1 | // ----------------------------------------------------------------------- |
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2 | // param.cc: Dealing with the set of parameters for Duchamp. |
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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 | #include <iostream> |
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29 | #include <iomanip> |
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30 | #include <fstream> |
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31 | #include <sstream> |
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32 | #include <string> |
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33 | #include <algorithm> |
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34 | #include <stdlib.h> |
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35 | #include <ctype.h> |
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36 | #include <math.h> |
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37 | #include <unistd.h> |
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38 | #include <duchamp/param.hh> |
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39 | #include <duchamp/fitsHeader.hh> |
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40 | #include <duchamp/duchamp.hh> |
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41 | #include <duchamp/pgheader.hh> |
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42 | #include <duchamp/ATrous/filter.hh> |
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43 | #include <duchamp/Utils/utils.hh> |
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44 | #include <duchamp/Utils/Section.hh> |
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45 | #include <duchamp/Utils/VOParam.hh> |
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46 | #include <duchamp/Outputs/columns.hh> |
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47 | |
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48 | namespace duchamp |
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49 | { |
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50 | const std::string defaultSection = "[*,*,*]"; |
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51 | |
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52 | /****************************************************************/ |
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53 | /////////////////////////////////////////////////// |
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54 | //// Accessor Functions for Parameter class: |
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55 | /////////////////////////////////////////////////// |
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56 | Param::~Param() |
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57 | { |
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58 | /// Deletes the offsets array if the sizeOffsets parameter is |
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59 | /// positive. |
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60 | if(this->sizeOffsets>0) delete [] this->offsets; |
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61 | } |
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62 | |
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63 | Param::Param() |
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64 | { |
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65 | this->defaultValues(); |
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66 | } |
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67 | |
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68 | void Param::defaultValues() |
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69 | { |
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70 | /// Provides default intial values for the parameters. Note that |
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71 | /// imageFile has no default value! |
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72 | |
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73 | // Input files |
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74 | this->imageFile = ""; |
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75 | this->flagSubsection = false; |
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76 | this->pixelSec.setSection(defaultSection); |
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77 | this->flagReconExists = false; |
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78 | this->reconFile = ""; |
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79 | this->flagSmoothExists = false; |
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80 | this->smoothFile = ""; |
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81 | this->usePrevious = false; |
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82 | this->objectList = ""; |
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83 | // Output files |
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84 | this->flagLog = false; |
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85 | this->logFile = "duchamp-Logfile.txt"; |
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86 | this->outFile = "duchamp-Results.txt"; |
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87 | this->flagSeparateHeader= false; |
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88 | this->headerFile = "duchamp-Results.hdr"; |
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89 | this->flagPlotSpectra = true; |
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90 | this->spectraFile = "duchamp-Spectra.ps"; |
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91 | this->flagTextSpectra = false; |
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92 | this->spectraTextFile = "duchamp-Spectra.txt"; |
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93 | this->flagOutputMomentMap = false; |
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94 | this->fileOutputMomentMap = ""; |
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95 | this->flagOutputMask = false; |
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96 | this->fileOutputMask = ""; |
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97 | this->flagMaskWithObjectNum = false; |
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98 | this->flagOutputSmooth = false; |
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99 | this->fileOutputSmooth = ""; |
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100 | this->flagOutputRecon = false; |
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101 | this->fileOutputRecon = ""; |
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102 | this->flagOutputResid = false; |
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103 | this->fileOutputResid = ""; |
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104 | this->flagVOT = false; |
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105 | this->votFile = "duchamp-Results.xml"; |
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106 | this->flagKarma = false; |
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107 | this->karmaFile = "duchamp-Results.ann"; |
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108 | this->flagDS9 = false; |
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109 | this->ds9File = "duchamp-Results.reg"; |
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110 | this->annotationType = "borders"; |
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111 | this->flagMaps = true; |
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112 | this->detectionMap = "duchamp-DetectionMap.ps"; |
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113 | this->momentMap = "duchamp-MomentMap.ps"; |
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114 | this->flagXOutput = true; |
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115 | this->precFlux = Catalogues::prFLUX; |
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116 | this->precVel = Catalogues::prVEL; |
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117 | this->precSNR = Catalogues::prSNR; |
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118 | // Cube related parameters |
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119 | this->flagBlankPix = false; |
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120 | this->blankPixValue = -8.00061; |
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121 | this->blankKeyword = 1; |
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122 | this->bscaleKeyword = -8.00061; |
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123 | this->bzeroKeyword = 0.; |
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124 | this->newFluxUnits = ""; |
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125 | // Milky-Way parameters |
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126 | this->flagMW = false; |
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127 | this->maxMW = 112; |
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128 | this->minMW = 75; |
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129 | this->areaBeam = 0.; |
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130 | this->fwhmBeam = 0.; |
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131 | this->beamAsUsed.empty(); |
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132 | this->searchType = "spatial"; |
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133 | // Trim-related |
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134 | this->flagTrim = false; |
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135 | this->hasBeenTrimmed = false; |
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136 | this->borderLeft = 0; |
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137 | this->borderRight = 0; |
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138 | this->borderBottom = 0; |
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139 | this->borderTop = 0; |
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140 | // Subsection offsets |
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141 | this->sizeOffsets = 0; |
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142 | this->xSubOffset = 0; |
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143 | this->ySubOffset = 0; |
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144 | this->zSubOffset = 0; |
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145 | // Baseline related |
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146 | this->flagBaseline = false; |
