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 <fstream> |
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17 | #include <iostream> |
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18 | #include <sstream> |
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19 | #include <string> |
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20 | #include <vector> |
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21 | // AIPS++ |
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22 | #include <casa/aips.h> |
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23 | #include <casa/Arrays/MaskedArray.h> |
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24 | #include <casa/Arrays/Vector.h> |
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25 | #include <casa/BasicSL/String.h> |
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26 | #include <casa/Containers/Record.h> |
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27 | #include <casa/Exceptions/Error.h> |
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28 | #include <casa/Quanta/Quantum.h> |
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29 | #include <casa/Utilities/CountedPtr.h> |
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30 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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31 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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32 | #include <scimath/Mathematics/FFTServer.h> |
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33 | #include <tables/Tables/ArrayColumn.h> |
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34 | #include <tables/Tables/ScalarColumn.h> |
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35 | #include <tables/Tables/Table.h> |
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36 | |
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37 | #include "MathUtils.h" |
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38 | #include "STBaselineEnum.h" |
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39 | #include "STFit.h" |
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40 | #include "STFitEntry.h" |
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41 | #include "STFocus.h" |
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42 | #include "STFrequencies.h" |
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43 | #include "STHeader.h" |
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44 | #include "STHistory.h" |
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45 | #include "STMolecules.h" |
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46 | #include "STPol.h" |
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47 | #include "STSelector.h" |
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48 | #include "STTcal.h" |
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49 | #include "STWeather.h" |
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50 | |
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51 | namespace asap { |
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52 | |
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53 | class Fitter; |
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54 | class STLineFinder; |
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55 | class STBaselineTable; |
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56 | |
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57 | /** |
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58 | * This class contains and wraps a casa::Table, which is used to store |
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59 | * all the information. This can be either a MemoryTable or a |
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60 | * disk based Table. |
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61 | * It provides access functions to the underlying table |
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62 | * It contains n subtables: |
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63 | * @li weather |
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64 | * @li frequencies |
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65 | * @li molecules |
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66 | * @li tcal |
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67 | * @li focus |
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68 | * @li fits |
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69 | * |
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70 | * @brief The main ASAP data container |
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71 | * @author Malte Marquarding |
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72 | * @date |
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73 | * @version |
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74 | */ |
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75 | class Scantable |
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76 | { |
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77 | |
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78 | friend class STMath; |
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79 | |
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80 | public: |
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81 | /** |
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82 | * Default constructor |
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83 | */ |
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84 | explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory); |
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85 | |
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86 | /** |
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87 | * Create a Scantable object from an existing table on disk |
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88 | * @param[in] name the name of the existing Scantable |
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89 | */ |
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90 | explicit Scantable(const std::string& name, |
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91 | casa::Table::TableType ttype = casa::Table::Memory); |
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92 | |
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93 | /// @fixme this is only sensible for MemoryTables.... |
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94 | Scantable(const Scantable& other, bool clear=true); |
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95 | |
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96 | /** |
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97 | * Destructor |
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98 | */ |
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99 | virtual ~Scantable(); |
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100 | |
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101 | /** |
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102 | * get a const reference to the underlying casa::Table |
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103 | * @return const \ref casa::Table reference |
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104 | */ |
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105 | const casa::Table& table() const; |
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106 | |
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107 | /** |
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108 | * get a reference to the underlying casa::Table with the Selection |
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109 | * object applied if set |
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110 | * @return casa::Table reference |
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111 | */ |
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112 | casa::Table& table(); |
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113 | |
