1 | // |
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2 | // C++ Interface: Scantable |
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3 | // |
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4 | // Description: |
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5 | // |
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6 | // |
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7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005 |
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8 | // |
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9 | // Copyright: See COPYING file that comes with this distribution |
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10 | // |
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11 | // |
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12 | #ifndef ASAPSCANTABLE_H |
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13 | #define ASAPSCANTABLE_H |
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14 | |
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15 | // STL |
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16 | #include <string> |
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17 | #include <vector> |
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18 | // AIPS++ |
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19 | #include <casa/aips.h> |
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20 | #include <casa/Containers/Record.h> |
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21 | #include <casa/Arrays/MaskedArray.h> |
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22 | #include <casa/BasicSL/String.h> |
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23 | #include <casa/Utilities/CountedPtr.h> |
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24 | |
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25 | #include <tables/Tables/Table.h> |
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26 | #include <tables/Tables/ArrayColumn.h> |
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27 | #include <tables/Tables/ScalarColumn.h> |
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28 | |
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29 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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30 | |
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31 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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32 | |
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33 | #include <casa/Arrays/Vector.h> |
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34 | #include <casa/Quanta/Quantum.h> |
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35 | |
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36 | #include <casa/Exceptions/Error.h> |
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37 | |
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38 | #include "Logger.h" |
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39 | #include "STHeader.h" |
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40 | #include "STFrequencies.h" |
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41 | #include "STWeather.h" |
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42 | #include "STFocus.h" |
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43 | #include "STTcal.h" |
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44 | #include "STMolecules.h" |
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45 | #include "STSelector.h" |
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46 | #include "STHistory.h" |
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47 | #include "STPol.h" |
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48 | #include "STFit.h" |
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49 | #include "STFitEntry.h" |
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50 | #include "STFitter.h" |
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51 | |
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52 | namespace asap { |
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53 | |
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54 | /** |
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55 | * This class contains and wraps a casa::Table, which is used to store |
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56 | * all the information. This can be either a MemoryTable or a |
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57 | * disk based Table. |
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58 | * It provides access functions to the underlying table |
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59 | * It contains n subtables: |
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60 | * @li weather |
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61 | * @li frequencies |
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62 | * @li molecules |
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63 | * @li tcal |
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64 | * @li focus |
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65 | * @li fits |
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66 | * |
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67 | * @brief The main ASAP data container |
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68 | * @author Malte Marquarding |
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69 | * @date |
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70 | * @version |
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71 | */ |
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72 | class Scantable : private Logger |
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73 | { |
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74 | |
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75 | friend class STMath; |
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76 | |
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77 | public: |
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78 | /** |
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79 | * Default constructor |
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80 | */ |
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81 | explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory); |
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82 | |
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83 | /** |
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84 | * Create a Scantable object form an existing table on disk |
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85 | * @param[in] name the name of the existing Scantable |
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86 | */ |
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87 | explicit Scantable(const std::string& name, casa::Table::TableType ttype = casa::Table::Memory); |
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88 | |
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89 | /// @fixme this is only sensible for MemoryTables.... |
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90 | Scantable(const Scantable& other, bool clear=true); |
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91 | |
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92 | /** |
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93 | * Destructor |
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94 | */ |
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95 | virtual ~Scantable(); |
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96 | |
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97 | /** |
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98 | * get a const reference to the underlying casa::Table |
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99 | * @return const \ref casa::Table reference |
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100 | */ |
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101 | const casa::Table& table() const; |
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102 | |
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103 | /** |
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104 | * get a reference to the underlying casa::Table with the Selection |
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105 | * object applied if set |
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106 | * @return casa::Table reference |
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107 | */ |
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108 | casa::Table& table(); |
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109 | |
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110 | |
