1 | #include <iostream> |
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2 | #include <iomanip> |
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3 | #include <fstream> |
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4 | #include <sstream> |
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5 | #include <string> |
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6 | #include <math.h> |
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7 | #include <wcs.h> |
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8 | #include <wcsunits.h> |
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9 | #include <param.hh> |
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10 | #include <config.h> |
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11 | #include <duchamp.hh> |
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12 | #include <Utils/utils.hh> |
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13 | |
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14 | // Define funtion to print bools as words, in case the compiler doesn't recognise |
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15 | // the setf(ios::boolalpha) command... |
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16 | #ifdef HAVE_STDBOOL_H |
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17 | string stringize(bool b){ |
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18 | std::stringstream ss; |
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19 | ss.setf(std::ios::boolalpha); |
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20 | ss << b; |
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21 | return ss.str(); |
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22 | } |
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23 | #else |
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24 | string stringize(bool b){ |
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25 | std::string output; |
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26 | if(b) output="true"; |
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27 | else output="false"; |
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28 | return output; |
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29 | } |
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30 | #endif |
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31 | |
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32 | using std::setw; |
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33 | using std::endl; |
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34 | |
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35 | /****************************************************************/ |
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36 | /////////////////////////////////////////////////// |
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37 | //// Functions for FitsHeader class: |
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38 | /////////////////////////////////////////////////// |
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39 | |
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40 | FitsHeader::FitsHeader(){ |
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41 | this->wcs = new wcsprm; |
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42 | this->wcs->flag=-1; |
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43 | wcsini(true,3,this->wcs); |
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44 | this->wcsIsGood = false; |
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45 | this->nwcs = 0; |
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46 | this->scale=1.; |
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47 | this->offset=0.; |
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48 | this->power=1.; |
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49 | this->fluxUnits="counts"; |
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50 | } |
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51 | |
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52 | FitsHeader::FitsHeader(const FitsHeader& h){ |
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53 | this->wcs = new wcsprm; |
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54 | this->wcs->flag=-1; |
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55 | wcsini(true,h.wcs->naxis,this->wcs); |
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56 | wcscopy(true,h.wcs,this->wcs); |
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57 | wcsset(this->wcs); |
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58 | this->nwcs = h.nwcs; |
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59 | this->wcsIsGood = h.wcsIsGood; |
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60 | this->spectralUnits = h.spectralUnits; |
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61 | this->fluxUnits = h.fluxUnits; |
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62 | this->intFluxUnits = h.intFluxUnits; |
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63 | this->beamSize = h.beamSize; |
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64 | this->bmajKeyword = h.bmajKeyword; |
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65 | this->bminKeyword = h.bminKeyword; |
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66 | this->blankKeyword = h.blankKeyword; |
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67 | this->bzeroKeyword = h.bzeroKeyword; |
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68 | this->bscaleKeyword = h.bscaleKeyword; |
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69 | this->scale = h.scale; |
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70 | this->offset = h.offset; |
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71 | this->power = h.power; |
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72 | } |
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73 | |
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74 | FitsHeader& FitsHeader::operator= (const FitsHeader& h){ |
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75 | this->wcs = new wcsprm; |
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76 | this->wcs->flag=-1; |
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77 | wcsini(true,h.wcs->naxis,this->wcs); |
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78 | wcscopy(true,h.wcs,this->wcs); |
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79 | wcsset(this->wcs); |
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80 | this->nwcs = h.nwcs; |
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81 | this->wcsIsGood = h.wcsIsGood; |
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82 | this->spectralUnits = h.spectralUnits; |
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83 | this->fluxUnits = h.fluxUnits; |
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84 | this->intFluxUnits = h.intFluxUnits; |
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85 | this->beamSize = h.beamSize; |
