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 | // return pixelToVelocity(this->wcs,x,y,z,this->spectralUnits);}; |
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137 | double *pix = new double[3]; |
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138 | double *world = new double[3]; |
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139 | pix[0] = x; pix[1] = y; pix[2] = z; |
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140 | pixToWCSSingle(this->wcs,pix,world); |
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141 | double vel = this->specToVel(world[2]); |
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142 | delete [] pix; |
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143 | delete [] world; |
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144 | return vel; |
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145 | } |
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146 | |
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147 | double* FitsHeader::pixToVel(double &x, double &y, double *zarray, int size) |
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148 | { |
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149 | // return pixelToVelocity(this->wcs,x,y,z,this->spectralUnits);}; |
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150 | double *pix = new double[size*3]; |
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151 | for(int i=0;i<size;i++){ |
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152 | pix[3*i] = x; pix[3*i+1] = y; pix[3*i+2] = zarray[i]; |
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153 | } |
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154 | double *world = new double[size*3]; |
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155 | pixToWCSMulti(this->wcs,pix,world,size); |
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156 | delete [] pix; |
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157 | double *newzarray = new double[size]; |
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158 | for(int i=0;i<size;i++) newzarray[i] = this->specToVel(world[3*i+2]); |
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159 | delete [] world; |
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160 | return newzarray; |
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161 | } |
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162 | |
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163 | double FitsHeader::specToVel(const double &coord) |
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164 | { |
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165 | double vel; |
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166 | if(power==1.0) vel = coord*this->scale + this->offset; |
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167 | else vel = pow( (coord*this->scale + this->offset), this->power); |
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168 | return vel; |
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169 | } |
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170 | |
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171 | double FitsHeader::velToSpec(const float &velocity) |
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172 | { |
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173 | // return velToCoord(this->wcs,velocity,this->spectralUnits);}; |
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174 | return (pow(velocity, 1./this->power) - this->offset) / this->scale;} |
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175 | |
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176 | string FitsHeader::getIAUName(double ra, double dec) |
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177 | { |
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178 | if(strcmp(this->wcs->lngtyp,"RA")==0) return getIAUNameEQ(ra, dec, this->wcs->equinox); |
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179 | else return getIAUNameGAL(ra, dec); |
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180 | } |
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181 | |
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182 | void FitsHeader::fixUnits(Param &par) |
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183 | { |
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184 | // define spectral units from the param set |
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185 | this->spectralUnits = par.getSpectralUnits(); |
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186 | |
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187 | double sc=1.; |
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188 | double of=0.; |
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189 | double po=1.;; |
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190 | if(this->wcsIsGood){ |
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191 | int flag = wcsunits( this->wcs->cunit[2], this->spectralUnits.c_str(), |
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192 | &sc, &of, &po); |
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193 | if(flag>0){ |
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194 | std::stringstream errmsg; |
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195 | errmsg << "WCSUNITS Error, Code = " << flag |
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196 | << ": "<< wcsunits_errmsg[flag]; |
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197 | if(flag==10) errmsg << "\nTried to get conversion from '" |
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198 | << wcs->cunit[2] << "' to '" |
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199 | << this->spectralUnits.c_str() << "'\n"; |