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147 | // Detection-related |
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148 | this->flagNegative = false; |
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149 | // Object growth |
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150 | this->flagGrowth = false; |
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151 | this->growthCut = 3.; |
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152 | this->flagUserGrowthThreshold = false; |
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153 | this->growthThreshold = 0.; |
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154 | // FDR analysis |
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155 | this->flagFDR = false; |
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156 | this->alphaFDR = 0.01; |
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157 | this->FDRnumCorChan = 2; |
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158 | // Other detection |
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159 | this->flagStatSec = false; |
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160 | this->statSec.setSection(defaultSection); |
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161 | this->flagRobustStats = true; |
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162 | this->snrCut = 5.; |
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163 | this->threshold = 0.; |
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164 | this->flagUserThreshold = false; |
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165 | // Smoothing |
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166 | this->flagSmooth = false; |
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167 | this->smoothType = "spectral"; |
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168 | this->hanningWidth = 5; |
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169 | this->kernMaj = 3.; |
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170 | this->kernMin = -1.; |
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171 | this->kernPA = 0.; |
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172 | // A trous reconstruction parameters |
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173 | this->flagATrous = false; |
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174 | this->reconDim = 1; |
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175 | this->scaleMin = 1; |
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176 | this->scaleMax = 0; |
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177 | this->snrRecon = 4.; |
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178 | this->reconConvergence = 0.005; |
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179 | this->filterCode = 1; |
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180 | this->reconFilter.define(this->filterCode); |
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181 | // Volume-merging parameters |
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182 | this->flagAdjacent = true; |
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183 | this->threshSpatial = 3.; |
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184 | this->threshVelocity = 7.; |
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185 | this->minChannels = 3; |
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186 | this->minPix = 2; |
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187 | this->minVoxels = 4; |
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188 | this->flagRejectBeforeMerge = false; |
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189 | this->flagTwoStageMerging = true; |
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190 | // Input-Output related |
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191 | this->spectralMethod = "peak"; |
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192 | this->spectralType = ""; |
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193 | this->restFrequency = -1.; |
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194 | this->restFrequencyUsed = false; |
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195 | this->spectralUnits = ""; |
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196 | this->pixelCentre = "centroid"; |
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197 | this->sortingParam = "vel"; |
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198 | this->borders = true; |
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199 | this->blankEdge = true; |
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200 | this->verbose = true; |
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201 | } |
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202 | |
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203 | Param::Param (const Param& p) |
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204 | { |
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205 | operator=(p); |
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206 | } |
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207 | |
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208 | Param& Param::operator= (const Param& p) |
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209 | { |
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210 | if(this == &p) return *this; |
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211 | this->imageFile = p.imageFile; |
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212 | this->flagSubsection = p.flagSubsection; |
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213 | this->pixelSec = p.pixelSec; |
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214 | this->flagReconExists = p.flagReconExists; |
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215 | this->reconFile = p.reconFile; |
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216 | this->flagSmoothExists = p.flagSmoothExists; |
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217 | this->smoothFile = p.smoothFile; |
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218 | this->usePrevious = p.usePrevious; |
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219 | this->objectList = p.objectList; |
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220 | this->flagLog = p.flagLog; |
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221 | this->logFile = p.logFile; |
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222 | this->outFile = p.outFile; |
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223 | this->flagSeparateHeader= p.flagSeparateHeader; |
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224 | this->headerFile = p.headerFile; |
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225 | this->flagPlotSpectra = p.flagPlotSpectra; |
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226 | this->spectraFile = p.spectraFile; |
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227 | this->flagTextSpectra = p.flagTextSpectra; |
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228 | this->spectraTextFile = p.spectraTextFile; |
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229 | this->flagOutputMomentMap = p.flagOutputMomentMap; |
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230 | this->fileOutputMomentMap = p.fileOutputMomentMap; |
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231 | this->flagOutputMask = p.flagOutputMask; |
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232 | this->fileOutputMask = p.fileOutputMask; |
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233 | this->flagMaskWithObjectNum = p.flagMaskWithObjectNum; |
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234 | this->flagOutputSmooth = p.flagOutputSmooth; |
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235 | this->fileOutputSmooth = p.fileOutputSmooth; |
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236 | this->flagOutputRecon = p.flagOutputRecon; |
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237 | this->fileOutputRecon = p.fileOutputRecon; |
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238 | this->flagOutputResid = p.flagOutputResid; |
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239 | this->fileOutputResid = p.fileOutputResid; |
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240 | this->flagVOT = p.flagVOT; |
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241 | this->votFile = p.votFile; |
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242 | this->flagKarma = p.flagKarma; |
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243 | this->karmaFile = p.karmaFile; |
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244 | this->flagDS9 = p.flagDS9; |
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245 | this->ds9File = p.ds9File; |
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246 | this->annotationType = p.annotationType; |
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247 | this->flagMaps = p.flagMaps; |
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248 | this->detectionMap = p.detectionMap; |
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249 | this->momentMap = p.momentMap; |
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250 | this->flagXOutput = p.flagXOutput; |
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251 | this->precFlux = p.precFlux; |
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252 | this->precVel = p.precVel; |
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253 | this->precSNR = p.precSNR; |
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254 | this->flagNegative = p.flagNegative; |
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255 | this->flagBlankPix = p.flagBlankPix; |
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256 | this->blankPixValue = p.blankPixValue; |
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257 | this->blankKeyword = p.blankKeyword; |
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258 | this->bscaleKeyword = p.bscaleKeyword; |
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259 | this->bzeroKeyword = p.bzeroKeyword; |
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260 | this->newFluxUnits = p.newFluxUnits; |
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261 | this->flagMW = p.flagMW; |
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262 | this->maxMW = p.maxMW; |
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263 | this->minMW = p.minMW; |
