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