1 | // ----------------------------------------------------------------------- |
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2 | // param.hh: Definition of the parameter set. |
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3 | // ----------------------------------------------------------------------- |
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4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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5 | // |
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6 | // This program is free software; you can redistribute it and/or modify it |
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7 | // under the terms of the GNU General Public License as published by the |
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8 | // Free Software Foundation; either version 2 of the License, or (at your |
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9 | // option) any later version. |
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10 | // |
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11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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14 | // for more details. |
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15 | // |
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16 | // You should have received a copy of the GNU General Public License |
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17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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19 | // |
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20 | // Correspondence concerning Duchamp may be directed to: |
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21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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22 | // Postal address: Dr. Matthew Whiting |
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23 | // Australia Telescope National Facility, CSIRO |
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24 | // PO Box 76 |
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25 | // Epping NSW 1710 |
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26 | // AUSTRALIA |
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27 | // ----------------------------------------------------------------------- |
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28 | #ifndef PARAM_H |
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29 | #define PARAM_H |
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30 | |
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31 | #include <iostream> |
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32 | #include <string> |
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33 | #include <vector> |
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34 | #include <math.h> |
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35 | #include <wcslib/wcs.h> |
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36 | #include <wcslib/wcshdr.h> |
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37 | #include <duchamp/Utils/Section.hh> |
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38 | #include <duchamp/ATrous/filter.hh> |
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39 | |
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40 | namespace duchamp |
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41 | { |
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42 | |
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43 | |
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44 | class FitsHeader; // foreshadow this so that Param knows it exists |
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45 | |
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46 | /** |
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47 | * Class to store general parameters. |
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48 | * |
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49 | * This is a general repository for parameters that are used by all |
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50 | * functions. This is how the user interacts with the program, as |
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51 | * parameters are read in from disk files through functions in this |
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52 | * class. |
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53 | */ |
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54 | |
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55 | class Param |
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56 | { |
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57 | public: |
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58 | /** Default constructor. */ |
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59 | Param(); |
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60 | |
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61 | /** Copy constructor for Param. */ |
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62 | Param(const Param& p); |
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63 | |
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64 | /** Assignment operator for Param.*/ |
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65 | Param& operator= (const Param& p); |
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66 | |
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67 | /** Destructor function. */ |
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68 | virtual ~Param(); |
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69 | |
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70 | /** Define the default values of each parameter.*/ |
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71 | void defaultValues(); |
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72 | |
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73 | //----------------- |
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74 | // Functions in param.cc |
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75 | // |
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76 | /** Parse the command line parameters correctly. */ |
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77 | int getopts(int argc, char ** argv); |
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78 | |
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79 | /** Read in parameters from a disk file. */ |
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80 | int readParams(std::string paramfile); |
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81 | |
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82 | /** Copy certain necessary FITS header parameters from a FitsHeader |
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83 | object */ |
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84 | void copyHeaderInfo(FitsHeader &head); |
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85 | |
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86 | /** Determine filename in which to save the mask array. */ |
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87 | std::string outputMaskFile(); |
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88 | |
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89 | /** Determine filename in which to save the smoothed array. */ |
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90 | std::string outputSmoothFile(); |
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91 | |
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92 | /** Determine filename in which to save the reconstructed array. */ |
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93 | std::string outputReconFile(); |
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94 | |
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95 | /** Determine filename in which to save the residual array from the |
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96 | atrous reconstruction. */ |