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111 | /** |
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112 | * Get a handle to the selection object |
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113 | * @return constant STSelector reference |
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114 | */ |
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115 | const STSelector& getSelection() const { return selector_; } |
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116 | |
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117 | /** |
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118 | * Set the data to be a subset as defined by the STSelector |
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119 | * @param selection a STSelector object |
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120 | */ |
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121 | void setSelection(const STSelector& selection); |
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122 | |
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123 | /** |
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124 | * unset the selection of the data |
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125 | */ |
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126 | void unsetSelection(); |
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127 | /** |
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128 | * set the header |
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129 | * @param[in] sth an STHeader object |
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130 | */ |
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131 | void setHeader( const STHeader& sth ); |
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132 | |
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133 | /** |
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134 | * get the header information |
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135 | * @return an STHeader object |
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136 | */ |
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137 | STHeader getHeader( ) const; |
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138 | |
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139 | /** |
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140 | * Checks if the "other" Scantable is conformant with this, |
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141 | * i.e. if header values are the same. |
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142 | * @param[in] other another Scantable |
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143 | * @return true or false |
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144 | */ |
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145 | bool conformant( const Scantable& other); |
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146 | |
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147 | /** |
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148 | * |
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149 | * @param stype The type of the source, 0 = on, 1 = off |
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150 | */ |
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151 | void setSourceType(int stype); |
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152 | |
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153 | |
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154 | /** |
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155 | * The number of scans in the table |
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156 | * @return number of scans in the table |
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157 | */ |
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158 | int nscan() const; |
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159 | |
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160 | casa::MEpoch::Types getTimeReference() const; |
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161 | |
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162 | |
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163 | casa::MEpoch getEpoch(int whichrow) const; |
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164 | |
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165 | /** |
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166 | * Get global antenna position |
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167 | * @return casa::MPosition |
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168 | */ |
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169 | casa::MPosition getAntennaPosition() const; |
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170 | |
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171 | /** |
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172 | * the @ref casa::MDirection for a specific row |
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173 | * @param[in] whichrow the row number |
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174 | * return casa::MDirection |
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175 | */ |
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176 | casa::MDirection getDirection( int whichrow ) const; |
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177 | |
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178 | /** |
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179 | * get the direction type as a string, e.g. "J2000" |
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180 | * @param[in] whichrow the row number |
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181 | * return the direction string |
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182 | */ |
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183 | std::string getDirectionString( int whichrow ) const; |
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184 | |
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185 | /** |
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186 | * set the direction type as a string, e.g. "J2000" |
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187 | * @param[in] refstr the direction type |
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188 | */ |
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189 | void setDirectionRefString(const std::string& refstr=""); |
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190 | |
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191 | /** |
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192 | * get the direction reference string |
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193 | * @return a string describing the direction reference |
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194 | */ |
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195 | std::string getDirectionRefString() const; |
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196 | |
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197 | /** |
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198 | * Return the Flux unit of the data, e.g. "Jy" or "K" |
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199 | * @return string |
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200 | */ |
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201 | std::string getFluxUnit() const; |
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202 | |
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203 | /** |
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204 | * Set the Flux unit of the data |
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205 | * @param unit a string representing the unit, e.g "Jy" or "K" |
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206 | */ |
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207 | void setFluxUnit( const std::string& unit ); |
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208 | |
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209 | /** |
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210 | * Set the Stokes type of the data |
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211 | * @param feedtype a string representing the type, e.g "circular" or "linear" |
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212 | */ |
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213 | void setFeedType( const std::string& feedtype ); |
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214 | |
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215 | /** |
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216 | * |
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217 | * @param instrument a string representing an insturment. see xxx |
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218 | */ |