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114 | |
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115 | /** |
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116 | * Get a handle to the selection object |
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117 | * @return constant STSelector reference |
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118 | */ |
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119 | const STSelector& getSelection() const { return selector_; } |
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120 | |
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121 | /** |
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122 | * Set the data to be a subset as defined by the STSelector |
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123 | * @param selection a STSelector object |
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124 | */ |
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125 | void setSelection(const STSelector& selection); |
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126 | |
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127 | /** |
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128 | * unset the selection of the data |
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129 | */ |
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130 | void unsetSelection(); |
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131 | /** |
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132 | * set the header |
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133 | * @param[in] sth an STHeader object |
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134 | */ |
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135 | void setHeader( const STHeader& sth ); |
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136 | |
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137 | /** |
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138 | * get the header information |
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139 | * @return an STHeader object |
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140 | */ |
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141 | STHeader getHeader( ) const; |
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142 | |
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143 | /** |
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144 | * Checks if the "other" Scantable is conformant with this, |
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145 | * i.e. if header values are the same. |
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146 | * @param[in] other another Scantable |
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147 | * @return true or false |
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148 | */ |
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149 | bool conformant( const Scantable& other); |
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150 | |
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151 | /** |
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152 | * |
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153 | * @param stype The type of the source, 0 = on, 1 = off |
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154 | */ |
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155 | void setSourceType(int stype); |
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156 | |
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157 | /** |
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158 | * |
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159 | * @param stype The name of the source |
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160 | */ |
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161 | void setSourceName(const std::string& name); |
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162 | |
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163 | |
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164 | /** |
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165 | * The number of scans in the table |
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166 | * @return number of scans in the table |
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167 | */ |
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168 | int nscan() const; |
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169 | |
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170 | casa::MEpoch::Types getTimeReference() const; |
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171 | |
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172 | |
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173 | casa::MEpoch getEpoch(int whichrow) const; |
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174 | |
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175 | /** |
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176 | * Get global antenna position |
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177 | * @return casa::MPosition |
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178 | */ |
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179 | casa::MPosition getAntennaPosition() const; |
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180 | |
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181 | /** |
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182 | * the @ref casa::MDirection for a specific row |
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183 | * @param[in] whichrow the row number |
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184 | * return casa::MDirection |
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185 | */ |
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186 | casa::MDirection getDirection( int whichrow ) const; |
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187 | |
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188 | /** |
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189 | * get the direction type as a string, e.g. "J2000" |
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190 | * @param[in] whichrow the row number |
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191 | * return the direction string |
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192 | */ |
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193 | std::string getDirectionString( int whichrow ) const; |
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194 | |
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195 | /** |
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196 | * set the direction type as a string, e.g. "J2000" |
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197 | * @param[in] refstr the direction type |
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198 | */ |
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199 | void setDirectionRefString(const std::string& refstr=""); |
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200 | |
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201 | /** |
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202 | * get the direction reference string |
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203 | * @return a string describing the direction reference |
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204 | */ |
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205 | std::string getDirectionRefString() const; |
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206 | |
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207 | /** |
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208 | * Return the Flux unit of the data, e.g. "Jy" or "K" |
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209 | * @return string |
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210 | */ |
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211 | std::string getFluxUnit() const; |
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212 | |
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213 | /** |