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97 | std::string outputResidFile(); |
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98 | |
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99 | /** Print the parameter set in a readable fashion. */ |
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100 | friend std::ostream& operator<< ( std::ostream& theStream, Param& par); |
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101 | friend class Image; |
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102 | |
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103 | //------------------ |
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104 | // Functions in FitsIO/subsection.cc |
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105 | // |
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106 | /** Make sure the subsection strings are OK. */ |
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107 | int verifySubsection(); |
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108 | |
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109 | /** Set the correct offset values for each axis */ |
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110 | void setOffsets(struct wcsprm *wcs); |
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111 | |
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112 | /** Set the correct offset values for each axis */ |
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113 | void setOffsets(struct wcsprm &wcs); |
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114 | |
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115 | //------------------ |
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116 | // These are in param.cc |
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117 | /** Is a pixel value a BLANK? */ |
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118 | bool isBlank(float &value); |
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119 | |
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120 | /** Is a given channel flagged as being in the Milky Way?*/ |
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121 | bool isInMW(int z); |
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122 | |
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123 | /** Is a given pixel position OK for use with stats calculations? */ |
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124 | bool isStatOK(int x, int y, int z); |
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125 | |
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126 | /** Make a mask array -- an array saying whether each pixel is BLANK |
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127 | or not*/ |
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128 | bool *makeBlankMask(float *array, int size); |
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129 | |
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130 | |
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131 | //-------------------- |
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132 | // Basic inline accessor functions |
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133 | // |
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134 | std::string getImageFile(){return imageFile;}; |
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135 | void setImageFile(std::string fname){imageFile = fname;}; |
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136 | std::string getFullImageFile(){ |
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137 | if(flagSubsection) return imageFile+pixelSec.getSection(); |
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138 | else return imageFile; |
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139 | }; |
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140 | bool getFlagSubsection(){return flagSubsection;}; |
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141 | void setFlagSubsection(bool flag){flagSubsection=flag;}; |
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142 | std::string getSubsection(){return pixelSec.getSection();}; |
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143 | void setSubsection(std::string range){pixelSec.setSection(range);}; |
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144 | Section §ion(){Section &rsection = pixelSec; return rsection;}; |
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145 | bool getFlagReconExists(){return flagReconExists;}; |
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146 | void setFlagReconExists(bool flag){flagReconExists=flag;}; |
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147 | std::string getReconFile(){return reconFile;}; |
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148 | void setReconFile(std::string file){reconFile = file;}; |
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149 | bool getFlagSmoothExists(){return flagSmoothExists;}; |
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150 | void setFlagSmoothExists(bool flag){flagSmoothExists=flag;}; |
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151 | std::string getSmoothFile(){return smoothFile;}; |
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152 | void setSmoothFile(std::string file){smoothFile = file;}; |
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153 | // |
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154 | bool getFlagLog(){return flagLog;}; |
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155 | void setFlagLog(bool flag){flagLog=flag;}; |
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156 | std::string getLogFile(){return logFile;}; |
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157 | void setLogFile(std::string fname){logFile = fname;}; |
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158 | std::string getOutFile(){return outFile;}; |
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159 | void setOutFile(std::string fname){outFile = fname;}; |
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160 | bool getFlagSeparateHeader(){return flagSeparateHeader;}; |
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161 | void setFlagSeparateHeader(bool b){flagSeparateHeader=b;}; |
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162 | std::string getHeaderFile(){return headerFile;}; |
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163 | void setHeaderFile(std::string s){headerFile=s;}; |
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164 | std::string getSpectraFile(){return spectraFile;}; |
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165 | void setSpectraFile(std::string fname){spectraFile = fname;}; |
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166 | bool getFlagTextSpectra(){return flagTextSpectra;}; |
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167 | void setFlagTextSpectra(bool b){flagTextSpectra = b;}; |
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168 | std::string getSpectraTextFile(){return spectraTextFile;}; |
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169 | void setSpectraTextFile(std::string fname){spectraTextFile = fname;}; |
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170 | bool getFlagOutputMask(){return flagOutputMask;}; |
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171 | void setFlagOutputMask(bool flag){flagOutputMask=flag;}; |
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172 | bool getFlagOutputSmooth(){return flagOutputSmooth;}; |
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173 | void setFlagOutputSmooth(bool flag){flagOutputSmooth=flag;}; |
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174 | bool getFlagOutputRecon(){return flagOutputRecon;}; |
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175 | void setFlagOutputRecon(bool flag){flagOutputRecon=flag;}; |
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176 | bool getFlagOutputResid(){return flagOutputResid;}; |
