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 <string> |
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32 | #include <wcslib/wcs.h> |
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33 | #include <math.h> |
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34 | #include <duchamp/duchamp.hh> |
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35 | #include <duchamp/param.hh> |
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36 | #include <duchamp/fitsHeader.hh> |
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37 | #include <duchamp/Utils/utils.hh> |
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38 | #include <duchamp/PixelMap/Voxel.hh> |
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39 | #include <duchamp/PixelMap/ChanMap.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 | |
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44 | using namespace PixelInfo; |
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45 | |
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46 | namespace duchamp |
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47 | { |
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48 | |
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49 | |
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50 | Detection::Detection(): |
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51 | Object3D() |
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52 | { |
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53 | this->flagWCS=false; |
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54 | this->negSource = false; |
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55 | this->flagText=""; |
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56 | this->totalFlux = this->peakFlux = this->intFlux = 0.; |
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57 | this->centreType="centroid"; |
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58 | this->id = -1; |
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59 | this->raS = this->decS = ""; |
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60 | this->ra = this->dec = this->vel = 0.; |
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61 | this->raWidth = this->decWidth = 0.; |
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62 | this->majorAxis = this->minorAxis = this->posang = 0.; |
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63 | this->w20 = this->w50 = this->velWidth = 0.; |
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64 | } |
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65 | |
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66 | Detection::Detection(const Object3D& o): |
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67 | Object3D(o) |
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68 | { |
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69 | this->flagWCS=false; |
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70 | this->negSource = false; |
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71 | this->flagText=""; |
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72 | this->totalFlux = this->peakFlux = this->intFlux = 0.; |
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73 | this->centreType="centroid"; |
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74 | this->id = -1; |
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75 | this->raS = this->decS = ""; |
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76 | this->ra = this->dec = this->vel = 0.; |
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77 | this->raWidth = this->decWidth = 0.; |
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78 | this->majorAxis = this->minorAxis = this->posang = 0.; |
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79 | this->w20 = this->w50 = this->velWidth = 0.; |
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80 | } |
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81 | |
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82 | Detection::Detection(const Detection& d): |
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83 | Object3D(d) |
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84 | { |
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85 | operator=(d); |
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86 | } |
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87 | |
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88 | Detection& Detection::operator= (const Detection& d) |
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89 | { |
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90 | // if(this == &d) return *this; |
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91 | // this->pixelArray = d.pixelArray; |
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92 | ((Object3D &) *this) = d; |
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93 | this->xSubOffset = d.xSubOffset; |
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94 | this->ySubOffset = d.ySubOffset; |
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95 | this->zSubOffset = d.zSubOffset; |
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96 | this->totalFlux = d.totalFlux; |
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97 | this->intFlux = d.intFlux; |
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98 | this->peakFlux = d.peakFlux; |
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99 | this->xpeak = d.xpeak; |
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100 | this->ypeak = d.ypeak; |
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101 | this->zpeak = d.zpeak; |
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102 | this->peakSNR = d.peakSNR; |
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103 | this->xCentroid = d.xCentroid; |
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104 | this->yCentroid = d.yCentroid; |
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105 | this->zCentroid = d.zCentroid; |
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106 | this->centreType = d.centreType; |
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107 | this->negSource = d.negSource; |
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108 | this->flagText = d.flagText; |
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109 | this->id = d.id; |
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110 | this->name = d.name; |
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111 | this->flagWCS = d.flagWCS; |
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112 | this->specOK = d.specOK; |
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113 | this->raS = d.raS; |
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114 | this->decS = d.decS; |
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115 | this->ra = d.ra; |
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116 | this->dec = d.dec; |
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117 | this->raWidth = d.raWidth; |
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118 | this->decWidth = d.decWidth; |
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119 | this->majorAxis = d.majorAxis; |
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120 | this->minorAxis = d.minorAxis; |
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121 | this->posang = d.posang; |
