1 | // ----------------------------------------------------------------------- |
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2 | // detection.cc : Member functions for the Detection class. |
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3 | // ----------------------------------------------------------------------- |
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4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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5 | // |
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6 | // This program is free software; you can redistribute it and/or modify it |
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7 | // under the terms of the GNU General Public License as published by the |
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8 | // Free Software Foundation; either version 2 of the License, or (at your |
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9 | // option) any later version. |
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10 | // |
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11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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14 | // for more details. |
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15 | // |
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16 | // You should have received a copy of the GNU General Public License |
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17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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19 | // |
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20 | // Correspondence concerning Duchamp may be directed to: |
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21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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22 | // Postal address: Dr. Matthew Whiting |
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23 | // Australia Telescope National Facility, CSIRO |
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24 | // PO Box 76 |
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25 | // Epping NSW 1710 |
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26 | // AUSTRALIA |
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27 | // ----------------------------------------------------------------------- |
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28 | #include <iostream> |
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29 | #include <iomanip> |
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30 | #include <vector> |
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31 | #include <map> |
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32 | #include <string> |
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33 | #include <wcslib/wcs.h> |
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34 | #include <math.h> |
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35 | #include <duchamp/duchamp.hh> |
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36 | #include <duchamp/param.hh> |
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37 | #include <duchamp/fitsHeader.hh> |
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38 | #include <duchamp/Utils/utils.hh> |
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39 | #include <duchamp/PixelMap/Voxel.hh> |
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40 | #include <duchamp/PixelMap/Object3D.hh> |
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41 | #include <duchamp/Detection/detection.hh> |
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42 | #include <duchamp/Cubes/cubeUtils.hh> |
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43 | #include <duchamp/Outputs/columns.hh> |
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44 | |
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45 | using namespace PixelInfo; |
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46 | |
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47 | namespace duchamp |
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48 | { |
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49 | |
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50 | void Detection::defaultDetection() |
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51 | { |
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52 | this->xSubOffset = 0; |
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53 | this->ySubOffset = 0; |
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54 | this->zSubOffset = 0; |
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55 | this->haveParams = false; |
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56 | this->totalFlux = 0.; |
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57 | this->peakFlux = 0.; |
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58 | this->intFlux = 0.; |
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59 | this->xpeak = 0; |
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60 | this->ypeak = 0; |
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61 | this->zpeak = 0; |
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62 | this->peakSNR = 0.; |
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63 | this->xCentroid = 0.; |
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64 | this->yCentroid = 0.; |
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65 | this->zCentroid = 0.; |
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66 | this->centreType="centroid"; |
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67 | this->negSource = false; |
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68 | this->flagText=""; |
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69 | this->id = -1; |
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70 | this->name = ""; |
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71 | this->flagWCS=false; |
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72 | this->specOK = true; |
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73 | this->raS = ""; |
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74 | this->decS = ""; |
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75 | this->ra = 0.; |
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76 | this->dec = 0.; |
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77 | this->raWidth = 0.; |
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78 | this->decWidth = 0.; |
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79 | this->majorAxis = 0.; |
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80 | this->minorAxis = 0.; |
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81 | this->posang = 0.; |
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82 | this->specUnits = ""; |
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83 | this->specType = ""; |
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84 | this->fluxUnits = ""; |
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85 | this->intFluxUnits = ""; |
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86 | this->lngtype = "RA"; |
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87 | this->lattype = "DEC"; |
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88 | this->vel = 0.; |
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89 | this->velWidth = 0.; |
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90 | this->velMin = 0.; |
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91 | this->velMax = 0.; |
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92 | this->w20 = 0.; |
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93 | this->v20min = 0.; |
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94 | this->v20max = 0.; |
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95 | this->w50 = 0.; |
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96 | this->v50min = 0.; |
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97 | this->v50max = 0.; |
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98 | this->posPrec = Catalogues::prPOS; |
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99 | this->xyzPrec = Catalogues::prXYZ; |
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100 | this->fintPrec = Catalogues::prFLUX; |
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101 | this->fpeakPrec = Catalogues::prFLUX; |
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102 | this->velPrec = Catalogues::prVEL; |
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103 | this->snrPrec = Catalogues::prSNR; |
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104 | } |
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105 | |
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106 | Detection::Detection(): |
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107 | Object3D() |
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108 | { |