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219 | void setInstrument( const std::string& instrument ); |
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220 | |
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221 | /** |
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222 | * (Re)calculate the azimuth and elevationnfor all rows |
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223 | */ |
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224 | void calculateAZEL(); |
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225 | |
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226 | /** |
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227 | * "hard" flag the data, this flags everything selected in setSelection() |
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228 | * param[in] msk a boolean mask of length nchan describing the points to |
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229 | * to be flagged |
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230 | */ |
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231 | //void flag( const std::vector<bool>& msk = std::vector<bool>()); |
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232 | void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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233 | |
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234 | /** |
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235 | * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki) |
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236 | * param[in] rows list of row numbers to be flagged |
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237 | */ |
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238 | void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false); |
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239 | |
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240 | /** |
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241 | * Get flagRow info at the specified row. If true, the whole data |
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242 | * at the row should be flagged. |
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243 | */ |
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244 | bool getFlagRow(int whichrow) const |
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245 | { return (flagrowCol_(whichrow) > 0); } |
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246 | |
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247 | /** |
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248 | * Flag the data outside a specified range (in a channel-based manner). |
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249 | * (CAS-1807 Wataru Kawasaki) |
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250 | */ |
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251 | void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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252 | |
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253 | /** |
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254 | * Return a list of booleans with the size of nchan for a specified row, to get info |
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255 | * about which channel is clipped. |
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256 | */ |
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257 | std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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258 | void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag, |
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259 | casa::Vector<casa::uChar> flgs); |
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260 | |
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261 | /** |
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262 | * Return a list of row numbers with respect to the original table. |
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263 | * @return a list of unsigned ints |
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264 | */ |
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265 | std::vector<unsigned int> rownumbers() const; |
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266 | |
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267 | |
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268 | /** |
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269 | * Get the number of beams in the data or a specific scan |
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270 | * @param scanno the scan number to get the number of beams for. |
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271 | * If scanno<0 the number is retrieved from the header. |
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272 | * @return an integer number |
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273 | */ |
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274 | int nbeam(int scanno=-1) const; |
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275 | /** |
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276 | * Get the number of IFs in the data or a specific scan |
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277 | * @param scanno the scan number to get the number of IFs for. |
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278 | * If scanno<0 the number is retrieved from the header. |
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279 | * @return an integer number |
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280 | */ |
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281 | int nif(int scanno=-1) const; |
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282 | /** |
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283 | * Get the number of polarizations in the data or a specific scan |
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284 | * @param scanno the scan number to get the number of polarizations for. |
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285 | * If scanno<0 the number is retrieved from the header. |
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286 | * @return an integer number |
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287 | */ |
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288 | int npol(int scanno=-1) const; |
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289 | |
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290 | std::string getPolType() const; |
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291 | |
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292 | |
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293 | /** |
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294 | * Get the number of integartion cycles |
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295 | * @param scanno the scan number to get the number of rows for. |
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296 | * If scanno<0 the number is retrieved from the header. |
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297 | * @return the number of rows (for the specified scanno) |
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298 | */ |
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299 | int nrow(int scanno=-1) const; |
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300 | |
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301 | int getBeam(int whichrow) const; |
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302 | std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); } |
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303 | |
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304 | int getIF(int whichrow) const; |
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305 | std::vector<uint> getIFNos() const { return getNumbers(ifCol_); } |
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306 | |
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307 | int getPol(int whichrow) const; |
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308 | std::vector<uint> getPolNos() const { return getNumbers(polCol_); } |
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309 | |
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310 | std::vector<uint> getScanNos() const { return getNumbers(scanCol_); } |
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311 | int getScan(int whichrow) const { return scanCol_(whichrow); } |
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312 | |
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313 | //TT addition |
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314 | std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); } |
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315 | |