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122 | this->specUnits = d.specUnits; |
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123 | this->fluxUnits = d.fluxUnits; |
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124 | this->intFluxUnits = d.intFluxUnits; |
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125 | this->lngtype = d.lngtype; |
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126 | this->lattype = d.lattype; |
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127 | this->vel = d.vel; |
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128 | this->velWidth = d.velWidth; |
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129 | this->velMin = d.velMin; |
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130 | this->velMax = d.velMax; |
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131 | this->w20 = d.w20; |
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132 | this->v20min = d.v20min; |
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133 | this->v20max = d.v20max; |
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134 | this->w50 = d.w50; |
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135 | this->v50min = d.v50min; |
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136 | this->v50max = d.v50max; |
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137 | this->posPrec = d.posPrec; |
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138 | this->xyzPrec = d.xyzPrec; |
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139 | this->fintPrec = d.fintPrec; |
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140 | this->fpeakPrec = d.fpeakPrec; |
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141 | this->velPrec = d.velPrec; |
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142 | this->snrPrec = d.snrPrec; |
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143 | return *this; |
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144 | } |
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145 | |
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146 | //-------------------------------------------------------------------- |
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147 | |
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148 | bool Detection::voxelListsMatch(std::vector<Voxel> voxelList) |
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149 | { |
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150 | /// @details |
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151 | /// A test to see whether there is a 1-1 correspondence between |
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152 | /// the given list of Voxels and the voxel positions contained in |
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153 | /// this Detection's pixel list. No testing of the fluxes of the |
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154 | /// Voxels is done. |
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155 | /// |
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156 | /// \param voxelList The std::vector list of Voxels to be tested. |
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157 | |
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158 | bool listsMatch = true; |
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159 | // compare sizes |
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160 | listsMatch = listsMatch && (voxelList.size() == this->getSize()); |
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161 | if(!listsMatch) return listsMatch; |
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162 | |
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163 | // make sure all Detection pixels are in voxel list |
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164 | listsMatch = listsMatch && this->voxelListCovered(voxelList); |
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165 | |
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166 | // make sure all voxels are in Detection |
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167 | for(unsigned int i=0;i<voxelList.size();i++) |
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168 | listsMatch = listsMatch && this->isInObject(voxelList[i]); |
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169 | // listsMatch = listsMatch && this->pixelArray.isInObject(voxelList[i]); |
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170 | |
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171 | return listsMatch; |
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172 | |
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173 | } |
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174 | //-------------------------------------------------------------------- |
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175 | |
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176 | //-------------------------------------------------------------------- |
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177 | |
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178 | bool Detection::voxelListCovered(std::vector<Voxel> voxelList) |
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179 | { |
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180 | /// @details |
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181 | /// A test to see whether the given list of Voxels contains each |
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182 | /// position in this Detection's pixel list. It does not look for |
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183 | /// a 1-1 correspondence: the given list can be a super-set of the |
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184 | /// Detection. No testing of the fluxes of the Voxels is done. |
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185 | /// |
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186 | /// \param voxelList The std::vector list of Voxels to be tested. |
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187 | |
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188 | bool listsMatch = true; |
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189 | |
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190 | // make sure all Detection pixels are in voxel list |
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191 | int v1=0, mysize=this->getSize(); |
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192 | while(listsMatch && v1<mysize){ |
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193 | bool inList = false; |
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194 | unsigned int v2=0; |
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195 | Voxel test = this->getPixel(v1); |
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196 | while(!inList && v2<voxelList.size()){ |
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197 | inList = inList || test.match(voxelList[v2]); |
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198 | v2++; |
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199 | } |
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200 | listsMatch = listsMatch && inList; |
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201 | v1++; |
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202 | } |
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203 | |
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204 | return listsMatch; |