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109 | this->defaultDetection(); |
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110 | } |
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111 | |
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112 | Detection::Detection(const Object3D& o): |
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113 | Object3D(o) |
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114 | { |
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115 | this->defaultDetection(); |
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116 | } |
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117 | |
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118 | Detection::Detection(const Detection& d): |
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119 | Object3D(d) |
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120 | { |
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121 | operator=(d); |
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122 | } |
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123 | |
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124 | Detection& Detection::operator= (const Detection& d) |
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125 | { |
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126 | ((Object3D &) *this) = d; |
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127 | this->xSubOffset = d.xSubOffset; |
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128 | this->ySubOffset = d.ySubOffset; |
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129 | this->zSubOffset = d.zSubOffset; |
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130 | this->haveParams = d.haveParams; |
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131 | this->totalFlux = d.totalFlux; |
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132 | this->intFlux = d.intFlux; |
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133 | this->peakFlux = d.peakFlux; |
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134 | this->xpeak = d.xpeak; |
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135 | this->ypeak = d.ypeak; |
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136 | this->zpeak = d.zpeak; |
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137 | this->peakSNR = d.peakSNR; |
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138 | this->xCentroid = d.xCentroid; |
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139 | this->yCentroid = d.yCentroid; |
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140 | this->zCentroid = d.zCentroid; |
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141 | this->centreType = d.centreType; |
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142 | this->negSource = d.negSource; |
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143 | this->flagText = d.flagText; |
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144 | this->id = d.id; |
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145 | this->name = d.name; |
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146 | this->flagWCS = d.flagWCS; |
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147 | this->specOK = d.specOK; |
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148 | this->raS = d.raS; |
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149 | this->decS = d.decS; |
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150 | this->ra = d.ra; |
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151 | this->dec = d.dec; |
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152 | this->raWidth = d.raWidth; |
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153 | this->decWidth = d.decWidth; |
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154 | this->majorAxis = d.majorAxis; |
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155 | this->minorAxis = d.minorAxis; |
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156 | this->posang = d.posang; |
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157 | this->specUnits = d.specUnits; |
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158 | this->specType = d.specType; |
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159 | this->fluxUnits = d.fluxUnits; |
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160 | this->intFluxUnits = d.intFluxUnits; |
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161 | this->lngtype = d.lngtype; |
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162 | this->lattype = d.lattype; |
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163 | this->vel = d.vel; |
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164 | this->velWidth = d.velWidth; |
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165 | this->velMin = d.velMin; |
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166 | this->velMax = d.velMax; |
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167 | this->w20 = d.w20; |
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168 | this->v20min = d.v20min; |
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169 | this->v20max = d.v20max; |
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170 | this->w50 = d.w50; |
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171 | this->v50min = d.v50min; |
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172 | this->v50max = d.v50max; |
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173 | this->posPrec = d.posPrec; |
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174 | this->xyzPrec = d.xyzPrec; |
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175 | this->fintPrec = d.fintPrec; |
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176 | this->fpeakPrec = d.fpeakPrec; |
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177 | this->velPrec = d.velPrec; |
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178 | this->snrPrec = d.snrPrec; |
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179 | return *this; |
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180 | } |
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181 | |
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182 | //-------------------------------------------------------------------- |
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183 | float Detection::getXcentre() |
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184 | { |
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185 | if(this->centreType=="peak") return this->xpeak; |
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186 | else if(this->centreType=="average") return this->getXaverage(); |
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187 | else return this->xCentroid; |
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188 | } |
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189 | |
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190 | float Detection::getYcentre() |
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191 | { |
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192 | if(this->centreType=="peak") return this->ypeak; |
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193 | else if(this->centreType=="average") return this->getYaverage(); |
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194 | else return this->yCentroid; |
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195 | } |
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196 | |
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197 | float Detection::getZcentre() |
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198 | { |
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199 | if(this->centreType=="peak") return this->zpeak; |
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200 | else if(this->centreType=="average") return this->getZaverage(); |
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201 | else return this->zCentroid; |
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202 | } |
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203 | |
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204 | //-------------------------------------------------------------------- |
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205 | |
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206 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
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207 | { |
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208 | /// @details |
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209 | /// A test to see whether there is a 1-1 correspondence between |
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210 | /// the given list of Voxels and the voxel positions contained in |
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211 | /// this Detection's pixel list. No testing of the fluxes of the |