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214 | * Set the Flux unit of the data |
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215 | * @param unit a string representing the unit, e.g "Jy" or "K" |
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216 | */ |
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217 | void setFluxUnit( const std::string& unit ); |
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218 | |
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219 | /** |
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220 | * Set the Stokes type of the data |
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221 | * @param feedtype a string representing the type, e.g "circular" or "linear" |
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222 | */ |
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223 | void setFeedType( const std::string& feedtype ); |
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224 | |
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225 | /** |
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226 | * |
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227 | * @param instrument a string representing an insturment. see xxx |
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228 | */ |
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229 | void setInstrument( const std::string& instrument ); |
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230 | |
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231 | /** |
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232 | * (Re)calculate the azimuth and elevationnfor all rows |
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233 | */ |
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234 | void calculateAZEL(); |
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235 | |
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236 | /** |
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237 | * "hard" flag the data, this flags everything selected in setSelection() |
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238 | * param[in] msk a boolean mask of length nchan describing the points to |
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239 | * to be flagged |
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240 | */ |
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241 | //void flag( const std::vector<bool>& msk = std::vector<bool>()); |
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242 | //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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243 | |
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244 | void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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245 | |
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246 | /** |
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247 | * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki) |
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248 | * param[in] rows list of row numbers to be flagged |
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249 | */ |
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250 | void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false); |
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251 | |
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252 | /** |
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253 | * Get flagRow info at the specified row. If true, the whole data |
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254 | * at the row should be flagged. |
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255 | */ |
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256 | bool getFlagRow(int whichrow) const |
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257 | { return (flagrowCol_(whichrow) > 0); } |
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258 | |
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259 | /** |
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260 | * Flag the data outside a specified range (in a channel-based manner). |
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261 | * (CAS-1807 Wataru Kawasaki) |
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262 | */ |
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263 | void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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264 | |
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265 | /** |
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266 | * Return a list of booleans with the size of nchan for a specified row, to get info |
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267 | * about which channel is clipped. |
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268 | */ |
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269 | std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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270 | void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag, |
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271 | casa::Vector<casa::uChar> flgs); |
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272 | |
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273 | /** |
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274 | * Return a list of row numbers with respect to the original table. |
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275 | * @return a list of unsigned ints |
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276 | */ |
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277 | std::vector<unsigned int> rownumbers() const; |
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278 | |
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279 | |
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280 | /** |
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281 | * Get the number of beams in the data or a specific scan |
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282 | * @param scanno the scan number to get the number of beams for. |
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283 | * If scanno<0 the number is retrieved from the header. |
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284 | * @return an integer number |
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285 | */ |
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286 | int nbeam(int scanno=-1) const; |
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287 | /** |
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288 | * Get the number of IFs in the data or a specific scan |
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289 | * @param scanno the scan number to get the number of IFs for. |
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290 | * If scanno<0 the number is retrieved from the header. |
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291 | * @return an integer number |
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292 | */ |
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293 | int nif(int scanno=-1) const; |
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294 | /** |
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295 | * Get the number of polarizations in the data or a specific scan |
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296 | * @param scanno the scan number to get the number of polarizations for. |
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297 | * If scanno<0 the number is retrieved from the header. |
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298 | * @return an integer number |
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299 | */ |
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300 | int npol(int scanno=-1) const; |
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301 | |
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302 | std::string getPolType() const; |
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303 | |
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304 | |
