1 | #include <iostream> |
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2 | #include <iomanip> |
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3 | #include <vector> |
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4 | #include <string> |
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5 | #include <wcs.h> |
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6 | #include <math.h> |
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7 | #include <param.hh> |
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8 | #include <Utils/utils.hh> |
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9 | #include <Detection/detection.hh> |
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10 | |
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11 | using std::setw; |
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12 | using std::setprecision; |
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13 | using std::endl; |
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14 | |
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15 | std::ostream& operator<< ( std::ostream& theStream, Voxel& vox) |
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16 | { |
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17 | /** |
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18 | * << operator for Voxel class |
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19 | * A convenient way of printing the coordinate |
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20 | * and flux values of a voxel. |
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21 | */ |
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22 | |
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23 | theStream << setw(4) << vox.itsX ; |
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24 | theStream << " " << setw(4) << vox.itsY; |
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25 | theStream << " " << setw(4) << vox.itsZ; |
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26 | theStream << setprecision(4); |
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27 | theStream << " " << vox.itsF; |
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28 | |
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29 | } |
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30 | //-------------------------------------------------------------------- |
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31 | |
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32 | void Detection::calcParams() |
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33 | { |
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34 | /** |
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35 | * Detection::calcParams() |
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36 | * A function that calculates centroid positions, |
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37 | * minima & maxima of coordinates, |
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38 | * and total & peak fluxes for a detection. |
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39 | */ |
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40 | |
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41 | this->xcentre = 0; |
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42 | this->ycentre = 0; |
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43 | this->zcentre = 0; |
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44 | this->totalFlux = 0; |
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45 | this->peakFlux = 0; |
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46 | this->xmin = 0; |
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47 | this->xmax = 0; |
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48 | this->ymin = 0; |
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49 | this->ymax = 0; |
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50 | this->zmin = 0; |
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51 | this->zmax = 0; |
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52 | if(this->pix.size()>0){ |
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53 | this->peakFlux = this->pix[0].itsF; |
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54 | for(int ctr=0;ctr<this->pix.size();ctr++){ |
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55 | this->xcentre += this->pix[ctr].itsX; |
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56 | this->ycentre += this->pix[ctr].itsY; |
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57 | this->zcentre += this->pix[ctr].itsZ; |
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58 | this->totalFlux += this->pix[ctr].itsF; |
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59 | if((ctr==0)||(this->pix[ctr].itsX<this->xmin)) |
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60 | this->xmin = this->pix[ctr].itsX; |
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61 | if((ctr==0)||(this->pix[ctr].itsX>this->xmax)) |
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62 | this->xmax = this->pix[ctr].itsX; |
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63 | if((ctr==0)||(this->pix[ctr].itsY<this->ymin)) |
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64 | this->ymin = this->pix[ctr].itsY; |
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65 | if((ctr==0)||(this->pix[ctr].itsY>this->ymax)) |
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66 | this->ymax = this->pix[ctr].itsY; |
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67 | if((ctr==0)||(this->pix[ctr].itsZ<this->zmin)) |
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68 | this->zmin = this->pix[ctr].itsZ; |
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69 | if((ctr==0)||(this->pix[ctr].itsZ>this->zmax)) |
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70 | this->zmax = this->pix[ctr].itsZ; |
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71 | if(this->negativeSource){ |
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72 | // if negative feature, peakFlux is most negative flux |
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73 | if((ctr==0)||(this->pix[ctr].itsF < this->peakFlux)){ |
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74 | this->peakFlux = this->pix[ctr].itsF; |
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75 | this->xpeak = this->pix[ctr].itsX; |
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76 | this->ypeak = this->pix[ctr].itsY; |
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77 | this->zpeak = this->pix[ctr].itsZ; |
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78 | } |
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79 | } |
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80 | else{ |
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81 | // otherwise, it's a regular detection, |
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82 | // and peakFlux is most positive flux |
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83 | if((ctr==0)||(this->pix[ctr].itsF > this->peakFlux)){ |
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84 | this->peakFlux = this->pix[ctr].itsF; |
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85 | this->xpeak = this->pix[ctr].itsX; |