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205 | |
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206 | } |
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207 | //-------------------------------------------------------------------- |
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208 | |
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209 | void Detection::calcFluxes(std::vector<Voxel> voxelList) |
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210 | { |
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211 | /// @details |
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212 | /// A function that calculates total & peak fluxes (and the location |
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213 | /// of the peak flux) for a Detection. |
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214 | /// |
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215 | /// \param fluxArray The array of flux values to calculate the |
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216 | /// flux parameters from. |
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217 | /// \param dim The dimensions of the flux array. |
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218 | |
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219 | this->totalFlux = this->peakFlux = 0; |
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220 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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221 | |
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222 | // first check that the voxel list and the Detection's pixel list |
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223 | // have a 1-1 correspondence |
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224 | |
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225 | if(!this->voxelListCovered(voxelList)){ |
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226 | duchampError("Detection::calcFluxes","Voxel list provided does not match"); |
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227 | return; |
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228 | } |
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229 | |
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230 | for(unsigned int i=0;i<voxelList.size();i++) { |
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231 | if(this->isInObject(voxelList[i])){ |
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232 | // if(this->pixelArray.isInObject(voxelList[i])){ |
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233 | long x = voxelList[i].getX(); |
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234 | long y = voxelList[i].getY(); |
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235 | long z = voxelList[i].getZ(); |
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236 | float f = voxelList[i].getF(); |
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237 | this->totalFlux += f; |
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238 | this->xCentroid += x*f; |
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239 | this->yCentroid += y*f; |
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240 | this->zCentroid += z*f; |
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241 | if( (i==0) || //first time round |
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242 | (this->negSource&&(f<this->peakFlux)) || |
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243 | (!this->negSource&&(f>this->peakFlux)) ) |
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244 | { |
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245 | this->peakFlux = f; |
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246 | this->xpeak = x; |
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247 | this->ypeak = y; |
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248 | this->zpeak = z; |
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249 | } |
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250 | } |
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251 | } |
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252 | |
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253 | this->xCentroid /= this->totalFlux; |
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254 | this->yCentroid /= this->totalFlux; |
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255 | this->zCentroid /= this->totalFlux; |
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256 | } |
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257 | //-------------------------------------------------------------------- |
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258 | |
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259 | void Detection::calcFluxes(float *fluxArray, long *dim) |
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260 | { |
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261 | /// @details |
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262 | /// A function that calculates total & peak fluxes (and the location |
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263 | /// of the peak flux) for a Detection. |
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264 | /// |
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265 | /// \param fluxArray The array of flux values to calculate the |
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266 | /// flux parameters from. |
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267 | /// \param dim The dimensions of the flux array. |
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268 | |
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269 | this->totalFlux = this->peakFlux = 0; |
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270 | this->xCentroid = this->yCentroid = this->zCentroid = 0.; |
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271 | |
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272 | // std::vector<Voxel> voxList = this->pixelArray.getPixelSet(); |
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273 | std::vector<Voxel> voxList = this->getPixelSet(); |
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274 | std::vector<Voxel>::iterator vox=voxList.begin(); |
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275 | for(;vox<voxList.end();vox++){ |
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276 | |
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277 | long x=vox->getX(); |
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278 | long y=vox->getY(); |
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279 | long z=vox->getZ(); |
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280 | long ind = vox->arrayIndex(dim); |
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281 | float f = fluxArray[ind]; |
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282 | this->totalFlux += f; |
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283 | this->xCentroid += x*f; |
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284 | this->yCentroid += y*f; |
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285 | this->zCentroid += z*f; |
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286 | if( (vox==voxList.begin()) || |
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287 | (this->negSource&&(f<this->peakFlux)) || |
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288 | (!this->negSource&&(f>this->peakFlux)) ) |