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212 | /// Voxels is done. |
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213 | /// |
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214 | /// \param voxelList The std::vector list of Voxels to be tested. |
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215 | |
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216 | bool listsMatch = true; |
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217 | // compare sizes |
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218 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
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219 | if(!listsMatch) return listsMatch; |
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220 | |
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221 | // make sure all Detection pixels are in voxel list |
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222 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
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223 | |
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224 | // make sure all voxels are in Detection |
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225 | std::vector<Voxel>::iterator vox; |
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226 | for(vox=voxelList.begin();vox<voxelList.end();vox++) |
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227 | listsMatch = listsMatch && this->isInObject(*vox); |
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228 | |
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229 | return listsMatch; |
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230 | |
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231 | } |
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232 | //-------------------------------------------------------------------- |
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233 | |
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234 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
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235 | { |
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236 | /// @details |
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237 | /// A test to see whether the given list of Voxels contains each |
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238 | /// position in this Detection's pixel list. It does not look for |
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239 | /// a 1-1 correspondence: the given list can be a super-set of the |
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240 | /// Detection. No testing of the fluxes of the Voxels is done. |
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241 | /// |
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242 | /// \param voxelList The std::vector list of Voxels to be tested. |
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243 | |
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244 | bool listsMatch = true; |
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245 | |
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246 | // make sure all Detection pixels are in voxel list |
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247 | size_t v1=0; |
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248 | std::vector<Voxel> detpixlist = this->getPixelSet(); |
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249 | while(listsMatch && v1<detpixlist.size()){ |
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250 | bool inList = false; |
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251 | size_t v2=0; |
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252 | while(!inList && v2<voxelList.size()){ |
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253 | inList = inList || detpixlist[v1].match(voxelList[v2]); |
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254 | v2++; |
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255 | } |
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256 | listsMatch = listsMatch && inList; |
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257 | v1++; |
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258 | } |
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259 | |
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260 | return listsMatch; |
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261 | |
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262 | } |
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263 | //-------------------------------------------------------------------- |
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264 | |
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265 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
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266 | { |
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267 | /// @details |
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268 | /// A function that calculates total & peak fluxes (and the location |
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269 | /// of the peak flux) for a Detection. |
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270 | /// |
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271 | /// \param fluxArray The array of flux values to calculate the |
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272 | /// flux parameters from. |
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273 | /// \param dim The dimensions of the flux array. |
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274 | |
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275 | // this->haveParams = true; |
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276 | |
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277 | this->totalFlux = this->peakFlux = 0; |
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278 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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279 | |
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280 | // first check that the voxel list and the Detection's pixel list |
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281 | // have a 1-1 correspondence |
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282 | |
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283 | if(!this->voxelListCovered(voxelList)){ |
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284 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
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285 | return; |
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286 | } |
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287 | |
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288 | std::vector<Voxel>::iterator vox; |
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289 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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290 | if(this->isInObject(*vox)){ |
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291 | long x = vox->getX(); |
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292 | long y = vox->getY(); |
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293 | long z = vox->getZ(); |
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294 | float f = vox->getF(); |
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295 | this->totalFlux += f; |
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296 | this->xCentroid += x*f; |
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297 | this->yCentroid += y*f; |
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298 | this->zCentroid += z*f; |
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299 | if( (vox==voxelList.begin()) || //first time round |
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300 | (this->negSource&&(f<this->peakFlux)) || |
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301 | (!this->negSource&&(f>this->peakFlux)) ) |
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302 | { |
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303 | this->peakFlux = f; |
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304 | this->xpeak = x; |
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305 | this->ypeak = y; |
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306 | this->zpeak = z; |
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307 | } |
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308 | } |
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309 | } |
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310 | |
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311 | this->xCentroid /= this->totalFlux; |
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312 | this->yCentroid /= this->totalFlux; |
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313 | this->zCentroid /= this->totalFlux; |
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314 | } |