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86 | this->bmajKeyword = h.bmajKeyword; |
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87 | this->bminKeyword = h.bminKeyword; |
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88 | this->blankKeyword = h.blankKeyword; |
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89 | this->bzeroKeyword = h.bzeroKeyword; |
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90 | this->bscaleKeyword = h.bscaleKeyword; |
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91 | this->scale = h.scale; |
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92 | this->offset = h.offset; |
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93 | this->power = h.power; |
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94 | } |
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95 | |
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96 | void FitsHeader::setWCS(wcsprm *w) |
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97 | { |
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98 | /** |
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99 | * FitsHeader::setWCS(wcsprm *) |
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100 | * A function that assigns the wcs parameters, and runs |
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101 | * wcsset to set it up correctly. |
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102 | * Performs a check to see if the WCS is good (by looking at |
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103 | * the lng and lat wcsprm parameters), and sets the wcsIsGood |
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104 | * flag accordingly. |
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105 | */ |
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106 | wcscopy(true,w,this->wcs); |
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107 | wcsset(this->wcs); |
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108 | if( (w->lng!=-1) && (w->lat!=-1) ) this->wcsIsGood = true; |
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109 | } |
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110 | |
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111 | wcsprm *FitsHeader::getWCS() |
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112 | { |
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113 | /** |
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114 | * FitsHeader::getWCS() |
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115 | * A function that returns a wcsprm object corresponding to the WCS. |
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116 | */ |
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117 | wcsprm *wNew = new wcsprm; |
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118 | wNew->flag=-1; |
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119 | wcsini(true,this->wcs->naxis,wNew); |
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120 | wcscopy(true,this->wcs,wNew); |
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121 | wcsset(wNew); |
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122 | return wNew; |
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123 | } |
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124 | |
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125 | int FitsHeader::wcsToPix(const double *world, double *pix){ |
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126 | return wcsToPixSingle(this->wcs,world,pix);} |
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127 | int FitsHeader::wcsToPix(const double *world, double *pix, const int npts){ |
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128 | return wcsToPixMulti(this->wcs,world,pix,npts);} |
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129 | int FitsHeader::pixToWCS(const double *pix, double *world){ |
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130 | return pixToWCSSingle(this->wcs,pix,world);} |
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131 | int FitsHeader::pixToWCS(const double *pix, double *world, const int npts){ |
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132 | return pixToWCSMulti(this->wcs,pix,world,npts);} |
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133 | |
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134 | double FitsHeader::pixToVel(double &x, double &y, double &z) |
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135 | { |
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136 | double vel; |
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137 | if(this->wcsIsGood){ |
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138 | double *pix = new double[3]; |
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139 | double *world = new double[3]; |
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140 | pix[0] = x; pix[1] = y; pix[2] = z; |
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141 | pixToWCSSingle(this->wcs,pix,world); |
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142 | vel = this->specToVel(world[2]); |
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143 | delete [] pix; |
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144 | delete [] world; |
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145 | } |
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146 | else vel = z; |
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147 | return vel; |
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148 | } |
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149 | |
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150 | double* FitsHeader::pixToVel(double &x, double &y, double *zarray, int size) |
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151 | { |
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152 | double *newzarray = new double[size]; |
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153 | if(this->wcsIsGood){ |
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154 | double *pix = new double[size*3]; |
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155 | for(int i=0;i<size;i++){ |
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156 | pix[3*i] = x; pix[3*i+1] = y; pix[3*i+2] = zarray[i]; |
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157 | } |
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158 | double *world = new double[size*3]; |
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159 | pixToWCSMulti(this->wcs,pix,world,size); |
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160 | delete [] pix; |
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161 | for(int i=0;i<size;i++) newzarray[i] = this->specToVel(world[3*i+2]); |
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162 | delete [] world; |
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163 | } |
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164 | else{ |
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165 | for(int i=0;i<size;i++) newzarray[i] = zarray[i]; |