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86 | this->ypeak = this->pix[ctr].itsY; |
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87 | this->zpeak = this->pix[ctr].itsZ; |
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88 | } |
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89 | } |
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90 | } |
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91 | this->xcentre /= this->pix.size(); |
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92 | this->ycentre /= this->pix.size(); |
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93 | this->zcentre /= this->pix.size(); |
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94 | } |
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95 | } |
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96 | //-------------------------------------------------------------------- |
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97 | |
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98 | void Detection::calcWCSparams(FitsHeader &head) |
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99 | { |
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100 | /** |
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101 | * Detection::calcWCSparams(FitsHeader &) |
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102 | * Use the input wcs to calculate the position and velocity |
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103 | * information for the Detection. |
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104 | * Quantities calculated: |
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105 | * RA: ra [deg], ra (string), ra width. |
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106 | * Dec: dec [deg], dec (string), dec width. |
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107 | * Vel: vel [km/s], min & max vel, vel width. |
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108 | * Other: coord type for all three axes, nuRest, |
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109 | * name (IAU-style, in equatorial or Galactic) |
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110 | * Uses getIntegFlux to calculate the integrated flux in (say) [Jy km/s] |
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111 | */ |
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112 | |
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113 | if(head.isWCS()){ |
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114 | |
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115 | this->calcParams(); // make sure this is up to date. |
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116 | |
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117 | double *pixcrd = new double[15]; |
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118 | double *world = new double[15]; |
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119 | /* |
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120 | define a five-point array in 3D: |
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121 | (x,y,z), (x,y,z1), (x,y,z2), (x1,y1,z), (x2,y2,z) |
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122 | [note: x = central point, x1 = minimum x, x2 = maximum x etc.] |
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123 | and convert to world coordinates. |
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124 | */ |
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125 | pixcrd[0] = pixcrd[3] = pixcrd[6] = this->xcentre; |
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126 | pixcrd[9] = this->xmin-0.5; |
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127 | pixcrd[12] = this->xmax+0.5; |
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128 | pixcrd[1] = pixcrd[4] = pixcrd[7] = this->ycentre; |
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129 | pixcrd[10] = this->ymin-0.5; |
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130 | pixcrd[13] = this->ymax+0.5; |
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131 | pixcrd[2] = pixcrd[11] = pixcrd[14] = this->zcentre; |
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132 | pixcrd[5] = this->zmin; |
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133 | pixcrd[8] = this->zmax; |
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134 | int flag = head.pixToWCS(pixcrd, world, 5); |
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135 | delete [] pixcrd; |
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136 | |
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137 | // world now has the WCS coords for the five points |
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138 | // -- use this to work out WCS params |
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139 | |
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140 | this->lngtype = head.getWCS()->lngtyp; |
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141 | this->lattype = head.getWCS()->lattyp; |
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142 | this->specUnits = head.getSpectralUnits(); |
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143 | this->fluxUnits = head.getFluxUnits(); |
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144 | // if fluxUnits are eg. Jy/beam, make intFluxUnits = Jy km/s |
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145 | this->intFluxUnits = head.getIntFluxUnits(); |
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146 | this->ra = world[0]; |
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147 | this->dec = world[1]; |
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148 | this->raS = decToDMS(this->ra, this->lngtype); |
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149 | this->decS = decToDMS(this->dec,this->lattype); |
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150 | this->raWidth = angularSeparation(world[9],world[1],world[12],world[1])*60.; |
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151 | this->decWidth = angularSeparation(world[0],world[10],world[0],world[13]) * 60.; |
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152 | this->name = head.getIAUName(this->ra, this->dec); |
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153 | this->vel = head.specToVel(world[2]); |
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154 | this->velMin = head.specToVel(world[5]); |
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155 | this->velMax = head.specToVel(world[8]); |
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156 | this->velWidth = fabs(this->velMax - this->velMin); |
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157 | |
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158 | this->getIntegFlux(head); |
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159 | |
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160 | this->flagWCS = true; |
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161 | |
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162 | delete [] world; |
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163 | |
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164 | } |
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165 | } |
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166 | //-------------------------------------------------------------------- |