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316 | /** |
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317 | * Get the number of channels in the data or a specific IF. This currently |
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318 | * varies only with IF number |
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319 | * @param ifno the IF number to get the number of channels for. |
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320 | * If ifno<0 the number is retrieved from the header. |
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321 | * @return an integer number |
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322 | */ |
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323 | int nchan(int ifno=-1) const; |
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324 | int getChannels(int whichrow) const; |
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325 | |
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326 | int ncycle(int scanno=-1) const; |
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327 | int getCycle(int whichrow) const { return cycleCol_(whichrow); } |
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328 | |
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329 | double getInterval(int whichrow) const |
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330 | { return integrCol_(whichrow); } |
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331 | |
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332 | float getTsys(int whichrow) const |
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333 | { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); } |
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334 | float getElevation(int whichrow) const |
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335 | { return elCol_(whichrow); } |
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336 | float getAzimuth(int whichrow) const |
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337 | { return azCol_(whichrow); } |
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338 | float getParAngle(int whichrow) const |
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339 | { return focus().getParAngle(mfocusidCol_(whichrow)); } |
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340 | int getTcalId(int whichrow) const |
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341 | { return mtcalidCol_(whichrow); } |
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342 | |
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343 | std::string getSourceName(int whichrow) const |
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344 | { return srcnCol_(whichrow); } |
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345 | |
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346 | std::vector<bool> getMask(int whichrow) const; |
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347 | std::vector<float> getSpectrum(int whichrow, |
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348 | const std::string& poltype = "" ) const; |
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349 | |
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350 | void setSpectrum(const std::vector<float>& spec, int whichrow); |
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351 | |
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352 | std::string getPolarizationLabel(int index, const std::string& ptype) const |
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353 | { return STPol::getPolLabel(index, ptype ); } |
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354 | |
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355 | /** |
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356 | * Write the Scantable to disk |
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357 | * @param filename the output file name |
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358 | */ |
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359 | void makePersistent(const std::string& filename); |
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360 | |
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361 | std::vector<std::string> getHistory() const |
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362 | { return historyTable_.getHistory(); }; |
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363 | |
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364 | void addHistory(const std::string& hist) { historyTable_.addEntry(hist); } |
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365 | |
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366 | void appendToHistoryTable(const STHistory& otherhist) |
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367 | { historyTable_.append(otherhist); } |
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368 | |
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369 | std::string summary(bool verbose=false); |
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370 | std::string getTime(int whichrow=-1, bool showdate=true) const; |
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371 | double getIntTime(int whichrow) const { return integrCol_(whichrow); } |
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372 | |
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373 | // returns unit, conversion frame, doppler, base-frame |
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374 | |
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375 | /** |
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376 | * Get the frequency set up |
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377 | * This is forwarded to the STFrequencies subtable |
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378 | * @return unit, frame, doppler |
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379 | */ |
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380 | std::vector<std::string> getCoordInfo() const |
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381 | { return freqTable_.getInfo(); }; |
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382 | |
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383 | void setCoordInfo(std::vector<string> theinfo) |
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384 | { return freqTable_.setInfo(theinfo); }; |
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385 | |
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386 | |
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387 | std::vector<double> getAbcissa(int whichrow) const; |
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388 | |
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389 | std::vector<float> getWeather(int whichrow) const; |
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390 | |
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391 | std::string getAbcissaLabel(int whichrow) const; |
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392 | std::vector<double> getRestFrequencies() const |
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393 | { return moleculeTable_.getRestFrequencies(); } |
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394 | std::vector<double> getRestFrequency(int id) const |
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395 | { return moleculeTable_.getRestFrequency(id); } |
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396 | |
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397 | /** |
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398 | void setRestFrequencies(double rf, const std::string& name = "", |
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399 | const std::string& = "Hz"); |
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400 | **/ |
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401 | // Modified by Takeshi Nakazato 05/09/2008 |
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402 | /*** |
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403 | void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "", |
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404 | const std::string& = "Hz"); |
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405 | ***/ |
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406 | void setRestFrequencies(vector<double> rf, |
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407 | const vector<std::string>& name = vector<std::string>(1,""), |
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408 | const std::string& = "Hz"); |
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409 | |
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410 | //void setRestFrequencies(const std::string& name); |
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411 | void setRestFrequencies(const vector<std::string>& name); |