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166 | } |
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167 | return newzarray; |
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168 | } |
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169 | |
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170 | double FitsHeader::specToVel(const double &coord) |
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171 | { |
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172 | double vel; |
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173 | if(power==1.0) vel = coord*this->scale + this->offset; |
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174 | else vel = pow( (coord*this->scale + this->offset), this->power); |
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175 | return vel; |
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176 | } |
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177 | |
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178 | double FitsHeader::velToSpec(const float &velocity) |
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179 | { |
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180 | // return velToCoord(this->wcs,velocity,this->spectralUnits);}; |
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181 | return (pow(velocity, 1./this->power) - this->offset) / this->scale;} |
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182 | |
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183 | string FitsHeader::getIAUName(double ra, double dec) |
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184 | { |
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185 | if(strcmp(this->wcs->lngtyp,"RA")==0) return getIAUNameEQ(ra, dec, this->wcs->equinox); |
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186 | else return getIAUNameGAL(ra, dec); |
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187 | } |
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188 | |
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189 | void FitsHeader::fixUnits(Param &par) |
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190 | { |
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191 | // define spectral units from the param set |
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192 | this->spectralUnits = par.getSpectralUnits(); |
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193 | |
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194 | double sc=1.; |
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195 | double of=0.; |
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196 | double po=1.;; |
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197 | if(this->wcsIsGood){ |
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198 | int flag = wcsunits( this->wcs->cunit[wcs->spec], |
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199 | this->spectralUnits.c_str(), |
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200 | &sc, &of, &po); |
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201 | if(flag>0){ |
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202 | std::stringstream errmsg; |
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203 | errmsg << "WCSUNITS Error, Code = " << flag |
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204 | << ": "<< wcsunits_errmsg[flag]; |
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205 | if(flag==10) errmsg << "\nTried to get conversion from '" |
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206 | << wcs->cunit[wcs->spec] << "' to '" |
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207 | << this->spectralUnits.c_str() << "'\n"; |
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208 | this->spectralUnits = this->wcs->cunit[wcs->spec]; |
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209 | if(this->spectralUnits==""){ |
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210 | errmsg << "Setting coordinates to 'XX' for clarity.\n"; |
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211 | this->spectralUnits = "XX"; |
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212 | } |
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213 | duchampError("fixUnits", errmsg.str()); |
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214 | |
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215 | } |
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216 | } |
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217 | this->scale = sc; |
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218 | this->offset= of; |
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219 | this->power = po; |
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220 | |
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221 | // Work out the integrated flux units, based on the spectral units. |
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222 | // If flux is per beam, trim the /beam from the flux units and multiply |
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223 | // by the spectral units. |
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224 | // Otherwise, just muliply by the spectral units. |
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225 | if(this->fluxUnits.size()>0){ |
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226 | if(this->fluxUnits.substr(this->fluxUnits.size()-5, |
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227 | this->fluxUnits.size() ) == "/beam"){ |
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228 | this->intFluxUnits = this->fluxUnits.substr(0,this->fluxUnits.size()-5) |
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229 | +" " +this->spectralUnits; |
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230 | } |
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231 | else this->intFluxUnits = this->fluxUnits + " " + this->spectralUnits; |
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232 | } |
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233 | |
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234 | } |
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235 | |
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236 | /****************************************************************/ |
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237 | /////////////////////////////////////////////////// |
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238 | //// Accessor Functions for Parameter class: |
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239 | /////////////////////////////////////////////////// |
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240 | Param::Param(){ |
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241 | /** |
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242 | * Param() |
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243 | * Default intial values for the parameters. |
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244 | * imageFile has no default value! |