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264 | this->areaBeam = p.areaBeam; |
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265 | this->fwhmBeam = p.fwhmBeam; |
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266 | this->beamAsUsed = p.beamAsUsed; |
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267 | this->searchType = p.searchType; |
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268 | this->flagTrim = p.flagTrim; |
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269 | this->hasBeenTrimmed = p.hasBeenTrimmed; |
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270 | this->borderLeft = p.borderLeft; |
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271 | this->borderRight = p.borderRight; |
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272 | this->borderBottom = p.borderBottom; |
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273 | this->borderTop = p.borderTop; |
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274 | if(this->sizeOffsets>0) delete [] this->offsets; |
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275 | this->sizeOffsets = p.sizeOffsets; |
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276 | if(this->sizeOffsets>0){ |
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277 | this->offsets = new long[this->sizeOffsets]; |
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278 | for(int i=0;i<this->sizeOffsets;i++) this->offsets[i] = p.offsets[i]; |
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279 | } |
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280 | this->xSubOffset = p.xSubOffset; |
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281 | this->ySubOffset = p.ySubOffset; |
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282 | this->zSubOffset = p.zSubOffset; |
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283 | this->flagBaseline = p.flagBaseline; |
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284 | this->flagGrowth = p.flagGrowth; |
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285 | this->growthCut = p.growthCut; |
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286 | this->growthThreshold = p.growthThreshold; |
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287 | this->flagUserGrowthThreshold = p.flagUserGrowthThreshold; |
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288 | this->flagFDR = p.flagFDR; |
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289 | this->alphaFDR = p.alphaFDR; |
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290 | this->FDRnumCorChan = p.FDRnumCorChan; |
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291 | this->flagStatSec = p.flagStatSec; |
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292 | this->statSec = p.statSec; |
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293 | this->flagRobustStats = p.flagRobustStats; |
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294 | this->snrCut = p.snrCut; |
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295 | this->threshold = p.threshold; |
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296 | this->flagUserThreshold = p.flagUserThreshold; |
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297 | this->flagSmooth = p.flagSmooth; |
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298 | this->smoothType = p.smoothType; |
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299 | this->hanningWidth = p.hanningWidth; |
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300 | this->kernMaj = p.kernMaj; |
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301 | this->kernMin = p.kernMin; |
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302 | this->kernPA = p.kernPA; |
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303 | this->flagATrous = p.flagATrous; |
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304 | this->reconDim = p.reconDim; |
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305 | this->scaleMin = p.scaleMin; |
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306 | this->scaleMax = p.scaleMax; |
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307 | this->snrRecon = p.snrRecon; |
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308 | this->reconConvergence = p.reconConvergence; |
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309 | this->filterCode = p.filterCode; |
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310 | this->reconFilter = p.reconFilter; |
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311 | this->flagAdjacent = p.flagAdjacent; |
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312 | this->threshSpatial = p.threshSpatial; |
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313 | this->threshVelocity = p.threshVelocity; |
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314 | this->minChannels = p.minChannels; |
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315 | this->minPix = p.minPix; |
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316 | this->minVoxels = p.minVoxels; |
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317 | this->flagRejectBeforeMerge = p.flagRejectBeforeMerge; |
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318 | this->flagTwoStageMerging = p.flagTwoStageMerging; |
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319 | this->spectralMethod = p.spectralMethod; |
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320 | this->spectralType = p.spectralType; |
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321 | this->restFrequency = p.restFrequency; |
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322 | this->restFrequencyUsed = p.restFrequencyUsed; |
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323 | this->spectralUnits = p.spectralUnits; |
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324 | this->pixelCentre = p.pixelCentre; |
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325 | this->sortingParam = p.sortingParam; |
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326 | this->borders = p.borders; |
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327 | this->blankEdge = p.blankEdge; |
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328 | this->verbose = p.verbose; |
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329 | return *this; |
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330 | } |
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331 | //-------------------------------------------------------------------- |
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332 | |
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333 | OUTCOME Param::getopts(int argc, char ** argv, std::string progname) |
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334 | { |
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335 | /// A function that reads in the command-line options, in a manner |
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336 | /// tailored for use with the main Duchamp program. |
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337 | /// |
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338 | /// \param argc The number of command line arguments. |
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339 | /// \param argv The array of command line arguments. |
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340 | |
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341 | OUTCOME returnValue = FAILURE; |
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342 | if(argc==1){ |
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343 | if(progname=="Selavy") std::cout << SELAVY_ERR_USAGE_MSG; |
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344 | else if(progname=="Duchamp") std::cout << ERR_USAGE_MSG; |
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345 | else std::cout << ERR_USAGE_MSG; |
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346 | returnValue = FAILURE; |
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347 | } |
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348 | else { |
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349 | std::string file; |
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350 | bool changeX = false; |
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351 | this->defaultValues(); |
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352 | char c; |
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353 | while( ( c = getopt(argc,argv,"p:f:hvx") )!=-1){ |
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354 | switch(c) { |
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355 | case 'p': |
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356 | file = optarg; |
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357 | if(this->readParams(file)==FAILURE){ |
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358 | DUCHAMPERROR(progname,"Could not open parameter file " << file); |
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359 | } |
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360 | else returnValue = SUCCESS; |
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361 | break; |
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362 | case 'f': |
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363 | file = optarg; |
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364 | this->imageFile = file; |
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365 | returnValue = SUCCESS; |
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366 | break; |
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367 | case 'v': |
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368 | std::cout << PROGNAME << " version " << VERSION << std::endl; |
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369 | break; |
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370 | case 'x': |
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371 | changeX = true; |
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372 | break; |
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373 | case 'h': |
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374 | default : |
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375 | if(progname=="Selavy") std::cout << SELAVY_ERR_USAGE_MSG; |
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376 | else if(progname=="Duchamp") std::cout << ERR_USAGE_MSG; |
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377 | else std::cout << ERR_USAGE_MSG; |
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378 | break; |
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379 | } |
