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 <duchamp.hh> |
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10 | #include <param.hh> |
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11 | #include <Utils/utils.hh> |
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12 | |
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13 | // Define funtion to print bools as words, in case the compiler doesn't recognise |
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14 | // the setf(ios::boolalpha) command... |
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15 | #ifdef HAVE_STDBOOL_H |
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16 | string stringize(bool b){ |
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17 | std::stringstream ss; |
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18 | ss.setf(std::ios::boolalpha); |
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19 | ss << b; |
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20 | return ss.str(); |
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21 | } |
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22 | #else |
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23 | string stringize(bool b){ |
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24 | std::string output; |
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25 | if(b) output="true"; |
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26 | else output="false"; |
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27 | return output; |
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28 | } |
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29 | #endif |
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30 | |
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31 | using std::setw; |
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32 | using std::endl; |
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33 | |
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34 | /****************************************************************/ |
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35 | /////////////////////////////////////////////////// |
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36 | //// Functions for FitsHeader class: |
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37 | /////////////////////////////////////////////////// |
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38 | |
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39 | FitsHeader::FitsHeader(){ |
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40 | this->wcs = new wcsprm; |
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41 | this->wcs->flag=-1; |
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42 | wcsini(true,3,this->wcs); |
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43 | this->wcsIsGood = false; |
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44 | this->nwcs = 0; |
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45 | this->scale=1.; |
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46 | this->offset=0.; |
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47 | this->power=1.; |
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48 | this->fluxUnits="counts"; |
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49 | } |
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50 | |
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51 | FitsHeader::FitsHeader(const FitsHeader& h){ |
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52 | this->wcs = new wcsprm; |
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53 | this->wcs->flag=-1; |
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54 | wcsini(true,h.wcs->naxis,this->wcs); |
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55 | wcscopy(true,h.wcs,this->wcs); |
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56 | wcsset(this->wcs); |
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57 | nwcs = h.nwcs; |
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58 | wcsIsGood = h.wcsIsGood; |
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59 | spectralUnits = h.spectralUnits; |
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60 | fluxUnits = h.fluxUnits; |
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61 | intFluxUnits = h.intFluxUnits; |
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62 | beamSize = h.beamSize; |
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63 | bmajKeyword = h.bmajKeyword; |
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64 | bminKeyword = h.bminKeyword; |
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65 | blankKeyword = h.blankKeyword; |
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66 | bzeroKeyword = h.bzeroKeyword; |
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67 | bscaleKeyword = h.bscaleKeyword; |
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68 | scale = h.scale; |
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69 | offset = h.offset; |
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70 | power = h.power; |
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71 | } |
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72 | |
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73 | FitsHeader& FitsHeader::operator= (const FitsHeader& h){ |
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74 | this->wcs = new wcsprm; |
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75 | this->wcs->flag=-1; |
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76 | wcsini(true,h.wcs->naxis,this->wcs); |
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77 | wcscopy(true,h.wcs,this->wcs); |
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78 | wcsset(this->wcs); |
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79 | nwcs = h.nwcs; |
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80 | wcsIsGood = h.wcsIsGood; |
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81 | spectralUnits = h.spectralUnits; |
