1 | // ----------------------------------------------------------------------- |
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2 | // detectionIO.cc: Screen and File output of the detected objects. |
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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 <sstream> |
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30 | #include <fstream> |
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31 | #include <iomanip> |
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32 | #include <string> |
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33 | #include <vector> |
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34 | #include <time.h> |
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35 | #include <duchamp/param.hh> |
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36 | #include <duchamp/fitsHeader.hh> |
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37 | #include <duchamp/Cubes/cubes.hh> |
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38 | #include <duchamp/PixelMap/Object3D.hh> |
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39 | #include <duchamp/Detection/detection.hh> |
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40 | #include <duchamp/Outputs/columns.hh> |
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41 | #include <duchamp/Utils/utils.hh> |
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42 | #include <duchamp/Utils/Statistics.hh> |
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43 | #include <duchamp/Outputs/ASCIICatalogueWriter.hh> |
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44 | #include <duchamp/Outputs/VOTableCatalogueWriter.hh> |
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45 | #include <duchamp/Outputs/KarmaAnnotationWriter.hh> |
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46 | #include <duchamp/Outputs/DS9AnnotationWriter.hh> |
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47 | #include <duchamp/Outputs/CasaAnnotationWriter.hh> |
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48 | |
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49 | using std::endl; |
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50 | using std::setw; |
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51 | using std::setprecision; |
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52 | using namespace PixelInfo; |
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53 | using namespace Statistics; |
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54 | |
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55 | namespace duchamp |
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56 | { |
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57 | |
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58 | void Cube::outputAnnotations() |
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59 | { |
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60 | |
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61 | for(int i=0;i<3;i++){ |
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62 | AnnotationWriter *writer=0; |
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63 | switch(i){ |
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64 | case 0: //Karma |
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65 | if(this->par.getFlagKarma()) |
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66 | writer = new KarmaAnnotationWriter(this->par.getKarmaFile()); |
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67 | break; |
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68 | case 1://DS9 |
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69 | if(this->par.getFlagDS9()) |
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70 | writer = new DS9AnnotationWriter(this->par.getDS9File()); |
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71 | break; |
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72 | case 2://CASA |
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73 | if(this->par.getFlagCasa()) |
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74 | writer = new CasaAnnotationWriter(this->par.getCasaFile()); |
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75 | break; |
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76 | } |
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77 | if(writer!=0){ |
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78 | writer->setup(this); |
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79 | writer->openCatalogue(); |
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80 | writer->writeHeader(); |
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81 | writer->writeParameters(); |
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82 | writer->writeStats(); |
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83 | writer->writeTableHeader(); |
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84 | writer->writeEntries(); |
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85 | writer->writeFooter(); |
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86 | writer->closeCatalogue(); |
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87 | } |
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88 | |
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89 | delete writer; |
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90 | } |
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91 | |
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92 | } |
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93 | |
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94 | void Cube::outputDetectionsKarma() |
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95 | { |
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96 | KarmaAnnotationWriter writer(this->pars().getKarmaFile()); |
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97 | writer.setup(this); |
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98 | writer.openCatalogue(); |
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99 | writer.writeHeader(); |
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100 | writer.writeParameters(); |
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101 | writer.writeStats(); |
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102 | writer.writeTableHeader(); |
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103 | writer.writeEntries(); |
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104 | writer.writeFooter(); |
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105 | writer.closeCatalogue(); |
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106 | |
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107 | } |
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108 | |
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109 | void Cube::outputDetectionsDS9() |
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110 | { |
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111 | DS9AnnotationWriter writer(this->pars().getDS9File()); |
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112 | writer.setup(this); |
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113 | writer.openCatalogue(); |
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114 | writer.writeHeader(); |
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115 | writer.writeParameters(); |
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116 | writer.writeStats(); |
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117 | writer.writeTableHeader(); |
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118 | writer.writeEntries(); |
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119 | writer.writeFooter(); |
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120 | writer.closeCatalogue(); |
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121 | |
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122 | } |
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123 | |
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124 | void Cube::outputDetectionsCasa() |
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125 | { |
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126 | CasaAnnotationWriter writer(this->pars().getCasaFile()); |