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315 | //-------------------------------------------------------------------- |
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316 | |
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317 | void Detection::calcFluxes(std::map<Voxel,float> &voxelMap) |
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318 | { |
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319 | /// @details |
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320 | /// A function that calculates total & peak fluxes (and the location |
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321 | /// of the peak flux) for a Detection. |
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322 | /// |
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323 | /// \param fluxArray The array of flux values to calculate the |
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324 | /// flux parameters from. |
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325 | /// \param dim The dimensions of the flux array. |
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326 | |
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327 | // this->haveParams = true; |
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328 | |
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329 | this->totalFlux = this->peakFlux = 0; |
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330 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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331 | |
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332 | std::vector<Voxel> voxelList = this->getPixelSet(); |
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333 | std::vector<Voxel>::iterator vox; |
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334 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
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335 | if(voxelMap.find(*vox) == voxelMap.end()){ |
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336 | DUCHAMPERROR("Detection::calcFluxes","Voxel list provided does not match"); |
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337 | return; |
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338 | } |
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339 | else { |
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340 | long x = vox->getX(); |
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341 | long y = vox->getY(); |
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342 | long z = vox->getZ(); |
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343 | float f = voxelMap[*vox]; |
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344 | this->totalFlux += f; |
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345 | this->xCentroid += x*f; |
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346 | this->yCentroid += y*f; |
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347 | this->zCentroid += z*f; |
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348 | if( (vox==voxelList.begin()) || //first time round |
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349 | (this->negSource&&(f<this->peakFlux)) || |
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350 | (!this->negSource&&(f>this->peakFlux)) ) |
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351 | { |
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352 | this->peakFlux = f; |
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353 | this->xpeak = x; |
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354 | this->ypeak = y; |
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355 | this->zpeak = z; |
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356 | } |
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357 | } |
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358 | } |
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359 | |
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360 | this->xCentroid /= this->totalFlux; |
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361 | this->yCentroid /= this->totalFlux; |
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362 | this->zCentroid /= this->totalFlux; |
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363 | } |
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364 | //-------------------------------------------------------------------- |
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365 | |
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366 | void Detection::calcFluxes(float *fluxArray, size_t *dim) |
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367 | { |
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368 | /// @details |
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369 | /// A function that calculates total & peak fluxes (and the location |
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370 | /// of the peak flux) for a Detection. |
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371 | /// |
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372 | /// \param fluxArray The array of flux values to calculate the |
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373 | /// flux parameters from. |
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374 | /// \param dim The dimensions of the flux array. |
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375 | |
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376 | // this->haveParams = true; |
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377 | |
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378 | this->totalFlux = this->peakFlux = 0; |
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379 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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380 | |
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381 | std::vector<Voxel> voxList = this->getPixelSet(); |
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382 | std::vector<Voxel>::iterator vox=voxList.begin(); |
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383 | for(;vox<voxList.end();vox++){ |
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384 | |
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385 | long x=vox->getX(); |
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386 | long y=vox->getY(); |
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387 | long z=vox->getZ(); |
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388 | size_t ind = vox->arrayIndex(dim); |
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389 | float f = fluxArray[ind]; |
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390 | this->totalFlux += f; |
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391 | this->xCentroid += x*f; |
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392 | this->yCentroid += y*f; |
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393 | this->zCentroid += z*f; |
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394 | if( (vox==voxList.begin()) || |
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395 | (this->negSource&&(f<this->peakFlux)) || |
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396 | (!this->negSource&&(f>this->peakFlux)) ) |
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397 | { |
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398 | this->peakFlux = f; |
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399 | this->xpeak = x; |
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400 | this->ypeak = y; |
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401 | this->zpeak = z; |
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402 | } |
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403 | |
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404 | } |
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405 | |
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406 | this->xCentroid /= this->totalFlux; |
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407 | this->yCentroid /= this->totalFlux; |
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408 | this->zCentroid /= this->totalFlux; |
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409 | } |
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410 | //-------------------------------------------------------------------- |
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411 | |
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412 | void Detection::calcWCSparams(FitsHeader &head) |
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413 | { |
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414 | /// @details |
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415 | /// Use the input wcs to calculate the position and velocity |
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416 | /// information for the Detection. |
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417 | /// Quantities calculated: |