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177 | void setFlagOutputResid(bool flag){flagOutputResid=flag;}; |
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178 | bool getFlagVOT(){return flagVOT;}; |
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179 | void setFlagVOT(bool flag){flagVOT=flag;}; |
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180 | std::string getVOTFile(){return votFile;}; |
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181 | void setVOTFile(std::string fname){votFile = fname;}; |
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182 | bool getFlagKarma(){return flagKarma;}; |
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183 | void setFlagKarma(bool flag){flagKarma=flag;}; |
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184 | std::string getKarmaFile(){return karmaFile;}; |
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185 | void setKarmaFile(std::string fname){karmaFile = fname;}; |
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186 | bool getFlagMaps(){return flagMaps;}; |
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187 | void setFlagMaps(bool flag){flagMaps=flag;}; |
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188 | std::string getDetectionMap(){return detectionMap;}; |
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189 | void setDetectionMap(std::string fname){detectionMap = fname;}; |
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190 | std::string getMomentMap(){return momentMap;}; |
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191 | void setMomentMap(std::string fname){momentMap = fname;}; |
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192 | bool getFlagXOutput(){return flagXOutput;}; |
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193 | void setFlagXOutput(bool b){flagXOutput=b;}; |
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194 | // |
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195 | bool getFlagNegative(){return flagNegative;}; |
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196 | void setFlagNegative(bool flag){flagNegative=flag;}; |
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197 | bool getFlagBlankPix(){return flagBlankPix;}; |
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198 | void setFlagBlankPix(bool flag){flagBlankPix=flag;}; |
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199 | float getBlankPixVal(){return blankPixValue;}; |
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200 | void setBlankPixVal(float v){blankPixValue=v;}; |
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201 | int getBlankKeyword(){return blankKeyword;}; |
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202 | void setBlankKeyword(int v){blankKeyword=v;}; |
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203 | float getBscaleKeyword(){return bscaleKeyword;}; |
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204 | void setBscaleKeyword(float v){bscaleKeyword=v;}; |
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205 | float getBzeroKeyword(){return bzeroKeyword;}; |
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206 | void setBzeroKeyword(float v){bzeroKeyword=v;}; |
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207 | bool getFlagMW(){return flagMW;}; |
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208 | void setFlagMW(bool flag){flagMW=flag;}; |
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209 | int getMaxMW(){return maxMW;}; |
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210 | void setMaxMW(int m){maxMW=m;}; |
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211 | int getMinMW(){return minMW;}; |
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212 | void setMinMW(int m){minMW=m;}; |
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213 | void setBeamSize(float s){numPixBeam = s;}; |
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214 | float getBeamSize(){return numPixBeam;}; |
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215 | bool getFlagUsingBeam(){return flagUsingBeam;}; |
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216 | void setFlagUsingBeam(bool b){flagUsingBeam=b;}; |
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217 | // |
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218 | bool getFlagTrim(){return flagTrim;}; |
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219 | void setFlagTrim(bool b){flagTrim=b;}; |
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220 | bool getFlagCubeTrimmed(){return hasBeenTrimmed;}; |
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221 | void setFlagCubeTrimmed(bool flag){hasBeenTrimmed = flag;}; |
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222 | long getBorderLeft(){return borderLeft;}; |
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223 | void setBorderLeft(long b){borderLeft = b;}; |
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224 | long getBorderRight(){return borderRight;}; |
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225 | void setBorderRight(long b){borderRight = b;}; |
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226 | long getBorderBottom(){return borderBottom;}; |
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227 | void setBorderBottom(long b){borderBottom = b;}; |
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228 | long getBorderTop(){return borderTop;}; |
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229 | void setBorderTop(long b){borderTop = b;}; |
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230 | // |
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231 | long getXOffset(){return xSubOffset;}; |
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232 | void setXOffset(long o){xSubOffset = o;}; |
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233 | long getYOffset(){return ySubOffset;}; |
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234 | void setYOffset(long o){ySubOffset = o;}; |
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235 | long getZOffset(){return zSubOffset;}; |
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236 | void setZOffset(long o){zSubOffset = o;}; |
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237 | // |
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238 | int getMinPix(){return minPix;}; |
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239 | void setMinPix(int m){minPix=m;}; |
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240 | // |
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241 | bool getFlagGrowth(){return flagGrowth;}; |
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242 | void setFlagGrowth(bool flag){flagGrowth=flag;}; |
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243 | float getGrowthCut(){return growthCut;}; |
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244 | void setGrowthCut(float c){growthCut=c;}; |
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245 | // |
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246 | bool getFlagFDR(){return flagFDR;}; |
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247 | void setFlagFDR(bool flag){flagFDR=flag;}; |
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248 | float getAlpha(){return alphaFDR;}; |
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249 | void setAlpha(float a){alphaFDR=a;}; |
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250 | // |
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251 | bool getFlagBaseline(){return flagBaseline;}; |
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252 | void setFlagBaseline(bool flag){flagBaseline = flag;}; |
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253 | // |
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254 | bool getFlagStatSec(){return flagStatSec;}; |
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255 | void setFlagStatSec(bool flag){flagStatSec=flag;}; |
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256 | std::string getStatSec(){return statSec.getSection();}; |