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127 | writer.setup(this); |
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128 | writer.openCatalogue(); |
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129 | writer.writeHeader(); |
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130 | writer.writeParameters(); |
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131 | writer.writeStats(); |
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132 | writer.writeTableHeader(); |
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133 | writer.writeEntries(); |
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134 | writer.writeFooter(); |
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135 | writer.closeCatalogue(); |
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136 | |
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137 | } |
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138 | |
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139 | void Cube::outputCatalogue() |
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140 | { |
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141 | this->setupColumns(); |
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142 | |
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143 | ASCIICatalogueWriter catWriter(this->par.getOutFile(),Catalogues::FILE); |
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144 | catWriter.setup(this); |
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145 | ASCIICatalogueWriter headerWriter(this->par.getHeaderFile(),Catalogues::FILE); |
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146 | headerWriter.setup(this); |
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147 | ASCIICatalogueWriter screenWriter(Catalogues::SCREEN); |
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148 | screenWriter.setup(this); |
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149 | ASCIICatalogueWriter *writer; |
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150 | |
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151 | // write the header information |
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152 | if(this->par.getFlagSeparateHeader()) writer = &headerWriter; |
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153 | else writer=&catWriter; |
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154 | |
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155 | writer->openCatalogue(); |
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156 | writer->writeHeader(); |
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157 | writer->writeParameters(); |
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158 | writer->writeStats(); |
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159 | |
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160 | if(this->par.getFlagSeparateHeader()){ |
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161 | writer->closeCatalogue(); |
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162 | writer = &catWriter; |
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163 | writer->openCatalogue(); |
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164 | } |
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165 | |
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166 | // write the catalogue |
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167 | writer->writeTableHeader(); |
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168 | writer->writeEntries(); |
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169 | writer->closeCatalogue(); |
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170 | |
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171 | screenWriter.openCatalogue(); |
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172 | screenWriter.writeTableHeader(); |
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173 | screenWriter.writeEntries(); |
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174 | screenWriter.closeCatalogue(); |
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175 | |
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176 | } |
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177 | |
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178 | |
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179 | void Cube::outputDetectionsVOTable() |
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180 | { |
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181 | VOTableCatalogueWriter writer(this->pars().getVOTFile()); |
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182 | writer.setup(this); |
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183 | writer.setTableName("Detections"); |
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184 | writer.setTableDescription("Detected sources and parameters from running the Duchamp source finder."); |
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185 | writer.openCatalogue(); |
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186 | writer.writeHeader(); |
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187 | writer.writeParameters(); |
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188 | writer.writeStats(); |
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189 | writer.writeTableHeader(); |
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190 | writer.writeEntries(); |
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191 | writer.writeFooter(); |
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192 | writer.closeCatalogue(); |
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193 | |
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194 | } |
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195 | |
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196 | |
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197 | void Cube::prepareOutputFile() |
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198 | { |
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199 | /// @details |
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200 | /// A function to write the paramters, time of execution, and |
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201 | /// statistical information to the output file. |
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202 | |
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203 | std::string outfile; |
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204 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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205 | else outfile = this->par.getOutFile(); |
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206 | std::ofstream output(outfile.c_str()); |
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207 | output<<"Results of the Duchamp source finder v."<<VERSION<<": "; |
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208 | time_t now = time(NULL); |
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209 | output << asctime( localtime(&now) ); |
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210 | this->showParam(output); |
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211 | output<<"--------------------\n"; |
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212 | output.close(); |
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213 | this->outputStats(); |
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214 | |
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215 | } |
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216 | |
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217 | void Cube::outputStats() |
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218 | { |
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219 | /// @details |
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220 | /// A function to write the statistical information to the output |
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221 | /// file. This writes the threshold, its equivalent S/N ratio, and |
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222 | /// the noise level and spread. |
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223 | /// |
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224 | /// If smoothing has been done, the noise level & spread for the |