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305 | /** |
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306 | * Get the number of integartion cycles |
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307 | * @param scanno the scan number to get the number of rows for. |
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308 | * If scanno<0 the number is retrieved from the header. |
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309 | * @return the number of rows (for the specified scanno) |
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310 | */ |
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311 | int nrow(int scanno=-1) const; |
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312 | |
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313 | int getBeam(int whichrow) const; |
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314 | std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); } |
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315 | |
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316 | int getIF(int whichrow) const; |
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317 | std::vector<uint> getIFNos() const { return getNumbers(ifCol_); } |
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318 | |
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319 | int getPol(int whichrow) const; |
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320 | std::vector<uint> getPolNos() const { return getNumbers(polCol_); } |
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321 | |
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322 | std::vector<uint> getScanNos() const { return getNumbers(scanCol_); } |
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323 | int getScan(int whichrow) const { return scanCol_(whichrow); } |
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324 | |
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325 | std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); } |
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326 | int getCycle(int whichrow) const { return cycleCol_(whichrow); } |
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327 | |
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328 | //TT addition |
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329 | std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); } |
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330 | |
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331 | /** |
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332 | * Get the number of channels in the data or a specific IF. This currently |
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333 | * varies only with IF number |
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334 | * @param ifno the IF number to get the number of channels for. |
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335 | * If ifno<0 the number is retrieved from the header. |
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336 | * @return an integer number |
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337 | */ |
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338 | int nchan(int ifno=-1) const; |
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339 | int getChannels(int whichrow) const; |
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340 | |
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341 | int ncycle(int scanno=-1) const; |
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342 | |
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343 | |
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344 | double getInterval(int whichrow) const |
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345 | { return integrCol_(whichrow); } |
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346 | |
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347 | float getTsys(int whichrow) const |
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348 | { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); } |
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349 | std::vector<float> getTsysSpectrum(int whichrow) const ; |
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350 | |
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351 | void setTsys(const std::vector<float>& newvals, int whichrow); |
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352 | |
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353 | float getElevation(int whichrow) const |
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354 | { return elCol_(whichrow); } |
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355 | float getAzimuth(int whichrow) const |
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356 | { return azCol_(whichrow); } |
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357 | float getParAngle(int whichrow) const |
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358 | { return focus().getParAngle(mfocusidCol_(whichrow)); } |
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359 | int getTcalId(int whichrow) const |
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360 | { return mtcalidCol_(whichrow); } |
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361 | |
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362 | std::string getSourceName(int whichrow) const |
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363 | { return srcnCol_(whichrow); } |
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364 | |
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365 | std::vector<bool> getMask(int whichrow) const; |
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366 | std::vector<float> getSpectrum(int whichrow, |
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367 | const std::string& poltype = "" ) const; |
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368 | |
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369 | void setSpectrum(const std::vector<float>& spec, int whichrow); |
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370 | |
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371 | std::string getPolarizationLabel(int index, const std::string& ptype) const |
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372 | { return STPol::getPolLabel(index, ptype ); } |
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373 | |
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374 | /** |
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375 | * Write the Scantable to disk |
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376 | * @param filename the output file name |
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377 | */ |
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378 | void makePersistent(const std::string& filename); |
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379 | |
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380 | std::vector<std::string> getHistory(int nrow=-1, int start=0) const |
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381 | { return historyTable_.getHistory(nrow, start); } |
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382 | |
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383 | uint historyLength() |
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384 | { return historyTable_.nrow(); } |
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385 | |
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386 | void dropHistory() { historyTable_.drop(); } |
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387 | |
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388 | void addHistory(const std::string& hist) { historyTable_.addEntry(hist); } |
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389 | |
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390 | void appendToHistoryTable(const STHistory& otherhist) |
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391 | { historyTable_.append(otherhist); } |
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392 | |