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289 | { |
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290 | this->peakFlux = f; |
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291 | this->xpeak = x; |
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292 | this->ypeak = y; |
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293 | this->zpeak = z; |
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294 | } |
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295 | |
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296 | } |
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297 | |
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298 | this->xCentroid /= this->totalFlux; |
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299 | this->yCentroid /= this->totalFlux; |
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300 | this->zCentroid /= this->totalFlux; |
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301 | } |
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302 | //-------------------------------------------------------------------- |
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303 | |
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304 | void Detection::calcWCSparams(FitsHeader &head) |
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305 | { |
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306 | /// @details |
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307 | /// Use the input wcs to calculate the position and velocity |
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308 | /// information for the Detection. |
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309 | /// Quantities calculated: |
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310 | /// <ul><li> RA: ra [deg], ra (string), ra width. |
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311 | /// <li> Dec: dec [deg], dec (string), dec width. |
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312 | /// <li> Vel: vel [km/s], min & max vel, vel width. |
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313 | /// <li> coord type for all three axes, nuRest, |
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314 | /// <li> name (IAU-style, in equatorial or Galactic) |
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315 | /// </ul> |
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316 | /// |
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317 | /// Note that the regular parameters are NOT recalculated! |
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318 | /// |
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319 | /// \param head FitsHeader object that contains the WCS information. |
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320 | |
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321 | if(head.isWCS()){ |
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322 | |
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323 | double *pixcrd = new double[15]; |
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324 | double *world = new double[15]; |
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325 | /* |
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326 | define a five-point array in 3D: |
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327 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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328 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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329 | and convert to world coordinates. |
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330 | */ |
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331 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->getXcentre(); |
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332 | pixcrd[9] = this->getXmin()-0.5; |
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333 | pixcrd[12] = this->getXmax()+0.5; |
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334 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->getYcentre(); |
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335 | pixcrd[10] = this->getYmin()-0.5; |
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336 | pixcrd[13] = this->getYmax()+0.5; |
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337 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->getZcentre(); |
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338 | pixcrd[5] = this->getZmin(); |
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339 | pixcrd[8] = this->getZmax(); |
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340 | int flag = head.pixToWCS(pixcrd, world, 5); |
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341 | delete [] pixcrd; |
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342 | if(flag!=0) duchampError("calcWCSparams", |
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343 | "Error in calculating the WCS for this object.\n"); |
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344 | else{ |
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345 | |
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346 | // world now has the WCS coords for the five points |
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347 | // -- use this to work out WCS params |
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348 | |
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349 | this->specOK = head.canUseThirdAxis(); |
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350 | this->lngtype = head.WCS().lngtyp; |
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351 | this->lattype = head.WCS().lattyp; |
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352 | this->specUnits = head.getSpectralUnits(); |
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353 | this->fluxUnits = head.getFluxUnits(); |
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354 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
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355 | this->intFluxUnits = head.getIntFluxUnits(); |
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356 | this->ra = world[0]; |
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357 | this->dec = world[1]; |
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358 | this->raS = decToDMS(this->ra, this->lngtype); |
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359 | this->decS = decToDMS(this->dec,this->lattype); |
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360 | this->raWidth = angularSeparation(world[9],world[1], |
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361 | world[12],world[1]) * 60.; |
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362 | this->decWidth = angularSeparation(world[0],world[10], |
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363 | world[0],world[13]) * 60.; |
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364 | |
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365 | // Object2D spatMap = this->pixelArray.getSpatialMap(); |
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366 | Object2D spatMap = this->getSpatialMap(); |
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367 | std::pair<double,double> axes = spatMap.getPrincipleAxes(); |
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368 | this->majorAxis = std::max(axes.first,axes.second) * head.getAvPixScale(); |