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225 | /// original array are calculated and printed as well. |
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226 | |
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227 | std::string outfile; |
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228 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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229 | else outfile = this->par.getOutFile(); |
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230 | std::ofstream output(outfile.c_str(),std::ios::app); |
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231 | output<<"Summary of statistics:\n"; |
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232 | output<<"Detection threshold = " << this->Stats.getThreshold() |
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233 | <<" " << this->head.getFluxUnits(); |
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234 | if(this->par.getFlagFDR()) |
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235 | output<<" (or S/N=" << this->Stats.getThresholdSNR()<<")"; |
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236 | if(this->par.getFlagSmooth()){ |
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237 | output << " in smoothed cube."; |
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238 | if(!this->par.getFlagUserThreshold()) |
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239 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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240 | <<", Noise spread = " << this->Stats.getSpread() |
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241 | <<" in smoothed cube."; |
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242 | |
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243 | // calculate the stats for the original array, so that we can |
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244 | // quote S/N values correctly. |
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245 | this->par.setFlagSmooth(false); |
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246 | bool verb=this->par.isVerbose(); |
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247 | bool fdrflag=this->par.getFlagFDR(); |
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248 | this->par.setVerbosity(false); |
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249 | this->par.setFlagFDR(false); |
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250 | this->setCubeStats(); |
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251 | this->par.setVerbosity(verb); |
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252 | this->par.setFlagFDR(fdrflag); |
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253 | this->par.setFlagSmooth(true); |
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254 | |
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255 | output << "\nNoise properties for the original cube are:"; |
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256 | } |
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257 | |
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258 | if(!this->par.getFlagUserThreshold()) |
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259 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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260 | <<", Noise spread = " << this->Stats.getSpread(); |
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261 | |
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262 | if(this->par.getFlagGrowth()){ |
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263 | StatsContainer<float> growthStats = this->Stats; |
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264 | if(this->par.getFlagUserGrowthThreshold()) |
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265 | growthStats.setThreshold(this->par.getGrowthThreshold()); |
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266 | else |
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267 | growthStats.setThresholdSNR(this->par.getGrowthCut()); |
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268 | growthStats.setUseFDR(false); |
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269 | output<<"\nDetections grown down to threshold of " |
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270 | << growthStats.getThreshold() << " " |
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271 | << this->head.getFluxUnits(); |
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272 | } |
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273 | |
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274 | if(!this->par.getFlagUserThreshold()) |
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275 | output << "\nFull stats:\n" << this->Stats; |
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276 | else |
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277 | output << "\n\nNot calculating full stats since threshold was provided directly.\n"; |
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278 | |
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279 | output<<"--------------------\n"; |
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280 | output.close(); |
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281 | } |
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282 | |
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283 | void Cube::prepareLogFile(int argc, char *argv[]) |
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284 | { |
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285 | /// @details |
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286 | /// Opens the log file so that it can be written to, and writes |
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287 | /// the parameter summary as well as the time of execution to the |
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288 | /// file. |
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289 | /// |
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290 | /// It also writes the command-line statement, hence the need for |
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291 | /// argv and argc. |
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292 | |
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293 | ASCIICatalogueWriter logwriter(this->par.getLogFile(),Catalogues::LOG); |
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294 | logwriter.setup(this); |
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295 | logwriter.openCatalogue(); |
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296 | logwriter.writeHeader(); |
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297 | logwriter.writeCommandLineEntry(argc,argv); |
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298 | logwriter.writeParameters(); |
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299 | logwriter.closeCatalogue(); |
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300 | } |
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301 | |
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302 | |
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303 | void Cube::logDetectionList(bool calcFluxes) |
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304 | { |
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305 | /// @details |
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306 | /// A front-end to writing a list of detected objects to the log file. |
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307 | /// Does not assume WCS is present. |
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308 | /// Designed to be used by searching routines before returning their |
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309 | /// final list. |
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310 | /// @param[in] calcFluxes If true (the default), calculate the various flux parameters for each object. |
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311 | |
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312 | if(this->objectList->size()>0){ |
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313 | |
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314 | long left = this->par.getBorderLeft(); |