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82 | fluxUnits = h.fluxUnits; |
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83 | intFluxUnits = h.intFluxUnits; |
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84 | beamSize = h.beamSize; |
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85 | bmajKeyword = h.bmajKeyword; |
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86 | bminKeyword = h.bminKeyword; |
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87 | blankKeyword = h.blankKeyword; |
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88 | bzeroKeyword = h.bzeroKeyword; |
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89 | bscaleKeyword = h.bscaleKeyword; |
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90 | scale = h.scale; |
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91 | offset = h.offset; |
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92 | power = h.power; |
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93 | } |
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94 | |
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95 | void FitsHeader::setWCS(wcsprm *w) |
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96 | { |
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97 | /** |
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98 | * FitsHeader::setWCS(wcsprm *) |
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99 | * A function that assigns the wcs parameters, and runs |
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100 | * wcsset to set it up correctly. |
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101 | * Performs a check to see if the WCS is good (by looking at |
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102 | * the lng and lat wcsprm parameters), and sets the wcsIsGood |
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103 | * flag accordingly. |
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104 | */ |
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105 | wcscopy(true,w,this->wcs); |
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106 | wcsset(this->wcs); |
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107 | if( (w->lng!=-1) && (w->lat!=-1) ) this->wcsIsGood = true; |
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108 | } |
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109 | |
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110 | wcsprm *FitsHeader::getWCS() |
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111 | { |
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112 | /** |
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113 | * FitsHeader::getWCS() |
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114 | * A function that returns a wcsprm object corresponding to the WCS. |
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115 | */ |
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116 | wcsprm *wNew = new wcsprm; |
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117 | wNew->flag=-1; |
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118 | wcsini(true,this->wcs->naxis,wNew); |
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119 | wcscopy(true,this->wcs,wNew); |
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120 | wcsset(wNew); |
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121 | return wNew; |
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122 | } |
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123 | |
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124 | int FitsHeader::wcsToPix(const double *world, double *pix){ |
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125 | return wcsToPixSingle(this->wcs,world,pix);} |
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126 | int FitsHeader::wcsToPix(const double *world, double *pix, const int npts){ |
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127 | return wcsToPixMulti(this->wcs,world,pix,npts);} |
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128 | int FitsHeader::pixToWCS(const double *pix, double *world){ |
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129 | return pixToWCSSingle(this->wcs,pix,world);} |
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130 | int FitsHeader::pixToWCS(const double *pix, double *world, const int npts){ |
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131 | return pixToWCSMulti(this->wcs,pix,world,npts);} |
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132 | |
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133 | double FitsHeader::pixToVel(double &x, double &y, double &z) |
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134 | { |
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135 | // return pixelToVelocity(this->wcs,x,y,z,this->spectralUnits);}; |
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136 | double *pix = new double[3]; |
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137 | double *world = new double[3]; |
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138 | pix[0] = x; pix[1] = y; pix[2] = z; |
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139 | pixToWCSSingle(this->wcs,pix,world); |
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140 | double vel = this->specToVel(world[2]); |
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141 | delete [] pix; |
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142 | delete [] world; |
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143 | return vel; |
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144 | } |
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145 | |
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146 | double* FitsHeader::pixToVel(double &x, double &y, double *zarray, int size) |
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147 | { |
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148 | // return pixelToVelocity(this->wcs,x,y,z,this->spectralUnits);}; |