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369 | this->minorAxis = std::min(axes.first,axes.second) * head.getAvPixScale(); |
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370 | this->posang = spatMap.getPositionAngle() * 180. / M_PI; |
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371 | |
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372 | this->name = head.getIAUName(this->ra, this->dec); |
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373 | this->vel = head.specToVel(world[2]); |
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374 | this->velMin = head.specToVel(world[5]); |
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375 | this->velMax = head.specToVel(world[8]); |
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376 | this->velWidth = fabs(this->velMax - this->velMin); |
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377 | |
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378 | // this->calcIntegFlux(fluxArray,dim,head); |
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379 | |
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380 | this->flagWCS = true; |
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381 | } |
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382 | delete [] world; |
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383 | |
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384 | } |
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385 | } |
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386 | //-------------------------------------------------------------------- |
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387 | |
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388 | void Detection::calcIntegFlux(std::vector<Voxel> voxelList, FitsHeader &head) |
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389 | { |
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390 | /// @details |
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391 | /// Uses the input WCS to calculate the velocity-integrated flux, |
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392 | /// putting velocity in units of km/s. |
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393 | /// The fluxes used are taken from the Voxels, rather than an |
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394 | /// array of flux values. |
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395 | /// Integrates over full spatial and velocity range as given |
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396 | /// by the extrema calculated by calcWCSparams. |
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397 | /// |
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398 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
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399 | /// corrected by the beam size (in pixels). This is done by |
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400 | /// multiplying the integrated flux by the number of spatial pixels, |
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401 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
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402 | /// pix/beam --> Jy) |
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403 | /// |
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404 | /// \param voxelList The list of Voxels with flux information |
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405 | /// \param head FitsHeader object that contains the WCS information. |
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406 | |
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407 | const int border = 1; |
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408 | |
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409 | if(!this->voxelListCovered(voxelList)){ |
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410 | duchampError("Detection::calcIntegFlux","Voxel list provided does not match"); |
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411 | return; |
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412 | } |
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413 | |
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414 | // if(head.getNumAxes() > 2) { |
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415 | if(!head.is2D()){ |
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416 | |
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417 | // include one pixel either side in each direction |
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418 | long xsize = (this->getXmax()-this->getXmin()+border*2+1); |
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419 | long ysize = (this->getYmax()-this->getYmin()+border*2+1); |
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420 | long zsize = (this->getZmax()-this->getZmin()+border*2+1); |
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421 | long size = xsize*ysize*zsize; |
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422 | std::vector <bool> isObj(size,false); |
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423 | double *localFlux = new double[size]; |
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424 | for(int i=0;i<size;i++) localFlux[i]=0.; |
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425 | |
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426 | for(unsigned int i=0;i<voxelList.size();i++){ |
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427 | if(this->isInObject(voxelList[i])){ |
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428 | // if(this->pixelArray.isInObject(voxelList[i])){ |
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429 | long x = voxelList[i].getX(); |
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430 | long y = voxelList[i].getY(); |
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431 | long z = voxelList[i].getZ(); |
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432 | long pos = (x-this->getXmin()+border) + (y-this->getYmin()+border)*xsize |
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433 | + (z-this->getZmin()+border)*xsize*ysize; |
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434 | localFlux[pos] = voxelList[i].getF(); |
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435 | isObj[pos] = true; |
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436 | } |
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437 | } |
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438 | |
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439 | // work out the WCS coords for each pixel |
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440 | double *world = new double[size]; |
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441 | double xpt,ypt,zpt; |
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442 | for(int i=0;i<xsize*ysize*zsize;i++){ |
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443 | xpt = double( this->getXmin() - border + i%xsize ); |
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444 | ypt = double( this->getYmin() - border + (i/xsize)%ysize ); |
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445 | zpt = double( this->getZmin() - border + i/(xsize*ysize) ); |
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446 | world[i] = head.pixToVel(xpt,ypt,zpt); |
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447 | } |