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245 | */ |
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246 | // Input files |
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247 | this->imageFile = ""; |
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248 | this->flagSubsection = false; |
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249 | this->subsection = "[*,*,*]"; |
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250 | this->flagReconExists = false; |
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251 | this->reconFile = ""; |
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252 | // Output files |
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253 | this->flagLog = true; |
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254 | this->logFile = "duchamp-Logfile.txt"; |
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255 | this->outFile = "duchamp-Results.txt"; |
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256 | this->spectraFile = "duchamp-Spectra.ps"; |
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257 | this->flagOutputRecon = false; |
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258 | this->flagOutputResid = false; |
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259 | this->flagVOT = false; |
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260 | this->votFile = "duchamp-Results.xml"; |
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261 | this->flagKarma = false; |
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262 | this->karmaFile = "duchamp-Results.ann"; |
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263 | this->flagMaps = true; |
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264 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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265 | this->momentMap = "duchamp-MomentMap.ps"; |
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266 | // Cube related parameters |
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267 | this->flagBlankPix = true; |
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268 | this->blankPixValue = -8.00061; |
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269 | this->blankKeyword = 1; |
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270 | this->bscaleKeyword = -8.00061; |
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271 | this->bzeroKeyword = 0.; |
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272 | this->flagUsingBlank = false; |
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273 | this->flagMW = false; |
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274 | this->maxMW = 112; |
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275 | this->minMW = 75; |
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276 | this->numPixBeam = 10.; |
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277 | this->flagUsingBeam = false; |
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278 | // Trim-related |
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279 | this->flagTrimmed = false; |
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280 | this->borderLeft = 0; |
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281 | this->borderRight = 0; |
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282 | this->borderBottom = 0; |
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283 | this->borderTop = 0; |
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284 | // Subsection offsets |
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285 | this->xSubOffset = 0; |
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286 | this->ySubOffset = 0; |
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287 | this->zSubOffset = 0; |
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288 | // Baseline related |
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289 | this->flagBaseline = false; |
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290 | // Detection-related |
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291 | this->flagNegative = false; |
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292 | // Object growth |
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293 | this->flagGrowth = false; |
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294 | this->growthCut = 2.; |
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295 | // FDR analysis |
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296 | this->flagFDR = false; |
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297 | this->alphaFDR = 0.01; |
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298 | // Other detection |
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299 | this->snrCut = 3.; |
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300 | // A trous reconstruction parameters |
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301 | this->flagATrous = true; |
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302 | this->reconDim = 3; |
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303 | this->scaleMin = 1; |
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304 | this->snrRecon = 4.; |
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305 | this->filterCode = 1; |
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306 | // Volume-merging parameters |
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307 | this->flagAdjacent = true; |
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308 | this->threshSpatial = 3.; |
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309 | this->threshVelocity = 7.; |
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310 | this->minChannels = 3; |
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311 | this->minPix = 2; |
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312 | // Input-Output related |
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313 | this->spectralMethod = "peak"; |
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314 | this->borders = true; |
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315 | this->blankEdge = true; |
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316 | this->verbose = true; |
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317 | this->spectralUnits = "km/s"; |
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318 | }; |
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319 | |
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320 | Param& Param::operator= (const Param& p) |
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321 | { |
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322 | this->imageFile = p.imageFile; |
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323 | this->flagSubsection = p.flagSubsection; |
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324 | this->subsection = p.subsection; |
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325 | this->flagReconExists = p.flagReconExists; |
