1 | //# SpectralEstimate.h: Get an initial estimate for spectral lines |
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2 | //# Copyright (C) 2001,2002,2003,2004 |
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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 | //# casacore::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 | //# |
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27 | //# $Id: SpectralEstimate.h 21229 2012-04-02 12:00:20Z gervandiepen $ |
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28 | |
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29 | #ifndef COMPONENTS_SPECTRALESTIMATE_H |
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30 | #define COMPONENTS_SPECTRALESTIMATE_H |
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31 | |
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32 | #include <casa/aips.h> |
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33 | #include <components/SpectralComponents/SpectralElement.h> |
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34 | #include <components/SpectralComponents/SpectralList.h> |
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35 | |
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36 | namespace casacore { |
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37 | template <class T> class Vector; |
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38 | } |
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39 | |
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40 | namespace casa { //# NAMESPACE CASA - BEGIN |
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41 | |
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42 | //# Forward Declarations |
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43 | class GaussianSpectralElement; |
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44 | |
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45 | // <summary> |
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46 | // Get an initial estimate for spectral lines |
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47 | // </summary> |
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48 | |
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49 | // <use visibility=export> |
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50 | |
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51 | // <reviewed reviewer="" date="yyyy/mm/dd" tests="tSpectralFit" demos=""> |
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52 | // </reviewed> |
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53 | |
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54 | // <prerequisite> |
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55 | // <li> <linkto class=SpectralFit>SpectralFit</linkto> class |
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56 | // </prerequisite> |
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57 | // |
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58 | // <etymology> |
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59 | // From spectral line and estimate |
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60 | // </etymology> |
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61 | // |
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62 | // <synopsis> |
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63 | // The SpectralEstimate class obtains an initial guess for spectral |
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64 | // components. The current implementation uses the entire |
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65 | // profile as signal region, or can set a window to be searched around |
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66 | // the highest peak automatically. A window can also be set manually. |
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67 | // The second derivative of |
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68 | // the profile in the signal region is calculated by fitting |
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69 | // a second degree polynomal. The smoothing parameter Q |
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70 | // determines the number of points used for this (=2*Q+1). |
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71 | // The gaussians can then be estimated as described by |
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72 | // Schwarz, 1968, Bull.Astr.Inst.Netherlands, Volume 19, 405. |
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73 | // |
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74 | // The elements guessed can be used in the |
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75 | // <linkto class=SpectralFit>SpectralFit</linkto> class. |
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76 | // |
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77 | // The default type found is a Gaussian, defined as: |
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78 | // <srcblock> |
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79 | // AMPL.exp[ -(x-CENTER)<sup>2</sup>/2 SIGMA<sup>2</sup>] |
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80 | // </srcblock> |
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81 | // |
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82 | // The parameter estimates are returned in units of zero-based |
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83 | // pixel indices. |
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84 | // </synopsis> |
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85 | // |
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86 | // <example> |
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87 | // </example> |
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88 | // |
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89 | // <motivation> |
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90 | // To have an automatic method to find spectral lines |
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91 | // </motivation> |
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92 | // |
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93 | // <todo asof="2001/02/14"> |
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94 | // <li> find a way to get to absorption lines as well |
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95 | // <li> add more estimation options |
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96 | // </todo> |
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97 | |
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98 | class SpectralEstimate { |
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99 | public: |
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100 | //# Constants |
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101 | // Default maximum number of components to be found |
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102 | static const casacore::uInt MAXPAR = 200; |
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103 | //# Enumerations |
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104 | //# Friends |
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105 | |
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106 | //# Constructors |
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107 | // Default constructor creates a default estimator (default max number |
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108 | // of components to be found is 200) with the given maximum number |
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109 | // of components that will be found. A value of zero will indicate |
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110 | // an unlimited number. |
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111 | explicit SpectralEstimate(const casacore::uInt maxpar=MAXPAR); |
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112 | // Create an estimator with the given maximum number of possible |
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113 | // elements. A value of zero will indicate an unlimited number. |
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114 | // Construct with a given rms in profiles, a cutoff for amplitudes |
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115 | // found, and a minimum width. Cutoff and minsigma default to 0.0, maximum |
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116 | // size of list produced to 200. |
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117 | explicit SpectralEstimate(const casacore::Double rms, |
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118 | const casacore::Double cutoff=0.0, const casacore::Double minsigma=0.0, |
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119 | const casacore::uInt maxpar=MAXPAR); |
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120 | // Copy constructor (deep copy) |
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121 | SpectralEstimate(const SpectralEstimate &other); |
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122 | |
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123 | //#Destructor |
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124 | // Destructor |
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125 | ~SpectralEstimate(); |
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126 | |
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127 | //# Operators |
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128 | // Assignment (copy semantics) |
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129 | SpectralEstimate &operator=(const SpectralEstimate &other); |
