1 | #include <iostream> |
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2 | #include <iomanip> |
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3 | #include <sstream> |
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4 | #include <string> |
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5 | #include <stdio.h> |
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6 | #include <cpgplot.h> |
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7 | #include <math.h> |
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8 | #include <wcs.h> |
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9 | #include <Cubes/cubes.hh> |
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10 | #include <Cubes/plots.hh> |
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11 | #include <Utils/utils.hh> |
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12 | |
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13 | void getSmallVelRange(Detection &obj, wcsprm *wcs, float *minvel, float *maxvel); |
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14 | void getSmallZRange(Detection &obj, float *minz, float *maxz); |
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15 | |
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16 | void Cube::outputSpectra() |
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17 | { |
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18 | /** |
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19 | * Cube::outputSpectra() |
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20 | * |
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21 | * The way to print out the spectra of the detected objects. |
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22 | * Make use of the SpectralPlot class in plots.h, which sizes everything correctly. |
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23 | * Main choice is whether to use the peak pixel, in which case the spectrum is just |
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24 | * that of the peak pixel, or the sum, where the spectrum is summed over all spatial |
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25 | * pixels that are in the object. |
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26 | * If a reconstruction has been done, that spectrum is plotted in red. |
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27 | * The limits of the detection are marked in blue. |
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28 | * A 0th moment map of the detection is also plotted, with a scale bar indicating the |
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29 | * spatial size. |
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30 | */ |
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31 | |
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32 | string spectrafile = this->par.getSpectraFile() + "/vcps"; |
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33 | Plot::SpectralPlot newplot; |
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34 | newplot.setUpPlot(spectrafile.c_str()); |
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35 | |
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36 | long xdim = this->axisDim[0]; |
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37 | long ydim = this->axisDim[1]; |
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38 | long zdim = this->axisDim[2]; |
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39 | int numObjects = this->objectList.size(); |
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40 | float beam = this->par.getBeamSize(); |
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41 | |
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42 | float *specx = new float[zdim]; |
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43 | float *specy = new float[zdim]; |
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44 | for(int i=0;i<zdim;i++) specy[i] = 0.; |
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45 | float *specy2 = new float[zdim]; |
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46 | for(int i=0;i<zdim;i++) specy2[i] = 0.; |
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47 | |
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48 | for(int nobj=0;nobj<numObjects;nobj++){ |
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49 | // for each object in the cube: |
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50 | Detection *obj = new Detection; |
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51 | *obj = this->objectList[nobj]; |
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52 | obj->calcParams(); |
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53 | |
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54 | for(int i=0;i<zdim;i++) specy[i] = 0.; |
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55 | if(this->par.getFlagATrous()) |
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56 | for(int i=0;i<zdim;i++) specy2[i] = 0.; |
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57 | |
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58 | double x = double(obj->getXcentre()); |
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59 | double y = double(obj->getYcentre()); |
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60 | if(this->flagWCS) |
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61 | for(double z=0;z<zdim;z++) specx[int(z)] = pixelToVelocity(this->wcs,x,y,z); |
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62 | else |
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63 | for(double z=0;z<zdim;z++) specx[int(z)] = z; |
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64 | |
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65 | string fluxLabel = "Flux"; |
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66 | |
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67 | if(par.getSpectralMethod()=="sum"){ |
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68 | if(this->flagWCS) fluxLabel += " [Jy]"; |
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69 | bool *done = new bool[xdim*ydim]; |
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70 | for(int i=0;i<xdim*ydim;i++) done[i]=false; |
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71 | int thisSize = obj->getSize(); |
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72 | for(int pix=0;pix<thisSize;pix++){ |
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73 | int pos = obj->getX(pix) + xdim * obj->getY(pix); |
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74 | if(!done[pos]){ |
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75 | done[pos] = true; |
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76 | for(int z=0;z<zdim;z++){ |
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77 | if(!(this->par.isBlank(this->array[pos+z*xdim*ydim]))){ |
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78 | specy[z] += this->array[pos + z*xdim*ydim] / beam; |
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79 | if(this->par.getFlagATrous()) |
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80 | specy2[z] += this->recon[pos + z*xdim*ydim] / beam; |
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81 | } |
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82 | } |
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83 | } |
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84 | } |
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85 | delete [] done; |