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257 | void setStatSec(std::string range){statSec.setSection(range);}; |
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258 | bool getFlagRobustStats(){return flagRobustStats;}; |
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259 | void setFlagRobustStats(bool flag){flagRobustStats=flag;}; |
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260 | float getCut(){return snrCut;}; |
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261 | void setCut(float c){snrCut=c;}; |
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262 | float getThreshold(){return threshold;}; |
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263 | void setThreshold(float f){threshold=f;}; |
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264 | bool getFlagUserThreshold(){return flagUserThreshold;}; |
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265 | void setFlagUserThreshold(bool b){flagUserThreshold=b;}; |
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266 | // |
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267 | bool getFlagSmooth(){return flagSmooth;}; |
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268 | void setFlagSmooth(bool b){flagSmooth=b;}; |
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269 | std::string getSmoothType(){return smoothType;}; |
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270 | void setSmoothType(std::string s){smoothType=s;}; |
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271 | int getHanningWidth(){return hanningWidth;}; |
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272 | void setHanningWidth(int f){hanningWidth=f;}; |
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273 | void setKernMaj(float f){kernMaj=f;}; |
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274 | float getKernMaj(){return kernMaj;}; |
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275 | void setKernMin(float f){kernMin=f;}; |
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276 | float getKernMin(){return kernMin;}; |
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277 | void setKernPA(float f){kernPA=f;}; |
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278 | float getKernPA(){return kernPA;}; |
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279 | // |
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280 | bool getFlagATrous(){return flagATrous;}; |
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281 | void setFlagATrous(bool flag){flagATrous=flag;}; |
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282 | int getReconDim(){return reconDim;}; |
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283 | void setReconDim(int i){reconDim=i;}; |
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284 | int getMinScale(){return scaleMin;}; |
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285 | void setMinScale(int s){scaleMin=s;}; |
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286 | int getMaxScale(){return scaleMax;}; |
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287 | void setMaxScale(int s){scaleMax=s;}; |
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288 | float getAtrousCut(){return snrRecon;}; |
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289 | void setAtrousCut(float c){snrRecon=c;}; |
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290 | int getFilterCode(){return filterCode;}; |
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291 | void setFilterCode(int c){filterCode=c;}; |
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292 | std::string getFilterName(){return reconFilter.getName();}; |
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293 | Filter& filter(){ Filter &rfilter = reconFilter; return rfilter; }; |
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294 | // |
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295 | bool getFlagAdjacent(){return flagAdjacent;}; |
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296 | void setFlagAdjacent(bool flag){flagAdjacent=flag;}; |
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297 | float getThreshS(){return threshSpatial;}; |
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298 | void setThreshS(float t){threshSpatial=t;}; |
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299 | float getThreshV(){return threshVelocity;}; |
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300 | void setThreshV(float t){threshVelocity=t;}; |
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301 | int getMinChannels(){return minChannels;}; |
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302 | void setMinChannels(int n){minChannels=n;}; |
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303 | // |
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304 | std::string getSpectralMethod(){return spectralMethod;}; |
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305 | void setSpectralMethod(std::string s){spectralMethod=s;}; |
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306 | std::string getSpectralUnits(){return spectralUnits;}; |
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307 | void setSpectralUnits(std::string s){spectralUnits=s;}; |
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308 | std::string getPixelCentre(){return pixelCentre;}; |
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309 | void setPixelCentre(std::string s){pixelCentre=s;}; |
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310 | bool drawBorders(){return borders;}; |
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311 | void setDrawBorders(bool f){borders=f;}; |
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312 | bool drawBlankEdge(){return blankEdge;}; |
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313 | void setDrawBlankEdge(bool f){blankEdge=f;}; |
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314 | |
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315 | /** Are we in verbose mode? */ |
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316 | bool isVerbose(){return verbose;}; |
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317 | void setVerbosity(bool f){verbose=f;}; |
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318 | |
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319 | private: |
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320 | // Input files |
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321 | std::string imageFile; ///< The image to be analysed. |
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322 | bool flagSubsection; ///< Whether we just want a subsection of |
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323 | /// the image |
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324 | Section pixelSec; ///< The Section object storing the pixel |
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325 | /// subsection information. |
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326 | bool flagReconExists; ///< The reconstructed array is in a FITS |
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327 | /// file on disk. |
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328 | std::string reconFile; ///< The FITS file containing the |
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329 | /// reconstructed array. |
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330 | bool flagSmoothExists;///< The smoothed array is in a FITS file. |
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331 | std::string smoothFile; ///< The FITS file containing the smoothed |
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332 | /// array. |
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333 | |
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334 | // Output files |
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335 | bool flagLog; ///< Should we do the intermediate logging? |
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336 | std::string logFile; ///< Where the intermediate logging goes. |