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393 | std::string headerSummary(); |
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394 | void summary(const std::string& filename=""); |
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395 | std::string oldheaderSummary(); |
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396 | // std::string summary(); |
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397 | void oldsummary(const std::string& filename=""); |
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398 | |
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399 | //std::string getTime(int whichrow=-1, bool showdate=true) const; |
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400 | std::string getTime(int whichrow=-1, bool showdate=true, |
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401 | casa::uInt prec=0) const; |
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402 | double getIntTime(int whichrow) const { return integrCol_(whichrow); } |
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403 | |
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404 | // returns unit, conversion frame, doppler, base-frame |
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405 | |
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406 | /** |
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407 | * Get the frequency set up |
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408 | * This is forwarded to the STFrequencies subtable |
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409 | * @return unit, frame, doppler |
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410 | */ |
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411 | std::vector<std::string> getCoordInfo() const |
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412 | { return freqTable_.getInfo(); }; |
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413 | |
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414 | void setCoordInfo(std::vector<string> theinfo) |
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415 | { return freqTable_.setInfo(theinfo); }; |
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416 | |
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417 | |
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418 | std::vector<double> getAbcissa(int whichrow) const; |
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419 | |
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420 | std::vector<float> getWeather(int whichrow) const; |
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421 | |
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422 | std::string getAbcissaLabel(int whichrow) const; |
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423 | std::vector<double> getRestFrequencies() const |
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424 | { return moleculeTable_.getRestFrequencies(); } |
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425 | std::vector<double> getRestFrequency(int id) const |
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426 | { return moleculeTable_.getRestFrequency(id); } |
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427 | |
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428 | /** |
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429 | void setRestFrequencies(double rf, const std::string& name = "", |
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430 | const std::string& = "Hz"); |
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431 | **/ |
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432 | // Modified by Takeshi Nakazato 05/09/2008 |
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433 | /*** |
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434 | void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "", |
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435 | const std::string& = "Hz"); |
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436 | ***/ |
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437 | void setRestFrequencies(vector<double> rf, |
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438 | const vector<std::string>& name = vector<std::string>(1,""), |
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439 | const std::string& = "Hz"); |
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440 | |
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441 | //void setRestFrequencies(const std::string& name); |
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442 | void setRestFrequencies(const vector<std::string>& name); |
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443 | |
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444 | void shift(int npix); |
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445 | |
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446 | casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const; |
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447 | |
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448 | void convertDirection(const std::string& newframe); |
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449 | |
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450 | STFrequencies& frequencies() { return freqTable_; } |
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451 | const STFrequencies& frequencies() const { return freqTable_; } |
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452 | STWeather& weather() { return weatherTable_; } |
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453 | const STWeather& weather() const { return weatherTable_; } |
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454 | STFocus& focus() { return focusTable_; } |
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455 | const STFocus& focus() const { return focusTable_; } |
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456 | STTcal& tcal() { return tcalTable_; } |
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457 | const STTcal& tcal() const { return tcalTable_; } |
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458 | STMolecules& molecules() { return moleculeTable_; } |
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459 | const STMolecules& molecules() const { return moleculeTable_; } |
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460 | STHistory& history() { return historyTable_; } |
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461 | const STHistory& history() const { return historyTable_; } |
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462 | STFit& fit() { return fitTable_; } |
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463 | const STFit& fit() const { return fitTable_; } |
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464 | |
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465 | std::vector<std::string> columnNames() const; |
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466 | |
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467 | void addFit(const STFitEntry& fit, int row); |
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468 | STFitEntry getFit(int row) const |
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469 | { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; } |
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470 | |
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471 | //Added by TT |
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472 | /** |
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473 | * Get the antenna name |
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474 | * @return antenna name string |
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475 | */ |
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476 | casa::String getAntennaName() const; |
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477 | |
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478 | /** |
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479 | * For GBT MS data only. check a scan list |