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412 | |
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413 | void shift(int npix); |
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414 | |
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415 | casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const; |
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416 | |
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417 | void convertDirection(const std::string& newframe); |
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418 | |
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419 | STFrequencies& frequencies() { return freqTable_; } |
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420 | const STFrequencies& frequencies() const { return freqTable_; } |
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421 | STWeather& weather() { return weatherTable_; } |
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422 | const STWeather& weather() const { return weatherTable_; } |
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423 | STFocus& focus() { return focusTable_; } |
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424 | const STFocus& focus() const { return focusTable_; } |
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425 | STTcal& tcal() { return tcalTable_; } |
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426 | const STTcal& tcal() const { return tcalTable_; } |
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427 | STMolecules& molecules() { return moleculeTable_; } |
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428 | const STMolecules& molecules() const { return moleculeTable_; } |
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429 | STHistory& history() { return historyTable_; } |
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430 | const STHistory& history() const { return historyTable_; } |
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431 | STFit& fit() { return fitTable_; } |
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432 | const STFit& fit() const { return fitTable_; } |
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433 | |
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434 | std::vector<std::string> columnNames() const; |
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435 | |
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436 | void addFit(const STFitEntry& fit, int row); |
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437 | STFitEntry getFit(int row) const |
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438 | { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; } |
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439 | |
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440 | //Added by TT |
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441 | /** |
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442 | * Get the antenna name |
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443 | * @return antenna name string |
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444 | */ |
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445 | casa::String getAntennaName() const; |
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446 | |
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447 | /** |
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448 | * For GBT MS data only. check a scan list |
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449 | * against the information found in GBT_GO table for |
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450 | * scan number orders to get correct pairs. |
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451 | * @param[in] scan list |
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452 | * @return status |
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453 | */ |
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454 | int checkScanInfo(const std::vector<int>& scanlist) const; |
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455 | |
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456 | /** |
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457 | * Get the direction as a vector, for a specific row |
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458 | * @param[in] whichrow the row numbyyer |
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459 | * @return the direction in a vector |
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460 | */ |
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461 | std::vector<double> getDirectionVector(int whichrow) const; |
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462 | |
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463 | /** |
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464 | * Set a flag indicating whether the data was parallactified |
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465 | * @param[in] flag true or false |
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466 | */ |
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467 | void parallactify(bool flag) |
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468 | { focus().setParallactify(flag); } |
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469 | |
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470 | /** |
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471 | * Reshape spectrum |
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472 | * @param[in] nmin, nmax minimum and maximum channel |
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473 | * @param[in] irow row number |
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474 | * |
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475 | * 30/07/2008 Takeshi Nakazato |
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476 | **/ |
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477 | void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError ); |
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478 | void reshapeSpectrum( int nmin, int nmax, int irow ) ; |
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479 | |
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480 | /** |
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481 | * Change channel number under fixed bandwidth |
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482 | * @param[in] nchan, dnu new channel number and spectral resolution |
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483 | * @param[in] irow row number |
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484 | * |
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485 | * 27/08/2008 Takeshi Nakazato |
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486 | **/ |
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487 | void regridChannel( int nchan, double dnu ) ; |
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488 | void regridChannel( int nchan, double dnu, int irow ) ; |
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489 | |
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490 | bool getFlagtraFast(int whichrow); |
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491 | |
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492 | void polyBaselineBatch(const std::vector<bool>& mask, int order); |
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493 | STFitEntry polyBaseline(const std::vector<bool>& mask, int order, int rowno); |
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494 | |
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495 | private: |
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496 | |
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497 | casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const; |
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498 | |
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499 | /** |
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500 | * Turns a time vale into a formatted string |
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501 | * @param x |
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502 | * @return |
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503 | */ |
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504 | std::string formatSec(casa::Double x) const; |
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505 | |
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506 | std::string formatTime(const casa::MEpoch& me, bool showdate)const; |
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507 | |
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508 | /** |
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509 | * Turns a casa::MDirection into a nicely formatted string |
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510 | * @param md an casa::MDirection |