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200 | this->spectralUnits = this->wcs->cunit[2]; |
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201 | if(this->spectralUnits==""){ |
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202 | errmsg << "Setting coordinates to 'XX' for clarity.\n"; |
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203 | this->spectralUnits = "XX"; |
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204 | } |
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205 | duchampError("fixUnits", errmsg.str()); |
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206 | |
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207 | } |
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208 | } |
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209 | this->scale = sc; |
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210 | this->offset= of; |
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211 | this->power = po; |
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212 | |
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213 | // Work out the integrated flux units, based on the spectral units. |
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214 | // If flux is per beam, trim the /beam from the flux units and multiply |
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215 | // by the spectral units. |
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216 | // Otherwise, just muliply by the spectral units. |
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217 | if(this->fluxUnits.size()>0){ |
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218 | if(this->fluxUnits.substr(this->fluxUnits.size()-5, |
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219 | this->fluxUnits.size() ) == "/beam"){ |
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220 | this->intFluxUnits = this->fluxUnits.substr(0,this->fluxUnits.size()-5) |
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221 | +" " +this->spectralUnits; |
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222 | } |
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223 | else this->intFluxUnits = fluxUnits + " " + this->spectralUnits; |
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224 | } |
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225 | |
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226 | } |
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227 | |
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228 | /****************************************************************/ |
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229 | /////////////////////////////////////////////////// |
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230 | //// Accessor Functions for Parameter class: |
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231 | /////////////////////////////////////////////////// |
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232 | Param::Param(){ |
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233 | /** |
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234 | * Param() |
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235 | * Default intial values for the parameters. |
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236 | * imageFile has no default value! |
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237 | */ |
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238 | // Input files |
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239 | this->imageFile = ""; |
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240 | this->flagSubsection = false; |
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241 | this->subsection = "[*,*,*]"; |
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242 | this->flagReconExists = false; |
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243 | this->reconFile = ""; |
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244 | // Output files |
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245 | this->flagLog = true; |
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246 | this->logFile = "duchamp-Logfile.txt"; |
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247 | this->outFile = "duchamp-Results.txt"; |
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248 | this->spectraFile = "duchamp-Spectra.ps"; |
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249 | this->flagOutputRecon = false; |
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250 | this->flagOutputResid = false; |
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251 | this->flagVOT = false; |
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252 | this->votFile = "duchamp-Results.xml"; |
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253 | this->flagKarma = false; |
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254 | this->karmaFile = "duchamp-Results.ann"; |
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255 | this->flagMaps = true; |
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256 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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257 | this->momentMap = "duchamp-MomentMap.ps"; |
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258 | // Cube related parameters |
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259 | this->flagBlankPix = true; |
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260 | this->blankPixValue = -8.00061; |
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261 | this->blankKeyword = 1; |
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262 | this->bscaleKeyword = -8.00061; |
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263 | this->bzeroKeyword = 0.; |
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264 | this->flagUsingBlank = false; |