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418 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
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419 | /// <li> Dec: dec [deg], dec (string), dec width. |
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420 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
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421 | /// <li> coord type for all three axes, nuRest, |
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422 | /// <li> name (IAU-style, in equatorial or Galactic) |
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423 | /// </ul> |
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424 | /// |
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425 | /// Note that the regular parameters are NOT recalculated! |
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426 | /// |
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427 | /// \param head FitsHeader object that contains the WCS information. |
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428 | |
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429 | if(head.isWCS()){ |
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430 | |
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431 | double *pixcrd = new double[15]; |
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432 | double *world = new double[15]; |
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433 | /* |
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434 | define a five-point array in 3D: |
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435 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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436 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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437 | and convert to world coordinates. |
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438 | */ |
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439 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
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440 | pixcrd[9] = this->getXmin()-0.5; |
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441 | pixcrd[12] = this->getXmax()+0.5; |
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442 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
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443 | pixcrd[10] = this->getYmin()-0.5; |
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444 | pixcrd[13] = this->getYmax()+0.5; |
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445 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
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446 | pixcrd[5] = this->getZmin(); |
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447 | pixcrd[8] = this->getZmax(); |
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448 | int flag = head.pixToWCS(pixcrd, world, 5); |
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449 | delete [] pixcrd; |
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450 | if(flag!=0) { |
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451 | DUCHAMPERROR("calcWCSparams", "Error in calculating the WCS for this object."); |
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452 | } |
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453 | else{ |
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454 | |
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455 | // world now has the WCS coords for the five points |
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456 | // -- use this to work out WCS params |
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457 | |
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458 | this->haveParams = true; |
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459 | |
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460 | this->specOK = head.canUseThirdAxis(); |
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461 | this->lngtype = head.lngtype(); |
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462 | this->lattype = head.lattype(); |
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463 | this->specUnits = head.getSpectralUnits(); |
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464 | this->specType = head.getSpectralType(); |
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465 | this->fluxUnits = head.getFluxUnits(); |
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466 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
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467 | this->intFluxUnits = head.getIntFluxUnits(); |
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468 | this->ra = world[0]; |
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469 | this->dec = world[1]; |
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470 | int precision = -int(log10(fabs(head.WCS().cdelt[head.WCS().lng]*3600./10.))); |
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471 | this->raS = decToDMS(this->ra, this->lngtype,precision); |
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472 | this->decS = decToDMS(this->dec,this->lattype,precision); |
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473 | this->raWidth = angularSeparation(world[9],world[1], |
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474 | world[12],world[1]) * 60.; |
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475 | this->decWidth = angularSeparation(world[0],world[10], |
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476 | world[0],world[13]) * 60.; |
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477 | |
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478 | Object2D spatMap = this->getSpatialMap(); |
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479 | std::pair<double,double> axes = spatMap.getPrincipleAxes(); |
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480 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale(); |
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481 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale(); |
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482 | this->posang = spatMap.getPositionAngle() * 180. / M_PI; |
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483 | |
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484 | this->name = head.getIAUName(this->ra, this->dec); |
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485 | this->vel = head.specToVel(world[2]); |
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486 | this->velMin = head.specToVel(world[5]); |
---|
487 | this->velMax = head.specToVel(world[8]); |
---|
488 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
489 | |
---|
490 | this->flagWCS = true; |
---|
491 | } |
---|
492 | delete [] world; |
---|
493 | |
---|
494 | } |
---|
495 | else { |
---|
496 | double x=this->getXcentre(),y=this->getYcentre(),z=this->getZmin(); |
---|
497 | this->velMin = head.pixToVel(x,y,z); |
---|
498 | z=this->getZmax(); |
---|
499 | this->velMax = head.pixToVel(x,y,z); |
---|
500 | this->velWidth = fabs(this->velMax - this->velMin); |
---|
501 | } |
---|
502 | |
---|
503 | |
---|
504 | } |
---|
505 | //-------------------------------------------------------------------- |
---|
506 | |
---|
507 | void Detection::calcIntegFlux(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
508 | { |
---|
509 | /// @details |
---|
510 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
511 | /// putting velocity in units of km/s. |
---|
512 | /// The fluxes used are taken from the Voxels, rather than an |
---|
513 | /// array of flux values. |
---|
514 | /// Integrates over full spatial and velocity range as given |
---|
515 | /// by the extrema calculated by calcWCSparams. |
---|
516 | /// |
---|
517 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
518 | /// corrected by the beam size (in pixels). This is done by |
---|
519 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
520 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
521 | /// pix/beam --> Jy) |
---|
522 | /// |
---|
523 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
524 | /// \param voxelList The list of Voxels with flux information |
---|
525 | /// \param head FitsHeader object that contains the WCS information. |
---|
526 | |
---|
527 | if(!this->voxelListCovered(voxelList)){ |
---|
528 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
529 | return; |
---|
530 | } |
---|
531 | |
---|
532 | if(!head.is2D()){ |
---|
533 | |
---|
534 | this->haveParams = true; |
---|
535 | |
---|
536 | const int border = 1; // include one pixel either side in each direction |
---|
537 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
538 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
539 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
540 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
541 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