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511 | * @return |
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512 | */ |
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513 | std::string formatDirection(const casa::MDirection& md) const; |
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514 | |
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515 | /** |
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516 | * Create a unique file name for the paged (temporary) table |
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517 | * @return just the name |
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518 | */ |
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519 | static casa::String generateName(); |
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520 | |
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521 | /** |
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522 | * attach to cached columns |
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523 | */ |
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524 | void attach(); |
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525 | |
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526 | /** |
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527 | * Set up the main casa::Table |
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528 | */ |
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529 | void setupMainTable(); |
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530 | |
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531 | void attachSubtables(); |
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532 | void copySubtables(const Scantable& other); |
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533 | |
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534 | /** |
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535 | * Convert an "old" asap1 style row index into a new index |
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536 | * @param[in] therow |
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537 | * @return and index into @table_ |
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538 | */ |
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539 | int rowToScanIndex(int therow); |
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540 | |
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541 | std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const; |
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542 | |
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543 | static const casa::uInt version_ = 3; |
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544 | |
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545 | STSelector selector_; |
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546 | |
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547 | casa::Table::TableType type_; |
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548 | |
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549 | // the actual data |
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550 | casa::Table table_; |
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551 | casa::Table originalTable_; |
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552 | |
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553 | STTcal tcalTable_; |
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554 | STFrequencies freqTable_; |
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555 | STWeather weatherTable_; |
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556 | STFocus focusTable_; |
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557 | STMolecules moleculeTable_; |
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558 | STHistory historyTable_; |
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559 | STFit fitTable_; |
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560 | |
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561 | // Cached Columns to avoid reconstructing them for each row get/put |
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562 | casa::ScalarColumn<casa::Double> integrCol_; |
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563 | casa::MDirection::ScalarColumn dirCol_; |
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564 | casa::MEpoch::ScalarColumn timeCol_; |
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565 | casa::ScalarColumn<casa::Float> azCol_; |
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566 | casa::ScalarColumn<casa::Float> elCol_; |
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567 | casa::ScalarColumn<casa::String> srcnCol_, fldnCol_; |
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568 | casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_; |
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569 | casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_; |
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570 | casa::ArrayColumn<casa::Float> specCol_, tsysCol_; |
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571 | casa::ArrayColumn<casa::uChar> flagsCol_; |
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572 | |
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573 | // id in frequencies table |
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574 | casa::ScalarColumn<casa::uInt> mfreqidCol_; |
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575 | // id in tcal table |
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576 | casa::ScalarColumn<casa::uInt> mtcalidCol_; |
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577 | |
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578 | casa::ArrayColumn<casa::String> histitemCol_; |
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579 | casa::ScalarColumn<casa::Int> mfitidCol_; |
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580 | casa::ScalarColumn<casa::uInt> mweatheridCol_; |
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581 | |
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582 | casa::ScalarColumn<casa::uInt> mfocusidCol_; |
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583 | |
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584 | casa::ScalarColumn<casa::uInt> mmolidCol_; |
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585 | |
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586 | static std::map<std::string, STPol::STPolFactory *> factories_; |
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587 | void initFactories(); |
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588 | |
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589 | /** |
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590 | * Add an auxiliary column to the main table and attach it to a |
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591 | * cached column. Use for adding new columns that the original asap2 |
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592 | * tables do not have. |
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593 | * @param[in] col reference to the cached column to be attached |
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594 | * @param[in] colName column name in asap table |
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595 | * @param[in] defValue default value to fill in the column |
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596 | * |
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597 | * 25/10/2009 Wataru Kawasaki |
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598 | */ |
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599 | template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&, |
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600 | const casa::String&, |
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601 | const T2&); |
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602 | template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&, |
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603 | const casa::String&, |
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604 | const casa::Array<T2>&); |
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605 | |
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606 | void doPolyBaseline(const std::vector<bool>& mask, int order, int rowno, Fitter& fitter); |
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607 | }; |
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608 | |
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609 | |
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610 | } // namespace |
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611 | |
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612 | #endif |
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