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167 | |
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168 | float Detection::getIntegFlux(FitsHeader &head) |
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169 | { |
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170 | /** |
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171 | * Detection::getIntegFlux(FitsHeader) |
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172 | * Uses the input wcs to calculate the velocity-integrated flux, |
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173 | * putting velocity in units of km/s. |
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174 | * Integrates over full spatial and velocity range as given |
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175 | * by the extrema calculated by calcWCSparams. |
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176 | * If the flux units end in "/beam" (eg. Jy/beam), then the |
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177 | * flux is corrected by the beam size (in pixels). |
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178 | */ |
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179 | |
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180 | // include one pixel either side in each direction |
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181 | int xsize = (this->xmax-this->xmin+3); |
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182 | int ysize = (this->ymax-this->ymin+3); |
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183 | int zsize = (this->zmax-this->zmin+3); |
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184 | vector <bool> isObj(xsize*ysize*zsize,false); |
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185 | vector <float> fluxArray(xsize*ysize*zsize,0.); |
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186 | // work out which pixels are object pixels |
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187 | for(int p=0;p<this->pix.size();p++){ |
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188 | int pos = (this->pix[p].getX()-this->xmin+1) |
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189 | + (this->pix[p].getY()-this->ymin+1)*xsize |
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190 | + (this->pix[p].getZ()-this->zmin+1)*xsize*ysize; |
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191 | fluxArray[pos] = this->pix[p].getF(); |
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192 | isObj[pos] = true; |
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193 | } |
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194 | |
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195 | // work out the WCS coords for each pixel |
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196 | double *world = new double[xsize*ysize*zsize]; |
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197 | double x,y,z; |
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198 | for(int i=0;i<xsize*ysize*zsize;i++){ |
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199 | x = double( this->xmin -1 + i%xsize ); |
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200 | y = double( this->ymin -1 + (i/xsize)%ysize ); |
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201 | z = double( this->zmin -1 + i/(xsize*ysize) ); |
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202 | world[i] = head.pixToVel(x,y,z); |
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203 | } |
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204 | |
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205 | this->intFlux = 0.; |
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206 | for(int pix=0; pix<xsize*ysize; pix++){ // loop over each spatial pixel. |
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207 | for(int z=0; z<zsize; z++){ |
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208 | int pos = z*xsize*ysize + pix; |
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209 | if(isObj[pos]){ // if it's an object pixel... |
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210 | float deltaVel; |
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211 | if(z==0) |
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212 | deltaVel = (world[pos+xsize*ysize] - world[pos]); |
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213 | else if(z==(zsize-1)) |
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214 | deltaVel = (world[pos] - world[pos-xsize*ysize]); |
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215 | else |
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216 | deltaVel = (world[pos+xsize*ysize] - world[pos-xsize*ysize]) / 2.; |
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217 | this->intFlux += fluxArray[pos] * fabs(deltaVel); |
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218 | } |
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219 | } |
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220 | } |
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221 | |
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222 | // correct for the beam size if the flux units string ends in "/beam" |
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223 | int size = this->fluxUnits.size(); |
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224 | string tailOfFluxUnits = this->fluxUnits.substr(size-5,size); |
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225 | if(tailOfFluxUnits == "/beam") this->intFlux /= head.getBeamSize(); |
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226 | |
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227 | delete [] world; |
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228 | } |
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229 | //-------------------------------------------------------------------- |
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230 | |
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231 | void Detection::addAnObject(Detection &toAdd) |
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232 | { |
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233 | /** |
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234 | * Detection::addAnObject(Detection &) |
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235 | * Combines two objects by adding all the pixels of the argument |
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236 | * to the instigator. |
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237 | * All pixel & flux parameters are recalculated (so that |
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238 | * calcParams does not need to be called a second time), |
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239 | * but WCS parameters are not. |
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240 | * If the instigator is empty (pix.size()==0) then we just make it |
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241 | * equal to the argument, and call calcParams to initialise the |
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242 | * necessary parameters |
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243 | */ |
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244 | |
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245 | int size = this->pix.size(); |
