1 | // |
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2 | // C++ Interface: STMath |
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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) 2006 |
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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 ASAPSTMATH_H |
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13 | #define ASAPSTMATH_H |
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14 | |
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15 | #include <string> |
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16 | #include <map> |
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17 | |
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18 | #include <casa/aips.h> |
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19 | #include <casa/Utilities/CountedPtr.h> |
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20 | #include <casa/BasicSL/String.h> |
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21 | #include <casa/Arrays/Vector.h> |
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22 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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23 | |
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24 | #include "Scantable.h" |
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25 | #include "STDefs.h" |
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26 | #include "STPol.h" |
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27 | #include "Logger.h" |
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28 | |
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29 | namespace asap { |
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30 | |
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31 | /** |
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32 | * Mathmatical operations on Scantable objects |
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33 | * @author Malte Marquarding |
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34 | */ |
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35 | class STMath : private Logger { |
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36 | public: |
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37 | // typedef for long method name |
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38 | typedef casa::InterpolateArray1D<casa::Double, |
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39 | casa::Float>::InterpolationMethod imethod; |
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40 | |
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41 | // typedef for std::map |
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42 | typedef std::map<std::string, imethod> imap; |
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43 | |
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44 | /** |
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45 | * whether to operate on the given Scantable or return a new one |
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46 | * @param insitu the toggle for this behaviour |
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47 | */ |
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48 | explicit STMath(bool insitu=true); |
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49 | |
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50 | virtual ~STMath(); |
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51 | |
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52 | /** |
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53 | * get the currnt @attr inistu_ state |
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54 | */ |
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55 | bool insitu() const { return insitu_;}; |
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56 | |
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57 | /** |
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58 | * set the currnt @attr inistu state |
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59 | * @param b the new state |
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60 | */ |
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61 | void setInsitu(bool b) { insitu_ = b; }; |
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62 | |
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63 | |
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64 | /** |
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65 | * average a vector of Scantables |
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66 | * @param in the vector of Scantables to average |
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67 | * @param mask an optional mask to apply on specific weights |
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68 | * @param weight weighting scheme |
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69 | * @param avmode the mode ov averaging. Per "SCAN" or "ALL". |
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70 | * @return a casa::CountedPtr<Scantable> which either holds a new Scantable |
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71 | * or returns the imput pointer. |
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72 | */ |
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73 | casa::CountedPtr<Scantable> |
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74 | average( const std::vector<casa::CountedPtr<Scantable> >& in, |
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75 | const std::vector<bool>& mask = std::vector<bool>(), |
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76 | const std::string& weight = "NONE", |
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77 | const std::string& avmode = "SCAN"); |
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78 | |
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79 | /** |
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80 | * median average a vector of Scantables. See also STMath::average |
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81 | * @param in the Scantable to average |
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82 | * @param mode the averaging mode. Currently only "MEDIAN" |
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83 | * @param avmode the mode ov averaging. Per "SCAN" or "ALL". |
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84 | * @return a casa::CountedPtr<Scantable> which either holds a new Scantable |
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85 | * or returns the imput pointer. |
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86 | */ |
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87 | casa::CountedPtr<Scantable> |
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88 | averageChannel( const casa::CountedPtr<Scantable> & in, |
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89 | const std::string& mode = "MEDIAN", |
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90 | const std::string& avmode = "SCAN"); |
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91 | |
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92 | /** |
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93 | * Average polarisations together. really only useful if only linears are |
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94 | * available. |
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95 | * @param in the input Scantable |
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96 | * @param mask an optional mask if weight allows one |
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97 | * @param weight weighting scheme |
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98 | * @return |
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99 | */ |
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100 | casa::CountedPtr< Scantable > |
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101 | averagePolarisations( const casa::CountedPtr< Scantable > & in, |
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102 | const std::vector<bool>& mask, |
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103 | const std::string& weight ); |
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104 | |
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105 | /** |
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106 | * Average beams together. |
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107 | * @param in the input Scantable |
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108 | * @param mask an optional mask if weight allows one |
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109 | * @param weight weighting scheme |
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110 | * @return |
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111 | */ |
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112 | casa::CountedPtr< Scantable > |
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113 | averageBeams( const casa::CountedPtr< Scantable > & in, |
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114 | const std::vector<bool>& mask, |
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115 | const std::string& weight ); |
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116 | |