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380 | } |
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381 | if(changeX){ |
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382 | if(returnValue == SUCCESS) this->setFlagXOutput(false); |
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383 | else { |
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384 | DUCHAMPERROR(progname, "You need to specify either a parameter file or FITS image.\n"); |
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385 | std::cout << "\n" << ERR_USAGE_MSG; |
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386 | } |
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387 | } |
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388 | } |
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389 | return returnValue; |
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390 | } |
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391 | //-------------------------------------------------------------------- |
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392 | |
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393 | bool Param::isBlank(float &value) |
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394 | { |
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395 | /// Tests whether the value passed as the argument is BLANK or not. |
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396 | /// \param value Pixel value to be tested. |
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397 | /// \return False if flagBlankPix is false. Else, compare to the |
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398 | /// relevant FITS keywords, using integer comparison. |
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399 | |
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400 | return this->flagBlankPix && |
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401 | (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword)); |
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402 | } |
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403 | |
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404 | bool *Param::makeBlankMask(float *array, size_t size) |
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405 | { |
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406 | /// This returns an array of bools, saying whether each pixel in the |
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407 | /// given array is BLANK or not. If the pixel is BLANK, set mask to |
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408 | /// false, else set to true. The array is allocated by the function. |
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409 | |
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410 | bool *mask = new bool[size]; |
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411 | for(size_t i=0;i<size;i++) mask[i] = !this->isBlank(array[i]); |
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412 | return mask; |
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413 | } |
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414 | |
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415 | |
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416 | bool *Param::makeStatMask(float *array, size_t *dim) |
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417 | { |
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418 | /// This returns an array of bools, saying whether each pixel in |
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419 | /// the given array is suitable for a stats calculation. It needs |
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420 | /// to be in the StatSec (if defined), not blank and not a MW |
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421 | /// channel. The array is allocated by the function with a 'new' call. |
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422 | |
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423 | bool *mask = new bool[dim[0]*dim[1]*dim[2]]; |
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424 | for(size_t x=0;x<dim[0];x++) { |
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425 | for(size_t y=0;y<dim[1];y++) { |
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426 | for(size_t z=0;z<dim[2];z++) { |
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427 | size_t i = x+y*dim[0]+z*dim[0]*dim[1]; |
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428 | mask[i] = !this->isBlank(array[i]) && !this->isInMW(z) && this->isStatOK(x,y,z); |
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429 | } |
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430 | } |
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431 | } |
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432 | return mask; |
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433 | } |
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434 | |
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435 | |
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436 | bool Param::isInMW(int z) |
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437 | { |
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438 | /// Tests whether we are flagging Milky Way channels, and if so |
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439 | /// whether the given channel number is in the Milky Way range. The |
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440 | /// channels are assumed to start at number 0. |
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441 | /// \param z The channel number |
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442 | /// \return True if we are flagging Milky Way channels and z is in |
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443 | /// the range. |
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444 | |
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445 | return ( this->flagMW && (z>=this->getMinMW()) && (z<=this->getMaxMW()) ); |
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446 | } |
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447 | |
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448 | bool Param::isStatOK(int x, int y, int z) |
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449 | { |
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450 | /// Test whether a given pixel position lies within the subsection |
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451 | /// given by the statSec parameter. Only tested if the flagSubsection |
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452 | /// parameter is true -- if it isn't, we just return true since all |
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453 | /// pixels are therefore available for statstical calculations. |
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454 | /// \param x X-value of pixel being tested. |
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455 | /// \param y Y-value of pixel being tested. |
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456 | /// \param z Z-value of pixel being tested. |
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457 | /// \return True if pixel is able to be used for statistical |
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458 | /// calculations. False otherwise. |
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459 | |
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460 | int xval=x,yval=y,zval=z; |
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461 | if(flagSubsection){ |
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462 | xval += pixelSec.getStart(0); |
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463 | yval += pixelSec.getStart(1); |
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464 | zval += pixelSec.getStart(2); |
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465 | } |
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466 | return !flagStatSec || statSec.isInside(xval,yval,zval); |
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467 | } |
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468 | |
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469 | std::vector<int> Param::getObjectRequest() |
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470 | { |
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471 | /// Returns a list of the object numbers requested via the objectList parameter. |
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472 | /// \return a vector of integers, one for each number in the objectList set. |
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473 | |
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474 | std::stringstream ss1; |
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475 | std::string tmp; |
---|
476 | std::vector<int> tmplist; |
---|
477 | ss1.str(this->objectList); |
---|
478 | while(!ss1.eof()){ |
---|
479 | getline(ss1,tmp,','); |
---|
480 | for(size_t i=0;i<tmp.size();i++) if(tmp[i]=='-') tmp[i]=' '; |
---|
481 | int a,b; |
---|
482 | std::stringstream ss2; |
---|
483 | ss2.str(tmp); |
---|
484 | ss2 >>a; |
---|
485 | if(!ss2.eof()) ss2 >> b; |
---|
486 | else b=a; |
---|
487 | for(int n=a;n<=b;n++){ |
---|
488 | tmplist.push_back(n); |
---|
489 | } |
---|
490 | } |
---|
491 | return tmplist; |
---|
492 | } |
---|
493 | |
---|
494 | std::vector<bool> Param::getObjectChoices() |
---|
495 | { |
---|
496 | /// Returns a list of bool values, indicating whether a given |
---|
497 | /// object was requested or not. The size of the vector is |
---|
498 | /// determined by the maximum value in objectList. For instance, |
---|
499 | /// if objectList="2,3,5-8", then the returned vector will be |
---|
500 | /// [0,1,1,0,1,1,1,1]. |
---|
501 | /// \return Vector of bool values. |
---|
502 | |
---|
503 | std::vector<int> objectChoices = this->getObjectRequest(); |
---|
504 | int maxNum = *std::max_element(objectChoices.begin(), objectChoices.end()); |
---|
505 | std::vector<bool> choices(maxNum,false); |
---|
506 | for(std::vector<int>::iterator obj = objectChoices.begin();obj!=objectChoices.end();obj++) |
---|
507 | choices[*obj-1] = true; |
---|
508 | return choices; |
---|
509 | } |
---|
510 | |
---|
511 | std::vector<bool> Param::getObjectChoices(int numObjects) |
---|
512 | { |
---|
513 | /// Returns a list of bool values, indicating whether a given |
---|
514 | /// object was requested or not. The size of the vector is given |
---|
515 | /// by the numObjects parameter. So, if objectList="2,3,5-8", then |
---|