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448 | |
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449 | double integrated = 0.; |
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450 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
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451 | for(int z=0; z<zsize; z++){ |
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452 | int pos = z*xsize*ysize + pix; |
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453 | if(isObj[pos]){ // if it's an object pixel... |
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454 | double deltaVel; |
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455 | if(z==0) |
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456 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
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457 | else if(z==(zsize-1)) |
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458 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
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459 | else |
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460 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
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461 | integrated += localFlux[pos] * fabs(deltaVel); |
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462 | } |
---|
463 | } |
---|
464 | } |
---|
465 | this->intFlux = integrated; |
---|
466 | |
---|
467 | delete [] world; |
---|
468 | delete [] localFlux; |
---|
469 | |
---|
470 | calcVelWidths(voxelList,head); |
---|
471 | |
---|
472 | } |
---|
473 | else // in this case there is just a 2D image. |
---|
474 | this->intFlux = this->totalFlux; |
---|
475 | |
---|
476 | if(head.isWCS()){ |
---|
477 | // correct for the beam size if the flux units string ends in "/beam" |
---|
478 | if(head.needBeamSize()) this->intFlux /= head.getBeamSize(); |
---|
479 | } |
---|
480 | |
---|
481 | } |
---|
482 | //-------------------------------------------------------------------- |
---|
483 | |
---|
484 | void Detection::calcIntegFlux(float *fluxArray, long *dim, FitsHeader &head) |
---|
485 | { |
---|
486 | /// @details |
---|
487 | /// Uses the input WCS to calculate the velocity-integrated flux, |
---|
488 | /// putting velocity in units of km/s. |
---|
489 | /// Integrates over full spatial and velocity range as given |
---|
490 | /// by the extrema calculated by calcWCSparams. |
---|
491 | /// |
---|
492 | /// If the flux units end in "/beam" (eg. Jy/beam), then the flux is |
---|
493 | /// corrected by the beam size (in pixels). This is done by |
---|
494 | /// multiplying the integrated flux by the number of spatial pixels, |
---|
495 | /// and dividing by the beam size in pixels (e.g. Jy/beam * pix / |
---|
496 | /// pix/beam --> Jy) |
---|
497 | /// |
---|
498 | /// \param fluxArray The array of flux values. |
---|
499 | /// \param dim The dimensions of the flux array. |
---|
500 | /// \param head FitsHeader object that contains the WCS information. |
---|
501 | |
---|
502 | // int numDim=0; |
---|
503 | // for(int i=0;i<3;i++) if(dim[i]>1) numDim++; |
---|
504 | // if(head.getNumAxes() > 2) { |
---|
505 | // if(numDim > 2) { |
---|
506 | if(!head.is2D()){ |
---|
507 | |
---|
508 | // include one pixel either side in each direction |
---|
509 | long xsize = (this->getXmax()-this->getXmin()+3); |
---|
510 | long ysize = (this->getYmax()-this->getYmin()+3); |
---|
511 | long zsize = (this->getZmax()-this->getZmin()+3); |
---|
512 | long size = xsize*ysize*zsize; |
---|
513 | std::vector <bool> isObj(size,false); |
---|
514 | double *localFlux = new double[size]; |
---|
515 | for(int i=0;i<size;i++) localFlux[i]=0.; |
---|
516 | // work out which pixels are object pixels |
---|
517 | // for(int m=0; m<this->pixelArray.getNumChanMap(); m++){ |
---|
518 | // ChanMap tempmap = this->pixelArray.getChanMap(m); |
---|
519 | // long z = this->pixelArray.getChanMap(m).getZ(); |
---|
520 | // for(int s=0; s<this->pixelArray.getChanMap(m).getNumScan(); s++){ |
---|
521 | // long y = this->pixelArray.getChanMap(m).getScan(s).getY(); |
---|
522 | // for(long x=this->pixelArray.getChanMap(m).getScan(s).getX(); |
---|
523 | // x<=this->pixelArray.getChanMap(m).getScan(s).getXmax(); |
---|
524 | // x++){ |
---|
525 | // long pos = (x-this->getXmin()+1) + (y-this->getYmin()+1)*xsize |
---|
526 | // + (z-this->getZmin()+1)*xsize*ysize; |
---|
527 | // localFlux[pos] = fluxArray[x + y*dim[0] + z*dim[0]*dim[1]]; |
---|
528 | // isObj[pos] = true; |
---|
529 | // } |
---|
530 | // } |
---|
531 | // } |
---|
532 | for(int m=0; m<this->getNumChanMap(); m++){ |
---|
533 | ChanMap tempmap = this->getChanMap(m); |
---|
534 | long z = this->getChanMap(m).getZ(); |
---|
535 | for(int s=0; s<this->getChanMap(m).getNumScan(); s++){ |
---|
536 | long y = this->getChanMap(m).getScan(s).getY(); |
---|
537 | for(long x=this->getChanMap(m).getScan(s).getX(); |
---|
538 | x<=this->getChanMap(m).getScan(s).getXmax(); |
---|
539 | x++){ |
---|
540 | long pos = (x-this->getXmin()+1) + (y-this->getYmin()+1)*xsize |
---|
541 | + (z-this->getZmin()+1)*xsize*ysize; |
---|
542 | localFlux[pos] = fluxArray[x + y*dim[0] + z*dim[0]*dim[1]]; |
---|
543 | isObj[pos] = true; |
---|
544 | } |
---|
545 | } |
---|
546 | } |
---|
547 | |
---|
548 | // work out the WCS coords for each pixel |
---|
549 | double *world = new double[size]; |
---|
550 | double xpt,ypt,zpt; |
---|
551 | for(int i=0;i<xsize*ysize*zsize;i++){ |
---|
552 | xpt = double( this->getXmin() -1 + i%xsize ); |
---|
553 | ypt = double( this->getYmin() -1 + (i/xsize)%ysize ); |
---|
554 | zpt = double( this->getZmin() -1 + i/(xsize*ysize) ); |
---|
555 | world[i] = head.pixToVel(xpt,ypt,zpt); |
---|
556 | } |
---|
557 | |
---|
558 | double integrated = 0.; |
---|
559 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
---|
560 | for(int z=0; z<zsize; z++){ |
---|
561 | int pos = z*xsize*ysize + pix; |
---|
562 | if(isObj[pos]){ // if it's an object pixel... |
---|
563 | double deltaVel; |
---|
564 | if(z==0) |
---|
565 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
---|
566 | else if(z==(zsize-1)) |
---|
567 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
---|
568 | else |
---|
569 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
---|
570 | integrated += localFlux[pos] * fabs(deltaVel); |
---|
571 | } |
---|
572 | } |
---|
573 | } |
---|
574 | this->intFlux = integrated; |
---|
575 | |
---|
576 | delete [] world; |
---|
577 | delete [] localFlux; |
---|
578 | |
---|
579 | calcVelWidths(fluxArray, dim, head); |
---|
580 | |
---|
581 | } |
---|
582 | else // in this case there is just a 2D image. |
---|
583 | this->intFlux = this->totalFlux; |
---|
584 | |
---|
585 | if(head.isWCS()){ |
---|
586 | // correct for the beam size if the flux units string ends in "/beam" |
---|
587 | if(head.needBeamSize()) this->intFlux /= head.getBeamSize(); |
---|
588 | } |
---|
589 | |
---|
590 | } |
---|
591 | //-------------------------------------------------------------------- |
---|
592 | |
---|
593 | void Detection::calcVelWidths(std::vector<Voxel> voxelList, FitsHeader &head) |
---|
594 | { |
---|
595 | /// @details |
---|
596 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
597 | /// peak integrated flux. The procedure is as follows: first |
---|
598 | /// generate an integrated flux spectrum (using all given voxels |
---|
599 | /// that lie in the object's spatial map); find the peak; starting |
