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