516 | /// the returned vector from a getObjectChoices(10) call will be |
---|
517 | /// [0,1,1,0,1,1,1,1,0,0]. |
---|
518 | /// \param numObjects How many objects there are in total. |
---|
519 | /// \return Vector of bool values. |
---|
520 | |
---|
521 | if(this->objectList==""){ |
---|
522 | std::vector<bool> choices(numObjects,true); |
---|
523 | return choices; |
---|
524 | } |
---|
525 | else{ |
---|
526 | std::vector<int> objectChoices = this->getObjectRequest(); |
---|
527 | std::vector<bool> choices(numObjects,false); |
---|
528 | for(std::vector<int>::iterator obj = objectChoices.begin();obj!=objectChoices.end();obj++) |
---|
529 | if(*obj<=numObjects) choices[*obj-1] = true; |
---|
530 | return choices; |
---|
531 | } |
---|
532 | } |
---|
533 | |
---|
534 | /****************************************************************/ |
---|
535 | /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// |
---|
536 | /// / Other Functions using the Parameter class: |
---|
537 | /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// /// |
---|
538 | |
---|
539 | OUTCOME Param::readParams(std::string paramfile) |
---|
540 | { |
---|
541 | /// The parameters are read in from a disk file, on the assumption that each |
---|
542 | /// line of the file has the format "parameter value" (eg. alphafdr 0.1) |
---|
543 | /// |
---|
544 | /// The case of the parameter name does not matter, nor does the |
---|
545 | /// formatting of the spaces (it can be any amount of whitespace or |
---|
546 | /// tabs). |
---|
547 | /// |
---|
548 | /// \param paramfile A std::string containing the parameter filename. |
---|
549 | /// |
---|
550 | /// \return FAILURE if the parameter file does not exist. SUCCESS if |
---|
551 | /// it is able to read it. |
---|
552 | |
---|
553 | if(!USE_PGPLOT){ |
---|
554 | // Change default values for these parameters when we don't use PGPlot |
---|
555 | this->flagXOutput = false; |
---|
556 | this->flagMaps = false; |
---|
557 | this->flagPlotSpectra = false; |
---|
558 | } |
---|
559 | |
---|
560 | std::ifstream fin(paramfile.c_str()); |
---|
561 | if(!fin.is_open()) return FAILURE; |
---|
562 | std::string line; |
---|
563 | while( !std::getline(fin,line,'\n').eof()){ |
---|
564 | |
---|
565 | if(line[0]!='#'){ |
---|
566 | std::stringstream ss; |
---|
567 | ss.str(line); |
---|
568 | std::string arg; |
---|
569 | ss >> arg; |
---|
570 | arg = makelower(arg); |
---|
571 | if(arg=="imagefile") this->imageFile = readFilename(ss); |
---|
572 | if(arg=="flagsubsection") this->flagSubsection = readFlag(ss); |
---|
573 | if(arg=="subsection") this->pixelSec.setSection(readSval(ss)); |
---|
574 | if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); |
---|
575 | if(arg=="reconfile") this->reconFile = readSval(ss); |
---|
576 | if(arg=="flagsmoothexists")this->flagSmoothExists = readFlag(ss); |
---|
577 | if(arg=="smoothfile") this->smoothFile = readSval(ss); |
---|
578 | if(arg=="beamarea") this->areaBeam = readFval(ss); |
---|
579 | if(arg=="beamfwhm") this->fwhmBeam = readFval(ss); |
---|
580 | if(arg=="useprevious") this->usePrevious = readFlag(ss); |
---|
581 | if(arg=="objectlist") this->objectList = readSval(ss); |
---|
582 | |
---|
583 | if(arg=="flaglog") this->flagLog = readFlag(ss); |
---|
584 | if(arg=="logfile") this->logFile = readSval(ss); |
---|
585 | if(arg=="outfile") this->outFile = readSval(ss); |
---|
586 | if(arg=="flagseparateheader") this->flagSeparateHeader = readFlag(ss); |
---|
587 | if(arg=="headerfile") this->headerFile = readFilename(ss); |
---|
588 | if(arg=="flagplotspectra") this->flagPlotSpectra = readFlag(ss); |
---|
589 | if(arg=="spectrafile") this->spectraFile = readFilename(ss); |
---|
590 | if(arg=="flagtextspectra") this->flagTextSpectra = readFlag(ss); |
---|
591 | if(arg=="spectratextfile") this->spectraTextFile = readFilename(ss); |
---|
592 | if(arg=="flagoutputmomentmap") this->flagOutputMomentMap = readFlag(ss); |
---|
593 | if(arg=="fileoutputmomentmap") this->fileOutputMomentMap = readFilename(ss); |
---|
594 | if(arg=="flagoutputmask") this->flagOutputMask = readFlag(ss); |
---|
595 | if(arg=="fileoutputmask") this->fileOutputMask = readFilename(ss); |
---|
596 | if(arg=="flagmaskwithobjectnum") this->flagMaskWithObjectNum = readFlag(ss); |
---|
597 | if(arg=="flagoutputsmooth")this->flagOutputSmooth = readFlag(ss); |
---|
598 | if(arg=="fileoutputsmooth")this->fileOutputSmooth = readFilename(ss); |
---|
599 | if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); |
---|
600 | if(arg=="fileoutputrecon") this->fileOutputRecon = readFilename(ss); |
---|
601 | if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); |
---|
602 | if(arg=="fileoutputresid") this->fileOutputResid = readFilename(ss); |
---|
603 | if(arg=="flagvot") this->flagVOT = readFlag(ss); |
---|
604 | if(arg=="votfile") this->votFile = readFilename(ss); |
---|
605 | if(arg=="flagkarma") this->flagKarma = readFlag(ss); |
---|
606 | if(arg=="karmafile") this->karmaFile = readFilename(ss); |
---|
607 | if(arg=="flagds9") this->flagDS9 = readFlag(ss); |
---|
608 | if(arg=="ds9file") this->ds9File = readFilename(ss); |
---|
609 | if(arg=="annotationtype") this->annotationType = readSval(ss); |
---|
610 | if(arg=="flagmaps") this->flagMaps = readFlag(ss); |
---|
611 | if(arg=="detectionmap") this->detectionMap = readFilename(ss); |
---|
612 | if(arg=="momentmap") this->momentMap = readFilename(ss); |
---|
613 | if(arg=="flagxoutput") this->flagXOutput = readFlag(ss); |
---|
614 | if(arg=="newfluxunits") this->newFluxUnits = readSval(ss); |
---|
615 | if(arg=="precflux") this->precFlux = readIval(ss); |
---|
616 | if(arg=="precvel") this->precVel = readIval(ss); |
---|
617 | if(arg=="precsnr") this->precSNR = readIval(ss); |
---|
618 | |
---|
619 | if(arg=="flagtrim") this->flagTrim = readFlag(ss); |
---|
620 | if(arg=="flagmw") this->flagMW = readFlag(ss); |
---|
621 | if(arg=="maxmw") this->maxMW = readIval(ss); |
---|
622 | if(arg=="minmw") this->minMW = readIval(ss); |
---|
623 | if(arg=="flagbaseline") this->flagBaseline = readFlag(ss); |
---|
624 | if(arg=="searchtype") this->searchType = readSval(ss); |
---|
625 | |
---|
626 | if(arg=="flagnegative") this->flagNegative = readFlag(ss); |
---|
627 | if(arg=="minpix") this->minPix = readIval(ss); |
---|
628 | if(arg=="flaggrowth") this->flagGrowth = readFlag(ss); |
---|
629 | if(arg=="growthcut") this->growthCut = readFval(ss); |
---|
630 | if(arg=="growththreshold"){ |
---|
631 | this->growthThreshold = readFval(ss); |
---|
632 | this->flagUserGrowthThreshold = true; |
---|
633 | } |
---|
634 | |
---|
635 | if(arg=="flagfdr") this->flagFDR = readFlag(ss); |
---|
636 | if(arg=="alphafdr") this->alphaFDR = readFval(ss); |
---|
637 | if(arg=="fdrnumcorchan") this->FDRnumCorChan = readIval(ss); |
---|
638 | if(arg=="flagstatsec") this->flagStatSec = readFlag(ss); |
---|
639 | if(arg=="statsec") this->statSec.setSection(readSval(ss)); |
---|
640 | if(arg=="flagrobuststats") this->flagRobustStats = readFlag(ss); |
---|
641 | if(arg=="snrcut") this->snrCut = readFval(ss); |
---|
642 | if(arg=="threshold"){ |
---|
643 | this->threshold = readFval(ss); |
---|
644 | this->flagUserThreshold = true; |
---|
645 | } |
---|
646 | |
---|
647 | if(arg=="flagsmooth") this->flagSmooth = readFlag(ss); |
---|
648 | if(arg=="smoothtype") this->smoothType = readSval(ss); |
---|
649 | if(arg=="hanningwidth") this->hanningWidth = readIval(ss); |
---|
650 | if(arg=="kernmaj") this->kernMaj = readFval(ss); |
---|
651 | if(arg=="kernmin") this->kernMin = readFval(ss); |
---|
652 | if(arg=="kernpa") this->kernPA = readFval(ss); |
---|
653 | |
---|
654 | if(arg=="flagatrous") this->flagATrous = readFlag(ss); |
---|
655 | if(arg=="recondim") this->reconDim = readIval(ss); |
---|
656 | if(arg=="scalemin") this->scaleMin = readIval(ss); |
---|
657 | if(arg=="scalemax") this->scaleMax = readIval(ss); |
---|
658 | if(arg=="snrrecon") this->snrRecon = readFval(ss); |
---|
659 | if(arg=="reconconvergence") this->reconConvergence = readFval(ss); |
---|
660 | if(arg=="filtercode") this->filterCode = readIval(ss); |
---|
661 | |
---|
662 | if(arg=="flagadjacent") this->flagAdjacent = readFlag(ss); |
---|
663 | if(arg=="threshspatial") this->threshSpatial = readFval(ss); |
---|
664 | if(arg=="threshvelocity") this->threshVelocity = readFval(ss); |
---|
665 | if(arg=="minchannels") this->minChannels = readIval(ss); |
---|
666 | if(arg=="minvoxels") this->minVoxels = readIval(ss); |
---|
667 | if(arg=="flagrejectbeforemerge") this->flagRejectBeforeMerge = readFlag(ss); |
---|
668 | if(arg=="flagtwostagemerging") this->flagTwoStageMerging = readFlag(ss); |
---|
669 | |
---|
670 | if(arg=="spectralmethod") this->spectralMethod=makelower(readSval(ss)); |
---|
671 | if(arg=="spectraltype") this->spectralType = readSval(ss); |
---|
672 | if(arg=="restfrequency") this->restFrequency = readFval(ss); |
---|
673 | if(arg=="spectralunits") this->spectralUnits = readSval(ss); |
---|
674 | if(arg=="pixelcentre") this->pixelCentre = makelower(readSval(ss)); |
---|
675 | if(arg=="sortingparam") this->sortingParam = makelower(readSval(ss)); |
---|
676 | if(arg=="drawborders") this->borders = readFlag(ss); |
---|
677 | if(arg=="drawblankedges") this->blankEdge = readFlag(ss); |
---|
678 | if(arg=="verbose") this->verbose = readFlag(ss); |
---|
679 | |
---|
680 | // Dealing with deprecated parameters. |
---|
681 | if(arg=="flagblankpix"){ |
---|
682 | this->flagTrim = readFlag(ss); |
---|
683 | DUCHAMPWARN("Reading parameters","The parameter flagBlankPix is deprecated. Please use the flagTrim parameter in future."); |
---|
684 | DUCHAMPWARN("Reading parameters","Setting flagTrim = " << stringize(this->flagTrim)); |
---|
685 | } |
---|
686 | if(arg=="blankpixvalue"){ |
---|
687 | DUCHAMPWARN("Reading parameters","The parameter blankPixValue is deprecated. This value is only taken from the FITS header."); |
---|
688 | } |
---|
689 | if(arg=="beamsize"){ |
---|
690 | this->areaBeam = readFval(ss); |
---|
691 | DUCHAMPWARN("Reading parameters","The parameter beamSize is deprecated. You can specify the beam size by beamArea or beamFWHM."); |
---|
692 | DUCHAMPWARN("Reading parameters","Setting beamArea = " << this->areaBeam); |
---|
693 | } |
---|
694 | |
---|
695 | } |
---|
696 | } |
---|
697 | |
---|
698 | this->checkPars(); |
---|
699 | |
---|
700 | return SUCCESS; |
---|
701 | |
---|
702 | } |
---|
703 | |
---|
704 | void Param::checkPars() |
---|
705 | { |
---|
706 | |
---|
707 | // If flagSubsection is false, but the parset had a subsection string in it, we want to set this back to the default. |
