1 | #include <iostream> |
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2 | #include <sstream> |
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3 | #include <fstream> |
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4 | #include <iomanip> |
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5 | #include <string> |
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6 | #include <vector> |
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7 | #include <time.h> |
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8 | #include <Cubes/cubes.hh> |
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9 | #include <PixelMap/Object3D.hh> |
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10 | #include <Detection/detection.hh> |
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11 | #include <Detection/columns.hh> |
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12 | #include <Utils/utils.hh> |
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13 | |
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14 | using std::endl; |
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15 | using std::setw; |
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16 | using std::setprecision; |
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17 | using namespace Column; |
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18 | using namespace PixelInfo; |
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19 | |
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20 | void Cube::outputDetectionsKarma(std::ostream &stream) |
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21 | { |
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22 | /** |
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23 | * Prints to a stream (provided) the list of detected objects in the cube |
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24 | * in the format of an annotation file for the Karma suite of programs. |
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25 | * Annotation file draws a box enclosing the detection, and writes the |
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26 | * ID number of the detection to the right of the box. |
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27 | */ |
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28 | |
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29 | std::string fname = this->par.getImageFile(); |
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30 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
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31 | stream << "# Duchamp Source Finder results for FITS file: " << fname << endl; |
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32 | if(this->par.getFlagFDR()) |
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33 | stream<<"# FDR Significance = " << this->par.getAlpha() << endl; |
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34 | else |
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35 | stream<<"# Threshold = " << this->par.getCut() << endl; |
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36 | if(this->par.getFlagATrous()){ |
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37 | stream<<"# The a trous reconstruction method was used, with the following parameters." << endl; |
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38 | stream<<"# ATrous Dimension = " << this->par.getReconDim() << endl; |
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39 | stream<<"# ATrous Threshold = " << this->par.getAtrousCut() << endl; |
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40 | stream<<"# ATrous Minimum Scale =" << this->par.getMinScale() << endl; |
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41 | stream<<"# ATrous Filter = " << this->par.getFilterName() << endl; |
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42 | } |
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43 | else stream << "# No ATrous reconstruction done." << endl; |
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44 | stream << "#\n"; |
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45 | stream << "COLOR RED" << endl; |
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46 | stream << "COORD W" << endl; |
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47 | for(int i=0;i<this->objectList.size();i++){ |
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48 | if(this->head.isWCS()){ |
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49 | float radius = this->objectList[i].getRAWidth()/120.; |
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50 | if(this->objectList[i].getDecWidth()/120.>radius) |
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51 | radius = this->objectList[i].getDecWidth()/120.; |
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52 | stream << "CIRCLE " |
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53 | << this->objectList[i].getRA() << " " |
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54 | << this->objectList[i].getDec() << " " |
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55 | << radius << endl; |
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56 | stream << "TEXT " |
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57 | << this->objectList[i].getRA() << " " |
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58 | << this->objectList[i].getDec() << " " |
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59 | << this->objectList[i].getID() << endl; |
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60 | } |
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61 | else{ |
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62 | float radius = this->objectList[i].getXmax() - |
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63 | this->objectList[i].getXmin() + 1; |
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64 | if(this->objectList[i].getYmax()-this->objectList[i].getYmin() + 1 |
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65 | > radius) |
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66 | radius = this->objectList[i].getYmax() - |
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67 | this->objectList[i].getYmin() + 1; |
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68 | stream << "CIRCLE " |
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69 | << this->objectList[i].getXcentre() << " " |
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70 | << this->objectList[i].getYcentre() << " " |
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71 | << radius << endl; |
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72 | stream << "TEXT " |
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73 | << this->objectList[i].getXcentre() << " " |
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74 | << this->objectList[i].getYcentre() << " " |
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75 | << this->objectList[i].getID() << endl; |
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76 | } |