---|
600 | /// at the spectral edges of the detection, move in or out until |
---|
601 | /// you reach the 20% or 50% peak flux level. Linear interpolation |
---|
602 | /// between points is done. |
---|
603 | /// |
---|
604 | /// \param voxelList The list of Voxels with flux information |
---|
605 | /// \param head FitsHeader object that contains the WCS information. |
---|
606 | |
---|
607 | const int border = 1; |
---|
608 | long zsize = (this->getZmax()-this->getZmin()+border*2+1); |
---|
609 | double xpt = double(this->getXcentre()); |
---|
610 | double ypt = double(this->getYcentre()); |
---|
611 | double zpt; |
---|
612 | |
---|
613 | float *intSpec = new float[zsize]; |
---|
614 | for(int i=0;i<zsize;i++) intSpec[i]=0; |
---|
615 | |
---|
616 | // Object2D spatMap = this->pixelArray.getSpatialMap(); |
---|
617 | Object2D spatMap = this->getSpatialMap(); |
---|
618 | for(int s=0;s<spatMap.getNumScan();s++){ |
---|
619 | for(unsigned int i=0;i<voxelList.size();i++){ |
---|
620 | if(spatMap.isInObject(voxelList[i])){ |
---|
621 | if(voxelList[i].getZ()>=this->getZmin()-border && |
---|
622 | voxelList[i].getZ()<=this->getZmax()+border) |
---|
623 | intSpec[voxelList[i].getZ()-this->getZmin()+1] += voxelList[i].getF(); |
---|
624 | } |
---|
625 | } |
---|
626 | } |
---|
627 | |
---|
628 | std::vector<std::pair<int,float> > goodPix; |
---|
629 | float peak; |
---|
630 | int peakLoc; |
---|
631 | for(int z=0;z<zsize;z++) { |
---|
632 | if(z==0 || peak<intSpec[z]){ |
---|
633 | peak = intSpec[z]; |
---|
634 | peakLoc = z; |
---|
635 | } |
---|
636 | goodPix.push_back(std::pair<int,float>(z,intSpec[z])); |
---|
637 | } |
---|
638 | |
---|
639 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
640 | // points. Then, if the int flux there is above the 20%/50% |
---|
641 | // limit, go out, otherwise go in. This is to deal with the |
---|
642 | // problems from double peaked sources. |
---|
643 | |
---|
644 | int z; |
---|
645 | bool goLeft; |
---|
646 | z=border; |
---|
647 | goLeft = intSpec[z]>peak*0.5; |
---|
648 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
---|
649 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
---|
650 | if(z==0) this->v50min = this->velMin; |
---|
651 | else{ |
---|
652 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
---|
653 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
---|
654 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
655 | } |
---|
656 | z=this->getZmax()-this->getZmin(); |
---|
657 | goLeft = intSpec[z]<peak*0.5; |
---|
658 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
659 | else while(z<zsize && intSpec[z]>peak*0.5) z++; |
---|
660 | if(z==zsize) this->v50max = this->velMax; |
---|
661 | else{ |
---|
662 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
---|
663 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
---|
664 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
665 | } |
---|
666 | z=border; |
---|
667 | goLeft = intSpec[z]>peak*0.5; |
---|
668 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
669 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
670 | if(z==0) this->v20min = this->velMin; |
---|
671 | else{ |
---|
672 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
---|
673 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
---|
674 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
675 | } |
---|
676 | z=this->getZmax()-this->getZmin(); |
---|
677 | goLeft = intSpec[z]<peak*0.5; |
---|
678 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
679 | else while(z<zsize && intSpec[z]>peak*0.2) z++; |
---|
680 | if(z==zsize) this->v20max = this->velMax; |
---|
681 | else{ |
---|
682 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]) + this->getZmin() - border; |
---|
683 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]) + this->getZmin() - border; |
---|
684 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
685 | } |
---|
686 | |
---|
687 | this->w20 = fabs(this->v20min - this->v20max); |
---|
688 | this->w50 = fabs(this->v50min - this->v50max); |
---|
689 | |
---|
690 | delete [] intSpec; |
---|
691 | |
---|
692 | } |
---|
693 | |
---|
694 | //-------------------------------------------------------------------- |
---|
695 | |
---|
696 | void Detection::calcVelWidths(float *fluxArray, long *dim, FitsHeader &head) |
---|
697 | { |
---|
698 | /// @details |
---|
699 | /// Calculates the widths of the detection at 20% and 50% of the |
---|
700 | /// peak integrated flux. The procedure is as follows: first |
---|
701 | /// generate an integrated flux spectrum (summing each spatial |
---|
702 | /// pixel's spectrum); find the peak; starting at the spectral |
---|
703 | /// edges of the detection, move in or out until you reach the 20% |
---|
704 | /// or 50% peak flux level. Linear interpolation between points is |
---|
705 | /// done. |
---|
706 | /// |
---|
707 | /// \param fluxArray The array of flux values. |
---|
708 | /// \param dim The dimensions of the flux array. |
---|
709 | /// \param head FitsHeader object that contains the WCS information. |
---|
710 | |
---|
711 | if(dim[2] > 2){ |
---|
712 | |
---|
713 | double xpt = double(this->getXcentre()); |
---|
714 | double ypt = double(this->getYcentre()); |
---|
715 | double zpt; |
---|
716 | |
---|
717 | float *intSpec = new float[dim[2]]; |
---|
718 | bool *mask = new bool[dim[0]*dim[1]*dim[2]]; |
---|
719 | for(int i=0;i<dim[0]*dim[1]*dim[2];i++) mask[i] = true; |
---|
720 | getIntSpec(*this,fluxArray,dim,mask,1.,intSpec); |
---|
721 | |
---|
722 | std::vector<std::pair<int,float> > goodPix; |
---|
723 | float peak; |
---|
724 | int peakLoc; |
---|
725 | for(int z=this->getZmin();z<=this->getZmax();z++) { |
---|
726 | if(z==this->getZmin() || peak<intSpec[z]){ |
---|
727 | peak = intSpec[z]; |
---|
728 | peakLoc = z; |
---|
729 | } |
---|
730 | goodPix.push_back(std::pair<int,float>(z,intSpec[z])); |
---|
731 | } |
---|
732 | |
---|
733 | // finding the 20% & 50% points. Start at the velmin & velmax |
---|
734 | // points. Then, if the int flux there is above the 20%/50% |
---|
735 | // limit, go out, otherwise go in. This is to deal with the |
---|
736 | // problems from double- (or multi-) peaked sources. |
---|
737 | |
---|
738 | int z; |
---|
739 | bool goLeft; |
---|
740 | z=this->getZmin(); |
---|
741 | goLeft = intSpec[z]>peak*0.5; |
---|
742 | if(goLeft) while(z>0 && intSpec[z]>peak*0.5) z--; |
---|
743 | else while(z<peakLoc && intSpec[z]<peak*0.5) z++; |
---|
744 | if(z==0) this->v50min = this->velMin; |
---|
745 | else{ |
---|
746 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
747 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
748 | this->v50min = head.pixToVel(xpt,ypt,zpt); |
---|
749 | } |
---|
750 | z=this->getZmax(); |
---|
751 | goLeft = intSpec[z]<peak*0.5; |
---|
752 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.5) z--; |
---|
753 | else while(z<dim[2] && intSpec[z]>peak*0.5) z++; |
---|
754 | if(z==dim[2]) this->v50max = this->velMax; |
---|
755 | else{ |
---|
756 | if(goLeft) zpt = z + (peak*0.5-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
757 | else zpt = z - (peak*0.5-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
758 | this->v50max = head.pixToVel(xpt,ypt,zpt); |
---|
759 | } |
---|
760 | z=this->getZmin(); |
---|
761 | goLeft = intSpec[z]>peak*0.5; |
---|
762 | if(goLeft) while(z>0 && intSpec[z]>peak*0.2) z--; |
---|
763 | else while(z<peakLoc && intSpec[z]<peak*0.2) z++; |