---|
708 | if(!this->flagSubsection){ |
---|
709 | this->pixelSec.setSection(defaultSection); |
---|
710 | } |
---|
711 | if(!this->flagStatSec){ |
---|
712 | this->statSec.setSection(defaultSection); |
---|
713 | } |
---|
714 | |
---|
715 | // If we have usePrevious=false, set the objectlist to blank so that we use all of them |
---|
716 | if(!this->usePrevious) this->objectList = ""; |
---|
717 | |
---|
718 | // If pgplot was not included in the compilation, need to set flagXOutput to false |
---|
719 | if(!USE_PGPLOT){ |
---|
720 | if(this->flagXOutput || this->flagMaps || this->flagPlotSpectra) |
---|
721 | DUCHAMPWARN("Reading parameters","PGPlot has not been enabled, so setting flagXOutput, flagMaps and flagPlotSpectra to false."); |
---|
722 | this->flagXOutput = false; |
---|
723 | this->flagMaps = false; |
---|
724 | this->flagPlotSpectra = false; |
---|
725 | } |
---|
726 | |
---|
727 | // Correcting bad precision values -- if negative, set to 0 |
---|
728 | if(this->precFlux<0) this->precFlux = 0; |
---|
729 | if(this->precVel<0) this->precVel = 0; |
---|
730 | if(this->precSNR<0) this->precSNR = 0; |
---|
731 | |
---|
732 | // Can only have "spatial" or "spectral" as search types |
---|
733 | if(this->searchType != "spatial" && this->searchType != "spectral"){ |
---|
734 | DUCHAMPWARN("Reading parameters","You have requested a search type of \""<<this->searchType<<"\" -- Only \"spectral\" and \"spatial\" are accepted, so setting to \"spatial\"."); |
---|
735 | this->searchType = "spatial"; |
---|
736 | } |
---|
737 | |
---|
738 | // The wavelet reconstruction takes precendence over the smoothing. |
---|
739 | if(this->flagATrous) this->flagSmooth = false; |
---|
740 | |
---|
741 | // Check validity of recon parameters |
---|
742 | if(this->flagATrous){ |
---|
743 | if(this->reconConvergence < 0.){ |
---|
744 | DUCHAMPWARN("Reading Parameters","Your reconConvergence value is negative ("<<this->reconConvergence<<") - setting to " << -this->reconConvergence <<"."); |
---|
745 | this->reconConvergence *= -1.; |
---|
746 | } |
---|
747 | |
---|
748 | this->reconFilter.define(this->filterCode); |
---|
749 | |
---|
750 | if((this->scaleMax) > 0 && (this->scaleMax < this->scaleMin)){ |
---|
751 | DUCHAMPWARN("Reading Parameters","Reconstruction scaleMax ("<<this->scaleMax<<") is less than scaleMin ("<<this->scaleMin<<"): setting both to "<<this->scaleMin); |
---|
752 | this->scaleMax = this->scaleMin; |
---|
753 | } |
---|
754 | |
---|
755 | if( (this->reconDim < 1) || (this->reconDim > 3) ){ |
---|
756 | DUCHAMPWARN("Reading Parameters", "You requested a " << this->reconDim << " dimensional reconstruction. Setting reconDim to 1"); |
---|
757 | this->reconDim = 1; |
---|
758 | } |
---|
759 | |
---|
760 | if( this->snrRecon < 0.){ |
---|
761 | DUCHAMPWARN("Reading Parameters", "Your snrRecon value is negative (" << this->snrRecon<<"). Turning reconstruction off -- fix your parameter file!"); |
---|
762 | this->flagATrous = false; |
---|
763 | } |
---|
764 | |
---|
765 | } |
---|
766 | |
---|
767 | if(this->flagUserThreshold){ |
---|
768 | |
---|
769 | // If we specify a manual threshold, need to also specify a manual growth threshold |
---|
770 | // If we haven't done so, turn growing off |
---|
771 | if(this->flagGrowth && !this->flagUserGrowthThreshold){ |
---|
772 | DUCHAMPWARN("Reading parameters","You have specified a manual search threshold, but not a manual growth threshold. You need to do so using the \"growthThreshold\" parameter."); |
---|
773 | DUCHAMPWARN("Reading parameters","The growth function is being turned off."); |
---|
774 | this->flagGrowth = false; |
---|
775 | } |
---|
776 | |
---|
777 | // If we specify a manual threshold, we don't need the FDR method, so turn it off if requested. |
---|
778 | if(this->flagFDR){ |
---|
779 | DUCHAMPWARN("Reading parameters","You have specified a manual search threshold, so we don't need to use the FDR method. Setting \"flagFDR=false\"."); |
---|
780 | this->flagFDR = false; |
---|
781 | } |
---|
782 | |
---|
783 | } |
---|
784 | |
---|
785 | // Make sure the growth level is less than the detection level. Else turn off growing. |
---|
786 | if(this->flagGrowth){ |
---|
787 | std::stringstream errmsg; |
---|
788 | bool doWarn = false; |
---|
789 | if(this->flagUserThreshold && |
---|
790 | ( (this->threshold < this->growthThreshold) |
---|
791 | || (this->snrCut < this->growthCut) ) ){ |
---|
792 | errmsg << "Your \"growthThreshold\" parameter" << this->growthThreshold <<" is larger than your \"threshold\"" << this->threshold; |
---|
793 | doWarn = true; |
---|
794 | } |
---|
795 | |
---|
796 | if(!this->flagUserThreshold && |
---|
797 | (this->snrCut < this->growthCut)) { |
---|
798 | errmsg << "Your \"growthCut\" parameter " << this->growthCut << " is larger than your \"snrCut\"" << this->snrCut; |
---|
799 | doWarn = true; |
---|
800 | } |
---|
801 | |
---|
802 | if(doWarn){ |
---|
803 | DUCHAMPWARN("Reading parameters",errmsg); |
---|
804 | DUCHAMPWARN("Reading parameters","The growth function is being turned off."); |
---|
805 | |
---|
806 | } |
---|
807 | } |
---|
808 | |
---|
809 | // Make sure the annnotationType is an acceptable option -- default is "borders" |
---|
810 | if((this->annotationType != "borders") && (this->annotationType!="circles")){ |
---|
811 | DUCHAMPWARN("Reading parameters","The requested value of the parameter annotationType, \"" << this->annotationType << "\", is invalid -- changing to \"borders\"."); |
---|
812 | this->annotationType = "borders"; |
---|
813 | } |
---|
814 | |
---|
815 | // Make sure smoothType is an acceptable type -- default is "spectral" |
---|
816 | if((this->smoothType!="spectral")&& |
---|
817 | (this->smoothType!="spatial")){ |
---|
818 | DUCHAMPWARN("Reading parameters","The requested value of the parameter smoothType, \"" << this->smoothType << "\", is invalid -- changing to \"spectral\"."); |
---|
819 | this->smoothType = "spectral"; |
---|
820 | } |
---|
821 | // If kernMin has not been given, or is negative, make it equal to kernMaj |
---|
822 | if(this->kernMin < 0) this->kernMin = this->kernMaj; |
---|
823 | |
---|
824 | // Make sure spectralMethod is an acceptable type -- default is "peak" |
---|
825 | if((this->spectralMethod!="peak")&& |
---|
826 | (this->spectralMethod!="sum")){ |
---|
827 | DUCHAMPWARN("Reading parameters","The requested value of the parameter spectralMethod, \"" << this->spectralMethod << "\", is invalid -- changing to \"peak\"."); |
---|
828 | this->spectralMethod = "peak"; |
---|
829 | } |
---|
830 | |
---|
831 | // make sure pixelCentre is an acceptable type -- default is "peak" |
---|
832 | if((this->pixelCentre!="centroid")&& |
---|
833 | (this->pixelCentre!="average") && |
---|
834 | (this->pixelCentre!="peak") ){ |
---|
835 | DUCHAMPWARN("Reading parameters","The requested value of the parameter pixelCentre, \"" << this->pixelCentre << "\", is invalid -- changing to \"centroid\"."); |
---|
836 | this->pixelCentre = "centroid"; |
---|
837 | } |
---|
838 | |
---|
839 | // Make sure sortingParam is an acceptable type -- default is "vel" |
---|
840 | bool OK = false; |
---|
841 | int loc=(this->sortingParam[0]=='-') ? 1 : 0; |
---|
842 | for(int i=0;i<numSortingParamOptions;i++) |
---|
843 | OK = OK || this->sortingParam.substr(loc)==sortingParamOptions[i]; |
---|
844 | if(!OK){ |
---|
845 | DUCHAMPWARN("Reading parameters","The requested value of the parameter sortingParam, \"" << this->sortingParam << "\", is invalid. -- changing to \"vel\"."); |
---|
846 | this->sortingParam = "vel"; |
---|
847 | } |
---|
848 | |
---|
849 | // Make sure minVoxels is appropriate given minChannels & minPixels |
---|
850 | if(this->minVoxels < (this->minPix + this->minChannels - 1) ){ |
---|
851 | DUCHAMPWARN("Reading parameters","Changing minVoxels to " << this->minPix + this->minChannels - 1 << " given minPix="<<this->minPix << " and minChannels="<<this->minChannels); |
---|
852 | this->minVoxels = this->minPix + this->minChannels - 1; |
---|
853 | } |
---|
854 | |
---|
855 | } |
---|
856 | |
---|
857 | OUTCOME Param::checkImageExists() |
---|
858 | { |
---|
859 | /// A simple check to see whether the image actually exists or not, using the cfitsio interface. |
---|
860 | /// If it does, we return SUCCESS, otherwise we throw an exception. |
---|
861 | |
---|
862 | int exists,status = 0; /* MUST initialize status */ |
---|
863 | fits_file_exists(this->imageFile.c_str(),&exists,&status); |
---|
864 | if(exists<=0){ |
---|
865 | fits_report_error(stderr, status); |
---|
866 | DUCHAMPTHROW("Cube Reader","Requested image " << this->imageFile << " does not exist!"); |
---|
867 | return FAILURE; |
---|
868 | } |
---|
869 | return SUCCESS; |
---|
870 | } |
---|
871 | |
---|
872 | |
---|
873 | void recordParameters(std::ostream& theStream, std::string paramName, std::string paramDesc, std::string paramValue) |
---|
874 | { |
---|
875 | |
---|
876 | const int width = 56; |
---|
877 | int widthText = width - paramName.size(); |
---|
878 | |
---|
879 | theStream << std::setw(widthText) << paramDesc |
---|
880 | << setiosflags(std::ios::right) << paramName |
---|
881 | << " = " << resetiosflags(std::ios::right) << paramValue |
---|
882 | <<std::endl; |
---|
883 | } |
---|
884 | |
---|
885 | std::string fileOption(bool flag, std::string file) |
---|
886 | { |
---|
887 | std::ostringstream ss; |
---|
888 | ss << stringize(flag); |
---|
889 | if(flag) ss << " --> " << file; |
---|
890 | return ss.str(); |
---|
891 | |
---|
892 | } |
---|
893 | |
---|
894 | std::ostream& operator<< ( std::ostream& theStream, Param& par) |
---|
895 | { |
---|
896 | /// Print out the parameter set in a formatted, easy to read style. |
---|
897 | /// Lists the parameters, a description of them, and their value. |
---|
898 | |
---|
899 | // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3? |
---|
900 | // theStream.setf(std::ios::boolalpha); |
---|
901 | theStream.setf(std::ios::left); |
---|
902 | theStream <<"\n---- Parameters ----"<<std::endl; |
---|
903 | theStream << std::setfill('.'); |
---|
904 | if(par.getFlagSubsection()) |
---|
905 | recordParam(theStream, "[imageFile]", "Image to be analysed", par.getImageFile()<<par.getSubsection()); |
---|
906 | else |
---|
907 | recordParam(theStream, "[imageFile]", "Image to be analysed", par.getImageFile()); |
---|
908 | if(par.getFlagRestFrequencyUsed()){ |
---|
909 | recordParam(theStream, "[restFrequency]","Rest frequency as used", par.getRestFrequency()); |
---|
910 | } |
---|
911 | if(par.getFlagReconExists() && par.getFlagATrous()){ |
---|