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265 | this->flagMW = false; |
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266 | this->maxMW = 112; |
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267 | this->minMW = 75; |
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268 | this->numPixBeam = 0.; |
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269 | // Trim-related |
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270 | this->flagTrimmed = false; |
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271 | this->borderLeft = 0; |
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272 | this->borderRight = 0; |
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273 | this->borderBottom = 0; |
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274 | this->borderTop = 0; |
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275 | // Subsection offsets |
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276 | this->xSubOffset = 0; |
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277 | this->ySubOffset = 0; |
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278 | this->zSubOffset = 0; |
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279 | // Baseline related |
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280 | this->flagBaseline = false; |
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281 | // Detection-related |
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282 | this->flagNegative = false; |
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283 | // Object growth |
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284 | this->flagGrowth = false; |
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285 | this->growthCut = 2.; |
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286 | // FDR analysis |
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287 | this->flagFDR = false; |
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288 | this->alphaFDR = 0.01; |
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289 | // Other detection |
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290 | this->snrCut = 3.; |
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291 | // A trous reconstruction parameters |
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292 | this->flagATrous = true; |
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293 | this->reconDim = 3; |
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294 | this->scaleMin = 1; |
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295 | this->snrRecon = 4.; |
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296 | this->filterCode = 1; |
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297 | // Volume-merging parameters |
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298 | this->flagAdjacent = true; |
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299 | this->threshSpatial = 3.; |
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300 | this->threshVelocity = 7.; |
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301 | this->minChannels = 3; |
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302 | this->minPix = 2; |
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303 | // Input-Output related |
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304 | this->spectralMethod = "peak"; |
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305 | this->borders = true; |
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306 | this->blankEdge = true; |
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307 | this->verbose = true; |
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308 | this->spectralUnits = "km/s"; |
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309 | }; |
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310 | |
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311 | Param& Param::operator= (const Param& p) |
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312 | { |
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313 | this->imageFile = p.imageFile; |
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314 | this->flagSubsection = p.flagSubsection; |
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315 | this->subsection = p.subsection; |
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316 | this->flagReconExists = p.flagReconExists; |
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317 | this->reconFile = p.reconFile; |
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318 | this->flagLog = p.flagLog; |
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319 | this->logFile = p.logFile; |
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320 | this->outFile = p.outFile; |
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321 | this->spectraFile = p.spectraFile; |
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322 | this->flagOutputRecon = p.flagOutputRecon; |
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323 | this->flagOutputResid = p.flagOutputResid; |
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324 | this->flagVOT = p.flagVOT; |
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325 | this->votFile = p.votFile; |
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326 | this->flagKarma = p.flagKarma; |
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327 | this->karmaFile = p.karmaFile; |
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328 | this->flagMaps = p.flagMaps; |
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329 | this->detectionMap = p.detectionMap; |
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330 | this->momentMap = p.momentMap; |
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331 | this->flagBlankPix = p.flagBlankPix; |
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332 | this->blankPixValue = p.blankPixValue; |