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149 | double *pix = new double[size*3]; |
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150 | for(int i=0;i<size;i++){ |
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151 | pix[3*i] = x; pix[3*i+1] = y; pix[3*i+2] = zarray[i]; |
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152 | } |
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153 | double *world = new double[size*3]; |
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154 | pixToWCSMulti(this->wcs,pix,world,size); |
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155 | delete [] pix; |
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156 | double *newzarray = new double[size]; |
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157 | for(int i=0;i<size;i++) newzarray[i] = this->specToVel(world[3*i+2]); |
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158 | delete [] world; |
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159 | return newzarray; |
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160 | } |
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161 | |
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162 | double FitsHeader::specToVel(const double &coord) |
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163 | { |
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164 | // return coordToVel(this->wcs,coord,this->spectralUnits);}; |
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165 | double vel; |
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166 | if(power==1.0){ |
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167 | // std::cerr << coord << " --> " << coord*this->scale + this->offset << std::endl; |
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168 | vel = coord*this->scale + this->offset; |
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169 | } |
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170 | else vel = pow( (coord*this->scale + this->offset), this->power); |
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171 | |
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172 | return vel; |
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173 | } |
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174 | |
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175 | double FitsHeader::velToSpec(const float &velocity) |
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176 | { |
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177 | // return velToCoord(this->wcs,velocity,this->spectralUnits);}; |
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178 | return (pow(velocity, 1./this->power) - this->offset) / this->scale;} |
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179 | |
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180 | string FitsHeader::getIAUName(double ra, double dec) |
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181 | { |
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182 | if(strcmp(this->wcs->lngtyp,"RA")==0) return getIAUNameEQ(ra, dec, this->wcs->equinox); |
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183 | else return getIAUNameGAL(ra, dec); |
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184 | } |
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185 | |
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186 | void FitsHeader::fixUnits(Param &par) |
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187 | { |
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188 | // define spectral units from the param set |
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189 | this->spectralUnits = par.getSpectralUnits(); |
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190 | |
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191 | double sc=1.; |
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192 | double of=0.; |
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193 | double po=1.;; |
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194 | if(this->wcsIsGood){ |
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195 | int flag = wcsunits( this->wcs->cunit[2], this->spectralUnits.c_str(), &sc, &of, &po); |
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196 | if(flag>0){ |
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197 | std::cerr << "ERROR <fixUnits> : WCSUNITS Error Code = " << flag << ": " |
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198 | << wcsunits_errmsg[flag] << std::endl; |
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199 | if(flag==10) |
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200 | std::cerr<<" Tried to get conversion from '" << wcs->cunit[2] |
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201 | << "' to '" << this->spectralUnits.c_str() << "'\n"; |
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202 | // std::cerr << " Using coordinate value instead\n"; |
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203 | this->spectralUnits = this->wcs->cunit[2]; |
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204 | if(this->spectralUnits==""){ |
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205 | std::cerr << " Setting coordinates to 'XX' for clarity.\n"; |
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206 | this->spectralUnits = "XX"; |
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207 | } |
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208 | } |
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209 | } |
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210 | this->scale = sc; |
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211 | this->offset= of; |
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212 | this->power = po; |
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213 | |
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214 | // work out the integrated flux units, based on the spectral units |
