1 | //# ProfileFit1D.cc: Class to fit Spectral components 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.tcc 21229 2012-04-02 12:00:20Z gervandiepen $ |
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27 | |
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28 | #include <components/SpectralComponents/ProfileFit1D.h> |
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29 | |
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30 | #include <casa/Arrays/ArrayLogical.h> |
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31 | #include <casa/Exceptions/Error.h> |
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32 | #include <components/SpectralComponents/SpectralEstimate.h> |
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33 | #include <components/SpectralComponents/SpectralElement.h> |
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34 | #include <casa/Utilities/DataType.h> |
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35 | #include <casa/Utilities/Assert.h> |
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36 | |
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37 | namespace casa { |
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38 | |
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39 | template <class T> |
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40 | ProfileFit1D<T>::ProfileFit1D() |
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41 | { |
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42 | checkType(); |
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43 | } |
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44 | |
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45 | template <class T> |
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46 | ProfileFit1D<T>::ProfileFit1D(const ProfileFit1D& other) |
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47 | { |
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48 | checkType(); |
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49 | copy(other); |
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50 | } |
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51 | |
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52 | template <class T> |
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53 | ProfileFit1D<T>& ProfileFit1D<T>::operator=(const ProfileFit1D& other) |
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54 | { |
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55 | if (this != &other) { |
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56 | copy(other); |
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57 | } |
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58 | return *this; |
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59 | } |
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60 | |
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61 | template <class T> |
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62 | ProfileFit1D<T>::~ProfileFit1D() |
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63 | {;} |
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64 | |
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65 | template <class T> |
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66 | Bool ProfileFit1D<T>::setData (const Vector<Double>& x, const Vector<T>& y, |
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67 | const Vector<Bool>& mask, const Vector<Double>& weight) |
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68 | { |
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69 | if (x.nelements()==0) { |
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70 | itsError = "The X vector must have some elements"; |
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71 | return False; |
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72 | } |
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73 | const uInt n = x.nelements(); |
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74 | // |
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75 | if (y.nelements() != n) { |
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76 | itsError = "The Y vector must have the same number of elements as the X vector"; |
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77 | return False; |
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78 | } |
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79 | // |
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80 | if (weight.nelements() != n && weight.nelements()!=0) { |
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81 | itsError = "The weights vector must have the same number of elements as the X vector"; |
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82 | return False; |
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83 | } |
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84 | // |
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85 | if (mask.nelements() != n && mask.nelements() != 0) { |
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86 | itsError = "The mask vector must have the same number of elements (or zero) as the data"; |
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87 | return False; |
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88 | } |
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89 | // |
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90 | itsX.resize(n); |
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91 | itsY.resize(n); |
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92 | itsDataMask.resize(n); |
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93 | // |
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94 | itsX = x; |
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95 | itsY = y; |
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96 | // |
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97 | if (weight.nelements()==0) { |
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98 | itsWeight.resize(0); |
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99 | } else { |
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100 | itsWeight.resize(n); |
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101 | itsWeight = weight; |
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102 | } |
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103 | // |
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104 | if (mask.nelements()==0) { |
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105 | itsDataMask = True; |
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106 | } else { |
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107 | itsDataMask = mask; |
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108 | } |
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109 | return True; |
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110 | } |
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111 | |
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112 | |
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113 | template <class T> |
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114 | Bool ProfileFit1D<T>::setData (const Vector<Double>& x, const Vector<T>& y, |
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115 | const Vector<Bool>& mask) |
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116 | { |
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117 | Vector<Double> weight; |
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118 | return setData (x, y, mask, weight); |
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119 | } |
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120 | |
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121 | template <class T> |
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122 | Bool ProfileFit1D<T>::setData (const Vector<Double>& x, const Vector<T>& y) |
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123 | { |
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124 | Vector<Bool> mask(x.nelements(), True); |
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125 | return setData (x, y, mask); |
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126 | } |
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127 | |
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128 | |
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129 | template <class T> |
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130 | void ProfileFit1D<T>::setElements (const SpectralList& list) |
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131 | { |
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132 | itsList = list; |
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133 | } |
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134 | |
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135 | template <class T> |
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136 | Bool ProfileFit1D<T>::setGaussianElements (uInt nGauss) |
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137 | { |
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138 | if (nGauss==0) { |
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139 | itsError = "You must specify some Gaussian components"; |
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140 | return False; |
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141 | } |
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142 | // |
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143 | if (itsY.nelements()==0) { |
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144 | itsError = "You must call function setData to set some data first"; |
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145 | return False; |
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146 | } |
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147 | |
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148 | // Clear list |
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149 | |
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150 | itsList.clear(); |
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151 | |
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152 | // Make estimate for Gaussians. |
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153 | |
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154 | SpectralEstimate estimator (nGauss); |
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155 | estimator.setQ(5); |
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156 | SpectralList listGauss = estimator.estimate (itsX, itsY); // Ignores masked data |
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157 | itsList.add (listGauss); |
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158 | return True; |
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159 | } |
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160 | |
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161 | template <class T> |
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162 | void ProfileFit1D<T>::addElements (const SpectralList& list) |
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163 | { |
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164 | itsList.add (list); |
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165 | } |
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166 | |