---|
764 | if(z==0) this->v20min = this->velMin; |
---|
765 | else{ |
---|
766 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
767 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
768 | this->v20min = head.pixToVel(xpt,ypt,zpt); |
---|
769 | } |
---|
770 | z=this->getZmax(); |
---|
771 | goLeft = intSpec[z]<peak*0.5; |
---|
772 | if(goLeft) while(z>peakLoc && intSpec[z]<peak*0.2) z--; |
---|
773 | else while(z<dim[2] && intSpec[z]>peak*0.2) z++; |
---|
774 | if(z==dim[2]) this->v20max = this->velMax; |
---|
775 | else{ |
---|
776 | if(goLeft) zpt = z + (peak*0.2-intSpec[z])/(intSpec[z+1]-intSpec[z]); |
---|
777 | else zpt = z - (peak*0.2-intSpec[z])/(intSpec[z-1]-intSpec[z]); |
---|
778 | this->v20max = head.pixToVel(xpt,ypt,zpt); |
---|
779 | } |
---|
780 | |
---|
781 | delete [] intSpec; |
---|
782 | delete [] mask; |
---|
783 | |
---|
784 | } |
---|
785 | else{ |
---|
786 | this->v50min = this->v20min = this->velMin; |
---|
787 | this->v50max = this->v20max = this->velMax; |
---|
788 | } |
---|
789 | |
---|
790 | this->w20 = fabs(this->v20min - this->v20max); |
---|
791 | this->w50 = fabs(this->v50min - this->v50max); |
---|
792 | |
---|
793 | } |
---|
794 | //-------------------------------------------------------------------- |
---|
795 | |
---|
796 | // Detection operator+ (Detection lhs, Detection rhs) |
---|
797 | // { |
---|
798 | // /// @details |
---|
799 | // /// Combines two objects by adding all the pixels using the Object3D |
---|
800 | // /// operator. |
---|
801 | // /// |
---|
802 | // /// The pixel parameters are recalculated in the process (equivalent |
---|
803 | // /// to calling pixels().calcParams()), but WCS parameters are not. |
---|
804 | |
---|
805 | // Detection output = lhs; |
---|
806 | // output.pixelArray = lhs.pixelArray + rhs.pixelArray; |
---|
807 | // return output; |
---|
808 | // } |
---|
809 | //-------------------------------------------------------------------- |
---|
810 | |
---|
811 | void Detection::setOffsets(Param &par) |
---|
812 | { |
---|
813 | /// @details |
---|
814 | /// This function stores the values of the offsets for each cube axis. |
---|
815 | /// The offsets are the starting values of the cube axes that may differ from |
---|
816 | /// the default value of 0 (for instance, if a subsection is being used). |
---|
817 | /// The values will be used when the detection is outputted. |
---|
818 | |
---|
819 | this->xSubOffset = par.getXOffset(); |
---|
820 | this->ySubOffset = par.getYOffset(); |
---|
821 | this->zSubOffset = par.getZOffset(); |
---|
822 | } |
---|
823 | //-------------------------------------------------------------------- |
---|
824 | |
---|
825 | bool Detection::hasEnoughChannels(int minNumber) |
---|
826 | { |
---|
827 | /// @details |
---|
828 | /// A function to determine if the Detection has enough |
---|
829 | /// contiguous channels to meet the minimum requirement |
---|
830 | /// given as the argument. |
---|
831 | /// \param minNumber How many channels is the minimum acceptable number? |
---|
832 | /// \return True if there is at least one occurence of minNumber consecutive |
---|
833 | /// channels present to return true. False otherwise. |
---|
834 | |
---|
835 | // Preferred method -- need a set of minNumber consecutive channels present. |
---|
836 | // this->pixelArray.order(); |
---|
837 | this->order(); |
---|
838 | int numChannels = 0; |
---|
839 | bool result = false; |
---|
840 | // int size = this->pixelArray.getNumChanMap(); |
---|
841 | int size = this->getNumChanMap(); |
---|
842 | if(size>0) numChannels++; |
---|
843 | if( numChannels >= minNumber) result = true; |
---|
844 | for(int i=1;(i<size && !result);i++) { |
---|
845 | // if( (this->pixelArray.getZ(i) - this->pixelArray.getZ(i-1)) == 1) |
---|
846 | // numChannels++; |
---|
847 | // else if( (this->pixelArray.getZ(i) - this->pixelArray.getZ(i-1)) >= 2) |
---|
848 | // numChannels = 1; |
---|
849 | if( (this->getZ(i) - this->getZ(i-1)) == 1) |
---|
850 | numChannels++; |
---|
851 | else if( (this->getZ(i) - this->getZ(i-1)) >= 2) |
---|
852 | numChannels = 1; |
---|
853 | |
---|
854 | if( numChannels >= minNumber) result = true; |
---|
855 | } |
---|
856 | return result; |
---|
857 | |
---|
858 | } |
---|
859 | //-------------------------------------------------------------------- |
---|
860 | |
---|
861 | std::vector<int> Detection::getVertexSet() |
---|
862 | { |
---|
863 | /// @details |
---|
864 | /// Gets a list of points being the end-points of 1-pixel long |
---|
865 | /// segments drawing a border around the spatial extend of a |
---|
866 | /// detection. The vector is a series of 4 integers, being: x_0, |
---|
867 | /// y_0, x_1, y_1. |
---|
868 | /// \return The vector of vertex positions. |
---|
869 | |
---|
870 | std::vector<int> vertexSet; |
---|
871 | |
---|
872 | int xmin = this->getXmin() - 1; |
---|
873 | int xmax = this->getXmax() + 1; |
---|
874 | int ymin = this->getYmin() - 1; |
---|
875 | int ymax = this->getYmax() + 1; |
---|
876 | int xsize = xmax - xmin + 1; |
---|
877 | int ysize = ymax - ymin + 1; |
---|
878 | |
---|
879 | // std::vector<Voxel> voxlist = this->pixelArray.getPixelSet(); |
---|
880 | std::vector<Voxel> voxlist = this->getPixelSet(); |
---|
881 | std::vector<bool> isObj(xsize*ysize,false); |
---|
882 | for(unsigned int i=0;i<voxlist.size();i++){ |
---|
883 | int pos = (voxlist[i].getX()-xmin) + |
---|
884 | (voxlist[i].getY()-ymin)*xsize; |
---|
885 | isObj[pos] = true; |
---|
886 | } |
---|
887 | voxlist.clear(); |
---|
888 | |
---|
889 | for(int x=xmin; x<=xmax; x++){ |
---|
890 | // for each column... |
---|
891 | for(int y=ymin+1;y<=ymax;y++){ |
---|
892 | int current = (y-ymin)*xsize + x-xmin; |
---|
893 | int previous = (y-ymin-1)*xsize + x-xmin; |
---|
894 | if((isObj[current]&&!isObj[previous]) || |
---|
895 | (!isObj[current]&&isObj[previous])){ |
---|
896 | vertexSet.push_back(x); |
---|
897 | vertexSet.push_back(y); |
---|
898 | vertexSet.push_back(x+1); |
---|
899 | vertexSet.push_back(y); |
---|
900 | } |
---|
901 | } |
---|
902 | } |
---|
903 | for(int y=ymin; y<=ymax; y++){ |
---|
904 | // now for each row... |
---|
905 | for(int x=xmin+1;x<=xmax;x++){ |
---|
906 | int current = (y-ymin)*xsize + x-xmin; |
---|
907 | int previous = (y-ymin)*xsize + x-xmin - 1; |
---|
908 | if((isObj[current]&&!isObj[previous]) || |
---|
909 | (!isObj[current]&&isObj[previous])){ |
---|
910 | vertexSet.push_back(x); |
---|
911 | vertexSet.push_back(y); |
---|
912 | vertexSet.push_back(x); |
---|
913 | vertexSet.push_back(y+1); |
---|
914 | } |
---|
915 | } |
---|
916 | } |
---|
917 | |
---|
918 | return vertexSet; |
---|
919 | |
---|
920 | } |
---|
921 | //-------------------------------------------------------------------- |
---|
922 | |
---|
923 | // std::ostream& operator<< ( std::ostream& theStream, Detection& obj) |
---|
924 | // { |
---|
925 | // /// @details |
---|
926 | // /// A convenient way of printing the coordinate values for each |
---|
927 | // /// pixel in the Detection. |
---|
928 | // /// |
---|
929 | // /// NOTE THAT THERE IS CURRENTLY NO FLUX INFORMATION BEING PRINTED! |
---|
930 | // /// |
---|
931 | // /// Use as front end to the Object3D::operator<< function. |
---|
932 | |
---|
933 | // theStream << obj.pixelArray << "---\n"; |
---|
934 | // return theStream; |
---|
935 | // } |
---|
936 | //-------------------------------------------------------------------- |
---|
937 | |
---|
938 | } |
---|