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337 | std::string outFile; ///< Where the final results get put. |
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338 | bool flagSeparateHeader;///< Should the header information |
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339 | /// (parameters & statistics) be written |
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340 | /// to a separate file to the table of |
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341 | /// results? |
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342 | std::string headerFile; ///< Where the header information to go with |
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343 | /// the results table should be written. |
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344 | std::string spectraFile;///< Where the spectra are displayed |
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345 | bool flagTextSpectra; ///< Should a text file with all spectra |
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346 | /// be written? |
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347 | std::string spectraTextFile;///< Where the text spectra are |
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348 | /// written. |
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349 | bool flagOutputMask; ///< Should the mask image be written? |
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350 | bool flagOutputSmooth;///< Should the smoothed cube be written? |
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351 | bool flagOutputRecon; ///< Should the reconstructed cube be |
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352 | /// written? |
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353 | bool flagOutputResid; ///< Should the reconstructed cube be |
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354 | /// written? |
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355 | bool flagVOT; ///< Should we save results in VOTable |
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356 | /// format? |
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357 | std::string votFile; ///< Where the VOTable goes. |
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358 | bool flagKarma; ///< Should we save results in Karma |
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359 | /// annotation format? |
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360 | std::string karmaFile; ///< Where the Karma annotation file goes. |
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361 | bool flagMaps; ///< Should we produce detection and moment |
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362 | /// maps in postscript form? |
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363 | std::string detectionMap;///< The name of the detection map |
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364 | /// (postscript file). |
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365 | std::string momentMap; ///< The name of the 0th moment map (ps file). |
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366 | bool flagXOutput; ///< Should there be an xwindows output of |
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367 | /// the detection map? |
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368 | |
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369 | // Cube related parameters |
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370 | bool flagNegative; ///< Are we going to search for negative |
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371 | /// features? |
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372 | bool flagBlankPix; ///< A flag that indicates whether there are |
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373 | /// pixels defined as BLANK and whether we |
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374 | /// need to remove & ignore them in |
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375 | /// processing. |
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376 | float blankPixValue; ///< Pixel value that is considered BLANK. |
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377 | int blankKeyword; ///< The FITS header keyword BLANK. |
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378 | float bscaleKeyword; ///< The FITS header keyword BSCALE. |
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379 | float bzeroKeyword; ///< The FITS header keyword BZERO. |
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380 | // Milky-Way parameters |
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381 | bool flagMW; ///< A flag that indicates whether to ignore |
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382 | /// the Milky Way channels. |
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383 | int maxMW; ///< Last Milky Way channel |
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384 | int minMW; ///< First Milky Way channel |
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385 | // Trim-related |
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386 | bool flagTrim; ///< Does the user want the cube trimmed? |
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387 | bool hasBeenTrimmed; ///< Has the cube been trimmed of excess |
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388 | /// BLANKs around the edge? |
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389 | long borderLeft; ///< The number of BLANK pixels trimmed from |
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390 | /// the left of the cube; |
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391 | long borderRight; ///< The number trimmed from the Right of |
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392 | /// the cube; |
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393 | long borderBottom; ///< The number trimmed from the Bottom of |
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394 | /// the cube; |
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395 | long borderTop; ///< The number trimmed from the Top of the |
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396 | /// cube; |
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397 | // Subsection offsets |
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398 | long *offsets; ///< The array of offsets for each FITS axis. |
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399 | long sizeOffsets; ///< The size of the offsets array. |
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400 | long xSubOffset; ///< The subsection's x-axis offset |
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401 | long ySubOffset; ///< The subsection's y-axis offset |
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402 | long zSubOffset; ///< The subsection's z-axis offset |
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403 | // Baseline related |
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404 | bool flagBaseline; ///< Whether to do baseline subtraction |
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405 | /// before reconstruction and/or searching. |
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406 | // Detection-related |
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407 | int minPix; ///< Minimum number of pixels for a detected |
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408 | /// object to be counted |
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409 | float numPixBeam; ///< Size (area) of the beam in pixels. |
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410 | bool flagUsingBeam; ///< If true, we are using the numPixBeam |
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411 | /// parameter, otherwise we use the value |
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412 | /// in the FITS header. |
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413 | // Object growth |
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414 | bool flagGrowth; ///< Are we growing objects once they are |
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415 | /// found? |