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130 | |
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131 | //# Member functions |
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132 | // Generate the estimates for a profile and return the |
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133 | // list found. The first function returns component parameters |
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134 | // in units of pixel indices. The second function calls the first |
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135 | // and then converts to the specified abcissa space (the supplied |
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136 | // vector must be monotonic); if the pixel-based center is out of range |
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137 | // of the supplied abcissa vector the conversion is done via extrapolation. |
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138 | // The der pointer is meant for debugging, and can return |
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139 | // the derivative profile. The second function throws an AipsError |
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140 | // if the vectors are not the same length. |
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141 | // <group> |
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142 | template <class MT> |
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143 | const SpectralList& estimate(const casacore::Vector<MT>& ordinate, |
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144 | casacore::Vector<MT> *der = 0); |
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145 | template <class MT> |
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146 | const SpectralList& estimate(const casacore::Vector<MT>& abcissa, |
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147 | const casacore::Vector<MT>& ordinate); |
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148 | // </group> |
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149 | |
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150 | // Return the list found. |
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151 | const SpectralList &list() const {return slist_p; }; |
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152 | |
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153 | // Set estimation parameters |
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154 | // <group> |
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155 | // Set the profile's estimated rms (forced to abs(rms)) |
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156 | void setRMS(const casacore::Double rms=0.0); |
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157 | // Set the amplitude cutoff for valid estimate (forced to max(0,cutoff)) |
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158 | void setCutoff(const casacore::Double cutoff=0.0); |
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159 | // Set the minimum width allowed (forced to max(0,minsigma)) |
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160 | void setMinSigma(const casacore::Double minsigma=0.0); |
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161 | // Set the number of points consider at each side of test point (i.e. a |
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162 | // width of 2q+1 is taken). Default internally is 2; max(1,q) taken. |
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163 | void setQ(const casacore::uInt q=2); |
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164 | // Set a region [lo,hi] over which to estimate. Lo and hi are given as |
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165 | // zero-based vector indices. |
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166 | void setRegion(const casacore::Int lo, const casacore::Int hi); |
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167 | // Do you want to look in an automatically determined window with signal? |
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168 | // Default is False, meaning the full (possibly regioned) profile. |
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169 | void setWindowing(const Bool win=False); |
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170 | // Set the maximum number of estimates to find (forced to >=1; 200 default) |
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171 | void setMaxN(const casacore::uInt maxpar=MAXPAR); |
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172 | // </group> |
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173 | |
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174 | private: |
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175 | //#Data |
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176 | // Use window search |
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177 | Bool useWindow_p; |
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178 | // rms estimate in profile |
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179 | casacore::Double rms_p; |
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180 | // Source cutoff amplitude |
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181 | casacore::Double cutoff_p; |
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182 | // Window low and end value |
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183 | // <group> |
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184 | casacore::Int windowLow_p; |
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185 | casacore::Int windowEnd_p; |
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186 | // </group> |
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187 | // Region low and high value |
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188 | // <group> |
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189 | casacore::Int regionLow_p; |
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190 | casacore::Int regionEnd_p; |
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191 | // </group> |
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192 | // Smoothing parameter. I.e. 2q+1 points are taken |
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193 | casacore::Int q_p; |
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194 | // casacore::Internal cashing of calculated values based on q |
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195 | // <group> |
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196 | casacore::Double a_p; |
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197 | casacore::Double b_p; |
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198 | // </group> |
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199 | // The minimum Gaussian width |
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200 | casacore::Double sigmin_p; |
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201 | // The second derivatives |
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202 | casacore::Double *deriv_p; |
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203 | // The list of components |
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204 | SpectralList slist_p; |
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205 | // The length of the current profile being estimated |
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206 | casacore::uInt lprof_p; |
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207 | |
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208 | //# Member functions |
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209 | // Get the window or the total spectrum |
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210 | template <class MT> |
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211 | casacore::uInt window(const casacore::Vector<MT> &prof); |
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212 | // Get the second derivatives |
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213 | template <class MT> |
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214 | void findc2(const casacore::Vector<MT> &prof); |
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215 | // Find the Gaussians |
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216 | template <class MT> |
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217 | void findga(const casacore::Vector<MT> &prof); |
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218 | // Convert the parameters of the components in the list from |
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219 | // pixel-based indices to the given abcissa-vector space. |
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220 | template <class MT> GaussianSpectralElement convertElement (const casacore::Vector<MT>& abcissa, |
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221 | const GaussianSpectralElement& el) const; |
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222 | }; |
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223 | |
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224 | |
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225 | } //# NAMESPACE CASA - END |
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226 | |
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227 | #ifndef CASACORE_NO_AUTO_TEMPLATES |
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228 | #include <components/SpectralComponents/Spectral2Estimate.tcc> |
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229 | #endif //# CASACORE_NO_AUTO_TEMPLATES |
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230 | #endif |
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