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77 | } |
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78 | |
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79 | } |
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80 | |
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81 | std::string fixUnitsVOT(std::string oldstring) |
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82 | { |
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83 | /** Fix a string containing units to make it acceptable for a VOTable. |
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84 | * |
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85 | * This function makes the provided units string acceptable |
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86 | * according to the standard found at |
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87 | * http://vizier.u-strasbg.fr/doc/catstd-3.2.htx |
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88 | * This should then be able to convert the units used in the text |
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89 | * table to units suitable for putting in a VOTable. |
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90 | * |
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91 | * Specifically, it removes any square brackets [] from the |
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92 | * start/end of the string, and replaces blank spaces (representing |
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93 | * multiplication) with a '.' (full stop). |
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94 | */ |
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95 | |
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96 | std::string newstring; |
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97 | for(int i=0;i<oldstring.size();i++){ |
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98 | if((oldstring[i]!='[')&&(oldstring[i]!=']')){ |
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99 | if(oldstring[i]==' ') newstring += '.'; |
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100 | else newstring += oldstring[i]; |
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101 | } |
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102 | } |
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103 | return newstring; |
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104 | } |
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105 | |
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106 | void Cube::outputDetectionsVOTable(std::ostream &stream) |
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107 | { |
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108 | /** |
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109 | * Prints to a stream (provided) the list of detected objects in the cube |
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110 | * in a VOTable format. |
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111 | * Uses WCS information and assumes WCS parameters have been calculated for each |
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112 | * detected object. |
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113 | * If they have not (given by the isWCS() function), then those objects are not written... |
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114 | */ |
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115 | |
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116 | // Set up Column definitions here |
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117 | std::vector<Col> localCol; |
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118 | std::string posUCD[4]; |
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119 | localCol.push_back(this->fullCols[NUM]); // objID |
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120 | localCol.push_back(this->fullCols[NAME]); // name |
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121 | localCol.push_back(this->fullCols[RA]); // ra |
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122 | if(makelower(localCol[2].getName())=="ra"){ |
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123 | posUCD[0] = "pos.eq.ra;meta.main"; |
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124 | posUCD[2] = "phys.angSize;pos.eq.ra"; |
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125 | } |
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126 | else{ |
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127 | posUCD[0] = "pos.galactic.lat;meta.main"; |
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128 | posUCD[2] = "phys.angSize;pos.galactic.lat"; |
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129 | } |
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130 | localCol.push_back(this->fullCols[DEC]); // dec |
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131 | if(makelower(localCol[2].getName())=="dec"){ |
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132 | posUCD[1] = "pos.eq.dec;meta.main"; |
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133 | posUCD[3] = "phys.angSize;pos.eq.dec"; |
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134 | } |
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135 | else{ |
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136 | posUCD[1] = "pos.galactic.lon;meta.main"; |
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137 | posUCD[3] = "phys.angSize;pos.galactic.lon"; |
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138 | } |
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139 | localCol.push_back(this->fullCols[WRA]); // w_ra |
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140 | localCol.push_back(this->fullCols[WDEC]); // w_dec |
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141 | localCol.push_back(this->fullCols[VEL]); // vel |
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142 | localCol.push_back(this->fullCols[WVEL]); // w_vel |
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143 | localCol.push_back(this->fullCols[FINT]); // f_int |
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144 | localCol.push_back(this->fullCols[FPEAK]); // f_peak |
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145 | localCol.push_back(this->fullCols[FLAG]); // flag |
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146 | |
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147 | stream<<"<?xml version=\"1.0\"?>\n"; |
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148 | stream<<"<VOTABLE version=\"1.1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n"; |
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149 | stream<<" xsi:noNamespaceSchemaLocation=\"http://www.ivoa.net/xml/VOTable/VOTable/v1.1\">\n"; |
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150 | |
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151 | stream<<" <COOSYS ID=\"J2000\" equinox=\"J2000.\" epoch=\"J2000.\" system=\"eq_FK5\"/>\n"; |
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152 | stream<<" <RESOURCE name=\"Duchamp Output\">\n"; |