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326 | this->reconFile = p.reconFile; |
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327 | this->flagLog = p.flagLog; |
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328 | this->logFile = p.logFile; |
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329 | this->outFile = p.outFile; |
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330 | this->spectraFile = p.spectraFile; |
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331 | this->flagOutputRecon = p.flagOutputRecon; |
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332 | this->flagOutputResid = p.flagOutputResid; |
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333 | this->flagVOT = p.flagVOT; |
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334 | this->votFile = p.votFile; |
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335 | this->flagKarma = p.flagKarma; |
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336 | this->karmaFile = p.karmaFile; |
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337 | this->flagMaps = p.flagMaps; |
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338 | this->detectionMap = p.detectionMap; |
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339 | this->momentMap = p.momentMap; |
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340 | this->flagBlankPix = p.flagBlankPix; |
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341 | this->blankPixValue = p.blankPixValue; |
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342 | this->blankKeyword = p.blankKeyword; |
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343 | this->bscaleKeyword = p.bscaleKeyword; |
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344 | this->bzeroKeyword = p.bzeroKeyword; |
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345 | this->flagUsingBlank = p.flagUsingBlank; |
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346 | this->flagMW = p.flagMW; |
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347 | this->maxMW = p.maxMW; |
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348 | this->minMW = p.minMW; |
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349 | this->numPixBeam = p.numPixBeam; |
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350 | this->flagTrimmed = p.flagTrimmed; |
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351 | this->borderLeft = p.borderLeft; |
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352 | this->borderRight = p.borderRight; |
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353 | this->borderBottom = p.borderBottom; |
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354 | this->borderTop = p.borderTop; |
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355 | this->xSubOffset = p.xSubOffset; |
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356 | this->ySubOffset = p.ySubOffset; |
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357 | this->zSubOffset = p.zSubOffset; |
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358 | this->flagBaseline = p.flagBaseline; |
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359 | this->flagNegative = p.flagNegative; |
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360 | this->flagGrowth = p.flagGrowth; |
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361 | this->growthCut = p.growthCut; |
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362 | this->flagFDR = p.flagFDR; |
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363 | this->alphaFDR = p.alphaFDR; |
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364 | this->snrCut = p.snrCut; |
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365 | this->flagATrous = p.flagATrous; |
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366 | this->reconDim = p.reconDim; |
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367 | this->scaleMin = p.scaleMin; |
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368 | this->snrRecon = p.snrRecon; |
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369 | this->filterCode = p.filterCode; |
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370 | this->flagAdjacent = p.flagAdjacent; |
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371 | this->threshSpatial = p.threshSpatial; |
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372 | this->threshVelocity = p.threshVelocity; |
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373 | this->minChannels = p.minChannels; |
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374 | this->minPix = p.minPix; |
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375 | this->spectralMethod = p.spectralMethod; |
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376 | this->borders = p.borders; |
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377 | this->verbose = p.verbose; |
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378 | this->spectralUnits = p.spectralUnits; |
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379 | } |
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380 | |
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381 | /****************************************************************/ |
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382 | /////////////////////////////////////////////////// |
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383 | //// Other Functions using the Parameter class: |
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384 | /////////////////////////////////////////////////// |
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385 | |
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386 | inline string makelower( string s ) |
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387 | { |
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388 | // "borrowed" from Matt Howlett's 'fred' |
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389 | string out = ""; |
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390 | for( int i=0; i<s.size(); ++i ) { |
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391 | out += tolower(s[i]); |
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392 | } |
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393 | return out; |
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394 | } |
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395 | |
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396 | inline bool boolify( string s ) |
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397 | { |
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398 | /** |
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399 | * bool boolify(string) |
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400 | * Convert a string to a bool variable |
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401 | * "1" and "true" get converted to true |
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402 | * "0" and "false" (and anything else) get converted to false |
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403 | */ |