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215 | // if flux is per beam, trim the /beam from the flux units and multiply 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,this->fluxUnits.size())=="/beam"){ |
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219 | this->intFluxUnits = this->fluxUnits.substr(0,this->fluxUnits.size()-5) |
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220 | +" " +this->spectralUnits; |
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221 | } |
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222 | else this->intFluxUnits = fluxUnits + " " + this->spectralUnits; |
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223 | } |
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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 | //// Accessor Functions for Parameter class: |
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230 | /////////////////////////////////////////////////// |
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231 | Param::Param(){ |
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232 | /** |
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233 | * Param() |
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234 | * Default intial values for the parameters. |
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235 | * imageFile has no default value! |
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236 | */ |
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237 | // Input files |
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238 | this->imageFile = ""; |
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239 | this->flagSubsection = false; |
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240 | this->subsection = "[*,*,*]"; |
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241 | this->flagReconExists = false; |
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242 | this->reconFile = ""; |
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243 | // Output files |
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244 | this->flagLog = true; |
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245 | this->logFile = "duchamp-Logfile.txt"; |
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246 | this->outFile = "duchamp-Results.txt"; |
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247 | this->spectraFile = "duchamp-Spectra.ps"; |
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248 | this->flagOutputRecon = false; |
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249 | this->flagOutputResid = false; |
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250 | this->flagVOT = false; |
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251 | this->votFile = "duchamp-Results.xml"; |
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252 | this->flagKarma = false; |
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253 | this->karmaFile = "duchamp-Results.ann"; |
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254 | this->flagMaps = true; |
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255 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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256 | this->momentMap = "duchamp-MomentMap.ps"; |
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257 | // Cube related parameters |
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258 | this->flagBlankPix = true; |
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259 | this->blankPixValue = -8.00061; |
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260 | this->blankKeyword = 1; |
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261 | this->bscaleKeyword = -8.00061; |
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262 | this->bzeroKeyword = 0.; |
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263 | this->flagUsingBlank = false; |
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264 | this->nanAsBlank = 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->verbose = true; |
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307 | this->spectralUnits = "km/s"; |
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308 | }; |
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309 | |
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310 | /****************************************************************/ |
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311 | /////////////////////////////////////////////////// |
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312 | //// Other Functions using the Parameter class: |
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313 | /////////////////////////////////////////////////// |
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314 | |
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315 | string makelower( string s ) |
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316 | { |
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317 | // "borrowed" from Matt Howlett's 'fred' |
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318 | string out = ""; |
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319 | for( int i=0; i<s.size(); ++i ) { |
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320 | out += tolower(s[i]); |
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321 | } |
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322 | return out; |
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323 | } |
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324 | |
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325 | void Param::readParams(string paramfile) |
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326 | { |
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327 | |
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328 | std::ifstream fin(paramfile.c_str()); |
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329 | string line; |
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330 | string sval; |