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333 | this->blankKeyword = p.blankKeyword; |
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334 | this->bscaleKeyword = p.bscaleKeyword; |
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335 | this->bzeroKeyword = p.bzeroKeyword; |
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336 | this->flagUsingBlank = p.flagUsingBlank; |
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337 | this->flagMW = p.flagMW; |
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338 | this->maxMW = p.maxMW; |
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339 | this->minMW = p.minMW; |
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340 | this->numPixBeam = p.numPixBeam; |
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341 | this->flagTrimmed = p.flagTrimmed; |
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342 | this->borderLeft = p.borderLeft; |
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343 | this->borderRight = p.borderRight; |
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344 | this->borderBottom = p.borderBottom; |
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345 | this->borderTop = p.borderTop; |
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346 | this->xSubOffset = p.xSubOffset; |
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347 | this->ySubOffset = p.ySubOffset; |
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348 | this->zSubOffset = p.zSubOffset; |
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349 | this->flagBaseline = p.flagBaseline; |
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350 | this->flagNegative = p.flagNegative; |
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351 | this->flagGrowth = p.flagGrowth; |
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352 | this->growthCut = p.growthCut; |
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353 | this->flagFDR = p.flagFDR; |
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354 | this->alphaFDR = p.alphaFDR; |
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355 | this->snrCut = p.snrCut; |
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356 | this->flagATrous = p.flagATrous; |
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357 | this->reconDim = p.reconDim; |
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358 | this->scaleMin = p.scaleMin; |
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359 | this->snrRecon = p.snrRecon; |
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360 | this->filterCode = p.filterCode; |
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361 | this->flagAdjacent = p.flagAdjacent; |
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362 | this->threshSpatial = p.threshSpatial; |
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363 | this->threshVelocity = p.threshVelocity; |
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364 | this->minChannels = p.minChannels; |
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365 | this->minPix = p.minPix; |
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366 | this->spectralMethod = p.spectralMethod; |
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367 | this->borders = p.borders; |
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368 | this->verbose = p.verbose; |
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369 | this->spectralUnits = p.spectralUnits; |
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370 | } |
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371 | |
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372 | /****************************************************************/ |
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373 | /////////////////////////////////////////////////// |
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374 | //// Other Functions using the Parameter class: |
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375 | /////////////////////////////////////////////////// |
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376 | |
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377 | string makelower( string s ) |
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378 | { |
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379 | // "borrowed" from Matt Howlett's 'fred' |
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380 | string out = ""; |
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381 | for( int i=0; i<s.size(); ++i ) { |
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382 | out += tolower(s[i]); |
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383 | } |
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384 | return out; |
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385 | } |
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386 | |
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387 | bool boolify( string s ) |
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388 | { |
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389 | /** |
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390 | * bool boolify(string) |
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391 | * Convert a string to a bool variable |
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392 | * "1" and "true" get converted to true |
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393 | * "0" and "false" (and anything else) get converted to false |
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394 | */ |
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395 | if((s=="1") || (makelower(s)=="true")) return true; |
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396 | else if((s=="0") || (makelower(s)=="false")) return false; |