912 | recordParam(theStream, "[reconExists]", "Reconstructed array exists?", stringize(par.getFlagReconExists())); |
---|
913 | recordParam(theStream, "[reconFile]", "FITS file containing reconstruction", par.getReconFile()); |
---|
914 | } |
---|
915 | if(par.getFlagSmoothExists() && par.getFlagSmooth()){ |
---|
916 | recordParam(theStream, "[smoothExists]", "Smoothed array exists?", stringize(par.getFlagSmoothExists())); |
---|
917 | recordParam(theStream, "[smoothFile]", "FITS file containing smoothed array", par.getSmoothFile()); |
---|
918 | } |
---|
919 | recordParam(theStream, "[logFile]", "Intermediate Logfile", par.logFile); |
---|
920 | recordParam(theStream, "[outFile]", "Final Results file", par.getOutFile()); |
---|
921 | if(par.getFlagSeparateHeader()){ |
---|
922 | recordParam(theStream, "[headerFile]", "Header for results file", par.getHeaderFile()); |
---|
923 | } |
---|
924 | if(USE_PGPLOT && par.getFlagPlotSpectra()){ |
---|
925 | recordParam(theStream, "[spectraFile]", "Spectrum file", par.getSpectraFile()); |
---|
926 | } |
---|
927 | if(par.getFlagTextSpectra()){ |
---|
928 | recordParam(theStream, "[spectraTextFile]", "Text file with ascii spectral data", par.getSpectraTextFile()); |
---|
929 | } |
---|
930 | if(par.getFlagVOT()){ |
---|
931 | recordParam(theStream, "[votFile]", "VOTable file", par.getVOTFile()); |
---|
932 | } |
---|
933 | if(par.getFlagKarma()){ |
---|
934 | recordParam(theStream, "[karmaFile]", "Karma annotation file" , par.getKarmaFile()); |
---|
935 | } |
---|
936 | if(par.getFlagDS9()){ |
---|
937 | recordParam(theStream, "[ds9File]", "DS9 annotation file" , par.getDS9File()); |
---|
938 | } |
---|
939 | if(USE_PGPLOT && par.getFlagMaps()){ |
---|
940 | recordParam(theStream, "[momentMap]", "0th Moment Map", par.getMomentMap()); |
---|
941 | recordParam(theStream, "[detectionMap]", "Detection Map", par.getDetectionMap()); |
---|
942 | } |
---|
943 | if(USE_PGPLOT){ |
---|
944 | recordParam(theStream, "[flagXOutput]", "Display a map in a pgplot xwindow?", stringize(par.getFlagXOutput())); |
---|
945 | } |
---|
946 | if(par.getFlagATrous()){ |
---|
947 | recordParam(theStream, "[flagOutputRecon]", "Saving reconstructed cube?", fileOption(par.getFlagOutputRecon(),par.outputReconFile())); |
---|
948 | recordParam(theStream, "[flagOutputResid]", "Saving residuals from reconstruction?", fileOption(par.getFlagOutputResid(),par.outputResidFile())); |
---|
949 | } |
---|
950 | if(par.getFlagSmooth()){ |
---|
951 | recordParam(theStream, "[flagOutputSmooth]", "Saving smoothed cube?", fileOption(par.getFlagOutputSmooth(),par.outputSmoothFile())); |
---|
952 | } |
---|
953 | recordParam(theStream, "[flagOutputMask]", "Saving mask cube?", fileOption(par.getFlagOutputMask(),par.outputMaskFile())); |
---|
954 | recordParam(theStream, "[flagOutputMask]", "Saving 0th moment to FITS file?", fileOption(par.getFlagOutputMomentMap(),par.outputMomentMapFile())); |
---|
955 | |
---|
956 | theStream <<"------"<<std::endl; |
---|
957 | |
---|
958 | recordParam(theStream, "[searchType]", "Type of searching performed", par.getSearchType()); |
---|
959 | if(par.getFlagBlankPix()){ |
---|
960 | recordParam(theStream, "", "Blank Pixel Value", par.getBlankPixVal()); |
---|
961 | } |
---|
962 | recordParam(theStream, "[flagTrim]", "Trimming Blank Pixels?", stringize(par.getFlagTrim())); |
---|
963 | recordParam(theStream, "[flagNegative]", "Searching for Negative features?", stringize(par.getFlagNegative())); |
---|
964 | recordParam(theStream, "[flagMW]", "Removing Milky Way channels?", stringize(par.getFlagMW())); |
---|
965 | if(par.getFlagMW()){ |
---|
966 | // need to remove the offset correction, as we want to report the parameters actually entered |
---|
967 | recordParam(theStream, "[minMW - maxMW]", "Milky Way Channels", par.getMinMW()+par.getZOffset()<<"-"<<par.getMaxMW()+par.getZOffset()); |
---|
968 | } |
---|
969 | if(par.beamAsUsed.origin()==EMPTY){ // No beam in FITS file and no information provided |
---|
970 | recordParam(theStream, "", "Area of Beam", "No beam"); |
---|
971 | } |
---|
972 | else if(par.beamAsUsed.origin()==HEADER){ // Report beam size from FITS file |
---|
973 | recordParam(theStream, "", "Area of Beam (pixels)", par.beamAsUsed.area() << " (beam: " << par.beamAsUsed.maj() << " x " << par.beamAsUsed.min() <<" pixels)"); |
---|
974 | } |
---|
975 | else if(par.beamAsUsed.origin()==PARAM){ // Report beam size requested in parameter set input |
---|
976 | if(par.fwhmBeam>0.) recordParam(theStream, "[beamFWHM]", "FWHM of Beam (pixels)", par.beamAsUsed.maj() << " (beam area = " << par.beamAsUsed.area() <<" pixels)"); |
---|
977 | else recordParam(theStream, "[beamArea]", "Area of Beam (pixels)", par.beamAsUsed.area()); |
---|
978 | } |
---|
979 | else{ |
---|
980 | recordParam(theStream, "[beam info]", "Size & shape of beam", "No information available!"); |
---|
981 | } |
---|
982 | recordParam(theStream, "[flagBaseline]", "Removing baselines before search?", stringize(par.getFlagBaseline())); |
---|
983 | recordParam(theStream, "[flagSmooth]", "Smoothing data prior to searching?", stringize(par.getFlagSmooth())); |
---|
984 | if(par.getFlagSmooth()){ |
---|
985 | recordParam(theStream, "[smoothType]", "Type of smoothing", par.getSmoothType()); |
---|
986 | if(par.getSmoothType()=="spectral") |
---|
987 | recordParam(theStream, "[hanningWidth]", "Width of hanning filter", par.getHanningWidth()); |
---|
988 | else{ |
---|
989 | recordParam(theStream, "[kernMaj]", "Gaussian kernel semi-major axis [pix]", par.getKernMaj()); |
---|
990 | recordParam(theStream, "[kernMin]", "Gaussian kernel semi-minor axis [pix]", par.getKernMin()); |
---|
991 | recordParam(theStream, "[kernPA]", "Gaussian kernel position angle [deg]", par.getKernPA()); |
---|
992 | } |
---|
993 | } |
---|
994 | recordParam(theStream, "[flagATrous]", "Using A Trous reconstruction?", stringize(par.getFlagATrous())); |
---|
995 | if(par.getFlagATrous()){ |
---|
996 | recordParam(theStream, "[reconDim]", "Number of dimensions in reconstruction", par.getReconDim()); |
---|
997 | if(par.getMaxScale()>0){ |
---|
998 | recordParam(theStream, "[scaleMin-scaleMax]", "Scales used in reconstruction", par.getMinScale()<<"-"<<par.getMaxScale()); |
---|
999 | } |
---|
1000 | else{ |
---|
1001 | recordParam(theStream, "[scaleMin]", "Minimum scale in reconstruction", par.getMinScale()); |
---|
1002 | } |
---|
1003 | recordParam(theStream, "[snrRecon]", "SNR Threshold within reconstruction", par.getAtrousCut()); |
---|
1004 | recordParam(theStream, "[reconConvergence]", "Residual convergence criterion", par.getReconConvergence()); |
---|
1005 | recordParam(theStream, "[filterCode]", "Filter being used for reconstruction", par.getFilterCode()<<" ("<<par.getFilterName()<<")"); |
---|
1006 | } |
---|
1007 | recordParam(theStream, "[flagRobustStats]", "Using Robust statistics?", stringize(par.getFlagRobustStats())); |
---|
1008 | if(par.getFlagStatSec()){ |
---|
1009 | recordParam(theStream, "[statSec]", "Section used by statistics calculation", par.statSec.getSection()); |
---|
1010 | } |
---|
1011 | recordParam(theStream, "[flagFDR]", "Using FDR analysis?", stringize(par.getFlagFDR())); |
---|
1012 | if(par.getFlagFDR()){ |
---|
1013 | recordParam(theStream, "[alphaFDR]", "Alpha value for FDR analysis", par.getAlpha()); |
---|
1014 | recordParam(theStream, "[FDRnumCorChan]", "Number of correlated channels for FDR", par.getFDRnumCorChan()); |
---|
1015 | } |
---|
1016 | else { |
---|
1017 | if(par.getFlagUserThreshold()){ |
---|
1018 | recordParam(theStream, "[threshold]", "Detection Threshold", par.getThreshold()); |
---|
1019 | } |
---|
1020 | else{ |
---|
1021 | recordParam(theStream, "[snrCut]", "SNR Threshold (in sigma)", par.getCut()); |
---|
1022 | } |
---|
1023 | } |
---|
1024 | recordParam(theStream, "[minPix]", "Minimum # Pixels in a detection", par.getMinPix()); |
---|
1025 | recordParam(theStream, "[minChannels]", "Minimum # Channels in a detection", par.getMinChannels()); |
---|
1026 | recordParam(theStream, "[minVoxels]", "Minimum # Voxels in a detection", par.getMinVoxels()); |
---|
1027 | recordParam(theStream, "[flagGrowth]", "Growing objects after detection?", stringize(par.getFlagGrowth())); |
---|
1028 | if(par.getFlagGrowth()) { |
---|
1029 | if(par.getFlagUserGrowthThreshold()){ |
---|
1030 | recordParam(theStream, "[growthThreshold]", "Threshold for growth", par.getGrowthThreshold()); |
---|
1031 | } |
---|
1032 | else{ |
---|
1033 | recordParam(theStream, "[growthCut]", "SNR Threshold for growth", par.getGrowthCut()); |
---|
1034 | } |
---|
1035 | } |
---|
1036 | recordParam(theStream, "[flagAdjacent]", "Using Adjacent-pixel criterion?", stringize(par.getFlagAdjacent())); |
---|
1037 | if(!par.getFlagAdjacent()){ |
---|
1038 | recordParam(theStream, "[threshSpatial]", "Max. spatial separation for merging", par.getThreshS()); |
---|
1039 | } |
---|
1040 | recordParam(theStream, "[threshVelocity]", "Max. velocity separation for merging", par.getThreshV()); |
---|
1041 | recordParam(theStream, "[flagRejectBeforeMerge]", "Reject objects before merging?", stringize(par.getFlagRejectBeforeMerge())); |
---|
1042 | recordParam(theStream, "[flagTwoStageMerging]", "Merge objects in two stages?", stringize(par.getFlagTwoStageMerging())); |
---|
1043 | recordParam(theStream, "[spectralMethod]", "Method of spectral plotting", par.getSpectralMethod()); |
---|
1044 | recordParam(theStream, "[pixelCentre]", "Type of object centre used in results", par.getPixelCentre()); |
---|
1045 | |
---|
1046 | theStream <<"--------------------\n"; |
---|
1047 | theStream << std::setfill(' '); |
---|
1048 | theStream.unsetf(std::ios::left); |
---|
1049 | // theStream.unsetf(std::ios::boolalpha); |
---|
1050 | return theStream; |
---|
1051 | } |
---|
1052 | |
---|
1053 | std::vector<VOParam> Param::getVOParams() |
---|
1054 | { |
---|
1055 | std::vector<VOParam> vopars; |
---|
1056 | vopars.push_back(VOParam("imageFile","meta.file;meta.fits","char",this->imageFile,this->imageFile.size(),"")); |
---|
1057 | vopars.push_back(VOParam("flagSubsection","meta.code","boolean",this->flagSubsection,0,"")); |
---|
1058 | if(this->flagSubsection) |
---|
1059 | vopars.push_back(VOParam("subsection","","char",this->pixelSec.getSection(),this->pixelSec.getSection().size(),"")); |
---|
1060 | vopars.push_back(VOParam("flagStatSec","meta.code","boolean",this->flagStatSec,0,"")); |
---|
1061 | if(this->flagSubsection) |
---|
1062 | vopars.push_back(VOParam("StatSec","","char",this->statSec.getSection(),this->statSec.getSection().size(),"")); |
---|