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331 | float fval; |
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332 | int ival; |
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333 | bool bval; |
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334 | while( !std::getline(fin,line,'\n').eof()){ |
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335 | |
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336 | if(line[0]!='#'){ |
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337 | std::stringstream ss; |
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338 | ss.str(line); |
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339 | string arg; |
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340 | ss >> arg; |
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341 | if(makelower(arg)=="imagefile"){ ss >> sval; this->imageFile = sval;} |
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342 | if(makelower(arg)=="flagsubsection"){ ss >> bval; this->flagSubsection = bval; } |
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343 | if(makelower(arg)=="subsection"){ ss >> sval; this->subsection = sval; } |
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344 | if(makelower(arg)=="flagreconexists"){ ss >> bval; this->flagReconExists = bval; } |
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345 | if(makelower(arg)=="reconfile"){ ss >> sval; this->reconFile = sval; } |
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346 | |
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347 | if(makelower(arg)=="flaglog"){ ss >> bval; this->flagLog = bval; } |
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348 | if(makelower(arg)=="logfile"){ ss >> sval; this->logFile = sval; } |
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349 | if(makelower(arg)=="outfile"){ ss >> sval; this->outFile = sval; } |
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350 | if(makelower(arg)=="spectrafile"){ ss >> sval; this->spectraFile = sval; } |
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351 | if(makelower(arg)=="flagoutputrecon"){ ss >> bval; this->flagOutputRecon = bval; } |
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352 | if(makelower(arg)=="flagoutputresid"){ ss >> bval; this->flagOutputResid = bval; } |
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353 | if(makelower(arg)=="flagvot"){ ss >> bval; this->flagVOT = bval; } |
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354 | if(makelower(arg)=="votfile"){ ss >> sval; this->votFile = sval; } |
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355 | if(makelower(arg)=="flagkarma"){ ss >> bval; this->flagKarma = bval; } |
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356 | if(makelower(arg)=="karmafile"){ ss >> sval; this->karmaFile = sval; } |
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357 | if(makelower(arg)=="flagmaps"){ ss >> bval; this->flagMaps = bval; } |
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358 | if(makelower(arg)=="detectionmap"){ ss >> sval; this->detectionMap = sval; } |
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359 | if(makelower(arg)=="momentmap"){ ss >> sval; this->momentMap = sval; } |
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360 | |
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361 | if(makelower(arg)=="flagnegative"){ ss >> bval; this->flagNegative = bval;} |
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362 | if(makelower(arg)=="flagblankpix"){ ss >> bval; this->flagBlankPix = bval; } |
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363 | if(makelower(arg)=="blankpixvalue"){ ss >> fval; this->blankPixValue = fval; } |
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364 | if(makelower(arg)=="flagmw"){ ss >> bval; this->flagMW = bval; } |
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365 | if(makelower(arg)=="maxmw"){ ss >> ival; this->maxMW = ival; } |
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366 | if(makelower(arg)=="minmw"){ ss >> ival; this->minMW = ival; } |
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367 | |
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368 | if(makelower(arg)=="flagbaseline"){ ss >> bval; this->flagBaseline = bval; } |
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369 | if(makelower(arg)=="minpix"){ ss >> ival; this->minPix = ival; } |
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370 | if(makelower(arg)=="flaggrowth"){ ss >> bval; this->flagGrowth = bval; } |
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371 | if(makelower(arg)=="growthcut"){ ss >> fval; this->growthCut = fval; } |
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372 | |
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373 | if(makelower(arg)=="flagfdr"){ ss >> bval; this->flagFDR = bval; } |
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374 | if(makelower(arg)=="alphafdr"){ ss >> fval; this->alphaFDR = fval; } |
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375 | |
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376 | if(makelower(arg)=="snrcut"){ ss >> fval; this->snrCut = fval; } |
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377 | |
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378 | if(makelower(arg)=="flagatrous"){ ss >> bval; this->flagATrous = bval; } |
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379 | if(makelower(arg)=="recondim"){ ss >> ival; this->reconDim = ival; } |
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380 | if(makelower(arg)=="scalemin"){ ss >> ival; this->scaleMin = ival; } |
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381 | if(makelower(arg)=="snrrecon"){ ss >> fval; this->snrRecon = fval; } |
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382 | if(makelower(arg)=="filtercode"){ ss >> ival; this->filterCode = ival; } |
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383 | |
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384 | if(makelower(arg)=="flagadjacent"){ ss >> bval; this->flagAdjacent = bval; } |