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404 | if((s=="1") || (makelower(s)=="true")) return true; |
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405 | else if((s=="0") || (makelower(s)=="false")) return false; |
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406 | else return false; |
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407 | } |
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408 | |
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409 | inline string readSval(std::stringstream& ss) |
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410 | { |
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411 | string val; ss >> val; return val; |
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412 | } |
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413 | |
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414 | inline bool readFlag(std::stringstream& ss) |
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415 | { |
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416 | string val; ss >> val; return boolify(val); |
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417 | } |
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418 | |
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419 | inline float readFval(std::stringstream& ss) |
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420 | { |
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421 | float val; ss >> val; return val; |
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422 | } |
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423 | |
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424 | inline int readIval(std::stringstream& ss) |
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425 | { |
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426 | int val; ss >> val; return val; |
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427 | } |
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428 | |
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429 | int Param::readParams(string paramfile) |
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430 | { |
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431 | |
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432 | std::ifstream fin(paramfile.c_str()); |
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433 | if(!fin.is_open()) return FAILURE; |
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434 | string line; |
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435 | while( !std::getline(fin,line,'\n').eof()){ |
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436 | |
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437 | if(line[0]!='#'){ |
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438 | std::stringstream ss; |
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439 | ss.str(line); |
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440 | string arg; |
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441 | ss >> arg; |
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442 | arg = makelower(arg); |
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443 | if(arg=="imagefile") this->imageFile = readSval(ss); |
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444 | if(arg=="flagsubsection") this->flagSubsection = readFlag(ss); |
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445 | if(arg=="subsection") this->subsection = readSval(ss); |
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446 | if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); |
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447 | if(arg=="reconfile") this->reconFile = readSval(ss); |
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448 | |
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449 | if(arg=="flaglog") this->flagLog = readFlag(ss); |
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450 | if(arg=="logfile") this->logFile = readSval(ss); |
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451 | if(arg=="outfile") this->outFile = readSval(ss); |
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452 | if(arg=="spectrafile") this->spectraFile = readSval(ss); |
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453 | if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); |
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454 | if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); |
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455 | if(arg=="flagvot") this->flagVOT = readFlag(ss); |
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456 | if(arg=="votfile") this->votFile = readSval(ss); |
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457 | if(arg=="flagkarma") this->flagKarma = readFlag(ss); |
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458 | if(arg=="karmafile") this->karmaFile = readSval(ss); |
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459 | if(arg=="flagmaps") this->flagMaps = readFlag(ss); |
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460 | if(arg=="detectionmap") this->detectionMap = readSval(ss); |
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461 | if(arg=="momentmap") this->momentMap = readSval(ss); |
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462 | |
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463 | if(arg=="flagnegative") this->flagNegative = readFlag(ss); |
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464 | if(arg=="flagblankpix") this->flagBlankPix = readFlag(ss); |
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465 | if(arg=="blankpixvalue") this->blankPixValue = readFval(ss); |
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466 | if(arg=="flagmw") this->flagMW = readFlag(ss); |
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467 | if(arg=="maxmw") this->maxMW = readIval(ss); |
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468 | if(arg=="minmw") this->minMW = readIval(ss); |
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469 | if(arg=="beamsize") this->numPixBeam = readFval(ss); |
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470 | |
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471 | if(arg=="flagbaseline") this->flagBaseline = readFlag(ss); |
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472 | if(arg=="minpix") this->minPix = readIval(ss); |
---|
473 | if(arg=="flaggrowth") this->flagGrowth = readFlag(ss); |
---|
474 | if(arg=="growthcut") this->growthCut = readFval(ss); |
---|
475 | |
---|
476 | if(arg=="flagfdr") this->flagFDR = readFlag(ss); |
---|
477 | if(arg=="alphafdr") this->alphaFDR = readFval(ss); |
---|
478 | |
---|
479 | if(arg=="snrcut") this->snrCut = readFval(ss); |
---|
480 | |
---|
481 | if(arg=="flagatrous") this->flagATrous = readFlag(ss); |
---|
482 | if(arg=="recondim") this->reconDim = readIval(ss); |
---|
483 | if(arg=="scalemin") this->scaleMin = readIval(ss); |
---|
484 | if(arg=="snrrecon") this->snrRecon = readFval(ss); |
---|
485 | if(arg=="filtercode") this->filterCode = readIval(ss); |