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397 | else return false; |
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398 | } |
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399 | |
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400 | void Param::readParams(string paramfile) |
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401 | { |
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402 | |
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403 | std::ifstream fin(paramfile.c_str()); |
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404 | string line; |
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405 | string sval; |
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406 | float fval; |
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407 | int ival; |
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408 | while( !std::getline(fin,line,'\n').eof()){ |
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409 | |
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410 | if(line[0]!='#'){ |
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411 | std::stringstream ss; |
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412 | ss.str(line); |
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413 | string arg; |
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414 | ss >> arg; |
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415 | if(makelower(arg)=="imagefile"){ ss >> sval; this->imageFile = sval;} |
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416 | if(makelower(arg)=="flagsubsection"){ ss >> sval; this->flagSubsection = boolify(sval); } |
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417 | if(makelower(arg)=="subsection"){ ss >> sval; this->subsection = sval; } |
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418 | if(makelower(arg)=="flagreconexists"){ ss >> sval; this->flagReconExists = boolify(sval); } |
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419 | if(makelower(arg)=="reconfile"){ ss >> sval; this->reconFile = sval; } |
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420 | |
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421 | if(makelower(arg)=="flaglog"){ ss >> sval; this->flagLog = boolify(sval); } |
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422 | if(makelower(arg)=="logfile"){ ss >> sval; this->logFile = sval; } |
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423 | if(makelower(arg)=="outfile"){ ss >> sval; this->outFile = sval; } |
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424 | if(makelower(arg)=="spectrafile"){ ss >> sval; this->spectraFile = sval; } |
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425 | if(makelower(arg)=="flagoutputrecon"){ ss >> sval; this->flagOutputRecon = boolify(sval); } |
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426 | if(makelower(arg)=="flagoutputresid"){ ss >> sval; this->flagOutputResid = boolify(sval); } |
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427 | if(makelower(arg)=="flagvot"){ ss >> sval; this->flagVOT = boolify(sval); } |
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428 | if(makelower(arg)=="votfile"){ ss >> sval; this->votFile = sval; } |
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429 | if(makelower(arg)=="flagkarma"){ ss >> sval; this->flagKarma = boolify(sval); } |
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430 | if(makelower(arg)=="karmafile"){ ss >> sval; this->karmaFile = sval; } |
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431 | if(makelower(arg)=="flagmaps"){ ss >> sval; this->flagMaps = boolify(sval); } |
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432 | if(makelower(arg)=="detectionmap"){ ss >> sval; this->detectionMap = sval; } |
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433 | if(makelower(arg)=="momentmap"){ ss >> sval; this->momentMap = sval; } |
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434 | |
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435 | if(makelower(arg)=="flagnegative"){ ss >> sval; this->flagNegative = boolify(sval);} |
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436 | if(makelower(arg)=="flagblankpix"){ ss >> sval; this->flagBlankPix = boolify(sval); } |
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437 | if(makelower(arg)=="blankpixvalue"){ ss >> fval; this->blankPixValue = fval; } |
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438 | if(makelower(arg)=="flagmw"){ ss >> sval; this->flagMW = boolify(sval); } |
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439 | if(makelower(arg)=="maxmw"){ ss >> ival; this->maxMW = ival; } |
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440 | if(makelower(arg)=="minmw"){ ss >> ival; this->minMW = ival; } |
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441 | |
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442 | if(makelower(arg)=="flagbaseline"){ ss >> sval; this->flagBaseline = boolify(sval); } |
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443 | if(makelower(arg)=="minpix"){ ss >> ival; this->minPix = ival; } |
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444 | if(makelower(arg)=="flaggrowth"){ ss >> sval; this->flagGrowth = boolify(sval); } |
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445 | if(makelower(arg)=="growthcut"){ ss >> fval; this->growthCut = fval; } |
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446 | |
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447 | if(makelower(arg)=="flagfdr"){ ss >> sval; this->flagFDR = boolify(sval); } |
---|
448 | if(makelower(arg)=="alphafdr"){ ss >> fval; this->alphaFDR = fval; } |
---|
449 | |
---|
450 | if(makelower(arg)=="snrcut"){ ss >> fval; this->snrCut = fval; } |
---|
451 | |
---|