542 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
543 | size_t spatsize=xsize*ysize; |
---|
544 | size_t size = xsize*ysize*zsize; |
---|
545 | std::vector <bool> isObj(size,false); |
---|
546 | double *localFlux = new double[size]; |
---|
547 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
548 | |
---|
549 | std::vector<Voxel>::iterator vox; |
---|
550 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
551 | if(this->isInObject(*vox)){ |
---|
552 | size_t pos=(vox->getX()-xzero) + (vox->getY()-yzero)*xsize + (vox->getZ()-zzero)*spatsize; |
---|
553 | localFlux[pos] = vox->getF(); |
---|
554 | isObj[pos] = true; |
---|
555 | } |
---|
556 | } |
---|
557 | |
---|
558 | // work out the WCS coords for each pixel |
---|
559 | double *world = new double[size]; |
---|
560 | double xpt,ypt,zpt; |
---|
561 | for(size_t i=0;i<size;i++){ |
---|
562 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
563 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
564 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
565 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
566 | } |
---|
567 | |
---|
568 | double integrated = 0.; |
---|
569 | for(size_t pix=0; pix<spatsize; pix++){ // loop over each spatial pixel. |
---|
570 | for(size_t z=0; z<zsize; z++){ |
---|
571 | size_t pos = z*xsize*ysize + pix; |
---|
572 | if(isObj[pos]){ // if it's an object pixel... |
---|
573 | double deltaVel; |
---|
574 | if(z==0) |
---|
575 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
576 | else if(z==(zsize-1)) |
---|
577 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
578 | else |
---|
579 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
580 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
581 | } |
---|
582 | } |
---|
583 | } |
---|
584 | this->intFlux = integrated; |
---|
585 | |
---|
586 | delete [] world; |
---|
587 | delete [] localFlux; |
---|
588 | |
---|
589 | calcVelWidths(zdim,voxelList,head); |
---|
590 | |
---|
591 | } |
---|
592 | else // in this case there is just a 2D image. |
---|
593 | this->intFlux = this->totalFlux; |
---|
594 | |
---|
595 | if(head.isWCS()){ |
---|
596 | // correct for the beam size if the flux units string ends in "/beam" |
---|
597 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
598 | } |
---|
599 | |
---|
600 | } |
---|
601 | //-------------------------------------------------------------------- |
---|
602 | |
---|
603 | void Detection::calcIntegFlux(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
604 | { |
---|
605 | /// @details |
---|
606 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
607 | /// putting velocity in units of km/s. |
---|
608 | /// The fluxes used are taken from the Voxels, rather than an |
---|
609 | /// array of flux values. |
---|
610 | /// Integrates over full spatial and velocity range as given |
---|
611 | /// by the extrema calculated by calcWCSparams. |
---|
612 | /// |
---|
613 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
614 | /// corrected by the beam size (in pixels). This is done by |
---|
615 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
616 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
617 | /// pix/beam --> Jy) |
---|
618 | /// |
---|
619 | /// \param zdim The size of the spectral axis (needed to find the velocity widths) |
---|
620 | /// \param voxelList The list of Voxels with flux information |
---|
621 | /// \param head FitsHeader object that contains the WCS information. |
---|
622 | |
---|
623 | if(!head.is2D()){ |
---|
624 | |
---|
625 | this->haveParams = true; |
---|
626 | |
---|
627 | const int border = 1; // include one pixel either side in each direction |
---|
628 | size_t xsize = size_t(this->xmax-this->xmin+2*border+1); |
---|
629 | size_t ysize = size_t(this->ymax-this->ymin+2*border+1); |
---|
630 | size_t zsize = size_t(this->zmax-this->zmin+2*border+1); |
---|
631 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
632 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
633 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
634 | size_t spatsize=xsize*ysize; |
---|
635 | size_t size = xsize*ysize*zsize; |
---|
636 | std::vector <bool> isObj(size,false); |
---|
637 | double *localFlux = new double[size]; |
---|
638 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
639 | |
---|
640 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
641 | std::vector<Voxel>::iterator vox; |
---|
642 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
643 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
644 | DUCHAMPERROR("Detection::calcIntegFlux","Voxel list provided does not match"); |
---|
645 | return; |
---|
646 | } |
---|
647 | else { |
---|
648 | size_t pos=(vox->getX()-xzero) + (vox->getY()-yzero)*xsize + (vox->getZ()-zzero)*spatsize; |
---|
649 | localFlux[pos] = voxelMap[*vox]; |
---|
650 | isObj[pos] = true; |
---|
651 | } |
---|
652 | } |
---|
653 | |
---|
654 | // work out the WCS coords for each pixel |
---|
655 | double *world = new double[size]; |
---|
656 | double xpt,ypt,zpt; |
---|
657 | for(size_t i=0;i<xsize*ysize*zsize;i++){ |
---|
658 | xpt = double( this->getXmin() - border + i%xsize ); |
---|
659 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
---|
660 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
---|
661 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
662 | } |
---|
663 | |
---|
664 | double integrated = 0.; |
---|
665 | for(size_t pix=0; pix<spatsize; pix++){ // loop over each spatial pixel. |
---|
666 | for(size_t z=0; z<zsize; z++){ |
---|
667 | size_t pos = z*xsize*ysize + pix; |
---|
668 | if(isObj[pos]){ // if it's an object pixel... |
---|
669 | double deltaVel; |
---|
670 | if(z==0) |
---|
671 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
672 | else if(z==(zsize-1)) |
---|
673 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
674 | else |
---|
675 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
676 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
677 | } |
---|
678 | } |
---|
679 | } |
---|
680 | this->intFlux = integrated; |
---|
681 | |
---|
682 | delete [] world; |
---|
683 | delete [] localFlux; |
---|
684 | |
---|
685 | calcVelWidths(zdim,voxelMap,head); |
---|
686 | |
---|
687 | } |
---|
688 | else // in this case there is just a 2D image. |
---|
689 | this->intFlux = this->totalFlux; |
---|
690 | |
---|
691 | if(head.isWCS()){ |
---|
692 | // correct for the beam size if the flux units string ends in "/beam" |
---|
693 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
694 | } |
---|
695 | |
---|
696 | } |
---|
697 | //-------------------------------------------------------------------- |
---|
698 | |
---|
699 | void Detection::calcIntegFlux(float *fluxArray, size_t *dim, FitsHeader &head) |
---|
700 | { |
---|
701 | /// @details |
---|
702 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
703 | /// putting velocity in units of km/s. |
---|
704 | /// Integrates over full spatial and velocity range as given |
---|
705 | /// by the extrema calculated by calcWCSparams. |
---|
706 | /// |
---|
707 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
708 | /// corrected by the beam size (in pixels). This is done by |
---|
709 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
710 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
711 | /// pix/beam --> Jy) |
---|
712 | /// |
---|
713 | /// \param fluxArray The array of flux values. |
---|
714 | /// \param dim The dimensions of the flux array. |
---|
715 | /// \param head FitsHeader object that contains the WCS information. |
---|
716 | |
---|
717 | if(!head.is2D()){ |
---|
718 | |
---|
719 | this->haveParams = true; |
---|
720 | |
---|
721 | const int border=1; // include one pixel either side in each direction |
---|
722 | size_t xsize = std::min(size_t(this->xmax-this->xmin+2*border+1),dim[0]); |
---|
723 | size_t ysize = std::min(size_t(this->ymax-this->ymin+2*border+1),dim[1]); |
---|
724 | size_t zsize = std::min(size_t(this->zmax-this->zmin+2*border+1),dim[2]); |
---|
725 | size_t xzero = size_t(std::max(0L,this->xmin-border)); |
---|
726 | size_t yzero = size_t(std::max(0L,this->ymin-border)); |
---|
727 | size_t zzero = size_t(std::max(0L,this->zmin-border)); |
---|
728 | size_t spatsize = xsize*ysize; |
---|
729 | size_t size = xsize*ysize*zsize; |
---|
730 | std::vector <bool> isObj(size,false); |
---|
731 | double *localFlux = new double[size]; |
---|
732 | for(size_t i=0;i<size;i++) localFlux[i]=0.; |
---|
733 | // work out which pixels are object pixels |
---|
734 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
735 | for(std::vector<Voxel>::iterator v=voxlist.begin();v<voxlist.end();v++){ |
---|
736 | size_t pos=(v->getX()-xzero) + (v->getY()-yzero)*xsize + (v->getZ()-zzero)*spatsize; |
---|
737 | localFlux[pos] = fluxArray[v->arrayIndex(dim)]; |
---|
738 | isObj[pos] = true; |
---|
739 | } |
---|
740 | |
---|
741 | // work out the WCS coords for each pixel |
---|