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153 | stream<<" <TABLE name=\"Detections\">\n"; |
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154 | stream<<" <DESCRIPTION>Detected sources and parameters from running the Duchamp source finder.</DESCRIPTION>\n"; |
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155 | |
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156 | // PARAM section -- parts that are not entry-specific ie. apply to whole dataset |
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157 | std::string fname = this->par.getImageFile(); |
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158 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
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159 | stream<<" <PARAM name=\"FITS file\" datatype=\"char\" ucd=\"meta.file;meta.fits\" value=\"" |
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160 | << fname << "\" arraysize=\""<<fname.size()<<"\"/>\n"; |
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161 | if(this->par.getFlagFDR()) |
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162 | stream<<" <PARAM name=\"FDR Significance\" datatype=\"float\" ucd=\"stat.param\" value=\"" |
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163 | << this->par.getAlpha() << "\"/>\n"; |
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164 | else |
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165 | stream<<" <PARAM name=\"Threshold\" datatype=\"float\" ucd=\"stat.snr\" value=\"" |
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166 | << this->par.getCut() << "\"/>\n"; |
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167 | if(this->par.getFlagATrous()){ |
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168 | std::string note = "The a trous reconstruction method was used, with the following parameters."; |
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169 | stream<<" <PARAM name=\"ATrous note\" datatype=\"char\" ucd=\"meta.note\" value=\"" |
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170 | <<note << "\" arraysize=\"" << note.size() << "\"/>\n"; |
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171 | stream<<" <PARAM name=\"ATrous Dimension\" datatype=\"int\" ucd=\"meta.code;stat\" value=\"" |
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172 | << this->par.getReconDim() << "\"/>\n"; |
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173 | stream<<" <PARAM name=\"ATrous Threshold\" datatype=\"float\" ucd=\"stat.snr\" value=\"" |
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174 | << this->par.getAtrousCut() << "\"/>\n"; |
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175 | stream<<" <PARAM name=\"ATrous Minimum Scale\" datatype=\"int\" ucd=\"stat.param\" value=\"" |
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176 | << this->par.getMinScale() << "\"/>\n"; |
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177 | stream<<" <PARAM name=\"ATrous Filter\" datatype=\"char\" ucd=\"meta.code;stat\" value=\"" |
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178 | << this->par.getFilterName() << "\" arraysize=\"" << this->par.getFilterName().size() << "\"/>\n"; |
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179 | } |
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180 | // FIELD section -- names, titles and info for each column. |
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181 | stream<<" <FIELD name=\"ID\" ID=\"col01\" ucd=\"meta.id\" datatype=\"int\" width=\"" |
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182 | <<localCol[0].getWidth()<<"\" unit=\"--\"/>\n"; |
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183 | stream<<" <FIELD name=\"Name\" ID=\"col02\" ucd=\"meta.id;meta.main\" datatype=\"char\" arraysize=\"" |
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184 | <<localCol[1].getWidth()<<"\" unit=\"--\"/>\n"; |
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185 | stream<<" <FIELD name=\""<<localCol[2].getName()<<"\" ID=\"col03\" ucd=\"" |
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186 | <<posUCD[0]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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187 | <<localCol[2].getWidth()<<"\" precision=\""<<prec[prPOS]<<"\" unit=\"deg\"/>\n"; |
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188 | stream<<" <FIELD name=\""<<localCol[3].getName()<<"\" ID=\"col04\" ucd=\"" |
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189 | <<posUCD[1]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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190 | <<localCol[3].getWidth()<<"\" precision=\""<<prec[prPOS]<<"\" unit=\"deg\"/>\n"; |
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191 | stream<<" <FIELD name=\""<<localCol[4].getName()<<"\" ID=\"col05\" ucd=\"" |
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192 | <<posUCD[2]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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193 | <<localCol[4].getWidth()<<"\" precision=\""<<prec[prWPOS]<<"\" unit=\"" |
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194 | <<fixUnitsVOT(localCol[4].getUnits())<<"\"/>\n"; |
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195 | stream<<" <FIELD name=\""<<localCol[5].getName()<<"\" ID=\"col06\" ucd=\"" |
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196 | <<posUCD[2]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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197 | <<localCol[5].getWidth()<<"\" precision=\""<<prec[prWPOS]<<"\" unit=\"" |
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198 | <<fixUnitsVOT(localCol[5].getUnits())<<"\"/>\n"; |
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199 | stream<<" <FIELD name=\"Vel\" ID=\"col07\" ucd=\"phys.veloc;src.dopplerVeloc\" datatype=\"float\" width=\"" |
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200 | <<localCol[6].getWidth()<<"\" precision=\""<<prec[prVEL]<<"\" unit=\"" |
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201 | <<fixUnitsVOT(localCol[6].getUnits())<<"\"/>\n"; |
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202 | stream<<" <FIELD name=\"w_Vel\" ID=\"col08\" ucd=\"phys.veloc;src.dopplerVeloc;spect.line.width\"" |
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203 | <<" datatype=\"float\" width=\""<<localCol[7].getWidth()<<"\" precision=\"" |
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204 | <<prec[prVEL]<<"\" unit=\""<<fixUnitsVOT(localCol[7].getUnits())<<"\"/>\n"; |
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205 | stream<<" <FIELD name=\"Integrated_Flux\" ID=\"col09\" ucd=\"phot.flux;spect.line.intensity\"" |
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206 | <<" datatype=\"float\" width=\""<<localCol[8].getWidth()<<"\" precision=\"" |
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207 | <<prec[prFLUX]<<"\" unit=\""<<fixUnitsVOT(localCol[8].getUnits())<<"\"/>\n"; |
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208 | stream<<" <FIELD name=\"Peak_Flux\" ID=\"col10\" ucd=\"phot.flux;spect.line.intensity\"" |