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86 | } |
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87 | else {// if(par.getSpectralMethod()=="peak"){ |
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88 | if(this->flagWCS) fluxLabel += " [Jy/beam]"; |
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89 | for(int z=0;z<zdim;z++){ |
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90 | int pos = obj->getXPeak() + xdim*obj->getYPeak(); |
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91 | specy[z] = this->array[pos + z*xdim*ydim]; |
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92 | if(this->par.getFlagATrous()) specy2[z] = this->recon[pos + z*xdim*ydim]; |
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93 | } |
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94 | } |
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95 | |
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96 | float vmax,vmin; |
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97 | vmax = vmin = specx[0]; |
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98 | for(int i=1;i<zdim;i++){ |
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99 | if(specx[i]>vmax) vmax=specx[i]; |
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100 | if(specx[i]<vmin) vmin=specx[i]; |
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101 | } |
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102 | float max,min; |
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103 | int loc=0; |
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104 | max = min = specy[0]; |
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105 | for(int i=1;i<zdim;i++){ |
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106 | if(specy[i]>max) max=specy[i]; |
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107 | if(specy[i]<min){ |
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108 | min=specy[i]; |
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109 | loc = i; |
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110 | } |
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111 | } |
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112 | // widen the flux range slightly so that the top & bottom don't lie on the axes. |
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113 | float width = max - min; |
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114 | max += width * 0.05; |
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115 | min -= width * 0.05; |
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116 | |
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117 | // now plot the resulting spectrum |
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118 | if(this->flagWCS) newplot.gotoHeader("Velocity [km s\\u-1\\d]"); |
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119 | else newplot.gotoHeader("Spectral pixel value"); |
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120 | |
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121 | string label; |
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122 | if(this->flagWCS){ |
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123 | label = obj->outputLabelWCS(); |
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124 | newplot.firstHeaderLine(label); |
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125 | } |
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126 | label = obj->outputLabelInfo(); |
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127 | newplot.secondHeaderLine(label); |
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128 | label = obj->outputLabelPix(); |
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129 | newplot.thirdHeaderLine(label); |
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130 | |
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131 | newplot.gotoMainSpectrum(vmin,vmax,min,max,fluxLabel); |
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132 | cpgline(zdim,specx,specy); |
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133 | if(this->par.getFlagATrous()){ |
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134 | cpgsci(2); |
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135 | cpgline(zdim,specx,specy2); |
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136 | cpgsci(1); |
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137 | } |
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138 | if(this->flagWCS) newplot.drawVelRange(obj->getVelMin(),obj->getVelMax()); |
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139 | else newplot.drawVelRange(obj->getZmin(),obj->getZmax()); |
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140 | |
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141 | /**************************/ |
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142 | // ZOOM IN SPECTRALLY ON THE DETECTION. |
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143 | |
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144 | float minvel,maxvel; |
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145 | if(this->flagWCS) getSmallVelRange(*obj,this->wcs,&minvel,&maxvel); |
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146 | else getSmallZRange(*obj,&minvel,&maxvel); |
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147 | |
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148 | // Find new max & min flux values |
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149 | swap(max,min); |
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150 | int ct = 0; |
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151 | for(int i=0;i<zdim;i++){ |
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152 | if((specx[i]>=minvel)&&(specx[i]<=maxvel)){ |
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153 | ct++; |
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154 | if(specy[i]>max) max=specy[i]; |
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155 | if(specy[i]<min) min=specy[i]; |
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156 | } |
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157 | } |
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158 | // widen the flux range slightly so that the top & bottom don't lie on the axes. |
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159 | width = max - min; |
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160 | max += width * 0.05; |
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161 | min -= width * 0.05; |
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162 | |
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163 | newplot.gotoZoomSpectrum(minvel,maxvel,min,max); |
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164 | cpgline(zdim,specx,specy); |
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165 | if(this->par.getFlagATrous()){ |
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166 | cpgsci(2); |
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167 | cpgline(zdim,specx,specy2); |
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168 | cpgsci(1); |
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169 | } |
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170 | if(this->flagWCS) newplot.drawVelRange(obj->getVelMin(),obj->getVelMax()); |
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171 | else newplot.drawVelRange(obj->getZmin(),obj->getZmax()); |