452 | if(makelower(arg)=="flagatrous"){ ss >> sval; this->flagATrous = boolify(sval); } |
---|
453 | if(makelower(arg)=="recondim"){ ss >> ival; this->reconDim = ival; } |
---|
454 | if(makelower(arg)=="scalemin"){ ss >> ival; this->scaleMin = ival; } |
---|
455 | if(makelower(arg)=="snrrecon"){ ss >> fval; this->snrRecon = fval; } |
---|
456 | if(makelower(arg)=="filtercode"){ ss >> ival; this->filterCode = ival; } |
---|
457 | |
---|
458 | if(makelower(arg)=="flagadjacent"){ ss >> sval; this->flagAdjacent = boolify(sval); } |
---|
459 | if(makelower(arg)=="threshspatial"){ ss >> fval; this->threshSpatial = fval; } |
---|
460 | if(makelower(arg)=="threshvelocity"){ ss >> fval; this->threshVelocity = fval; } |
---|
461 | if(makelower(arg)=="minchannels"){ ss >> ival; this->minChannels = ival; } |
---|
462 | |
---|
463 | if(makelower(arg)=="spectralmethod"){ ss >> sval; this->spectralMethod = makelower(sval); } |
---|
464 | if(makelower(arg)=="spectralunits"){ ss >> sval; this->spectralUnits = makelower(sval); } |
---|
465 | if(makelower(arg)=="drawborders"){ ss >> sval; this->borders = boolify(sval); } |
---|
466 | if(makelower(arg)=="drawblankedges"){ ss >> sval; this->blankEdge = boolify(sval); } |
---|
467 | if(makelower(arg)=="verbose"){ ss >> sval; this->verbose = boolify(sval); } |
---|
468 | } |
---|
469 | } |
---|
470 | } |
---|
471 | |
---|
472 | |
---|
473 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
474 | { |
---|
475 | // Only show the [blankPixValue] bit if we are using the parameter |
---|
476 | // otherwise we have read it from the FITS header. |
---|
477 | string blankParam = ""; |
---|
478 | if(par.getFlagUsingBlank()) blankParam = "[blankPixValue]"; |
---|
479 | |
---|
480 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
481 | // theStream.setf(std::ios::boolalpha); |
---|
482 | theStream.setf(std::ios::left); |
---|
483 | theStream <<"---- Parameters ----"<<endl; |
---|
484 | theStream << std::setfill('.'); |
---|
485 | if(par.getFlagSubsection()) |
---|
486 | theStream<<setw(38)<<"Image to be analysed" |
---|
487 | <<setw(18)<<setiosflags(std::ios::right) <<"[imageFile]" |
---|
488 | <<" = " <<resetiosflags(std::ios::right) |
---|
489 | <<(par.getImageFile()+par.getSubsection()) <<endl; |
---|
490 | else |
---|
491 | theStream<<setw(38)<<"Image to be analysed" |
---|
492 | <<setw(18)<<setiosflags(std::ios::right) <<"[imageFile]" |
---|
493 | <<" = " <<resetiosflags(std::ios::right)<<par.getImageFile() <<endl; |
---|
494 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
495 | theStream<<setw(38)<<"Reconstructed array exists?" |
---|
496 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconExists]" |
---|
497 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagReconExists())<<endl; |
---|
498 | theStream<<setw(38)<<"FITS file containing reconstruction" |
---|
499 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconFile]" |
---|
500 | <<" = " <<resetiosflags(std::ios::right)<<par.getReconFile() <<endl; |
---|
501 | } |
---|
502 | theStream <<setw(38)<<"Intermediate Logfile" |
---|
503 | <<setw(18)<<setiosflags(std::ios::right) <<"[logFile]" |
---|
504 | <<" = " <<resetiosflags(std::ios::right)<<par.getLogFile() <<endl; |
---|
505 | theStream <<setw(38)<<"Final Results file" |
---|
506 | <<setw(18)<<setiosflags(std::ios::right) <<"[outFile]" |
---|
507 | <<" = " <<resetiosflags(std::ios::right)<<par.getOutFile() <<endl; |
---|
508 | theStream <<setw(38)<<"Spectrum file" |
---|
509 | <<setw(18)<<setiosflags(std::ios::right) <<"[spectraFile]" |
---|
510 | <<" = " <<resetiosflags(std::ios::right)<<par.getSpectraFile() <<endl; |
---|
511 | if(par.getFlagVOT()){ |
---|
512 | theStream<<setw(38)<<"VOTable file" |
---|
513 | <<setw(18)<<setiosflags(std::ios::right) <<"[votFile]" |
---|
514 | <<" = " <<resetiosflags(std::ios::right)<<par.getVOTFile() <<endl; |
---|
515 | } |
---|
516 | if(par.getFlagKarma()){ |
---|
517 | theStream<<setw(38)<<"Karma annotation file" |
---|
518 | <<setw(18)<<setiosflags(std::ios::right) <<"[karmaFile]" |
---|
519 | <<" = " <<resetiosflags(std::ios::right)<<par.getKarmaFile() <<endl; |
---|
520 | } |
---|
521 | if(par.getFlagMaps()){ |
---|
522 | theStream<<setw(38)<<"0th Moment Map" |
---|
523 | <<setw(18)<<setiosflags(std::ios::right) <<"[momentMap]" |
---|
524 | <<" = " <<resetiosflags(std::ios::right)<<par.getMomentMap() <<endl; |
---|
525 | theStream<<setw(38)<<"Detection Map" |
---|
526 | <<setw(18)<<setiosflags(std::ios::right) <<"[detectionMap]" |
---|
527 | <<" = " <<resetiosflags(std::ios::right)<<par.getDetectionMap() <<endl; |
---|
528 | } |
---|
529 | if(par.getFlagATrous()){ |
---|
530 | theStream<<setw(38)<<"Saving reconstructed cube?" |
---|
531 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagoutputrecon]" |
---|
532 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagOutputRecon())<<endl; |
---|
533 | theStream<<setw(38)<<"Saving residuals from reconstruction?" |
---|
534 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagoutputresid]" |
---|
535 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagOutputResid())<<endl; |
---|
536 | } |
---|
537 | theStream <<"------"<<endl; |
---|
538 | theStream <<setw(38)<<"Searching for Negative features?" |
---|
539 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagNegative]" |
---|
540 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagNegative()) <<endl; |
---|
541 | theStream <<setw(38)<<"Fixing Blank Pixels?" |
---|
542 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagBlankPix]" |
---|
543 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagBlankPix()) <<endl; |
---|
544 | if(par.getFlagBlankPix()){ |
---|
545 | theStream<<setw(38)<<"Blank Pixel Value" |
---|
546 | <<setw(18)<<setiosflags(std::ios::right) << blankParam |
---|