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246 | if(size==0){ |
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247 | *this = toAdd; |
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248 | this->calcParams(); |
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249 | } |
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250 | else if(size>0){ |
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251 | |
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252 | this->xcentre *= size; |
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253 | this->ycentre *= size; |
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254 | this->zcentre *= size; |
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255 | |
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256 | for(int ctr=0;ctr<toAdd.getSize();ctr++){ |
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257 | long x = toAdd.getX(ctr); |
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258 | long y = toAdd.getY(ctr); |
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259 | long z = toAdd.getZ(ctr); |
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260 | float f = toAdd.getF(ctr); |
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261 | bool isNewPix = true; |
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262 | int ctr2 = 0; |
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263 | // For each pixel in the new object, test to see if it already |
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264 | // appears in the object |
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265 | while( isNewPix && (ctr2<this->pix.size()) ){ |
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266 | isNewPix = isNewPix && (( this->pix[ctr2].itsX != x ) || |
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267 | ( this->pix[ctr2].itsY != y ) || |
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268 | ( this->pix[ctr2].itsZ != z ) ); |
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269 | ctr2++; |
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270 | } |
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271 | if(isNewPix){ |
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272 | // If the pixel is new, add it to the object and |
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273 | // re-calculate the parameters. |
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274 | this->pix.push_back(toAdd.getPixel(ctr)); |
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275 | this->xcentre += x; |
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276 | this->ycentre += y; |
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277 | this->zcentre += z; |
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278 | this->totalFlux += f; |
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279 | if (x < this->xmin) this->xmin = x; |
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280 | else if(x > this->xmax) this->xmax = x; |
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281 | if (y < this->ymin) this->ymin = y; |
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282 | else if(y > this->ymax) this->ymax = y; |
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283 | if (z < this->zmin) this->zmin = z; |
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284 | else if(z > this->zmax) this->zmax = z; |
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285 | if(f > this->peakFlux) this->peakFlux = f; |
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286 | } |
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287 | } |
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288 | size = this->pix.size(); |
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289 | this->xcentre /= size; |
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290 | this->ycentre /= size; |
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291 | this->zcentre /= size; |
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292 | |
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293 | } |
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294 | } |
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295 | //-------------------------------------------------------------------- |
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296 | |
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297 | void Detection::addOffsets(Param &par) |
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298 | { |
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299 | this->xSubOffset = par.getXOffset(); |
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300 | this->ySubOffset = par.getYOffset(); |
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301 | this->zSubOffset = par.getZOffset(); |
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302 | } |
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303 | //-------------------------------------------------------------------- |
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304 | |
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305 | bool Detection::hasEnoughChannels(int minNumber) |
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306 | { |
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307 | /** |
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308 | * bool hasEnoughChannels(int) |
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309 | * A function to determine if the Detection has enough |
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310 | * contiguous channels to meet the minimum requirement |
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311 | * given as the argument. |
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312 | * Needs to have at least one occurence of minNumber consecutive |
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313 | * channels present to return true. Otherwise returns false. |
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314 | */ |
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315 | |
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316 | // Original requirement -- based on total span |
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317 | // int numChannels = this->getZmax() - this->getZmin() + 1; |
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318 | |
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319 | // Alternative -- number of distinct channels detected |
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320 | // int numChannels = 0; |
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321 | // this->SortByZ(); |
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322 | // if(this->getSize()>0) numChannels++; |
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323 | // for(int i=1;i<this->getSize();i++) |
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324 | // if(this->getZ(i)>this->getZ(i-1)) numChannels++; |
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325 | // return (numChannels < minNumber); |
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326 | |
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327 | // Preferred method -- need a set of minNumber consecutive channels present. |
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328 | this->SortByZ(); |