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209 | <<" datatype=\"float\" width=\""<<localCol[9].getWidth()<<"\" precision=\"" |
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210 | <<prec[prFLUX]<<"\" unit=\""<<fixUnitsVOT(localCol[9].getUnits())<<"\"/>\n"; |
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211 | stream<<" <FIELD name=\"Flag\" ID=\"col11\" ucd=\"meta.code.qual\" datatype=\"char\" arraysize=\"3\" unit=\"--\"/>\n"; |
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212 | |
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213 | |
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214 | stream<<" <DATA>\n" |
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215 | <<" <TABLEDATA>\n"; |
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216 | |
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217 | stream.setf(std::ios::fixed); |
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218 | for(int i=0;i<this->objectList.size();i++){ |
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219 | if(this->objectList[i].isWCS()){ |
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220 | stream<<" <TR>\n"; |
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221 | stream<<" <TD>"<<setw(localCol[0].getWidth())<<i+1<<"</TD>"; |
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222 | stream<<"<TD>" << setw(localCol[1].getWidth()) << this->objectList[i].getName() <<"</TD>"; |
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223 | stream<<setprecision(prec[prPOS]); |
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224 | stream<<"<TD>" << setw(localCol[2].getWidth()) << this->objectList[i].getRA() <<"</TD>"; |
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225 | stream<<"<TD>" << setw(localCol[3].getWidth()) << this->objectList[i].getDec() <<"</TD>"; |
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226 | stream<<setprecision(prec[prWPOS]); |
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227 | stream<<"<TD>" << setw(localCol[4].getWidth()) << this->objectList[i].getRAWidth() <<"</TD>"; |
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228 | stream<<"<TD>" << setw(localCol[5].getWidth()) << this->objectList[i].getDecWidth() <<"</TD>"; |
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229 | stream<<setprecision(prec[prVEL]); |
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230 | stream<<"<TD>" << setw(localCol[6].getWidth()) << this->objectList[i].getVel() <<"</TD>"; |
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231 | stream<<"<TD>" << setw(localCol[7].getWidth()) << this->objectList[i].getVelWidth() <<"</TD>"; |
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232 | stream<<setprecision(prec[prFLUX]); |
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233 | stream<<"<TD>" << setw(localCol[8].getWidth()) << this->objectList[i].getIntegFlux() <<"</TD>"; |
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234 | stream<<"<TD>" << setw(localCol[9].getWidth()) << this->objectList[i].getPeakFlux() <<"</TD>"; |
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235 | stream<<"<TD>" << setw(localCol[10].getWidth())<< this->objectList[i].getFlagText() <<"</TD>"; |
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236 | |
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237 | stream<<endl; |
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238 | stream<<" </TR>\n"; |
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239 | } |
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240 | } |
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241 | stream<<" </TABLEDATA>\n"; |
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242 | stream<<" </DATA>\n"; |
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243 | stream<<" </TABLE>\n"; |
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244 | stream<<" </RESOURCE>\n"; |
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245 | stream<<"</VOTABLE>\n"; |
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246 | resetiosflags(std::ios::fixed); |
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247 | |
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248 | } |
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249 | |
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250 | |
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251 | void Cube::outputDetectionList() |
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252 | { |
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253 | /** |
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254 | * A front-end to writing the full list of detected objects to a results |
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255 | * file and to cout. |
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256 | * Uses outputDetectionTextWCS for each objects. |
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257 | * Leaves the testing of whether the WCS parameters for each object |
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258 | * have been calculated to outputDetectionTextWCS. |
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259 | */ |
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260 | |
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261 | int count=0; |
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262 | int flag; |
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263 | std::ofstream output(this->par.getOutFile().c_str()); |
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264 | output<<"Results of the Duchamp source finder: "; |
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265 | time_t now = time(NULL); |
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266 | output << asctime( localtime(&now) ); |
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267 | this->showParam(output); |
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268 | output<<"--------------------\n"; |
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269 | output<<"Detection threshold = " << this->Stats.getThreshold() |
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270 | <<" " << this->head.getFluxUnits(); |
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271 | if(this->par.getFlagFDR()) |
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272 | output<<" (or S/N=" << this->Stats.getThresholdSNR()<<")"; |
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273 | output<<endl; |
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274 | if(!this->par.getFlagUserThreshold()) |
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275 | output<<" Noise level = " << this->Stats.getMiddle() |
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276 | <<", Noise spread = " << this->Stats.getSpread() << endl; |
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277 | output<<"Total number of detections = "<<this->objectList.size()<<endl; |
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278 | output<<"--------------------\n"; |