547 | <<" = " <<resetiosflags(std::ios::right)<<par.getBlankPixVal() <<endl; |
---|
548 | } |
---|
549 | theStream <<setw(38)<<"Removing Milky Way channels?" |
---|
550 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagMW]" |
---|
551 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagMW()) <<endl; |
---|
552 | if(par.getFlagMW()){ |
---|
553 | theStream<<setw(38)<<"Milky Way Channels" |
---|
554 | <<setw(18)<<setiosflags(std::ios::right) <<"[minMW - maxMW]" |
---|
555 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinMW() |
---|
556 | <<"-" <<par.getMaxMW() <<endl; |
---|
557 | } |
---|
558 | theStream <<setw(38)<<"Beam Size (pixels)" |
---|
559 | <<setw(18)<<setiosflags(std::ios::right) <<"" |
---|
560 | <<" = " <<resetiosflags(std::ios::right)<<par.getBeamSize() <<endl; |
---|
561 | theStream <<setw(38)<<"Removing baselines before search?" |
---|
562 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagBaseline]" |
---|
563 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagBaseline()) <<endl; |
---|
564 | theStream <<setw(38)<<"Minimum # Pixels in a detection" |
---|
565 | <<setw(18)<<setiosflags(std::ios::right) <<"[minPix]" |
---|
566 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinPix() <<endl; |
---|
567 | theStream <<setw(38)<<"Minimum # Channels in a detection" |
---|
568 | <<setw(18)<<setiosflags(std::ios::right) <<"[minChannels]" |
---|
569 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinChannels() <<endl; |
---|
570 | theStream <<setw(38)<<"Growing objects after detection?" |
---|
571 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagGrowth]" |
---|
572 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagGrowth()) <<endl; |
---|
573 | if(par.getFlagGrowth()) { |
---|
574 | theStream<<setw(38)<<"SNR Threshold for growth" |
---|
575 | <<setw(18)<<setiosflags(std::ios::right) <<"[growthCut]" |
---|
576 | <<" = " <<resetiosflags(std::ios::right)<<par.getGrowthCut() <<endl; |
---|
577 | } |
---|
578 | theStream <<setw(38)<<"Using A Trous reconstruction?" |
---|
579 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagATrous]" |
---|
580 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagATrous()) <<endl; |
---|
581 | if(par.getFlagATrous()){ |
---|
582 | theStream<<setw(38)<<"Number of dimensions in reconstruction" |
---|
583 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconDim]" |
---|
584 | <<" = " <<resetiosflags(std::ios::right)<<par.getReconDim() <<endl; |
---|
585 | theStream<<setw(38)<<"Minimum scale in reconstruction" |
---|
586 | <<setw(18)<<setiosflags(std::ios::right) <<"[scaleMin]" |
---|
587 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinScale() <<endl; |
---|
588 | theStream<<setw(38)<<"SNR Threshold within reconstruction" |
---|
589 | <<setw(18)<<setiosflags(std::ios::right) <<"[snrRecon]" |
---|
590 | <<" = " <<resetiosflags(std::ios::right)<<par.getAtrousCut() <<endl; |
---|
591 | theStream<<setw(38)<<"Filter being used for reconstruction" |
---|
592 | <<setw(18)<<setiosflags(std::ios::right) <<"[filterCode]" |
---|
593 | <<" = " <<resetiosflags(std::ios::right)<<par.getFilterCode() |
---|
594 | << " (" << par.getFilterName() << ")" <<endl; |
---|
595 | } |
---|
596 | theStream <<setw(38)<<"Using FDR analysis?" |
---|
597 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagFDR]" |
---|
598 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagFDR()) <<endl; |
---|
599 | if(par.getFlagFDR()){ |
---|
600 | theStream<<setw(38)<<"Alpha value for FDR analysis" |
---|
601 | <<setw(18)<<setiosflags(std::ios::right) <<"[alphaFDR]" |
---|
602 | <<" = " <<resetiosflags(std::ios::right)<<par.getAlpha() <<endl; |
---|
603 | } |
---|
604 | else { |
---|
605 | theStream<<setw(38)<<"SNR Threshold" |
---|
606 | <<setw(18)<<setiosflags(std::ios::right) <<"[snrCut]" |
---|
607 | <<" = " <<resetiosflags(std::ios::right)<<par.getCut() <<endl; |
---|
608 | } |
---|
609 | theStream <<setw(38)<<"Using Adjacent-pixel criterion?" |
---|
610 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagAdjacent]" |
---|
611 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagAdjacent()) <<endl; |
---|
612 | if(!par.getFlagAdjacent()){ |
---|
613 | theStream<<setw(38)<<"Max. spatial separation for merging" |
---|
614 | <<setw(18)<<setiosflags(std::ios::right) <<"[threshSpatial]" |
---|
615 | <<" = " <<resetiosflags(std::ios::right)<<par.getThreshS() <<endl; |
---|
616 | } |
---|
617 | theStream <<setw(38)<<"Max. velocity separation for merging" |
---|
618 | <<setw(18)<<setiosflags(std::ios::right) <<"[threshVelocity]" |
---|
619 | <<" = " <<resetiosflags(std::ios::right)<<par.getThreshV() <<endl; |
---|
620 | theStream <<setw(38)<<"Method of spectral plotting" |
---|
621 | <<setw(18)<<setiosflags(std::ios::right) <<"[spectralMethod]" |
---|
622 | <<" = " <<resetiosflags(std::ios::right)<<par.getSpectralMethod() <<endl; |
---|
623 | theStream <<"--------------------"<<endl; |
---|
624 | theStream << std::setfill(' '); |
---|
625 | theStream.unsetf(std::ios::left); |
---|
626 | // theStream.unsetf(std::ios::boolalpha); |
---|
627 | } |
---|
628 | |
---|
629 | void Param::parseSubsection() |
---|
630 | { |
---|
631 | /** |
---|
632 | * Param::parseSubsection() |
---|
633 | * |
---|
634 | * Convert the Param::subsection string to a series of offset values |
---|
635 | * for each dimension. |
---|
636 | * This involves reading the individual substrings and converting to |
---|
637 | * integers, and storing in the {x,y,z}SubOffset parameters. |
---|
638 | * Steps in the subsection string are not dealt with -- a warning message |
---|
639 | * is written to the screen, and the step values are ignored. |
---|
640 | */ |
---|
641 | |
---|
642 | std::stringstream ss; |
---|
643 | ss.str(this->subsection); |
---|
644 | bool removeStep = false; |
---|
645 | string x,y,z; |
---|
646 | getline(ss,x,'['); |