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315 | long bottom = this->par.getBorderBottom(); |
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316 | |
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317 | if(calcFluxes) this->calcObjectFluxes(); |
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318 | this->setupColumns(); |
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319 | |
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320 | ASCIICatalogueWriter logwriter(this->par.getLogFile(),Catalogues::LOG); |
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321 | logwriter.setup(this); |
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322 | logwriter.openCatalogue(std::ios::app); |
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323 | logwriter.writeTableHeader(); |
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324 | |
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325 | if(this->par.getFlagBaseline()){ |
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326 | for(size_t i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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327 | this->array[i] += this->baseline[i]; |
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328 | } |
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329 | |
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330 | for(size_t objCtr=0;objCtr<this->objectList->size();objCtr++){ |
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331 | Detection obj = this->objectList->at(objCtr); |
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332 | obj.setOffsets(par); |
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333 | if(this->par.getFlagCubeTrimmed()){ |
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334 | obj.addOffsets(left,bottom,0); |
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335 | } |
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336 | if(calcFluxes) obj.calcFluxes(this->array, this->axisDim); |
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337 | obj.setID(objCtr+1); |
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338 | logwriter.writeEntry(&obj); |
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339 | } |
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340 | |
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341 | if(this->par.getFlagBaseline()){ |
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342 | for(size_t i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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343 | this->array[i] -= this->baseline[i]; |
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344 | } |
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345 | |
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346 | logwriter.closeCatalogue(); |
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347 | |
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348 | } |
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349 | |
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350 | } |
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351 | |
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352 | void Cube::logSummary() |
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353 | { |
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354 | ASCIICatalogueWriter logwriter(this->par.getLogFile(),Catalogues::LOG); |
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355 | logwriter.setup(this); |
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356 | logwriter.openCatalogue(std::ios::app); |
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357 | logwriter.writeCubeSummary(); |
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358 | logwriter.closeCatalogue(); |
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359 | } |
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360 | |
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361 | void Cube::writeBinaryCatalogue() |
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362 | { |
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363 | if(this->par.getFlagWriteBinaryCatalogue()){ |
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364 | |
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365 | std::ofstream bincat(this->par.getBinaryCatalogue().c_str(), std::ios::out | std::ios::binary); |
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366 | writeStringToBinaryFile(bincat,PACKAGE_VERSION); |
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367 | time_t now = time(NULL); |
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368 | std::string nowstr(asctime(localtime(&now))); |
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369 | writeStringToBinaryFile(bincat,nowstr); |
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370 | bincat.close(); |
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371 | this->par.writeToBinaryFile(); |
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372 | |
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373 | this->Stats.writeToBinaryFile(this->par.getBinaryCatalogue()); |
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374 | |
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375 | bincat.open(this->par.getBinaryCatalogue().c_str(), std::ios::out | std::ios::binary | std::ios::app); |
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376 | size_t numObj=this->objectList->size(); |
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377 | bincat.write(reinterpret_cast<const char*>(&numObj), sizeof numObj); |
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378 | bincat.close(); |
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379 | |
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380 | for(size_t i=0;i<numObj;i++) |
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381 | this->objectList->at(i).write(this->par.getBinaryCatalogue()); |
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382 | |
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383 | } |
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384 | } |
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385 | |
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386 | OUTCOME Cube::readBinaryCatalogue() |
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387 | { |
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388 | std::ifstream bincat(this->par.getBinaryCatalogue().c_str(), std::ios::in | std::ios::binary); |
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389 | if(!bincat.is_open()){ |
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390 | DUCHAMPERROR("read binary catalogue", "Could not open binary catalogue \""<<this->par.getBinaryCatalogue()<<"\"."); |
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391 | return FAILURE; |
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392 | } |
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393 | std::string bincatVersion = readStringFromBinaryFile(bincat); |
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394 | if(bincatVersion != std::string(PACKAGE_VERSION)) |
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395 | DUCHAMPWARN("read binary catalogue","Duchamp versions don't match: Binary catalogue has " << bincatVersion << " compared to " << PACKAGE_VERSION<<". Attempting to continue, but beware!"); |
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396 | |
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397 | std::string nowstr=readStringFromBinaryFile(bincat); |
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398 | if(this->par.isVerbose()) std::cout << " Reading from binary catalogue " << this->par.getBinaryCatalogue() << " made on " << nowstr << std::flush; |
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399 | std::streampos loc=bincat.tellg(); |
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400 | bincat.close(); |
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401 | |
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402 | loc = this->par.readFromBinaryFile(loc); |
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403 | if(loc<0) { |
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404 | DUCHAMPERROR("read binary catalogue","Error reading catalogue"); |