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279 | this->setupColumns(); |
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280 | this->objectList[0].outputDetectionTextHeader(output,this->fullCols); |
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281 | this->objectList[0].outputDetectionTextHeader(std::cout,this->fullCols); |
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282 | for(int i=0;i<this->objectList.size();i++){ |
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283 | this->objectList[i].outputDetectionTextWCS(output,this->fullCols); |
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284 | this->objectList[i].outputDetectionTextWCS(std::cout,this->fullCols); |
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285 | } |
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286 | } |
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287 | |
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288 | void Cube::logDetectionList() |
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289 | { |
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290 | /** |
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291 | * logDetectionList |
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292 | * A front-end to writing a list of detected objects to the log file. |
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293 | * Does not assume WCS, so uses outputDetectionText. |
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294 | * Designed to be used by searching routines before returning their final list. |
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295 | */ |
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296 | |
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297 | long left = this->par.getBorderLeft(); |
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298 | long right = this->par.getBorderRight(); |
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299 | long top = this->par.getBorderTop(); |
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300 | long bottom = this->par.getBorderBottom(); |
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301 | |
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302 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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303 | this->setupColumns(); |
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304 | this->objectList[0].outputDetectionTextHeader(fout,this->logCols); |
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305 | long pos; |
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306 | |
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307 | // std::ofstream ftemp("temp2.txt"); |
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308 | // for(int objCtr=0;objCtr<this->objectList.size();objCtr++){ |
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309 | // this->objectList[objCtr].pixels().order(); |
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310 | // ftemp << "Object #" << objCtr+1 |
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311 | // << ": size = " << this->objectList[objCtr].getSize()<<"\n"; |
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312 | // ftemp << this->objectList[objCtr]; |
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313 | // } |
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314 | // ftemp.close(); |
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315 | |
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316 | |
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317 | // // Need to deal with possibility of trimmed array |
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318 | // long *tempDim = new long[3]; |
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319 | // tempDim[0] = (this->axisDim[0] + left + right); |
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320 | // tempDim[1] = (this->axisDim[1] + bottom + top); |
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321 | // tempDim[2] = this->axisDim[2]; |
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322 | // long tempsize = tempDim[0] * tempDim[1] * tempDim[2]; |
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323 | // float *temparray = new float[tempsize]; |
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324 | // // for(int i=0;i<this->numPixels;i++){ // loop over this->array |
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325 | // for(int z=0;z<tempDim[2];z++){ |
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326 | // for(int y=0;y<tempDim[1];y++){ |
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327 | // for(int x=0;x<tempDim[0];x++){ |
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328 | |
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329 | // bool isDud = (x<left) || (x>=this->axisDim[0]+left) || |
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330 | // (y<bottom) || (y>=this->axisDim[1]+bottom); |
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331 | |
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332 | // int temppos = x + tempDim[0]*y + tempDim[1]*tempDim[0]*z; |
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333 | |
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334 | // int pos = (x-left) + (y-bottom)*this->axisDim[0] + |
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335 | // z*this->axisDim[0]*this->axisDim[1]; |
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336 | |
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337 | // if(isDud) temparray[temppos] = this->par.getBlankPixVal(); |
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338 | // else temparray[temppos] = this->array[pos]; |
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339 | |
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340 | // if(this->par.getFlagBaseline() && !isDud) |
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341 | // temparray[temppos] += this->baseline[pos]; |
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342 | |
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343 | // } |
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344 | // } |
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345 | // } |
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346 | |
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347 | if(this->par.getFlagBaseline()){ |
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348 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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349 | this->array[i] += this->baseline[i]; |
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350 | } |
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351 | |
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352 | for(int objCtr=0;objCtr<this->objectList.size();objCtr++){ |
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353 | Detection *obj = new Detection; |
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354 | *obj = objectList[objCtr]; |