---|
647 | getline(ss,x,','); |
---|
648 | getline(ss,y,','); |
---|
649 | getline(ss,z,']'); |
---|
650 | char *end; |
---|
651 | if(x!="*") { |
---|
652 | int x1,x2,dx; |
---|
653 | int a = x.find(':'); // first occurence of ':' in x-subsection string |
---|
654 | int b = x.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
---|
655 | x1 = atoi( x.substr(0,a).c_str() ); // minimum x in subsection |
---|
656 | this->xSubOffset = x1 - 1; |
---|
657 | if(b>0){ // there is a dx component |
---|
658 | x2 = atoi( x.substr(a+1,b-a-1).c_str() ); // maximum x in subsection |
---|
659 | dx = atoi( x.substr(b+1,x.size()).c_str() ); // delta x in subsection |
---|
660 | x = x.substr(0,b); // rewrite x without the delta-x part. |
---|
661 | removeStep = true; |
---|
662 | } |
---|
663 | } |
---|
664 | if(y!="*") { |
---|
665 | int y1,y2,dy; |
---|
666 | int a = y.find(':'); // first occurence of ':' in y-subsection string |
---|
667 | int b = y.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
---|
668 | y1 = atoi( y.substr(0,a).c_str() ); // minimum y in subsection |
---|
669 | this->ySubOffset = y1 - 1; |
---|
670 | if(b>0){ // there is a dy component |
---|
671 | y2 = atoi( y.substr(a+1,b-a-1).c_str() ); // maximum y in subsection |
---|
672 | dy = atoi( y.substr(b+1,y.size()).c_str() ); // delta y in subsection |
---|
673 | y = y.substr(0,b); // rewrite y without the delta-y part. |
---|
674 | removeStep = true; |
---|
675 | } |
---|
676 | } |
---|
677 | if(z!="*") { |
---|
678 | int z1,z2,dz; |
---|
679 | int a = z.find(':'); // first occurence of ':' in z-subsection string |
---|
680 | int b = z.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
---|
681 | z1 = atoi( z.substr(0,a).c_str() ); // minimum z in subsection |
---|
682 | this->zSubOffset = z1 - 1; |
---|
683 | if(b>0){ // there is a dz component |
---|
684 | z2 = atoi( z.substr(a+1,b-a-1).c_str() ); // maximum z in subsection |
---|
685 | dz = atoi( z.substr(b+1,z.size()).c_str() ); // delta z in subsection |
---|
686 | z = z.substr(0,b); // rewrite z without the delta-z part. |
---|
687 | removeStep = true; |
---|
688 | } |
---|
689 | } |
---|
690 | |
---|
691 | if(removeStep){ |
---|
692 | std::stringstream errmsg; |
---|
693 | errmsg << "\aThe subsection given is " << this->subsection <<".\n" |
---|
694 | << "Duchamp is currently unable to deal with pixel steps" |
---|
695 | << " in the subsection.\n" |
---|
696 | << "These have been ignored, and so the subection used is "; |
---|
697 | // rewrite subsection without any step sizes. |
---|
698 | this->subsection = "[" + x + "," + y + "," + z + "]"; |
---|
699 | errmsg << this->subsection << std::endl; |
---|
700 | duchampWarning("parseSubsection", errmsg.str()); |
---|
701 | } |
---|
702 | |
---|
703 | } |
---|
704 | |
---|
705 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
706 | { |
---|
707 | /** |
---|
708 | * Param::copyHeaderInfo(FitsHeader &head) |
---|
709 | * A function to copy across relevant header keywords from the |
---|
710 | * FitsHeader class to the Param class, as they are needed by |
---|
711 | * functions in the Param class. |
---|
712 | */ |
---|
713 | |
---|
714 | this->blankKeyword = head.getBlankKeyword(); |
---|
715 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
716 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
717 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + this->bzeroKeyword; |
---|
718 | |
---|
719 | this->numPixBeam = head.getBeamSize(); |
---|
720 | } |
---|
721 | |
---|
722 | bool Param::isBlank(float &value) |
---|
723 | { |
---|
724 | /** |
---|
725 | * Param::isBlank(float) |
---|
726 | * Tests whether the value passed as the argument is BLANK or not. |
---|
727 | * If flagBlankPix is false, return false. |
---|
728 | * Otherwise, compare to the relevant FITS keywords, using integer comparison. |
---|
729 | * Return a bool. |
---|
730 | */ |
---|
731 | |
---|
732 | return this->flagBlankPix && |
---|
733 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
---|
734 | } |
---|
735 | |
---|
736 | string Param::outputReconFile() |
---|
737 | { |
---|
738 | /** |
---|
739 | * outputReconFile() |
---|
740 | * |
---|
741 | * This function produces the required filename in which to save |
---|
742 | * the reconstructed array. If the input image is image.fits, then |
---|
743 | * the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
744 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
745 | */ |
---|
746 | string inputName = this->imageFile; |
---|
747 | std::stringstream ss; |
---|
748 | ss << inputName.substr(0,inputName.size()-5); // remove the ".fits" on the end. |
---|
749 | if(this->flagSubsection) ss<<".sub"; |
---|
750 | ss << ".RECON-" << this->reconDim |
---|
751 | << "-" << this->filterCode |
---|
752 | << "-" << this->snrRecon |
---|
753 | << "-" << this->scaleMin |
---|
754 | << ".fits"; |
---|
755 | return ss.str(); |
---|
756 | } |
---|
757 | |
---|
758 | string Param::outputResidFile() |
---|
759 | { |
---|
760 | /** |
---|
761 | * outputResidFile() |
---|
762 | * |
---|
763 | * This function produces the required filename in which to save |
---|
764 | * the reconstructed array. If the input image is image.fits, then |
---|
765 | * the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
766 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
767 | */ |
---|
768 | string inputName = this->imageFile; |
---|
769 | std::stringstream ss; |
---|
770 | ss << inputName.substr(0,inputName.size()-5); // remove the ".fits" on the end. |
---|
771 | if(this->flagSubsection) ss<<".sub"; |
---|
772 | ss << ".RESID-" << this->reconDim |
---|
773 | << "-" << this->filterCode |
---|
774 | << "-" << this->snrRecon |
---|
775 | << "-" << this->scaleMin |
---|
776 | << ".fits"; |
---|
777 | return ss.str(); |
---|
778 | } |
---|