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172 | |
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173 | /**************************/ |
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174 | |
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175 | // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS |
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176 | newplot.gotoMap(); |
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177 | drawMomentCutout(*this,*obj); |
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178 | |
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179 | delete obj; |
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180 | |
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181 | }// end of loop over objects. |
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182 | |
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183 | delete [] specx; |
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184 | delete [] specy; |
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185 | delete [] specy2; |
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186 | |
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187 | } |
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188 | |
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189 | void getSmallVelRange(Detection &obj, wcsprm *wcs, float *minvel, float *maxvel) |
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190 | { |
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191 | /** |
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192 | * getSmallVelRange(obj,wcs,minvel,maxvel) |
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193 | * Routine to calculate the velocity range for the zoomed-in region. |
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194 | * This range should be the maximum of 20 pixels, or 3x the wdith of the detection. |
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195 | * Need to : |
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196 | * Calculate pixel width of a 3x-detection-width region. |
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197 | * If smaller than 20, calculate velocities of central vel +- 10 pixels |
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198 | * If not, use the 3x-detection-width |
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199 | * Range returned via "minvel" and "maxvel" parameters. |
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200 | */ |
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201 | |
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202 | double *pixcrd = new double[3]; |
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203 | double *world = new double[3]; |
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204 | float minpix,maxpix; |
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205 | // define new velocity extrema -- make it 3x wider than the width of the detection. |
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206 | *minvel = 0.5*(obj.getVelMin()+obj.getVelMax()) - 1.5*obj.getVelWidth(); |
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207 | *maxvel = 0.5*(obj.getVelMin()+obj.getVelMax()) + 1.5*obj.getVelWidth(); |
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208 | // Find velocity range in number of pixels: |
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209 | world[0] = obj.getRA(); |
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210 | world[1] = obj.getDec(); |
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211 | world[2] = velToCoord(wcs,*minvel); |
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212 | wcsToPixSingle(wcs,world,pixcrd); |
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213 | minpix = pixcrd[2]; |
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214 | world[2] = velToCoord(wcs,*maxvel); |
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215 | wcsToPixSingle(wcs,world,pixcrd); |
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216 | maxpix = pixcrd[2]; |
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217 | if(maxpix<minpix) swap(maxpix,minpix); |
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218 | |
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219 | if((maxpix - minpix + 1) < 20){ |
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220 | pixcrd[0] = double(obj.getXcentre()); |
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221 | pixcrd[1] = double(obj.getYcentre()); |
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222 | pixcrd[2] = obj.getZcentre() - 10.; |
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223 | pixToWCSSingle(wcs,pixcrd,world); |
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224 | *minvel = setVel_kms(wcs,world[2]); |
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225 | pixcrd[2] = obj.getZcentre() + 10.; |
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226 | pixToWCSSingle(wcs,pixcrd,world); |
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227 | *maxvel = setVel_kms(wcs,world[2]); |
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228 | if(*maxvel<*minvel) swap(*maxvel,*minvel); |
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229 | } |
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230 | delete [] pixcrd; |
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231 | delete [] world; |
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232 | |
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233 | } |
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234 | |
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235 | void getSmallZRange(Detection &obj, float *minz, float *maxz) |
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236 | { |
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237 | /** |
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238 | * getSmallZRange(obj,minz,maxz) |
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239 | * Routine to calculate the pixel range for the zoomed-in spectrum. |
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240 | * This range should be the maximum of 20 pixels, or 3x the wdith of the detection. |
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241 | * Need to : |
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242 | * Calculate pixel width of a 3x-detection-width region. |
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243 | * If smaller than 20, use central pixel +- 10 pixels |
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244 | * Range returned via "minz" and "maxz" parameters. |
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245 | */ |
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246 | |
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247 | *minz = 2.*obj.getZmin() - obj.getZmax(); |
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248 | *maxz = 2.*obj.getZmax() - obj.getZmin(); |
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249 | |
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250 | if((*maxz - *minz + 1) < 20){ |
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251 | *minz = obj.getZcentre() - 10.; |
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252 | *maxz = obj.getZcentre() + 10.; |
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253 | } |
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254 | |
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255 | } |
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