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385 | if(makelower(arg)=="threshspatial"){ ss >> fval; this->threshSpatial = fval; } |
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386 | if(makelower(arg)=="threshvelocity"){ ss >> fval; this->threshVelocity = fval; } |
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387 | if(makelower(arg)=="minchannels"){ ss >> ival; this->minChannels = ival; } |
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388 | |
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389 | if(makelower(arg)=="spectralmethod"){ ss >> sval; this->spectralMethod = makelower(sval); } |
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390 | if(makelower(arg)=="spectralunits"){ ss >> sval; this->spectralUnits = makelower(sval); } |
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391 | if(makelower(arg)=="drawborders"){ ss >> bval; this->borders = bval; } |
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392 | if(makelower(arg)=="verbose"){ ss >> bval; this->verbose = bval; } |
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393 | } |
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394 | } |
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395 | } |
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396 | |
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397 | |
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398 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
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399 | { |
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400 | // Only show the [blankPixValue] bit if we are using the parameter |
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401 | // otherwise we have read it from the FITS header. |
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402 | string blankParam = ""; |
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403 | if(par.getFlagUsingBlank()) blankParam = "[blankPixValue]"; |
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404 | |
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405 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
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406 | // theStream.setf(std::ios::boolalpha); |
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407 | theStream.setf(std::ios::left); |
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408 | theStream <<"---- Parameters ----"<<endl; |
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409 | theStream << std::setfill('.'); |
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410 | if(par.getFlagSubsection()) |
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411 | theStream<<setw(38)<<"Image to be analysed" |
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412 | <<setw(18)<<setiosflags(std::ios::right) <<"[imageFile]" |
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413 | <<" = " <<resetiosflags(std::ios::right) |
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414 | <<(par.getImageFile()+par.getSubsection()) <<endl; |
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415 | else |
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416 | theStream<<setw(38)<<"Image to be analysed" |
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417 | <<setw(18)<<setiosflags(std::ios::right) <<"[imageFile]" |
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418 | <<" = " <<resetiosflags(std::ios::right)<<par.getImageFile() <<endl; |
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419 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
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420 | theStream<<setw(38)<<"Reconstructed array exists?" |
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421 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconExists]" |
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422 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagReconExists())<<endl; |
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423 | theStream<<setw(38)<<"FITS file containing reconstruction" |
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424 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconFile]" |
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425 | <<" = " <<resetiosflags(std::ios::right)<<par.getReconFile() <<endl; |
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426 | } |
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427 | theStream <<setw(38)<<"Intermediate Logfile" |
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428 | <<setw(18)<<setiosflags(std::ios::right) <<"[logFile]" |
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429 | <<" = " <<resetiosflags(std::ios::right)<<par.getLogFile() <<endl; |
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430 | theStream <<setw(38)<<"Final Results file" |
---|
431 | <<setw(18)<<setiosflags(std::ios::right) <<"[outFile]" |
---|
432 | <<" = " <<resetiosflags(std::ios::right)<<par.getOutFile() <<endl; |
---|
433 | theStream <<setw(38)<<"Spectrum file" |
---|
434 | <<setw(18)<<setiosflags(std::ios::right) <<"[spectraFile]" |
---|
435 | <<" = " <<resetiosflags(std::ios::right)<<par.getSpectraFile() <<endl; |
---|
436 | if(par.getFlagVOT()){ |
---|
437 | theStream<<setw(38)<<"VOTable file" |
---|
438 | <<setw(18)<<setiosflags(std::ios::right) <<"[votFile]" |
---|
439 | <<" = " <<resetiosflags(std::ios::right)<<par.getVOTFile() <<endl; |
---|
440 | } |
---|
441 | if(par.getFlagKarma()){ |
---|
442 | theStream<<setw(38)<<"Karma annotation file" |
---|
443 | <<setw(18)<<setiosflags(std::ios::right) <<"[karmaFile]" |
---|
444 | <<" = " <<resetiosflags(std::ios::right)<<par.getKarmaFile() <<endl; |
---|
445 | } |
---|
446 | if(par.getFlagMaps()){ |
---|
447 | theStream<<setw(38)<<"0th Moment Map" |
---|
448 | <<setw(18)<<setiosflags(std::ios::right) <<"[momentMap]" |
---|
449 | <<" = " <<resetiosflags(std::ios::right)<<par.getMomentMap() <<endl; |