1063 | if(this->flagReconExists) |
---|
1064 | vopars.push_back(VOParam("reconfile","meta.file;meta.fits","char",this->reconFile, this->reconFile.size(),"")); |
---|
1065 | if(this->flagSmoothExists) |
---|
1066 | vopars.push_back(VOParam("smoothfile","meta.file;meta.fits","char",this->smoothFile, this->smoothFile.size(),"")); |
---|
1067 | if(this->usePrevious) |
---|
1068 | vopars.push_back(VOParam("objectlist","","char",this->objectList,this->objectList.size(),"")); |
---|
1069 | |
---|
1070 | vopars.push_back(VOParam("searchType","meta.note","char",this->searchType,this->searchType.size(),"")); |
---|
1071 | vopars.push_back(VOParam("flagNegative","meta.code","boolean",this->flagNegative,0,"")); |
---|
1072 | vopars.push_back(VOParam("flagBaseline","meta.code","boolean",this->flagBaseline,0,"")); |
---|
1073 | vopars.push_back(VOParam("flagRobustStats","meta.code","boolean",this->flagRobustStats,0,"")); |
---|
1074 | vopars.push_back(VOParam("flagFDR","meta.code","boolean",this->flagFDR,0,"")); |
---|
1075 | if(this->flagFDR){ |
---|
1076 | vopars.push_back(VOParam("alphaFDR","stat.param","float",this->alphaFDR,0,"")); |
---|
1077 | vopars.push_back(VOParam("FDRnumCorChan","stat.param","int",this->FDRnumCorChan,0,"")); |
---|
1078 | } |
---|
1079 | else{ |
---|
1080 | if(this->flagUserThreshold) |
---|
1081 | vopars.push_back(VOParam("threshold","phot.flux;stat.min","float",this->threshold,0,"")); |
---|
1082 | else |
---|
1083 | vopars.push_back(VOParam("snrCut","stat.snr;phot;stat.min","float",this->snrCut,0,"")); |
---|
1084 | } |
---|
1085 | vopars.push_back(VOParam("flagGrowth","meta.code","boolean",this->flagGrowth,0,"")); |
---|
1086 | if(this->flagGrowth){ |
---|
1087 | if(this->flagUserGrowthThreshold) |
---|
1088 | vopars.push_back(VOParam("growthThreshold","phot.flux;stat.min","float",this->growthThreshold,0,"")); |
---|
1089 | else |
---|
1090 | vopars.push_back(VOParam("growthCut","stat.snr;phot;stat.min","float",this->growthCut,0,"")); |
---|
1091 | } |
---|
1092 | vopars.push_back(VOParam("minVoxels","","int",minVoxels,0,"")); |
---|
1093 | vopars.push_back(VOParam("minPix","","int",minPix,0,"")); |
---|
1094 | vopars.push_back(VOParam("minChannels","","int",minChannels,0,"")); |
---|
1095 | vopars.push_back(VOParam("flagAdjacent","meta.code","boolean",this->flagAdjacent,0,"")); |
---|
1096 | if(!this->flagAdjacent) |
---|
1097 | vopars.push_back(VOParam("threshSpatial","","float",this->threshSpatial,0,"")); |
---|
1098 | vopars.push_back(VOParam("threshVelocity","","float",this->threshSpatial,0,"")); |
---|
1099 | vopars.push_back(VOParam("flagRejectBeforeMerge","","boolean",this->flagRejectBeforeMerge,0,"")); |
---|
1100 | vopars.push_back(VOParam("flagTwoStageMerging","","boolean",this->flagTwoStageMerging,0,"")); |
---|
1101 | vopars.push_back(VOParam("pixelCentre","","char",this->pixelCentre,this->pixelCentre.size(),"")); |
---|
1102 | vopars.push_back(VOParam("flagSmooth","meta.code","boolean",this->flagSmooth,0,"")); |
---|
1103 | if(this->flagSmooth){ |
---|
1104 | vopars.push_back(VOParam("smoothType","","char",this->smoothType,this->smoothType.size(),"")); |
---|
1105 | if(this->smoothType=="spectral") |
---|
1106 | vopars.push_back(VOParam("hanningWidth","","int",this->hanningWidth,0,"")); |
---|
1107 | else{ |
---|
1108 | vopars.push_back(VOParam("kernMaj","","float",this->kernMaj,0,"")); |
---|
1109 | vopars.push_back(VOParam("kernMin","","float",this->kernMin,0,"")); |
---|
1110 | vopars.push_back(VOParam("kernPA","","float",this->kernPA,0,"")); |
---|
1111 | } |
---|
1112 | } |
---|
1113 | vopars.push_back(VOParam("flagATrous","meta.code","boolean",this->flagATrous,0,"")); |
---|
1114 | if(this->flagATrous){ |
---|
1115 | vopars.push_back(VOParam("reconDim","","int",this->reconDim,0,"")); |
---|
1116 | vopars.push_back(VOParam("scaleMin","","int",this->scaleMin,0,"")); |
---|
1117 | if(this->scaleMax>0) |
---|
1118 | vopars.push_back(VOParam("scaleMax","","int",this->scaleMax,0,"")); |
---|
1119 | vopars.push_back(VOParam("snrRecon","","float",this->snrRecon,0,"")); |
---|
1120 | vopars.push_back(VOParam("reconConvergence","","float",this->reconConvergence,0,"")); |
---|
1121 | vopars.push_back(VOParam("filterCode","","int",this->filterCode,0,"")); |
---|
1122 | } |
---|
1123 | if(this->beamAsUsed.origin()==PARAM){ |
---|
1124 | if(this->fwhmBeam>0) |
---|
1125 | vopars.push_back(VOParam("beamFWHM","","float",this->fwhmBeam,0,"")); |
---|
1126 | else |
---|
1127 | vopars.push_back(VOParam("beamArea","","float",this->areaBeam,0,"")); |
---|
1128 | } |
---|
1129 | if(this->restFrequencyUsed){ |
---|
1130 | vopars.push_back(VOParam("restFrequency","em.freq","float",this->restFrequency,0,"Hz")); |
---|
1131 | } |
---|
1132 | |
---|
1133 | return vopars; |
---|
1134 | |
---|
1135 | } |
---|
1136 | |
---|
1137 | |
---|
1138 | |
---|
1139 | void Param::copyHeaderInfo(FitsHeader &head) |
---|
1140 | { |
---|
1141 | /// A function to copy across relevant header keywords from the |
---|
1142 | /// FitsHeader class to the Param class, as they are needed by |
---|
1143 | /// functions in the Param class. |
---|
1144 | /// The parameters are the keywords BLANK, BSCALE, BZERO, and the beam size. |
---|
1145 | |
---|
1146 | this->blankKeyword = head.getBlankKeyword(); |
---|
1147 | this->bscaleKeyword = head.getBscaleKeyword(); |
---|
1148 | this->bzeroKeyword = head.getBzeroKeyword(); |
---|
1149 | this->blankPixValue = this->blankKeyword * this->bscaleKeyword + |
---|
1150 | this->bzeroKeyword; |
---|
1151 | } |
---|
1152 | |
---|
1153 | std::string Param::outputMaskFile() |
---|
1154 | { |
---|
1155 | /// This function produces the required filename in which to save |
---|
1156 | /// the mask image, indicating which pixels have been detected as |
---|
1157 | /// part of an object. If the input image is image.fits, then the |
---|
1158 | /// output will be image.MASK.fits. |
---|
1159 | |
---|
1160 | if(this->fileOutputMask==""){ |
---|
1161 | std::string inputName = this->imageFile; |
---|
1162 | std::stringstream ss; |
---|
1163 | ss << inputName.substr(0,inputName.size()-5); |
---|
1164 | // remove the ".fits" on the end. |
---|
1165 | ss << ".MASK.fits"; |
---|
1166 | return ss.str(); |
---|
1167 | } |
---|
1168 | else return this->fileOutputMask; |
---|
1169 | } |
---|
1170 | |
---|
1171 | std::string Param::outputMomentMapFile() |
---|
1172 | { |
---|
1173 | /// This function produces the required filename in which to save |
---|
1174 | /// the moment-0 FITS image. If the input image is image.fits, then the |
---|
1175 | /// output will be image.MOM0.fits. |
---|
1176 | |
---|
1177 | if(this->fileOutputMomentMap==""){ |
---|
1178 | std::string inputName = this->imageFile; |
---|
1179 | std::stringstream ss; |
---|
1180 | ss << inputName.substr(0,inputName.size()-5); |
---|
1181 | // remove the ".fits" on the end. |
---|
1182 | ss << ".MOM0.fits"; |
---|
1183 | return ss.str(); |
---|
1184 | } |
---|
1185 | else return this->fileOutputMomentMap; |
---|
1186 | } |
---|
1187 | |
---|
1188 | std::string Param::outputSmoothFile() |
---|
1189 | { |
---|
1190 | /// This function produces the required filename in which to save |
---|
1191 | /// the smoothed array. If the input image is image.fits, then |
---|
1192 | /// the output will be: |
---|
1193 | /// <ul><li> Spectral smoothing: image.SMOOTH-1D-3.fits, where the |
---|
1194 | /// width of the Hanning filter was 3 pixels. |
---|
1195 | /// <li> Spatial smoothing : image.SMOOTH-2D-3-2-20.fits, where |
---|
1196 | /// kernMaj=3, kernMin=2 and kernPA=20 degrees. |
---|
1197 | /// </ul> |
---|
1198 | |
---|
1199 | if(this->fileOutputSmooth==""){ |
---|
1200 | std::string inputName = this->imageFile; |
---|
1201 | std::stringstream ss; |
---|
1202 | ss << inputName.substr(0,inputName.size()-5); |
---|
1203 | // remove the ".fits" on the end. |
---|
1204 | if(this->flagSubsection) ss<<".sub"; |
---|
1205 | if(this->smoothType=="spectral") |
---|
1206 | ss << ".SMOOTH-1D-" << this->hanningWidth << ".fits"; |
---|
1207 | else if(this->smoothType=="spatial") |
---|
1208 | ss << ".SMOOTH-2D-" |
---|
1209 | << this->kernMaj << "-" |
---|
1210 | << this->kernMin << "-" |
---|
1211 | << this->kernPA << ".fits"; |
---|
1212 | return ss.str(); |
---|
1213 | } |
---|
1214 | else return this->fileOutputSmooth; |
---|
1215 | } |
---|
1216 | |
---|
1217 | std::string Param::outputReconFile() |
---|
1218 | { |
---|
1219 | /// This function produces the required filename in which to save |
---|
1220 | /// the reconstructed array. If the input image is image.fits, then |
---|
1221 | /// the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are |
---|
1222 | /// 3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale |
---|
1223 | |
---|
1224 | if(this->fileOutputRecon==""){ |
---|
1225 | std::string inputName = this->imageFile; |
---|
1226 | std::stringstream ss; |
---|
1227 | // First we remove the ".fits" from the end of the filename. |
---|
1228 | ss << inputName.substr(0,inputName.size()-5); |
---|
1229 | if(this->flagSubsection) ss<<".sub"; |
---|
1230 | ss << ".RECON-" << this->reconDim |
---|
1231 | << "-" << this->filterCode |
---|
1232 | << "-" << this->snrRecon |
---|
1233 | << "-" << this->scaleMin |
---|
1234 | << "-" << this->scaleMax |
---|
1235 | << "-" << this->reconConvergence |
---|
1236 | << ".fits"; |
---|
1237 | return ss.str(); |
---|
1238 | } |
---|
1239 | else return this->fileOutputRecon; |
---|
1240 | } |
---|
1241 | |
---|
1242 | std::string Param::outputResidFile() |
---|
1243 | { |
---|
1244 | /// This function produces the required filename in which to save |
---|
1245 | /// the reconstructed array. If the input image is image.fits, then |
---|
1246 | /// the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are |
---|
1247 | /// 3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin |
---|
1248 | |
---|
1249 | if(this->fileOutputResid==""){ |
---|
1250 | std::string inputName = this->imageFile; |
---|
1251 | std::stringstream ss; |
---|
1252 | // First we remove the ".fits" from the end of the filename. |
---|
1253 | ss << inputName.substr(0,inputName.size()-5); |
---|
1254 | if(this->flagSubsection) ss<<".sub"; |
---|
1255 | ss << ".RESID-" << this->reconDim |
---|
1256 | << "-" << this->filterCode |
---|
1257 | << "-" << this->snrRecon |
---|
1258 | << "-" << this->scaleMin |
---|
1259 | << "-" << this->scaleMax |
---|
1260 | << "-" << this->reconConvergence |
---|
1261 | << ".fits"; |
---|
1262 | return ss.str(); |
---|
1263 | } |
---|
1264 | else return this->fileOutputResid; |
---|
1265 | } |
---|
1266 | |
---|
1267 | } |
---|