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329 | int numChannels = 0; |
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330 | bool result = false; |
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331 | if(this->getSize()>0) numChannels++; |
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332 | for(int i=1;i<this->getSize();i++) { |
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333 | if( (this->getZ(i) - this->getZ(i-1)) == 1) numChannels++; |
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334 | else if( (this->getZ(i) - this->getZ(i-1)) >= 2) numChannels = 1; |
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335 | |
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336 | if( numChannels >= minNumber) result = true; |
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337 | } |
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338 | return result; |
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339 | |
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340 | } |
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341 | //-------------------------------------------------------------------- |
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342 | |
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343 | int Detection::getSpatialSize() |
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344 | { |
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345 | /** |
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346 | * int getSpatialSize() |
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347 | * A function that returns the number of distinct spatial |
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348 | * pixels in a Detection. |
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349 | */ |
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350 | |
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351 | vector<Pixel> spatialPix; |
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352 | Pixel newpix; |
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353 | bool addThisOne; |
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354 | newpix.setXY(this->getX(0),this->getY(0)); |
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355 | spatialPix.push_back(newpix); |
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356 | for(int i=1;i<this->pix.size();i++){ |
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357 | newpix.setXY(this->getX(i),this->getY(i)); |
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358 | addThisOne = true; |
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359 | for(int j=0;(j<spatialPix.size())&&addThisOne;j++) { |
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360 | // do whole list or until addThisOne=false |
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361 | addThisOne = ( (newpix.getX()!=spatialPix[j].getX()) || |
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362 | (newpix.getY()!=spatialPix[j].getY()) ); |
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363 | // ie. if one of X or Y is different, addThisOne is true. |
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364 | } |
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365 | if(addThisOne) spatialPix.push_back(newpix); |
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366 | } |
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367 | return spatialPix.size(); |
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368 | } |
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369 | //-------------------------------------------------------------------- |
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370 | |
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371 | std::ostream& operator<< ( std::ostream& theStream, Detection& obj) |
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372 | { |
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373 | /** |
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374 | * << operator for Detection class |
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375 | * A convenient way of printing the coordinate & flux |
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376 | * values for each pixel in the Detection |
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377 | * --> use as front end to the << operator for Voxels. |
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378 | */ |
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379 | |
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380 | for(int i=0;i<obj.pix.size();i++) theStream << obj.pix[i] << endl; |
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381 | theStream<<"---"<<endl; |
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382 | } |
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383 | //-------------------------------------------------------------------- |
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384 | |
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385 | Detection combineObjects(Detection &first, Detection &second) |
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386 | { |
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387 | // make the new object |
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388 | Detection *newObject = new Detection; |
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389 | for(int ctr=0;ctr<first.getSize();ctr++){ |
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390 | newObject->addPixel(first.getPixel(ctr)); |
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391 | } |
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392 | for(int ctr=0;ctr<second.getSize();ctr++){ |
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393 | newObject->addPixel(second.getPixel(ctr)); |
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394 | } |
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395 | newObject->calcParams(); |
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396 | return *newObject; |
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397 | } |
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398 | //-------------------------------------------------------------------- |
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399 | |
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400 | vector <Detection> combineLists(vector <Detection> &first, |
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401 | vector <Detection> &second) |
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402 | { |
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403 | // make the new object |
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404 | vector <Detection> newList(first.size()+second.size()); |
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405 | for(int i=0;i<first.size();i++) newList[i] = first[i]; |
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406 | for(int i=0;i<second.size();i++) newList[i+first.size()] = second[i]; |
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407 | |
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408 | return newList; |
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409 | } |
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410 | |
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