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480 | * against the information found in GBT_GO table for |
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481 | * scan number orders to get correct pairs. |
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482 | * @param[in] scan list |
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483 | * @return status |
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484 | */ |
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485 | int checkScanInfo(const std::vector<int>& scanlist) const; |
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486 | |
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487 | /** |
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488 | * Get the direction as a vector, for a specific row |
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489 | * @param[in] whichrow the row numbyyer |
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490 | * @return the direction in a vector |
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491 | */ |
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492 | std::vector<double> getDirectionVector(int whichrow) const; |
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493 | |
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494 | /** |
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495 | * Set a flag indicating whether the data was parallactified |
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496 | * @param[in] flag true or false |
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497 | */ |
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498 | void parallactify(bool flag) |
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499 | { focusTable_.setParallactify(flag); } |
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500 | |
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501 | /** |
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502 | * Reshape spectrum |
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503 | * @param[in] nmin, nmax minimum and maximum channel |
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504 | * @param[in] irow row number |
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505 | * |
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506 | * 30/07/2008 Takeshi Nakazato |
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507 | **/ |
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508 | void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError ); |
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509 | void reshapeSpectrum( int nmin, int nmax, int irow ) ; |
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510 | |
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511 | /** |
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512 | * Change channel number under fixed bandwidth |
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513 | * @param[in] nchan, dnu new channel number and spectral resolution |
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514 | * @param[in] irow row number |
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515 | * |
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516 | * 27/08/2008 Takeshi Nakazato |
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517 | **/ |
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518 | void regridChannel( int nchan, double dnu ) ; |
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519 | void regridChannel( int nchan, double dnu, int irow ) ; |
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520 | void regridChannel( int nchan, double dnu, double fmin, int irow ) ; |
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521 | void regridSpecChannel( double dnu, int nchan=-1 ) ; |
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522 | |
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523 | bool isAllChannelsFlagged(casa::uInt whichrow); |
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524 | |
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525 | std::vector<std::string> applyBaselineTable(const std::string& bltable, |
---|
526 | const bool returnfitresult, |
---|
527 | const std::string& outbltable, |
---|
528 | const bool outbltableexists, |
---|
529 | const bool overwrite); |
---|
530 | std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, |
---|
531 | const bool returnfitresult, |
---|
532 | const std::string& outbltable, |
---|
533 | const bool outbltableexists, |
---|
534 | const bool overwrite); |
---|
535 | void polyBaseline(const std::vector<bool>& mask, |
---|
536 | int order, |
---|
537 | float thresClip, |
---|
538 | int nIterClip, |
---|
539 | bool getResidual=true, |
---|
540 | const std::string& progressInfo="true,1000", |
---|
541 | const bool outLogger=false, |
---|
542 | const std::string& blfile="", |
---|
543 | const std::string& bltable=""); |
---|
544 | void autoPolyBaseline(const std::vector<bool>& mask, |
---|
545 | int order, |
---|
546 | float thresClip, |
---|
547 | int nIterClip, |
---|
548 | const std::vector<int>& edge, |
---|
549 | float threshold=3.0, |
---|
550 | int chanAvgLimit=1, |
---|
551 | bool getResidual=true, |
---|
552 | const std::string& progressInfo="true,1000", |
---|
553 | const bool outLogger=false, |
---|
554 | const std::string& blfile="", |
---|
555 | const std::string& bltable=""); |
---|
556 | void chebyshevBaseline(const std::vector<bool>& mask, |
---|
557 | int order, |
---|
558 | float thresClip, |
---|
559 | int nIterClip, |
---|
560 | bool getResidual=true, |
---|
561 | const std::string& progressInfo="true,1000", |
---|
562 | const bool outLogger=false, |
---|
563 | const std::string& blfile="", |
---|
564 | const std::string& bltable=""); |
---|
565 | void autoChebyshevBaseline(const std::vector<bool>& mask, |
---|
566 | int order, |
---|
567 | float thresClip, |
---|
568 | int nIterClip, |
---|
569 | const std::vector<int>& edge, |
---|
570 | float threshold=3.0, |
---|
571 | int chanAvgLimit=1, |
---|
572 | bool getResidual=true, |
---|
573 | const std::string& progressInfo="true,1000", |
---|
574 | const bool outLogger=false, |
---|
575 | const std::string& blfile="", |
---|
576 | const std::string& bltable=""); |
---|
577 | void cubicSplineBaseline(const std::vector<bool>& mask, |
---|
578 | int nPiece, |
---|
579 | float thresClip, |
---|
580 | int nIterClip, |
---|
581 | bool getResidual=true, |
---|
582 | const std::string& progressInfo="true,1000", |
---|
583 | const bool outLogger=false, |
---|
584 | const std::string& blfile="", |
---|
585 | const std::string& bltable=""); |
---|
586 | void autoCubicSplineBaseline(const std::vector<bool>& mask, |
---|
587 | int nPiece, |
---|
588 | float thresClip, |
---|
589 | int nIterClip, |
---|
590 | const std::vector<int>& edge, |
---|
591 | float threshold=3.0, |
---|
592 | int chanAvgLimit=1, |
---|
593 | bool getResidual=true, |
---|
594 | const std::string& progressInfo="true,1000", |
---|
595 | const bool outLogger=false, |
---|
596 | const std::string& blfile="", |
---|
597 | const std::string& bltable=""); |
---|
598 | void sinusoidBaseline(const std::vector<bool>& mask, |
---|
599 | const std::string& fftInfo, |
---|
600 | const std::vector<int>& addNWaves, |
---|
601 | const std::vector<int>& rejectNWaves, |
---|
602 | float thresClip, |
---|
603 | int nIterClip, |
---|
604 | bool getResidual=true, |
---|
605 | const std::string& progressInfo="true,1000", |
---|
606 | const bool outLogger=false, |
---|
607 | const std::string& blfile="", |
---|
608 | const std::string& bltable=""); |
---|
609 | void autoSinusoidBaseline(const std::vector<bool>& mask, |
---|
610 | const std::string& fftInfo, |
---|
611 | const std::vector<int>& addNWaves, |
---|
612 | const std::vector<int>& rejectNWaves, |
---|
613 | float thresClip, |
---|
614 | int nIterClip, |
---|
615 | const std::vector<int>& edge, |
---|
616 | float threshold=3.0, |
---|
617 | int chanAvgLimit=1, |
---|
618 | bool getResidual=true, |
---|
619 | const std::string& progressInfo="true,1000", |
---|
620 | const bool outLogger=false, |
---|
621 | const std::string& blfile="", |