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167 | template <class T> |
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168 | void ProfileFit1D<T>::addElement (const SpectralElement& el) |
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169 | { |
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170 | itsList.add (el); |
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171 | } |
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172 | |
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173 | |
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174 | template <class T> |
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175 | void ProfileFit1D<T>::clearList () |
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176 | { |
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177 | itsList.clear(); |
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178 | } |
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179 | |
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180 | |
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181 | template <class T> |
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182 | Bool ProfileFit1D<T>::setRangeMask (const Vector<uInt>& start, |
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183 | const Vector<uInt>& end, |
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184 | Bool insideIsGood) |
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185 | { |
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186 | AlwaysAssert(start.nelements()==end.nelements(), AipsError); |
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187 | if (itsX.nelements()==0) { |
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188 | itsError = "You must call function setData to set some data first"; |
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189 | return False; |
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190 | } |
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191 | // |
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192 | const uInt n = itsX.nelements(); |
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193 | itsRangeMask.resize(n); |
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194 | Bool value = !insideIsGood; |
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195 | itsRangeMask = value; |
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196 | // |
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197 | for (uInt i=0; i<start.nelements(); i++) { |
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198 | if (start[i] > end[i]) { |
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199 | itsError = "The start index must be < the end index"; |
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200 | return False; |
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201 | } |
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202 | if (start[i]>=n) { |
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203 | itsError = "The start index must be in the range 0->nElements-1"; |
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204 | return False; |
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205 | } |
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206 | if (end[i]>=n) { |
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207 | itsError = "The end index must be in the range 0->nElements-1"; |
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208 | return False; |
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209 | } |
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210 | // |
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211 | for (uInt j=start[i]; j<end[i]+1; j++) { |
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212 | itsRangeMask[j] = !value; |
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213 | } |
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214 | } |
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215 | return True; |
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216 | } |
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217 | |
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218 | |
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219 | |
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220 | template <class T> |
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221 | Bool ProfileFit1D<T>::setRangeMask (const Vector<T>& start, |
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222 | const Vector<T>& end, |
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223 | Bool insideIsGood) |
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224 | { |
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225 | if (start.nelements()!=end.nelements()) { |
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226 | itsError = "Start and end vectors must be the same length"; |
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227 | return False; |
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228 | } |
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229 | if (itsX.nelements()==0) { |
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230 | itsError = "You must call function setData to set some data first"; |
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231 | return False; |
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232 | } |
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233 | // |
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234 | const uInt n = itsX.nelements(); |
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235 | itsRangeMask.resize(n); |
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236 | Bool value = !insideIsGood; |
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237 | itsRangeMask = value; |
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238 | // |
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239 | Vector<uInt> startIndex(start.nelements()); |
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240 | Vector<uInt> endIndex(end.nelements()); |
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241 | |
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242 | for (uInt i=0; i<start.nelements(); i++) { |
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243 | if (start[i] > end[i]) { |
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244 | itsError = "The start range must be < the end range"; |
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245 | return False; |
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246 | } |
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247 | if (start[i]<itsX[0] || start[i]>itsX[n-1]) { |
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248 | itsError = "The start range must be in the X-range of the data"; |
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249 | return False; |
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250 | } |
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251 | if (end[i]<itsX[0] || end[i]>itsX[n-1]) { |
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252 | itsError = "The end range must be in the X-range of the data"; |
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253 | return False; |
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254 | } |
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255 | |
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256 | // Find the indices for this range |
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257 | |
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258 | Bool doneStart = False; |
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259 | Bool doneEnd = False; |
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260 | for (uInt j=0; j<n; j++) { |
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261 | if (!doneStart && itsX[j] >= start[i]) { |
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262 | startIndex[i] = j; |
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263 | doneStart = True; |
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264 | } |
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265 | if (!doneEnd && itsX[j] >= end[i]) { |
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266 | endIndex[i] = j; |
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267 | doneEnd = True; |
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268 | } |
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269 | if (!doneEnd) endIndex[i] = n-1; |
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270 | } |
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271 | } |
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272 | // |
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273 | return setRangeMask (startIndex, endIndex); |
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274 | } |
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275 | |
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276 | |
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277 | template <class T> |
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278 | Bool ProfileFit1D<T>::fit () |
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279 | { |
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280 | if (itsX.nelements()==0) { |
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281 | itsError = "You must call function setData to set some data first"; |
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282 | return False; |
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283 | } |
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284 | if (itsList.nelements()==0) { |
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285 | itsError = "You must call function setElements to set some fit components first"; |
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286 | return False; |
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287 | } |
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288 | |
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289 | // Set list in fitter |
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290 | itsFitter.clear(); |
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291 | itsFitter.addFitElement (itsList); |
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292 | // Do the fit with the total mask |
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293 | |
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294 | Bool converged(False); |
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295 | if (itsWeight.nelements()==0) { |
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296 | converged = itsFitter.fit (itsY, itsX, makeTotalMask()); |
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297 | } else { |
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298 | converged = itsFitter.fit (itsWeight, itsY, itsX, makeTotalMask()); |
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299 | } |
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300 | return converged; |
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301 | } |
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302 | |
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303 | template <class T> |
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304 | const SpectralList& ProfileFit1D<T>::getList (Bool fit) const |