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405 | return FAILURE; |
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406 | } |
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407 | |
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408 | loc=this->Stats.readFromBinaryFile(this->par.getBinaryCatalogue(),loc); |
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409 | if(loc<0) { |
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410 | DUCHAMPERROR("read binary catalogue","Error reading catalogue"); |
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411 | return FAILURE; |
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412 | } |
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413 | |
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414 | bincat.open(this->par.getBinaryCatalogue().c_str(), std::ios::in | std::ios::binary); |
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415 | bincat.seekg(loc); |
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416 | size_t numObj; |
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417 | bincat.read(reinterpret_cast<char*>(&numObj), sizeof numObj); |
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418 | loc=bincat.tellg(); |
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419 | bincat.close(); |
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420 | |
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421 | for(size_t i=0;i<numObj;i++){ |
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422 | Object3D obj; |
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423 | loc=obj.read(this->par.getBinaryCatalogue(),loc); |
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424 | this->objectList->push_back(obj); |
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425 | } |
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426 | |
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427 | if(this->par.isVerbose()) std::cout << " Successfully read " << numObj << " objects from the binary catalogue.\n"; |
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428 | |
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429 | if(this->arrayAllocated) |
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430 | this->updateDetectMap(); |
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431 | |
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432 | return SUCCESS; |
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433 | |
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434 | } |
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435 | |
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436 | |
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437 | void Cube::writeSpectralData() |
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438 | { |
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439 | /// @details |
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440 | /// A function to write, in ascii form, the spectra of each |
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441 | /// detected object to a file. The file consists of a column for |
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442 | /// the spectral coordinates, and one column for each object |
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443 | /// showing the flux at that spectral position. The units are the |
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444 | /// same as those shown in the graphical output. The filename is |
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445 | /// given by the Param::spectraTextFile parameter in the Cube::par |
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446 | /// parameter set. |
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447 | |
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448 | const int zdim = this->axisDim[2]; |
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449 | float *specxOut = new float[zdim]; |
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450 | |
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451 | std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size()); |
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452 | size_t numObj = 0; |
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453 | for(size_t i=0;i<this->objectList->size();i++) if(objectChoice[i]) numObj++; |
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454 | |
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455 | float *spectra = new float[numObj*zdim]; |
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456 | |
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457 | size_t obj=0; |
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458 | for(size_t i=0;i<this->objectList->size();i++){ |
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459 | if(objectChoice[i]){ |
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460 | float *temp = new float[zdim]; |
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461 | float *specx = new float[zdim]; |
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462 | float *recon = new float[zdim]; |
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463 | float *base = new float[zdim]; |
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464 | this->getSpectralArrays(i, specx, temp, recon, base); |
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465 | for(int z=0;z<zdim;z++) spectra[obj*zdim+z] = temp[z]; |
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466 | if(obj==0) for(int z=0;z<zdim;z++) specxOut[z] = specx[z]; |
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467 | obj++; |
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468 | delete [] specx; |
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469 | delete [] recon; |
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470 | delete [] base; |
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471 | delete [] temp; |
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472 | } |
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473 | } |
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474 | |
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475 | std::ofstream fspec(this->par.getSpectraTextFile().c_str()); |
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476 | fspec.setf(std::ios::fixed); |
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477 | |
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478 | for(int z=0;z<zdim;z++){ |
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479 | |
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480 | fspec << std::setprecision(8); |
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481 | fspec << specxOut[z] << " "; |
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482 | obj=0; |
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483 | for(size_t i=0;i<this->objectList->size();i++){ |
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484 | if(objectChoice[i]){ |
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485 | fspec << spectra[obj*zdim+z] << " "; |
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486 | obj++; |
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487 | } |
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488 | } |
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489 | fspec << "\n"; |
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490 | |
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491 | } |
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492 | fspec.close(); |
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493 | |
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494 | delete [] spectra; |
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495 | delete [] specxOut; |
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496 | |
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497 | } |
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498 | //-------------------------------------------------------------------- |
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499 | |
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500 | |
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501 | } |
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