---|
622 | const std::string& bltable=""); |
---|
623 | std::vector<float> execFFT(const int whichrow, |
---|
624 | const std::vector<bool>& inMask, |
---|
625 | bool getRealImag=false, |
---|
626 | bool getAmplitudeOnly=false); |
---|
627 | float getRms(const std::vector<bool>& mask, int whichrow); |
---|
628 | std::string formatBaselineParams(const std::vector<float>& params, |
---|
629 | const std::vector<bool>& fixed, |
---|
630 | float rms, |
---|
631 | int nClipped, |
---|
632 | const std::string& masklist, |
---|
633 | int whichrow, |
---|
634 | bool verbose=false, |
---|
635 | bool csvformat=false, |
---|
636 | int start=-1, |
---|
637 | int count=-1, |
---|
638 | bool resetparamid=false) const; |
---|
639 | std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges, |
---|
640 | const std::vector<float>& params, |
---|
641 | const std::vector<bool>& fixed, |
---|
642 | float rms, |
---|
643 | int nClipped, |
---|
644 | const std::string& masklist, |
---|
645 | int whichrow, |
---|
646 | bool verbose=false, |
---|
647 | bool csvformat=false) const; |
---|
648 | std::vector<uint> getMoleculeIdColumnData() const; |
---|
649 | void setMoleculeIdColumnData(const std::vector<uint>& molids); |
---|
650 | |
---|
651 | /** |
---|
652 | * Get row idx of root table |
---|
653 | **/ |
---|
654 | std::vector<uint> getRootTableRowNumbers() const; |
---|
655 | |
---|
656 | double calculateModelSelectionCriteria(const std::string& valname, |
---|
657 | const std::string& blfunc, |
---|
658 | int order, |
---|
659 | const std::vector<bool>& inMask, |
---|
660 | int whichrow, |
---|
661 | bool useLineFinder, |
---|
662 | const std::vector<int>& edge, |
---|
663 | float threshold, |
---|
664 | int chanAvgLimit); |
---|
665 | static std::vector<bool> getMaskFromMaskList(const int nchan, |
---|
666 | const std::vector<int>& masklist); |
---|
667 | static casa::Vector<casa::uInt> getMaskListFromMask( |
---|
668 | const std::vector<bool>& mask); |
---|
669 | static std::vector<int> splitToIntList(const std::string& str, |
---|
670 | const char delim); |
---|
671 | static std::vector<string> splitToStringList(const std::string& str, |
---|
672 | const char delim); |
---|
673 | |
---|
674 | void dropXPol(); |
---|
675 | |
---|
676 | private: |
---|
677 | |
---|
678 | casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const; |
---|
679 | |
---|
680 | /** |
---|
681 | * Turns a time value into a formatted string |
---|
682 | * @param x |
---|
683 | * @return |
---|
684 | */ |
---|
685 | std::string formatSec(casa::Double x) const; |
---|
686 | |
---|
687 | std::string formatTime(const casa::MEpoch& me, bool showdate)const; |
---|
688 | std::string formatTime(const casa::MEpoch& me, bool showdate, |
---|
689 | casa::uInt prec)const; |
---|
690 | |
---|
691 | /** |
---|
692 | * Turns a casa::MDirection into a nicely formatted string |
---|
693 | * @param md an casa::MDirection |
---|
694 | * @param prec output precision of direction |
---|
695 | * @return |
---|
696 | */ |
---|
697 | std::string formatDirection(const casa::MDirection& md, casa::Int prec=7) const; |
---|
698 | |
---|
699 | /** |
---|
700 | * Create a unique file name for the paged (temporary) table |
---|
701 | * @return just the name |
---|
702 | */ |
---|
703 | static casa::String generateName(); |
---|
704 | |
---|
705 | /** |
---|
706 | * attach to cached columns |
---|
707 | */ |
---|
708 | void attach(); |
---|
709 | |
---|
710 | /** |
---|
711 | * Set up the main casa::Table |
---|
712 | */ |
---|
713 | void setupMainTable(); |
---|
714 | |
---|
715 | void attachSubtables(); |
---|
716 | void copySubtables(const Scantable& other); |
---|
717 | |
---|
718 | /** |
---|
719 | * Convert an "old" asap1 style row index into a new index |
---|
720 | * @param[in] therow |
---|
721 | * @return and index into @table_ |
---|
722 | */ |
---|
723 | int rowToScanIndex(int therow); |
---|
724 | |
---|
725 | std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const; |
---|
726 | |
---|
727 | static const casa::uInt version_ = 4; |
---|
728 | |
---|
729 | STSelector selector_; |
---|
730 | |
---|
731 | casa::Table::TableType type_; |
---|
732 | |
---|
733 | // the actual data |
---|
734 | casa::Table table_; |
---|
735 | casa::Table originalTable_; |
---|
736 | |
---|
737 | STTcal tcalTable_; |
---|
738 | STFrequencies freqTable_; |
---|
739 | STWeather weatherTable_; |
---|
740 | STFocus focusTable_; |
---|
741 | STMolecules moleculeTable_; |
---|
742 | STHistory historyTable_; |
---|
743 | STFit fitTable_; |
---|
744 | |
---|
745 | // Cached Columns to avoid reconstructing them for each row get/put |
---|
746 | casa::ScalarColumn<casa::Double> integrCol_; |
---|
747 | casa::MDirection::ScalarColumn dirCol_; |
---|
748 | casa::MEpoch::ScalarColumn timeCol_; |
---|
749 | casa::ScalarColumn<casa::Float> azCol_; |
---|
750 | casa::ScalarColumn<casa::Float> elCol_; |
---|
751 | casa::ScalarColumn<casa::String> srcnCol_, fldnCol_; |
---|
752 | casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_; |
---|
753 | casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_; |
---|
754 | casa::ArrayColumn<casa::Float> specCol_, tsysCol_; |
---|
755 | casa::ArrayColumn<casa::uChar> flagsCol_; |
---|
756 | |
---|
757 | // id in frequencies table |
---|
758 | casa::ScalarColumn<casa::uInt> mfreqidCol_; |
---|
759 | // id in tcal table |
---|
760 | casa::ScalarColumn<casa::uInt> mtcalidCol_; |
---|
761 | |
---|
762 | casa::ArrayColumn<casa::String> histitemCol_; |
---|
763 | casa::ScalarColumn<casa::Int> mfitidCol_; |
---|
764 | casa::ScalarColumn<casa::uInt> mweatheridCol_; |
---|
765 | |
---|
766 | casa::ScalarColumn<casa::uInt> mfocusidCol_; |
---|
767 | |
---|
768 | casa::ScalarColumn<casa::uInt> mmolidCol_; |
---|
769 | |
---|
770 | static std::map<std::string, STPol::STPolFactory *> factories_; |
---|
771 | void initFactories(); |
---|
772 | |
---|
773 | /** |
---|
774 | * Add an auxiliary column to the main table and attach it to a |
---|
775 | * cached column. Use for adding new columns that the original asap2 |
---|
776 | * tables do not have. |
---|
777 | * @param[in] col reference to the cached column to be attached |
---|
778 | * @param[in] colName column name in asap table |
---|
779 | * @param[in] defValue default value to fill in the column |
---|
780 | * |
---|
781 | * 25/10/2009 Wataru Kawasaki |
---|
782 | */ |
---|
783 | template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&, |
---|
784 | const casa::String&, |
---|
785 | const T2&); |
---|
786 | template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&, |
---|
787 | const casa::String&, |
---|
788 | const casa::Array<T2>&); |
---|
789 | |
---|
790 | double getNormalPolynomial(int n, double x); |
---|
791 | double getChebyshevPolynomial(int n, double x); |
---|
792 | std::vector<std::vector<double> > getPolynomialModel(int order, |
---|
793 | int nchan, |
---|
794 | double (Scantable::*pfunc)(int, double)); |
---|
795 | std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order, |
---|
796 | double (Scantable::*pfunc)(int, double), |
---|
797 | std::vector<int>& nChanNos); |
---|
798 | std::vector<float> doPolynomialFitting(const std::vector<float>& data, |
---|
799 | const std::vector<bool>& mask, |
---|
800 | int order, |
---|
801 | std::vector<float>& params, |
---|
802 | float& rms, |
---|
803 | std::vector<bool>& finalMask, |
---|
804 | float clipth, |
---|
805 | int clipn); |
---|
806 | std::vector<float> doPolynomialFitting(const std::vector<float>& data, |
---|
807 | const std::vector<bool>& mask, |
---|
808 | int order, |
---|
809 | std::vector<float>& params, |
---|
810 | float& rms, |
---|
811 | std::vector<bool>& finalMask, |
---|
812 | int& nClipped, |
---|
813 | float thresClip=3.0, |
---|
814 | int nIterClip=0, |
---|
815 | bool getResidual=true); |
---|
816 | std::vector<float> doChebyshevFitting(const std::vector<float>& data, |
---|
817 | const std::vector<bool>& mask, |
---|
818 | int order, |
---|
819 | std::vector<float>& params, |
---|
820 | float& rms, |
---|
821 | std::vector<bool>& finalMask, |
---|