742 | double *world = new double[size]; |
---|
743 | double xpt,ypt,zpt; |
---|
744 | size_t i=0; |
---|
745 | for(size_t z=zzero;z<zzero+zsize;z++){ |
---|
746 | for(size_t y=yzero;y<yzero+ysize;y++){ |
---|
747 | for(size_t x=xzero;x<xzero+xsize;x++){ |
---|
748 | xpt=double(x); |
---|
749 | ypt=double(y); |
---|
750 | zpt=double(z); |
---|
751 | world[i++] = head.pixToVel(xpt,ypt,zpt); |
---|
752 | } |
---|
753 | } |
---|
754 | } |
---|
755 | |
---|
756 | double integrated = 0.; |
---|
757 | for(size_t pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
758 | for(size_t z=0; z<zsize; z++){ |
---|
759 | size_t pos = z*xsize*ysize + pix; |
---|
760 | if(isObj[pos]){ // if it's an object pixel... |
---|
761 | double deltaVel; |
---|
762 | if(z==0) |
---|
763 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
764 | else if(z==(zsize-1)) |
---|
765 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
766 | else |
---|
767 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
768 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
769 | } |
---|
770 | } |
---|
771 | } |
---|
772 | this->intFlux = integrated; |
---|
773 | |
---|
774 | delete [] world; |
---|
775 | delete [] localFlux; |
---|
776 | |
---|
777 | calcVelWidths(fluxArray, dim, head); |
---|
778 | |
---|
779 | } |
---|
780 | else // in this case there is just a 2D image. |
---|
781 | this->intFlux = this->totalFlux; |
---|
782 | |
---|
783 | if(head.isWCS()){ |
---|
784 | // correct for the beam size if the flux units string ends in "/beam" and we have beam info |
---|
785 | if(head.needBeamSize()) this->intFlux /= head.beam().area(); |
---|
786 | } |
---|
787 | |
---|
788 | } |
---|
789 | //-------------------------------------------------------------------- |
---|
790 | |
---|
791 | void Detection::calcVelWidths(size_t zdim, std::vector<Voxel> voxelList, FitsHeader &head) |
---|
792 | { |
---|
793 | /// @details |
---|
794 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
795 | /// peak integrated flux. The procedure is as follows: first |
---|
796 | /// generate an integrated flux spectrum (using all given voxels |
---|
797 | /// that lie in the object's spatial map); find the peak; starting |
---|
798 | /// at the spectral edges of the detection, move in or out until |
---|
799 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
800 | /// between points is done. |
---|
801 | /// |
---|
802 | /// \param zdim The size of the spectral axis in the cube |
---|
803 | /// \param voxelList The list of Voxels with flux information |
---|
804 | /// \param head FitsHeader object that contains the WCS information. |
---|
805 | |
---|
806 | float *intSpec = new float[zdim]; |
---|
807 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
808 | |
---|
809 | Object2D spatMap = this->getSpatialMap(); |
---|
810 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
811 | std::vector<Voxel>::iterator vox; |
---|
812 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
813 | if(spatMap.isInObject(*vox)){ |
---|
814 | intSpec[vox->getZ()] += vox->getF(); |
---|
815 | } |
---|
816 | } |
---|
817 | } |
---|
818 | |
---|
819 | calcVelWidths(zdim, intSpec, head); |
---|
820 | |
---|
821 | delete [] intSpec; |
---|
822 | |
---|
823 | } |
---|
824 | |
---|
825 | //-------------------------------------------------------------------- |
---|
826 | |
---|
827 | void Detection::calcVelWidths(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head) |
---|
828 | { |
---|
829 | /// @details |
---|
830 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
831 | /// peak integrated flux. The procedure is as follows: first |
---|
832 | /// generate an integrated flux spectrum (using all given voxels |
---|
833 | /// that lie in the object's spatial map); find the peak; starting |
---|
834 | /// at the spectral edges of the detection, move in or out until |
---|
835 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
836 | /// between points is done. |
---|
837 | /// |
---|
838 | /// \param zdim The size of the spectral axis in the cube |
---|
839 | /// \param voxelList The list of Voxels with flux information |
---|
840 | /// \param head FitsHeader object that contains the WCS information. |
---|
841 | |
---|
842 | float *intSpec = new float[zdim]; |
---|
843 | for(size_t i=0;i<zdim;i++) intSpec[i]=0; |
---|
844 | |
---|
845 | std::vector<Voxel> voxelList = this->getPixelSet(); |
---|
846 | std::vector<Voxel>::iterator vox; |
---|
847 | for(vox=voxelList.begin();vox<voxelList.end();vox++){ |
---|
848 | if(voxelMap.find(*vox) == voxelMap.end()){ |
---|
849 | DUCHAMPERROR("Detection::calcVelWidths","Voxel list provided does not match"); |
---|
850 | return; |
---|
851 | } |
---|
852 | else { |
---|
853 | intSpec[vox->getZ()] += voxelMap[*vox]; |
---|
854 | } |
---|
855 | } |
---|
856 | |
---|
857 | calcVelWidths(zdim, intSpec, head); |
---|
858 | |
---|
859 | delete [] intSpec; |
---|
860 | |
---|
861 | } |
---|
862 | |
---|
863 | //-------------------------------------------------------------------- |
---|
864 | |
---|
865 | void Detection::calcVelWidths(size_t zdim, float *intSpec, FitsHeader &head) |
---|
866 | { |
---|
867 | |
---|
868 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
869 | // points. Then, if the int flux there is above the 20%/50% |
---|
870 | // limit, go out, otherwise go in. This is to deal with the |
---|
871 | // problems from double- (or multi-) peaked sources. |
---|
872 | |
---|
873 | this->haveParams = true; |
---|
874 | |
---|
875 | double zpt,xpt=double(this->getXcentre()),ypt=double(this->getYcentre()); |
---|
876 | bool goLeft; |
---|
877 | |
---|
878 | if(this->negSource){ |
---|
879 | // if we've inverted the source, need to make the feature |
---|
880 | // positive for the interpolation/extrapolation to work |
---|
881 | for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
882 | } |
---|
883 | |
---|
884 | float peak=0.; |
---|
885 | size_t peakLoc=0; |
---|
886 | for(size_t z=this->getZmin();z<=size_t(this->getZmax());z++) { |
---|
887 | if(z==0 || peak<intSpec[z]){ |
---|
888 | peak = intSpec[z]; |
---|
889 | peakLoc = z; |
---|
890 | } |
---|
891 | } |
---|
892 | |
---|
893 | size_t z=this->getZmin(); |
---|
894 | goLeft = intSpec[z]>peak*0.5; |
---|
895 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
---|
896 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
---|
897 | if(z==0) this->v50min = this->velMin; |
---|
898 | else{ |
---|
899 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
900 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
901 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
902 | } |
---|
903 | z=this->getZmax(); |
---|
904 | goLeft = intSpec[z]<peak*0.5; |
---|
905 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
906 | else while(z<zdim && intSpec[z]>peak*0.5) z++; |
---|
907 | if(z==zdim) this->v50max = this->velMax; |
---|
908 | else{ |
---|
909 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
910 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
911 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
912 | } |
---|
913 | z=this->getZmin(); |
---|
914 | goLeft = intSpec[z]>peak*0.2; |
---|
915 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
916 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
917 | if(z==0) this->v20min = this->velMin; |
---|
918 | else{ |
---|
919 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
920 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
921 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
922 | } |
---|
923 | z=this->getZmax(); |
---|
924 | goLeft = intSpec[z]<peak*0.2; |
---|
925 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
926 | else while(z<zdim && intSpec[z]>peak*0.2) z++; |
---|
927 | if(z==zdim) this->v20max = this->velMax; |
---|
928 | else{ |
---|
929 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
930 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
931 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
932 | } |
---|
933 | |
---|
934 | this->w20 = fabs(this->v20min - this->v20max); |
---|
935 | this->w50 = fabs(this->v50min - this->v50max); |
---|
936 | |
---|
937 | if(this->negSource){ |
---|
938 | // un-do the inversion, in case intSpec is needed elsewhere |
---|
939 | for(size_t i=0;i<zdim;i++) intSpec[i] *= -1.; |
---|
940 | } |
---|
941 | |
---|
942 | |
---|
943 | } |
---|
944 | //-------------------------------------------------------------------- |
---|
945 | |
---|
946 | void Detection::calcVelWidths(float *fluxArray, size_t *dim, FitsHeader &head) |
---|
947 | { |
---|
948 | /// @details |
---|
949 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
950 | /// peak integrated flux. The procedure is as follows: first |
---|
951 | /// generate an integrated flux spectrum (summing each spatial |
---|
952 | /// pixel's spectrum); find the peak; starting at the spectral |
---|
953 | /// edges of the detection, move in or out until you reach the 20% |