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117 | casa::CountedPtr<Scantable> |
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118 | unaryOperate( const casa::CountedPtr<Scantable>& in, float val, |
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119 | const std::string& mode, bool tsys=false ); |
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120 | |
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121 | // array operation |
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122 | casa::CountedPtr<Scantable> |
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123 | arrayOperate( const casa::CountedPtr<Scantable>& in, |
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124 | const std::vector<float> val, |
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125 | const std::string& mode, |
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126 | const std::string& opmode="channel", |
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127 | bool tsys=false ); |
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128 | |
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129 | // channel operation |
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130 | casa::CountedPtr<Scantable> |
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131 | arrayOperateChannel( const casa::CountedPtr<Scantable>& in, |
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132 | const std::vector<float> val, |
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133 | const std::string& mode, bool tsys=false ); |
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134 | |
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135 | // row operation |
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136 | casa::CountedPtr<Scantable> |
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137 | arrayOperateRow( const casa::CountedPtr<Scantable>& in, |
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138 | const std::vector<float> val, |
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139 | const std::string& mode, bool tsys=false ); |
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140 | |
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141 | // 2d array operation |
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142 | casa::CountedPtr<Scantable> |
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143 | array2dOperate( const casa::CountedPtr<Scantable>& in, |
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144 | const std::vector< std::vector<float> > val, |
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145 | const std::string& mode, bool tsys=false ); |
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146 | |
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147 | casa::CountedPtr<Scantable> |
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148 | binaryOperate( const casa::CountedPtr<Scantable>& left, |
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149 | const casa::CountedPtr<Scantable>& right, |
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150 | const std::string& mode); |
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151 | |
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152 | casa::CountedPtr<Scantable> autoQuotient(const casa::CountedPtr<Scantable>& in, |
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153 | const std::string& mode = "NEAREST", |
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154 | bool preserve = true); |
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155 | |
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156 | casa::CountedPtr<Scantable> quotient( const casa::CountedPtr<Scantable>& on, |
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157 | const casa::CountedPtr<Scantable>& off, |
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158 | bool preserve = true ); |
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159 | |
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160 | /** |
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161 | * Calibrate total power scans (translated from GBTIDL) |
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162 | * @param calon uncalibrated Scantable with CAL noise signal |
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163 | * @param caloff uncalibrated Scantable with no CAL signal |
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164 | * @param tcal optional scalar Tcal, CAL temperature (K) |
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165 | * @return casa::CountedPtr<Scantable> which holds a calibrated Scantable |
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166 | * (spectrum - average of the two CAL on and off spectra; |
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167 | * tsys - mean Tsys = <caloff>*Tcal/<calon-caloff> + Tcal/2) |
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168 | */ |
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169 | casa::CountedPtr<Scantable> dototalpower( const casa::CountedPtr<Scantable>& calon, |
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170 | const casa::CountedPtr<Scantable>& caloff, |
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171 | casa::Float tcal=1.0 ); |
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172 | |
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173 | /** |
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174 | * Combine signal and reference scans (translated from GBTIDL) |
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175 | * @param sig Scantable which contains signal scans |
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176 | * @param ref Scantable which contains reference scans |
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177 | * @param smoothref optional Boxcar smooth width of the reference scans |
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178 | * default: no smoothing (=1) |
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179 | * @param tsysv optional scalar Tsys value at the zenith, required to |
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180 | * set tau, as well |
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181 | * @param tau optional scalar Tau value |
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182 | * @return casa::CountedPtr<Scantable> which holds combined scans |
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183 | * (spectrum = (sig-ref)/ref * Tsys ) |
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184 | */ |
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185 | casa::CountedPtr<Scantable> dosigref( const casa::CountedPtr<Scantable>& sig, |
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186 | const casa::CountedPtr<Scantable>& ref, |
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187 | int smoothref=1, |
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188 | casa::Float tsysv=0.0, |
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189 | casa::Float tau=0.0 ); |
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190 | |
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191 | /** |
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192 | * Calibrate GBT Nod scan pairs (translated from GBTIDL) |
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193 | * @param s Scantable which contains Nod scans |
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194 | * @param scans Vector of scan numbers |
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195 | * @param smoothref optional Boxcar smooth width of the reference scans |
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196 | * @param tsysv optional scalar Tsys value at the zenith, required to |
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197 | * set tau, as well |
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198 | * @param tau optional scalar Tau value |
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199 | * @param tcal optional scalar Tcal, CAL temperature (K) |
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200 | * @return casa::CountedPtr<Scantable> which holds calibrated scans |
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201 | */ |
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202 | casa::CountedPtr<Scantable> donod( const casa::CountedPtr<Scantable>& s, |
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203 | const std::vector<int>& scans, |
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204 | int smoothref=1, |
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205 | casa::Float tsysv=0.0, |
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206 | casa::Float tau=0.0, |
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207 | casa::Float tcal=0.0 ); |
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208 | |
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209 | /** |
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210 | * Calibrate frequency switched scans (translated from GBTIDL) |
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211 | * @param s Scantable which contains frequency switched scans |
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212 | * @param scans Vector of scan numbers |