822 | float clipth, |
---|
823 | int clipn); |
---|
824 | std::vector<float> doChebyshevFitting(const std::vector<float>& data, |
---|
825 | const std::vector<bool>& mask, |
---|
826 | int order, |
---|
827 | std::vector<float>& params, |
---|
828 | float& rms, |
---|
829 | std::vector<bool>& finalMask, |
---|
830 | int& nClipped, |
---|
831 | float thresClip=3.0, |
---|
832 | int nIterClip=0, |
---|
833 | bool getResidual=true); |
---|
834 | std::vector<float> doLeastSquareFitting(const std::vector<float>& data, |
---|
835 | const std::vector<bool>& mask, |
---|
836 | const std::vector<std::vector<double> >& model, |
---|
837 | std::vector<float>& params, |
---|
838 | float& rms, |
---|
839 | std::vector<bool>& finalMask, |
---|
840 | int& nClipped, |
---|
841 | float thresClip=3.0, |
---|
842 | int nIterClip=0, |
---|
843 | bool getResidual=true); |
---|
844 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
845 | const std::vector<bool>& mask, |
---|
846 | std::vector<int>& idxEdge, |
---|
847 | std::vector<float>& params, |
---|
848 | float& rms, |
---|
849 | std::vector<bool>& finalMask, |
---|
850 | float clipth, |
---|
851 | int clipn); |
---|
852 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
853 | const std::vector<bool>& mask, |
---|
854 | int nPiece, |
---|
855 | std::vector<int>& idxEdge, |
---|
856 | std::vector<float>& params, |
---|
857 | float& rms, |
---|
858 | std::vector<bool>& finalMask, |
---|
859 | float clipth, |
---|
860 | int clipn); |
---|
861 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
862 | const std::vector<bool>& mask, |
---|
863 | int nPiece, |
---|
864 | bool useGivenPieceBoundary, |
---|
865 | std::vector<int>& idxEdge, |
---|
866 | std::vector<float>& params, |
---|
867 | float& rms, |
---|
868 | std::vector<bool>& finalMask, |
---|
869 | int& nClipped, |
---|
870 | float thresClip=3.0, |
---|
871 | int nIterClip=0, |
---|
872 | bool getResidual=true); |
---|
873 | std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data, |
---|
874 | const std::vector<bool>& mask, |
---|
875 | const std::vector<std::vector<double> >& model, |
---|
876 | int nPiece, |
---|
877 | bool useGivenPieceBoundary, |
---|
878 | std::vector<int>& idxEdge, |
---|
879 | std::vector<float>& params, |
---|
880 | float& rms, |
---|
881 | std::vector<bool>& finalMask, |
---|
882 | int& nClipped, |
---|
883 | float thresClip=3.0, |
---|
884 | int nIterClip=0, |
---|
885 | bool getResidual=true); |
---|
886 | std::vector<float> doSinusoidFitting(const std::vector<float>& data, |
---|
887 | const std::vector<bool>& mask, |
---|
888 | const std::vector<int>& waveNumbers, |
---|
889 | std::vector<float>& params, |
---|
890 | float& rms, |
---|
891 | std::vector<bool>& finalMask, |
---|
892 | float clipth, |
---|
893 | int clipn); |
---|
894 | std::vector<float> doSinusoidFitting(const std::vector<float>& data, |
---|
895 | const std::vector<bool>& mask, |
---|
896 | const std::vector<int>& waveNumbers, |
---|
897 | std::vector<float>& params, |
---|
898 | float& rms, |
---|
899 | std::vector<bool>& finalMask, |
---|
900 | int& nClipped, |
---|
901 | float thresClip=3.0, |
---|
902 | int nIterClip=0, |
---|
903 | bool getResidual=true); |
---|
904 | std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan); |
---|
905 | std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers, |
---|
906 | std::vector<int>& nChanNos); |
---|
907 | std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves, |
---|
908 | const std::vector<int>& rejectNWaves); |
---|
909 | std::vector<int> selectWaveNumbers(const int whichrow, |
---|
910 | const std::vector<bool>& chanMask, |
---|
911 | //const std::string& fftInfo, |
---|
912 | const bool applyFFT, |
---|
913 | const std::string& fftMethod, |
---|
914 | const std::string& fftThresh, |
---|
915 | const std::vector<int>& addNWaves, |
---|
916 | const std::vector<int>& rejectNWaves); |
---|
917 | int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos); |
---|
918 | void parseFFTInfo(const std::string& fftInfo, |
---|
919 | bool& applyFFT, |
---|
920 | std::string& fftMethod, |
---|
921 | std::string& fftThresh); |
---|
922 | void parseFFTThresholdInfo(const std::string& fftThresh, |
---|
923 | std::string& fftThAttr, |
---|
924 | float& fftThSigma, |
---|
925 | int& fftThTop); |
---|
926 | void doSelectWaveNumbers(const int whichrow, |
---|
927 | const std::vector<bool>& chanMask, |
---|
928 | const std::string& fftMethod, |
---|
929 | const float fftThSigma, |
---|
930 | const int fftThTop, |
---|
931 | const std::string& fftThAttr, |
---|
932 | std::vector<int>& nWaves); |
---|
933 | void addAuxWaveNumbers(const int whichrow, |
---|
934 | const std::vector<int>& addNWaves, |
---|
935 | const std::vector<int>& rejectNWaves, |
---|
936 | std::vector<int>& nWaves); |
---|
937 | void setWaveNumberListUptoNyquistFreq(const int whichrow, |
---|
938 | std::vector<int>& nWaves); |
---|
939 | void initialiseBaselining(const std::string& blfile, |
---|
940 | std::ofstream& ofs, |
---|
941 | const bool outLogger, |
---|
942 | bool& outTextFile, |
---|
943 | bool& csvFormat, |
---|
944 | casa::String& coordInfo, |
---|
945 | bool& hasSameNchan, |
---|
946 | const std::string& progressInfo, |
---|
947 | bool& showProgress, |
---|
948 | int& minNRow, |
---|
949 | casa::Vector<casa::Double>& timeSecCol); |
---|
950 | void finaliseBaselining(const bool outBaselineTable, |
---|
951 | STBaselineTable* pbt, |
---|
952 | const string& bltable, |
---|
953 | const bool outTextFile, |
---|
954 | std::ofstream& ofs); |
---|
955 | void initLineFinder(const std::vector<int>& edge, |
---|
956 | const float threshold, |
---|
957 | const int chanAvgLimit, |
---|
958 | STLineFinder& lineFinder); |
---|
959 | bool hasSameNchanOverIFs(); |
---|
960 | std::string getMaskRangeList(const std::vector<bool>& mask, |
---|
961 | int whichrow, |
---|
962 | const casa::String& coordInfo, |
---|
963 | bool hasSameNchan, |
---|
964 | bool verbose=false); |
---|
965 | std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask); |
---|
966 | std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const; |
---|
967 | std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const; |
---|
968 | std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask); |
---|
969 | std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder); |
---|
970 | void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped); |
---|
971 | void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped); |
---|
972 | void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow); |
---|
973 | void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000); |
---|
974 | |
---|
975 | void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval); |
---|
976 | |
---|
977 | double doCalculateModelSelectionCriteria(const std::string& valname, |
---|
978 | const std::vector<float>& spec, |
---|
979 | const std::vector<bool>& mask, |
---|
980 | const std::string& blfunc, |
---|
981 | int order); |
---|
982 | double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec); |
---|
983 | std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms); |
---|
984 | void parseBlInfo(const std::string& blInfo, int& whichrow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF); |
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985 | std::vector<float> doApplyBaselineTable(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms); |
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986 | std::vector<float> doSubtractBaseline(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, std::vector<bool>& finalmask, float clipth, int clipn, bool uself, int irow, float lfth, std::vector<int>& lfedge, int lfavg); |
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987 | |
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988 | }; |
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989 | } // namespace |
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990 | |
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991 | #endif |
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