---|
954 | /// or 50% peak flux level. Linear interpolation between points is |
---|
955 | /// done. |
---|
956 | /// |
---|
957 | /// \param fluxArray The array of flux values. |
---|
958 | /// \param dim The dimensions of the flux array. |
---|
959 | /// \param head FitsHeader object that contains the WCS information. |
---|
960 | |
---|
961 | if(dim[2] > 2){ |
---|
962 | |
---|
963 | float *intSpec = new float[dim[2]]; |
---|
964 | size_t size=dim[0]*dim[1]*dim[2]; |
---|
965 | std::vector<bool> mask(size,true); |
---|
966 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
---|
967 | |
---|
968 | this->calcVelWidths(dim[2],intSpec,head); |
---|
969 | |
---|
970 | delete [] intSpec; |
---|
971 | |
---|
972 | } |
---|
973 | else{ |
---|
974 | this->v50min = this->v20min = this->velMin; |
---|
975 | this->v50max = this->v20max = this->velMax; |
---|
976 | this->w20 = fabs(this->v20min - this->v20max); |
---|
977 | this->w50 = fabs(this->v50min - this->v50max); |
---|
978 | } |
---|
979 | |
---|
980 | } |
---|
981 | //-------------------------------------------------------------------- |
---|
982 | |
---|
983 | void Detection::setOffsets(Param &par) |
---|
984 | { |
---|
985 | /// @details |
---|
986 | /// This function stores the values of the offsets for each cube axis. |
---|
987 | /// The offsets are the starting values of the cube axes that may differ from |
---|
988 | /// the default value of 0 (for instance, if a subsection is being used). |
---|
989 | /// The values will be used when the detection is outputted. |
---|
990 | |
---|
991 | this->xSubOffset = par.getXOffset(); |
---|
992 | this->ySubOffset = par.getYOffset(); |
---|
993 | this->zSubOffset = par.getZOffset(); |
---|
994 | } |
---|
995 | //-------------------------------------------------------------------- |
---|
996 | |
---|
997 | bool Detection::hasEnoughChannels(int minNumber) |
---|
998 | { |
---|
999 | /// @details |
---|
1000 | /// A function to determine if the Detection has enough |
---|
1001 | /// contiguous channels to meet the minimum requirement |
---|
1002 | /// given as the argument. |
---|
1003 | /// \param minNumber How many channels is the minimum acceptable number? |
---|
1004 | /// \return True if there is at least one occurence of minNumber consecutive |
---|
1005 | /// channels present to return true. False otherwise. |
---|
1006 | |
---|
1007 | // Preferred method -- need a set of minNumber consecutive channels present. |
---|
1008 | |
---|
1009 | int numChan = this->getMaxAdjacentChannels(); |
---|
1010 | bool result = (numChan >= minNumber); |
---|
1011 | |
---|
1012 | return result; |
---|
1013 | |
---|
1014 | } |
---|
1015 | //-------------------------------------------------------------------- |
---|
1016 | |
---|
1017 | std::vector<int> Detection::getVertexSet() |
---|
1018 | { |
---|
1019 | /// @details |
---|
1020 | /// Gets a list of points being the end-points of 1-pixel long |
---|
1021 | /// segments drawing a border around the spatial extend of a |
---|
1022 | /// detection. The vector is a series of 4 integers, being: x_0, |
---|
1023 | /// y_0, x_1, y_1. |
---|
1024 | /// \return The vector of vertex positions. |
---|
1025 | |
---|
1026 | std::vector<int> vertexSet; |
---|
1027 | |
---|
1028 | int xmin = this->getXmin() - 1; |
---|
1029 | int xmax = this->getXmax() + 1; |
---|
1030 | int ymin = this->getYmin() - 1; |
---|
1031 | int ymax = this->getYmax() + 1; |
---|
1032 | int xsize = xmax - xmin + 1; |
---|
1033 | int ysize = ymax - ymin + 1; |
---|
1034 | |
---|
1035 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
1036 | std::vector<bool> isObj(xsize*ysize,false); |
---|
1037 | std::vector<Voxel>::iterator vox; |
---|
1038 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
---|
1039 | size_t pos = (vox->getX()-xmin) + |
---|
1040 | (vox->getY()-ymin)*xsize; |
---|
1041 | isObj[pos] = true; |
---|
1042 | } |
---|
1043 | voxlist.clear(); |
---|
1044 | |
---|
1045 | for(int x=xmin; x<=xmax; x++){ |
---|
1046 | // for each column... |
---|
1047 | for(int y=ymin+1;y<=ymax;y++){ |
---|
1048 | int current = (y-ymin)*xsize + x-xmin; |
---|
1049 | int previous = (y-ymin-1)*xsize + x-xmin; |
---|
1050 | if((isObj[current]&&!isObj[previous]) || |
---|
1051 | (!isObj[current]&&isObj[previous])){ |
---|
1052 | vertexSet.push_back(x); |
---|
1053 | vertexSet.push_back(y); |
---|
1054 | vertexSet.push_back(x+1); |
---|
1055 | vertexSet.push_back(y); |
---|
1056 | } |
---|
1057 | } |
---|
1058 | } |
---|
1059 | for(int y=ymin; y<=ymax; y++){ |
---|
1060 | // now for each row... |
---|
1061 | for(int x=xmin+1;x<=xmax;x++){ |
---|
1062 | int current = (y-ymin)*xsize + x-xmin; |
---|
1063 | int previous = (y-ymin)*xsize + x-xmin - 1; |
---|
1064 | if((isObj[current]&&!isObj[previous]) || |
---|
1065 | (!isObj[current]&&isObj[previous])){ |
---|
1066 | vertexSet.push_back(x); |
---|
1067 | vertexSet.push_back(y); |
---|
1068 | vertexSet.push_back(x); |
---|
1069 | vertexSet.push_back(y+1); |
---|
1070 | } |
---|
1071 | } |
---|
1072 | } |
---|
1073 | |
---|
1074 | return vertexSet; |
---|
1075 | |
---|
1076 | } |
---|
1077 | |
---|
1078 | |
---|
1079 | void Detection::addDetection(Detection &other) |
---|
1080 | { |
---|
1081 | for(std::map<long, Object2D>::iterator it = other.chanlist.begin(); it!=other.chanlist.end();it++) |
---|
1082 | // this->addChannel(*it); |
---|
1083 | this->addChannel(it->first, it->second); |
---|
1084 | this->haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
1085 | } |
---|
1086 | |
---|
1087 | Detection operator+ (Detection &lhs, Detection &rhs) |
---|
1088 | { |
---|
1089 | Detection output = lhs; |
---|
1090 | for(std::map<long, Object2D>::iterator it = rhs.chanlist.begin(); it!=rhs.chanlist.end();it++) |
---|
1091 | output.addChannel(it->first, it->second); |
---|
1092 | output.haveParams = false; // make it appear as if the parameters haven't been calculated, so that we can re-calculate them |
---|
1093 | return output; |
---|
1094 | } |
---|
1095 | |
---|
1096 | |
---|
1097 | bool Detection::canMerge(Detection &other, Param &par) |
---|
1098 | { |
---|
1099 | bool near = this->isNear(other,par); |
---|
1100 | if(near) return this->isClose(other,par); |
---|
1101 | else return near; |
---|
1102 | } |
---|
1103 | |
---|
1104 | bool Detection::isNear(Detection &other, Param &par) |
---|
1105 | { |
---|
1106 | |
---|
1107 | bool flagAdj = par.getFlagAdjacent(); |
---|
1108 | float threshS = par.getThreshS(); |
---|
1109 | float threshV = par.getThreshV(); |
---|
1110 | |
---|
1111 | long gap; |
---|
1112 | if(flagAdj) gap = 1; |
---|
1113 | else gap = long( ceil(threshS) ); |
---|
1114 | |
---|
1115 | bool areNear; |
---|
1116 | // Test X ranges |
---|
1117 | if((this->xmin-gap)<other.xmin) areNear=((this->xmax+gap)>=other.xmin); |
---|
1118 | else areNear=(other.xmax>=(this->xmin-gap)); |
---|
1119 | // Test Y ranges |
---|
1120 | if(areNear){ |
---|
1121 | if((this->ymin-gap)<other.ymin) areNear=areNear&&((this->ymax+gap)>=other.ymin); |
---|
1122 | else areNear=areNear&&(other.ymax>=(this->ymin-gap)); |
---|
1123 | } |
---|
1124 | // Test Z ranges |
---|
1125 | if(areNear){ |
---|
1126 | gap = long(ceil(threshV)); |
---|
1127 | if((this->zmin-gap)<other.zmin) areNear=areNear&&((this->zmax+gap)>=other.zmin); |
---|
1128 | else areNear=areNear&&(other.zmax>=(this->zmin-gap)); |
---|
1129 | } |
---|
1130 | |
---|
1131 | return areNear; |
---|
1132 | |
---|
1133 | } |
---|
1134 | |
---|
1135 | bool Detection::isClose(Detection &other, Param &par) |
---|
1136 | { |
---|
1137 | bool close = false; // this will be the value returned |
---|
1138 | |
---|
1139 | bool flagAdj = par.getFlagAdjacent(); |
---|
1140 | float threshS = par.getThreshS(); |
---|
1141 | float threshV = par.getThreshV(); |
---|
1142 | |
---|
1143 | // |
---|
1144 | // If we get to here, the pixel ranges overlap -- so we do a |
---|
1145 | // pixel-by-pixel comparison to make sure they are actually |
---|
1146 | // "close" according to the thresholds. Otherwise, close=false, |
---|
1147 | // and so don't need to do anything else before returning. |
---|
1148 | // |
---|
1149 | |
---|
1150 | std::vector<long> zlist1 = this->getChannelList(); |
---|
1151 | std::vector<long> zlist2 = other.getChannelList(); |
---|
1152 | Scan test1,test2; |
---|
1153 | |
---|
1154 | for(size_t ct1=0; (!close && (ct1<zlist1.size())); ct1++){ |
---|
1155 | for(size_t ct2=0; (!close && (ct2<zlist2.size())); ct2++){ |
---|
1156 | |
---|
1157 | if(abs(zlist1[ct1]-zlist2[ct2])<=threshV){ |
---|
1158 | |
---|
1159 | Object2D temp1 = this->getChanMap(zlist1[ct1]); |
---|
1160 | Object2D temp2 = other.getChanMap(zlist2[ct2]); |
---|
1161 | |
---|
1162 | close = temp1.canMerge(temp2,threshS,flagAdj); |
---|
1163 | |
---|
1164 | } |
---|
1165 | |
---|
1166 | } |
---|
1167 | } |
---|
1168 | |
---|
1169 | return close; |
---|
1170 | |
---|
1171 | } |
---|
1172 | |
---|
1173 | |
---|
1174 | |
---|
1175 | } |
---|