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305 | { |
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306 | if (fit) { |
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307 | return itsFitter.list(); |
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308 | } else { |
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309 | return itsList; |
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310 | } |
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311 | } |
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312 | |
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313 | |
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314 | template <class T> |
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315 | Vector<T> ProfileFit1D<T>::getEstimate (Int which) const |
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316 | { |
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317 | Vector<T> tmp; |
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318 | if (itsX.nelements()==0) { |
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319 | itsError = "You must call function setData to set some data first"; |
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320 | return tmp; |
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321 | } |
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322 | // |
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323 | if (which<0) { |
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324 | itsList.evaluate(tmp, itsX); |
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325 | } else { |
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326 | SpectralList list = getSubsetList (itsList, which); |
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327 | list.evaluate(tmp, itsX); |
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328 | } |
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329 | // |
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330 | return tmp; |
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331 | } |
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332 | |
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333 | template <class T> |
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334 | Vector<T> ProfileFit1D<T>::getFit (Int which) const |
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335 | { |
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336 | Vector<T> tmp; |
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337 | if (itsX.nelements()==0) { |
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338 | itsError = "You must call function setData to set some data first"; |
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339 | return tmp; |
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340 | } |
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341 | // |
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342 | const SpectralList& fitList = itsFitter.list(); |
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343 | if (fitList.nelements()==0) { |
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344 | itsError = "You must call function fit first"; |
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345 | return tmp; |
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346 | } |
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347 | // |
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348 | |
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349 | if (which<0) { |
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350 | fitList.evaluate(tmp, itsX); |
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351 | } else { |
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352 | SpectralList list = getSubsetList (fitList, which); |
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353 | list.evaluate(tmp, itsX); |
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354 | } |
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355 | // |
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356 | return tmp; |
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357 | } |
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358 | |
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359 | template <class T> |
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360 | Vector<T> ProfileFit1D<T>::getResidual (Int which, Bool fit) const |
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361 | { |
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362 | Vector<T> tmp; |
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363 | if (itsX.nelements()==0) { |
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364 | itsError = "You must call function setData to set some data first"; |
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365 | return tmp; |
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366 | } |
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367 | // |
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368 | SpectralList list; |
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369 | if (fit) { |
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370 | list = itsFitter.list(); |
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371 | if (list.nelements()==0) { |
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372 | throw (AipsError("You must call function fit first")); |
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373 | } |
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374 | } else { |
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375 | list = itsList; |
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376 | } |
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377 | // |
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378 | tmp = itsY; |
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379 | if (which<0) { |
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380 | list.residual(tmp, itsX); |
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381 | } else { |
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382 | SpectralList subList = getSubsetList (list, which); |
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383 | subList.residual(tmp, itsX); |
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384 | } |
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385 | // |
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386 | return tmp; |
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387 | } |
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388 | |
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389 | |
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390 | // Private functions |
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391 | |
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392 | |
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393 | template <class T> |
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394 | SpectralList ProfileFit1D<T>::getSubsetList (const SpectralList& list, Int which) const |
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395 | { |
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396 | const Int n = list.nelements(); |
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397 | if (which+1 > n) { |
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398 | throw AipsError("Illegal spectral element index"); |
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399 | } |
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400 | SpectralList listOut; |
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401 | listOut.add(*list[which]); |
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402 | return listOut; |
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403 | } |
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404 | |
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405 | template <class T> |
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406 | Vector<Bool> ProfileFit1D<T>::makeTotalMask () const |
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407 | { |
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408 | Vector<Bool> mask; |
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409 | if (itsRangeMask.nelements()==0) { |
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410 | mask = itsDataMask; |
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411 | } else { |
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412 | mask = itsDataMask && itsRangeMask; |
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413 | } |
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414 | return mask; |
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415 | } |
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416 | |
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417 | template <class T> |
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418 | void ProfileFit1D<T>::copy(const ProfileFit1D& other) |
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419 | { |
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420 | itsX.resize(0); |
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421 | itsX = other.itsX; |
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422 | // |
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423 | itsY.resize(0); |
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424 | itsY = other.itsY; |
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425 | // |
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426 | itsWeight.resize(0); |
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427 | itsWeight = other.itsWeight; |
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428 | // |
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429 | itsDataMask.resize(0); |
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430 | itsDataMask = other.itsDataMask; |
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431 | // |
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432 | itsRangeMask.resize(0); |
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433 | itsRangeMask = other.itsRangeMask; |
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434 | // |
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435 | itsList = other.itsList; |
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436 | // |
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437 | itsFitter = other.itsFitter; |
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438 | // |
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439 | itsError = other.itsError; |
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440 | } |
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441 | |
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442 | template <class T> |
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443 | void ProfileFit1D<T>::checkType() const |
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444 | { |
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445 | T* p=0; |
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446 | AlwaysAssert(whatType(p)==TpDouble,AipsError); |
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447 | } |
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448 | |
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449 | } //#End casa namespace |
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