---|
450 | theStream<<setw(38)<<"Detection Map" |
---|
451 | <<setw(18)<<setiosflags(std::ios::right) <<"[detectionMap]" |
---|
452 | <<" = " <<resetiosflags(std::ios::right)<<par.getDetectionMap() <<endl; |
---|
453 | } |
---|
454 | if(par.getFlagATrous()){ |
---|
455 | theStream<<setw(38)<<"Saving reconstructed cube?" |
---|
456 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagoutputrecon]" |
---|
457 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagOutputRecon())<<endl; |
---|
458 | theStream<<setw(38)<<"Saving residuals from reconstruction?" |
---|
459 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagoutputresid]" |
---|
460 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagOutputResid())<<endl; |
---|
461 | } |
---|
462 | theStream <<"------"<<endl; |
---|
463 | theStream <<setw(38)<<"Searching for Negative features?" |
---|
464 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagNegative]" |
---|
465 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagNegative()) <<endl; |
---|
466 | theStream <<setw(38)<<"Fixing Blank Pixels?" |
---|
467 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagBlankPix]" |
---|
468 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagBlankPix()) <<endl; |
---|
469 | if(par.getFlagBlankPix()){ |
---|
470 | theStream<<setw(38)<<"Blank Pixel Value" |
---|
471 | <<setw(18)<<setiosflags(std::ios::right) << blankParam |
---|
472 | <<" = " <<resetiosflags(std::ios::right)<<par.getBlankPixVal() <<endl; |
---|
473 | } |
---|
474 | theStream <<setw(38)<<"Removing Milky Way channels?" |
---|
475 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagMW]" |
---|
476 | <<" = " <<resetiosflags(std::ios::right)<<par.getFlagMW() <<endl; |
---|
477 | if(par.getFlagMW()){ |
---|
478 | theStream<<setw(38)<<"Milky Way Channels" |
---|
479 | <<setw(18)<<setiosflags(std::ios::right) <<"[minMW - maxMW]" |
---|
480 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinMW() |
---|
481 | <<"-" <<par.getMaxMW() <<endl; |
---|
482 | } |
---|
483 | theStream <<setw(38)<<"Beam Size (pixels)" |
---|
484 | <<setw(18)<<setiosflags(std::ios::right) <<"" |
---|
485 | <<" = " <<resetiosflags(std::ios::right)<<par.getBeamSize() <<endl; |
---|
486 | theStream <<setw(38)<<"Removing baselines before search?" |
---|
487 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagBaseline]" |
---|
488 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagBaseline()) <<endl; |
---|
489 | theStream <<setw(38)<<"Minimum # Pixels in a detection" |
---|
490 | <<setw(18)<<setiosflags(std::ios::right) <<"[minPix]" |
---|
491 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinPix() <<endl; |
---|
492 | theStream <<setw(38)<<"Minimum # Channels in a detection" |
---|
493 | <<setw(18)<<setiosflags(std::ios::right) <<"[minChannels]" |
---|
494 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinChannels() <<endl; |
---|
495 | theStream <<setw(38)<<"Growing objects after detection?" |
---|
496 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagGrowth]" |
---|
497 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagGrowth()) <<endl; |
---|
498 | if(par.getFlagGrowth()) { |
---|
499 | theStream<<setw(38)<<"SNR Threshold for growth" |
---|
500 | <<setw(18)<<setiosflags(std::ios::right) <<"[growthCut]" |
---|
501 | <<" = " <<resetiosflags(std::ios::right)<<par.getGrowthCut() <<endl; |
---|
502 | } |
---|
503 | theStream <<setw(38)<<"Using A Trous reconstruction?" |
---|
504 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagATrous]" |
---|
505 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagATrous()) <<endl; |
---|
506 | if(par.getFlagATrous()){ |
---|
507 | theStream<<setw(38)<<"Number of dimensions in reconstruction" |
---|
508 | <<setw(18)<<setiosflags(std::ios::right) <<"[reconDim]" |
---|
509 | <<" = " <<resetiosflags(std::ios::right)<<par.getReconDim() <<endl; |
---|
510 | theStream<<setw(38)<<"Minimum scale in reconstruction" |
---|
511 | <<setw(18)<<setiosflags(std::ios::right) <<"[scaleMin]" |
---|
512 | <<" = " <<resetiosflags(std::ios::right)<<par.getMinScale() <<endl; |
---|
513 | theStream<<setw(38)<<"SNR Threshold within reconstruction" |
---|
514 | <<setw(18)<<setiosflags(std::ios::right) <<"[snrRecon]" |
---|
515 | <<" = " <<resetiosflags(std::ios::right)<<par.getAtrousCut() <<endl; |
---|
516 | theStream<<setw(38)<<"Filter being used for reconstruction" |
---|
517 | <<setw(18)<<setiosflags(std::ios::right) <<"[filterCode]" |
---|
518 | <<" = " <<resetiosflags(std::ios::right)<<par.getFilterCode() |
---|
519 | << " (" << par.getFilterName() << ")" <<endl; |
---|
520 | } |
---|
521 | theStream <<setw(38)<<"Using FDR analysis?" |
---|
522 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagFDR]" |
---|
523 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagFDR()) <<endl; |
---|
524 | if(par.getFlagFDR()){ |
---|
525 | theStream<<setw(38)<<"Alpha value for FDR analysis" |
---|
526 | <<setw(18)<<setiosflags(std::ios::right) <<"[alphaFDR]" |
---|
527 | <<" = " <<resetiosflags(std::ios::right)<<par.getAlpha() <<endl; |
---|
528 | } |
---|
529 | else { |
---|
530 | theStream<<setw(38)<<"SNR Threshold" |
---|
531 | <<setw(18)<<setiosflags(std::ios::right) <<"[snrCut]" |
---|
532 | <<" = " <<resetiosflags(std::ios::right)<<par.getCut() <<endl; |
---|
533 | } |
---|
534 | theStream <<setw(38)<<"Using Adjacent-pixel criterion?" |
---|
535 | <<setw(18)<<setiosflags(std::ios::right) <<"[flagAdjacent]" |
---|
536 | <<" = " <<resetiosflags(std::ios::right)<<stringize(par.getFlagAdjacent()) <<endl; |
---|
537 | if(!par.getFlagAdjacent()){ |
---|
538 | theStream<<setw(38)<<"Max. spatial separation for merging" |
---|
539 | <<setw(18)<<setiosflags(std::ios::right) <<"[threshSpatial]" |
---|
540 | <<" = " <<resetiosflags(std::ios::right)<<par.getThreshS() <<endl; |
---|
541 | } |
---|
542 | theStream <<setw(38)<<"Max. velocity separation for merging" |
---|
543 | <<setw(18)<<setiosflags(std::ios::right) <<"[threshVelocity]" |
---|