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416 | float growthCut; ///< The SNR that we are growing objects |
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417 | /// down to. |
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418 | // FDR analysis |
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419 | bool flagFDR; ///< Should the FDR method be used? |
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420 | float alphaFDR; ///< Alpha value for FDR detection algorithm |
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421 | // Basic detection |
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422 | bool flagStatSec; ///< Whether we just want to use a |
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423 | /// subsection of the image to calculate |
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424 | /// the statistics. |
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425 | Section statSec; ///< The Section object storing the statistics |
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426 | /// subsection information. |
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427 | bool flagRobustStats; ///< Whether to use robust statistics. |
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428 | float snrCut; ///< How many sigma above mean is a |
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429 | /// detection when sigma-clipping |
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430 | float threshold; ///< What the threshold is (when |
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431 | /// sigma-clipping). |
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432 | bool flagUserThreshold;///< Whether the user has defined a |
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433 | /// threshold of their own. |
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434 | // Smoothing of the cube |
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435 | bool flagSmooth; ///< Should the cube be smoothed before |
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436 | /// searching? |
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437 | std::string smoothType; ///< The type of smoothing to be done. |
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438 | int hanningWidth; ///< Width for hanning smoothing. |
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439 | float kernMaj; ///< Semi-Major axis of gaussian smoothing kernel |
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440 | float kernMin; ///< Semi-Minor axis of gaussian smoothing kernel |
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441 | float kernPA; ///< Position angle of gaussian smoothing |
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442 | /// kernel, in degrees east of north |
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443 | /// (i.e. anticlockwise). |
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444 | // A trous reconstruction parameters |
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445 | bool flagATrous; ///< Are we using the a trous reconstruction? |
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446 | int reconDim; ///< How many dimensions to use for the |
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447 | /// reconstruction? |
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448 | int scaleMin; ///< Min scale used in a trous reconstruction |
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449 | int scaleMax; ///< Max scale used in a trous reconstruction |
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450 | float snrRecon; ///< SNR cutoff used in a trous |
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451 | /// reconstruction (only wavelet coefficients |
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452 | /// that survive this threshold are kept) |
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453 | Filter reconFilter; ///< The filter used for reconstructions. |
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454 | int filterCode; ///< The code number for the filter to be |
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455 | /// used (saves having to parse names) |
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456 | std::string filterName; ///< The code number converted into a name, |
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457 | /// for outputting purposes. |
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458 | |
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459 | // Volume-merging parameters |
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460 | bool flagAdjacent; ///< Whether to use the adjacent criterion |
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461 | /// for judging if objects are to be merged. |
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462 | float threshSpatial; ///< Maximum spatial separation between |
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463 | /// objects |
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464 | float threshVelocity; ///< Maximum channels separation between |
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465 | /// objects |
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466 | int minChannels; ///< Minimum no. of channels to make an object |
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467 | |
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468 | // Input-Output related |
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469 | std::string spectralMethod; ///< A string indicating choice of |
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470 | /// spectral plotting method: choices are |
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471 | /// "peak" (default) or "sum" |
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472 | std::string spectralUnits; ///< A string indicating what units the |
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473 | /// spectral axis should be quoted in. |
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474 | std::string pixelCentre;///< A string indicating which type of |
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475 | /// centre to give the results in: "average", |
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476 | /// "centroid", or "peak"(flux). |
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477 | bool borders; ///< Whether to draw a border around the |
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478 | /// individual pixels of a detection in the |
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479 | /// spectral display |
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480 | bool blankEdge; ///< Whether to draw a border around the |
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481 | /// BLANK pixel region in the moment maps and |
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482 | /// cutout images |
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483 | bool verbose; ///< Whether to use maximum verbosity -- use |
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484 | /// progress indicators in the reconstruction |
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485 | /// & merging steps. |
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486 | |
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487 | }; |
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488 | |
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489 | //=========================================================================== |
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490 | |
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491 | |
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492 | std::string makelower( std::string s ); |
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493 | |
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494 | } |
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495 | #endif |
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