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355 | obj->setOffsets(par); |
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356 | obj->calcFluxes(this->array, this->axisDim); |
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357 | if(this->par.getFlagCubeTrimmed()){ |
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358 | obj->pixels().addOffsets(left,bottom,0); |
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359 | } |
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360 | obj->outputDetectionText(fout,this->logCols,objCtr+1); |
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361 | delete obj; |
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362 | } |
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363 | |
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364 | if(this->par.getFlagBaseline()){ |
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365 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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366 | this->array[i] -= this->baseline[i]; |
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367 | } |
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368 | |
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369 | // delete [] temparray; |
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370 | // delete [] tempDim; |
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371 | fout.close(); |
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372 | } |
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373 | |
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374 | void Cube::logDetection(Detection obj, int counter) |
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375 | { |
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376 | /** |
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377 | * A front-end to writing a detected object to the log file. |
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378 | * Does not assume WCS, so uses outputDetectionText. |
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379 | * Corrects for changes to positions of pixels and removal of baselines. |
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380 | * Designed to be used by searching routines before returning their final |
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381 | * list. |
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382 | * \param obj Detection object to be written : passed by value, as we want |
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383 | * to potentially change positions etc, but not for the object in the |
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384 | * calling function. |
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385 | * \param counter The number to assign to the object : ideally its number |
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386 | * in a list of some kind. |
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387 | */ |
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388 | |
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389 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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390 | // Need to deal with possibility of trimmed array |
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391 | long left = this->par.getBorderLeft(); |
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392 | long right = this->par.getBorderRight(); |
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393 | long top = this->par.getBorderTop(); |
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394 | long bottom = this->par.getBorderBottom(); |
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395 | long *tempDim = new long[3]; |
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396 | tempDim[0] = (this->axisDim[0] + left + right); |
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397 | tempDim[1] = (this->axisDim[1] + bottom + top); |
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398 | tempDim[2] = this->axisDim[2]; |
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399 | long tempsize = tempDim[0] * tempDim[1] * tempDim[2]; |
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400 | float *temparray = new float[tempsize]; |
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401 | // for(int i=0;i<this->numPixels;i++){ // loop over this->array |
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402 | for(int z=0;z<tempDim[2];z++){ |
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403 | for(int y=0;y<tempDim[1];y++){ |
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404 | for(int x=0;x<tempDim[0];x++){ |
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405 | |
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406 | bool isDud = (x<left) || (x>=this->axisDim[0]+left) || |
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407 | (y<bottom) || (y>=this->axisDim[1]+bottom); |
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408 | |
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409 | int temppos = x + tempDim[0]*y + tempDim[1]*tempDim[0]*z; |
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410 | |
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411 | int pos = (x-left) + (y-bottom)*this->axisDim[0] + |
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412 | z*this->axisDim[0]*this->axisDim[1]; |
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413 | |
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414 | if(isDud) temparray[temppos] = this->par.getBlankPixVal(); |
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415 | else temparray[temppos] = this->array[pos]; |
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416 | |
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417 | if(this->par.getFlagBaseline() && !isDud) |
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418 | temparray[temppos] += this->baseline[pos]; |
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419 | |
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420 | } |
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421 | } |
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422 | } |
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423 | |
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424 | if(this->par.getFlagCubeTrimmed()){ |
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425 | obj.pixels().addOffsets(left,bottom,0); |
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426 | } |
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427 | obj.calcFluxes(temparray, this->axisDim); |
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428 | obj.outputDetectionText(fout,this->logCols,counter); |
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429 | delete [] temparray; |
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430 | delete [] tempDim; |
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431 | fout.close(); |
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432 | } |
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