---|
486 | |
---|
487 | if(arg=="flagadjacent") this->flagAdjacent = readFlag(ss); |
---|
488 | if(arg=="threshspatial") this->threshSpatial = readFval(ss); |
---|
489 | if(arg=="threshvelocity") this->threshVelocity = readFval(ss); |
---|
490 | if(arg=="minchannels") this->minChannels = readIval(ss); |
---|
491 | |
---|
492 | if(arg=="spectralmethod") this->spectralMethod=makelower(readSval(ss)); |
---|
493 | if(arg=="spectralunits") this->spectralUnits=makelower(readSval(ss)); |
---|
494 | if(arg=="drawborders") this->borders = readFlag(ss); |
---|
495 | if(arg=="drawblankedges") this->blankEdge = readFlag(ss); |
---|
496 | if(arg=="verbose") this->verbose = readFlag(ss); |
---|
497 | } |
---|
498 | } |
---|
499 | return SUCCESS; |
---|
500 | } |
---|
501 | |
---|
502 | |
---|
503 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
504 | { |
---|
505 | // Only show the [blankPixValue] bit if we are using the parameter |
---|
506 | // otherwise we have read it from the FITS header. |
---|
507 | string blankParam = ""; |
---|
508 | if(par.getFlagUsingBlank()) blankParam = "[blankPixValue]"; |
---|
509 | string beamParam = ""; |
---|
510 | if(par.getFlagUsingBeam()) beamParam = "[beamSize]"; |
---|
511 | |
---|
512 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
513 | // theStream.setf(std::ios::boolalpha); |
---|
514 | theStream.setf(std::ios::left); |
---|
515 | theStream <<"---- Parameters ----"<<endl; |
---|
516 | theStream << std::setfill('.'); |
---|
517 | if(par.getFlagSubsection()) |
---|
518 | theStream<<setw(38)<<"Image to be analysed" |
---|
519 | <<setw(18)<<setiosflags(std::ios::right) <<"[imageFile]" |
---|
520 | <<" = " <<resetiosflags(std::ios::right) |
---|
521 | <<(par.getImageFile()+par.getSubsection()) <<endl; |
---|
522 | else |
---|
523 | theStream<<setw(38)<<"Image to be analysed" |
---|
524 | <<setw(18)<<setiosflags(std::ios::right) <<"[imageFile]" |
---|
525 | <<" = " <<resetiosflags(std::ios::right) |
---|
526 | <<par.getImageFile() <<endl; |
---|
527 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
528 | theStream<<setw(38)<<"Reconstructed array exists?" |
---|
529 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconExists]" |
---|
530 | <<" = " <<resetiosflags(std::ios::right) |
---|
531 | <<stringize(par.getFlagReconExists())<<endl; |
---|
532 | theStream<<setw(38)<<"FITS file containing reconstruction" |
---|
533 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconFile]" |
---|
534 | <<" = " <<resetiosflags(std::ios::right) |
---|
535 | <<par.getReconFile() <<endl; |
---|
536 | } |
---|
537 | theStream <<setw(38)<<"Intermediate Logfile" |
---|
538 | <<setw(18)<<setiosflags(std::ios::right) <<"[logFile]" |
---|
539 | <<" = " <<resetiosflags(std::ios::right) |
---|
540 | <<par.getLogFile() <<endl; |
---|
541 | theStream <<setw(38)<<"Final Results file" |
---|
542 | <<setw(18)<<setiosflags(std::ios::right) <<"[outFile]" |
---|
543 | <<" = " <<resetiosflags(std::ios::right) |
---|
544 | <<par.getOutFile() <<endl; |
---|
545 | theStream <<setw(38)<<"Spectrum file" |
---|
546 | <<setw(18)<<setiosflags(std::ios::right) <<"[spectraFile]" |
---|
547 | <<" = " <<resetiosflags(std::ios::right) |
---|
548 | <<par.getSpectraFile() <<endl; |
---|
549 | if(par.getFlagVOT()){ |
---|
550 | theStream<<setw(38)<<"VOTable file" |
---|
551 | <<setw(18)<<setiosflags(std::ios::right) <<"[votFile]" |
---|
552 | <<" = " <<resetiosflags(std::ios::right) |
---|
553 | <<par.getVOTFile() <<endl; |
---|
554 | } |
---|
555 | if(par.getFlagKarma()){ |
---|
556 | theStream<<setw(38)<<"Karma annotation file" |
---|
557 | <<setw(18)<<setiosflags(std::ios::right) <<"[karmaFile]" |
---|
558 | <<" = " <<resetiosflags(std::ios::right) |
---|
559 | |
---|
560 | <<par.getKarmaFile() <<endl; |
---|
561 | } |
---|
562 | if(par.getFlagMaps()){ |
---|
563 | theStream<<setw(38)<<"0th Moment Map" |
---|
564 | <<setw(18)<<setiosflags(std::ios::right) <<"[momentMap]" |
---|
565 | <<" = " <<resetiosflags(std::ios::right) |
---|
566 | <<par.getMomentMap() <<endl; |
---|
567 | theStream<<setw(38)<<"Detection Map" |
---|
568 | <<setw(18)<<setiosflags(std::ios::right) <<"[detectionMap]" |
---|
569 | <<" = " <<resetiosflags(std::ios::right) |
---|
570 | <<par.getDetectionMap() <<endl; |
---|
571 | } |
---|
572 | if(par.getFlagATrous()){ |
---|
573 | theStream<<setw(38)<<"Saving reconstructed cube?" |
---|
574 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagoutputrecon]" |
---|
575 | <<" = " <<resetiosflags(std::ios::right) |
---|
576 | <<stringize(par.getFlagOutputRecon())<<endl; |
---|
577 | theStream<<setw(38)<<"Saving residuals from reconstruction?" |
---|
578 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagoutputresid]" |
---|
579 | <<" = " <<resetiosflags(std::ios::right) |
---|
580 | <<stringize(par.getFlagOutputResid())<<endl; |
---|
581 | } |
---|
582 | theStream <<"------"<<endl; |
---|
583 | theStream <<setw(38)<<"Searching for Negative features?" |
---|
584 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagNegative]" |
---|
585 | <<" = " <<resetiosflags(std::ios::right) |
---|
586 | <<stringize(par.getFlagNegative()) <<endl; |
---|
587 | theStream <<setw(38)<<"Fixing Blank Pixels?" |
---|
588 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagBlankPix]" |
---|
589 | <<" = " <<resetiosflags(std::ios::right) |
---|
590 | <<stringize(par.getFlagBlankPix()) <<endl; |
---|
591 | if(par.getFlagBlankPix()){ |
---|
592 | theStream<<setw(38)<<"Blank Pixel Value" |
---|
593 | <<setw(18)<<setiosflags(std::ios::right) << blankParam |
---|
594 | <<" = " <<resetiosflags(std::ios::right) |
---|
595 | <<par.getBlankPixVal() <<endl; |
---|
596 | } |
---|
597 | theStream <<setw(38)<<"Removing Milky Way channels?" |
---|
598 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagMW]" |
---|
599 | <<" = " <<resetiosflags(std::ios::right) |
---|
600 | <<stringize(par.getFlagMW()) <<endl; |
---|
601 | if(par.getFlagMW()){ |
---|
602 | theStream<<setw(38)<<"Milky Way Channels" |
---|
603 | <<setw(18)<<setiosflags(std::ios::right) <<"[minMW - maxMW]" |
---|
604 | <<" = " <<resetiosflags(std::ios::right) |
---|
605 | <<par.getMinMW() |
---|
606 | <<"-" <<par.getMaxMW() <<endl; |
---|
607 | } |
---|
608 | theStream <<setw(38)<<"Beam Size (pixels)" |
---|
609 | <<setw(18)<<setiosflags(std::ios::right) << beamParam |
---|
610 | <<" = " <<resetiosflags(std::ios::right) |
---|
611 | <<par.getBeamSize() <<endl; |
---|
612 | theStream <<setw(38)<<"Removing baselines before search?" |
---|
613 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagBaseline]" |
---|
614 | <<" = " <<resetiosflags(std::ios::right) |
---|
615 | <<stringize(par.getFlagBaseline()) <<endl; |
---|
616 | theStream <<setw(38)<<"Minimum # Pixels in a detection" |
---|
617 | <<setw(18)<<setiosflags(std::ios::right) <<"[minPix]" |
---|
618 | <<" = " <<resetiosflags(std::ios::right) |
---|
619 | <<par.getMinPix() <<endl; |
---|
620 | theStream <<setw(38)<<"Minimum # Channels in a detection" |
---|
621 | <<setw(18)<<setiosflags(std::ios::right) <<"[minChannels]" |