544 | <<" = " <<resetiosflags(std::ios::right)<<par.getThreshV() <<endl; |
---|
545 | theStream <<setw(38)<<"Method of spectral plotting" |
---|
546 | <<setw(18)<<setiosflags(std::ios::right) <<"[spectralMethod]" |
---|
547 | <<" = " <<resetiosflags(std::ios::right)<<par.getSpectralMethod() <<endl; |
---|
548 | theStream <<"--------------------"<<endl; |
---|
549 | theStream << std::setfill(' '); |
---|
550 | theStream.unsetf(std::ios::left); |
---|
551 | // theStream.unsetf(std::ios::boolalpha); |
---|
552 | } |
---|
553 | |
---|
554 | void Param::parseSubsection() |
---|
555 | { |
---|
556 | std::stringstream ss; |
---|
557 | ss.str(this->subsection); |
---|
558 | bool removeStep = false; |
---|
559 | string x,y,z; |
---|
560 | getline(ss,x,'['); |
---|
561 | getline(ss,x,','); |
---|
562 | getline(ss,y,','); |
---|
563 | getline(ss,z,']'); |
---|
564 | char *end; |
---|
565 | if(x!="*") { |
---|
566 | int x1,x2,dx; |
---|
567 | int a = x.find(':'); // first occurence of ':' in x-subsection string |
---|
568 | int b = x.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
---|
569 | x1 = atoi( x.substr(0,a).c_str() ); // minimum x in subsection |
---|
570 | this->xSubOffset = x1 - 1; |
---|
571 | if(b>0){ // there is a dx component |
---|
572 | x2 = atoi( x.substr(a+1,b-a-1).c_str() ); // maximum x in subsection |
---|
573 | dx = atoi( x.substr(b+1,x.size()).c_str() ); // delta x in subsection |
---|
574 | x = x.substr(0,b); // rewrite x without the delta-x part. |
---|
575 | removeStep = true; |
---|
576 | } |
---|
577 | } |
---|
578 | if(y!="*") { |
---|
579 | int y1,y2,dy; |
---|
580 | int a = y.find(':'); // first occurence of ':' in y-subsection string |
---|
581 | int b = y.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
---|
582 | y1 = atoi( y.substr(0,a).c_str() ); // minimum y in subsection |
---|
583 | this->ySubOffset = y1 - 1; |
---|
584 | if(b>0){ // there is a dy component |
---|
585 | y2 = atoi( y.substr(a+1,b-a-1).c_str() ); // maximum y in subsection |
---|
586 | dy = atoi( y.substr(b+1,y.size()).c_str() ); // delta y in subsection |
---|
587 | y = y.substr(0,b); // rewrite y without the delta-y part. |
---|
588 | removeStep = true; |
---|
589 | } |
---|
590 | } |
---|
591 | if(z!="*") { |
---|
592 | int z1,z2,dz; |
---|
593 | int a = z.find(':'); // first occurence of ':' in z-subsection string |
---|
594 | int b = z.find(':',a+1); // location of second ':' -- will be -1 if there is no second occurence. |
---|
595 | z1 = atoi( z.substr(0,a).c_str() ); // minimum z in subsection |
---|
596 | this->zSubOffset = z1 - 1; |
---|
597 | if(b>0){ // there is a dz component |
---|
598 | z2 = atoi( z.substr(a+1,b-a-1).c_str() ); // maximum z in subsection |
---|
599 | dz = atoi( z.substr(b+1,z.size()).c_str() ); // delta z in subsection |
---|
600 | z = z.substr(0,b); // rewrite z without the delta-z part. |
---|
601 | removeStep = true; |
---|
602 | } |
---|
603 | } |
---|
604 | |
---|
605 | if(removeStep){ |
---|
606 | std::cerr << "\a\tThe subsection given is " << this->subsection <<".\n"; |
---|
607 | std::cerr << "\tDuchamp is currently unable to deal with pixel steps in the subsection.\n"; |
---|
608 | std::cerr << "\tThese have been ignored, and so the subection used is "; |
---|
609 | this->subsection = "[" + x + "," + y + "," + z + "]"; // rewrite subsection without any step sizes. |
---|
610 | std::cerr << this->subsection << std::endl; |
---|
611 | } |
---|
612 | |
---|
613 | // if(x!="*") this->xSubOffset = strtol(x.c_str(),&end,10) - 1; |
---|
614 | // if(y!="*") this->ySubOffset = strtol(y.c_str(),&end,10) - 1; |
---|
615 | // if(z!="*") this->zSubOffset = strtol(z.c_str(),&end,10) - 1; |
---|
616 | } |
---|
617 | |
---|
618 | bool Param::isBlank(float &val) |
---|
619 | { |
---|
620 | // std::cerr << "val = " << val << " " << int((val-this->bzeroKeyword)/this->bscaleKeyword) |
---|
621 | // <<" " <<this->blankKeyword << std::endl; |
---|
622 | if(this->flagBlankPix){ |
---|
623 | if(this->nanAsBlank) return bool(isnan(val)); |
---|
624 | else// return (val == this->blankPixValue); |
---|
625 | return ( this->blankKeyword == int((val-this->bzeroKeyword)/this->bscaleKeyword) ); |
---|
626 | } |
---|
627 | else return false; |
---|
628 | } |
---|
629 | |
---|
630 | string Param::outputReconFile() |
---|
631 | { |
---|
632 | /** |
---|
633 | * outputReconFile() |
---|
634 | * |
---|
635 | * This function produces the required filename in which to save |
---|
636 | * the reconstructed array. If the input image is image.fits, then |
---|
637 | * the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
638 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
639 | */ |
---|
640 | string inputName = this->imageFile; |
---|
641 | std::stringstream ss; |
---|
642 | ss << inputName.substr(0,inputName.size()-5); // remove the ".fits" on the end. |
---|
643 | if(this->flagSubsection) ss<<".sub"; |
---|
644 | ss << ".RECON-" << this->reconDim |
---|
645 | << "-" << this->filterCode |
---|
646 | << "-" << this->snrRecon |
---|
647 | << "-" << this->scaleMin |
---|
648 | << ".fits"; |
---|
649 | return ss.str(); |
---|
650 | } |
---|
651 | |
---|
652 | string Param::outputResidFile() |
---|
653 | { |
---|
654 | /** |
---|
655 | * outputResidFile() |
---|
656 | * |
---|
657 | * This function produces the required filename in which to save |
---|
658 | * the reconstructed array. If the input image is image.fits, then |
---|
659 | * the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
660 | * 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
661 | */ |
---|
662 | string inputName = this->imageFile; |
---|
663 | std::stringstream ss; |
---|
664 | ss << inputName.substr(0,inputName.size()-5); // remove the ".fits" on the end. |
---|
665 | if(this->flagSubsection) ss<<".sub"; |
---|
666 | ss << ".RESID-" << this->reconDim |
---|
667 | << "-" << this->filterCode |
---|
668 | << "-" << this->snrRecon |
---|
669 | << "-" << this->scaleMin |
---|
670 | << ".fits"; |
---|
671 | return ss.str(); |
---|
672 | } |
---|