---|
622 | <<" = " <<resetiosflags(std::ios::right) |
---|
623 | <<par.getMinChannels() <<endl; |
---|
624 | theStream <<setw(38)<<"Growing objects after detection?" |
---|
625 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagGrowth]" |
---|
626 | <<" = " <<resetiosflags(std::ios::right) |
---|
627 | <<stringize(par.getFlagGrowth()) <<endl; |
---|
628 | if(par.getFlagGrowth()) { |
---|
629 | theStream<<setw(38)<<"SNR Threshold for growth" |
---|
630 | <<setw(18)<<setiosflags(std::ios::right) <<"[growthCut]" |
---|
631 | <<" = " <<resetiosflags(std::ios::right) |
---|
632 | <<par.getGrowthCut() <<endl; |
---|
633 | } |
---|
634 | theStream <<setw(38)<<"Using A Trous reconstruction?" |
---|
635 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagATrous]" |
---|
636 | <<" = " <<resetiosflags(std::ios::right) |
---|
637 | <<stringize(par.getFlagATrous()) <<endl; |
---|
638 | if(par.getFlagATrous()){ |
---|
639 | theStream<<setw(38)<<"Number of dimensions in reconstruction" |
---|
640 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconDim]" |
---|
641 | <<" = " <<resetiosflags(std::ios::right) |
---|
642 | <<par.getReconDim() <<endl; |
---|
643 | theStream<<setw(38)<<"Minimum scale in reconstruction" |
---|
644 | <<setw(18)<<setiosflags(std::ios::right) <<"[scaleMin]" |
---|
645 | <<" = " <<resetiosflags(std::ios::right) |
---|
646 | <<par.getMinScale() <<endl; |
---|
647 | theStream<<setw(38)<<"SNR Threshold within reconstruction" |
---|
648 | <<setw(18)<<setiosflags(std::ios::right) <<"[snrRecon]" |
---|
649 | <<" = " <<resetiosflags(std::ios::right) |
---|
650 | <<par.getAtrousCut() <<endl; |
---|
651 | theStream<<setw(38)<<"Filter being used for reconstruction" |
---|
652 | <<setw(18)<<setiosflags(std::ios::right) <<"[filterCode]" |
---|
653 | <<" = " <<resetiosflags(std::ios::right) |
---|
654 | <<par.getFilterCode() |
---|
655 | << " (" << par.getFilterName() << ")" <<endl; |
---|
656 | } |
---|
657 | theStream <<setw(38)<<"Using FDR analysis?" |
---|
658 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagFDR]" |
---|
659 | <<" = " <<resetiosflags(std::ios::right) |
---|
660 | <<stringize(par.getFlagFDR()) <<endl; |
---|
661 | if(par.getFlagFDR()){ |
---|
662 | theStream<<setw(38)<<"Alpha value for FDR analysis" |
---|
663 | <<setw(18)<<setiosflags(std::ios::right) <<"[alphaFDR]" |
---|
664 | <<" = " <<resetiosflags(std::ios::right) |
---|
665 | <<par.getAlpha() <<endl; |
---|
666 | } |
---|
667 | else { |
---|
668 | theStream<<setw(38)<<"SNR Threshold" |
---|
669 | <<setw(18)<<setiosflags(std::ios::right) <<"[snrCut]" |
---|
670 | <<" = " <<resetiosflags(std::ios::right) |
---|
671 | <<par.getCut() <<endl; |
---|
672 | } |
---|
673 | theStream <<setw(38)<<"Using Adjacent-pixel criterion?" |
---|
674 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagAdjacent]" |
---|
675 | <<" = " <<resetiosflags(std::ios::right) |
---|
676 | <<stringize(par.getFlagAdjacent()) <<endl; |
---|
677 | if(!par.getFlagAdjacent()){ |
---|
678 | theStream<<setw(38)<<"Max. spatial separation for merging" |
---|
679 | <<setw(18)<<setiosflags(std::ios::right) <<"[threshSpatial]" |
---|
680 | <<" = " <<resetiosflags(std::ios::right) |
---|
681 | <<par.getThreshS() <<endl; |
---|
682 | } |
---|
683 | theStream <<setw(38)<<"Max. velocity separation for merging" |
---|
684 | <<setw(18)<<setiosflags(std::ios::right) <<"[threshVelocity]" |
---|
685 | <<" = " <<resetiosflags(std::ios::right) |
---|
686 | <<par.getThreshV() <<endl; |
---|
687 | theStream <<setw(38)<<"Method of spectral plotting" |
---|
688 | <<setw(18)<<setiosflags(std::ios::right) <<"[spectralMethod]" |
---|
689 | <<" = " <<resetiosflags(std::ios::right) |
---|
690 | <<par.getSpectralMethod() <<endl; |
---|
691 | theStream <<"--------------------"<<endl; |
---|
692 | theStream << std::setfill(' '); |
---|
693 | theStream.unsetf(std::ios::left); |
---|
694 | // theStream.unsetf(std::ios::boolalpha); |
---|
695 | } |
---|
696 | |
---|
697 | |
---|
698 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
699 | { |
---|
700 | /** |
---|
701 | * Param::copyHeaderInfo(FitsHeader &head) |
---|
702 | * A function to copy across relevant header keywords from the |
---|
703 | * FitsHeader class to the Param class, as they are needed by |
---|
704 | * functions in the Param class. |
---|
705 | */ |
---|
706 | |
---|
707 | this->blankKeyword = head.getBlankKeyword(); |
---|
708 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
709 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
710 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + |
---|
711 | this->bzeroKeyword; |
---|
712 | |
---|
713 | this->numPixBeam = head.getBeamSize(); |
---|
714 | } |
---|
715 | |
---|
716 | bool Param::isBlank(float &value) |
---|
717 | { |
---|
718 | /** |
---|
719 | * Param::isBlank(float) |
---|
720 | * Tests whether the value passed as the argument is BLANK or not. |
---|
721 | * If flagBlankPix is false, return false. |
---|
722 | * Otherwise, compare to the relevant FITS keywords, using integer |
---|
723 | * comparison. |
---|
724 | * Return a bool. |
---|
725 | */ |
---|
726 | |
---|
727 | return this->flagBlankPix && |
---|
728 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
---|
729 | } |
---|
730 | |
---|
731 | string Param::outputReconFile() |
---|
732 | { |
---|
733 | /** |
---|
734 | * outputReconFile() |
---|
735 | * |
---|
736 | * This function produces the required filename in which to save |
---|
737 | * the reconstructed array. If the input image is image.fits, then |
---|
738 | * the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
739 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
740 | */ |
---|
741 | string inputName = this->imageFile; |
---|
742 | std::stringstream ss; |
---|
743 | ss << inputName.substr(0,inputName.size()-5); // remove the ".fits" on the end. |
---|
744 | if(this->flagSubsection) ss<<".sub"; |
---|
745 | ss << ".RECON-" << this->reconDim |
---|
746 | << "-" << this->filterCode |
---|
747 | << "-" << this->snrRecon |
---|
748 | << "-" << this->scaleMin |
---|
749 | << ".fits"; |
---|
750 | return ss.str(); |
---|
751 | } |
---|
752 | |
---|
753 | string Param::outputResidFile() |
---|
754 | { |
---|
755 | /** |
---|
756 | * outputResidFile() |
---|
757 | * |
---|
758 | * This function produces the required filename in which to save |
---|
759 | * the reconstructed array. If the input image is image.fits, then |
---|
760 | * the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
761 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
762 | */ |
---|
763 | string inputName = this->imageFile; |
---|
764 | std::stringstream ss; |
---|
765 | ss << inputName.substr(0,inputName.size()-5); // remove the ".fits" on the end. |
---|
766 | if(this->flagSubsection) ss<<".sub"; |
---|
767 | ss << ".RESID-" << this->reconDim |
---|
768 | << "-" << this->filterCode |
---|
769 | << "-" << this->snrRecon |
---|
770 | << "-" << this->scaleMin |
---|
771 | << ".fits"; |
---|
772 | return ss.str(); |
---|
773 | } |
---|