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213 | * @param smoothref optional Boxcar smooth width of the reference scans |
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214 | * @param tsysv optional scalar Tsys value at the zenith, required to |
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215 | * set tau, as well |
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216 | * @param tau optional scalar Tau value |
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217 | * @param tcal optional scalar Tcal, CAL temperature (K) |
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218 | * @return casa::CountedPtr<Scantable> which holds calibrated scans |
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219 | */ |
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220 | casa::CountedPtr<Scantable> dofs( const casa::CountedPtr<Scantable>& s, |
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221 | const std::vector<int>& scans, |
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222 | int smoothref=1, |
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223 | casa::Float tsysv=0.0, |
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224 | casa::Float tau=0.0, |
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225 | casa::Float tcal=0.0 ); |
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226 | |
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227 | /** |
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228 | * Calibrate data with Chopper-Wheel like calibration method |
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229 | * which adopts position switching by antenna motion, |
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230 | * wobbler (nutator) switching and On-The-Fly observation. |
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231 | * |
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232 | * The method is applicable to APEX, and other telescopes other than GBT. |
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233 | * |
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234 | * @param a Scantable which contains ON and OFF scans |
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235 | * @param a string that indicates calibration mode |
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236 | * @param a string that indicates antenna name |
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237 | **/ |
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238 | casa::CountedPtr<Scantable> cwcal( const casa::CountedPtr<Scantable>& s, |
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239 | const casa::String calmode, |
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240 | const casa::String antname ); |
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241 | |
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242 | /** |
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243 | * Calibrate frequency switched scans with Chopper-Wheel like |
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244 | * calibration method. |
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245 | * |
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246 | * The method is applicable to APEX, and other telescopes other than GBT. |
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247 | * |
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248 | * @param a Scantable which contains ON and OFF scans |
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249 | * @param a string that indicates antenna name |
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250 | **/ |
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251 | casa::CountedPtr<Scantable> cwcalfs( const casa::CountedPtr<Scantable>& s, |
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252 | const casa::String antname ); |
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253 | |
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254 | |
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255 | /** |
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256 | * Folding frequency-switch data |
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257 | * @param sig |
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258 | * @param ref |
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259 | * @param choffset |
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260 | **/ |
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261 | casa::CountedPtr<Scantable> dofold( const casa::CountedPtr<Scantable> &sig, |
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262 | const casa::CountedPtr<Scantable> &ref, |
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263 | casa::Double choffset, |
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264 | casa::Double choffset = 0.0 ); |
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265 | |
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266 | /** |
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267 | * ALMA calibration |
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268 | **/ |
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269 | casa::CountedPtr<Scantable> almacal( const casa::CountedPtr<Scantable>& s, |
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270 | const casa::String calmode ) ; |
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271 | casa::CountedPtr<Scantable> almacalfs( const casa::CountedPtr<Scantable>& s ) ; |
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272 | |
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273 | casa::CountedPtr<Scantable> |
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274 | freqSwitch( const casa::CountedPtr<Scantable>& in ); |
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275 | |
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276 | std::vector<float> statistic(const casa::CountedPtr<Scantable>& in, |
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277 | const std::vector<bool>& mask, |
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278 | const std::string& which); |
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279 | |
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280 | std::vector<float> statisticRow(const casa::CountedPtr<Scantable>& in, |
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281 | const std::vector<bool>& mask, |
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282 | const std::string& which, |
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283 | int row); |
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284 | |
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285 | std::vector< int > minMaxChan(const casa::CountedPtr<Scantable>& in, |
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286 | const std::vector<bool>& mask, |
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287 | const std::string& which); |
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288 | |
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289 | casa::CountedPtr<Scantable> bin( const casa::CountedPtr<Scantable>& in, |
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290 | int width=5); |
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291 | casa::CountedPtr<Scantable> |
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292 | resample(const casa::CountedPtr<Scantable>& in, |
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293 | const std::string& method, float width); |
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294 | |
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295 | casa::CountedPtr<Scantable> |
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296 | smooth(const casa::CountedPtr<Scantable>& in, const std::string& kernel, |
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297 | float width, int order=2); |
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298 | |
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299 | casa::CountedPtr<Scantable> |
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300 | gainElevation(const casa::CountedPtr<Scantable>& in, |
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301 | const std::vector<float>& coeff, |
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302 | const std::string& fileName, |
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303 | const std::string& method); |
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304 | casa::CountedPtr<Scantable> |
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305 | convertFlux(const casa::CountedPtr<Scantable>& in, float d, |
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306 | float etaap, float jyperk); |
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307 | |
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308 | casa::CountedPtr<Scantable> opacity(const casa::CountedPtr<Scantable>& in, |
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309 | const std::vector<float>& tau); |
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310 | |
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311 | casa::CountedPtr<Scantable> |
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312 | merge(const std::vector<casa::CountedPtr<Scantable> >& in); |
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313 | |
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314 | casa::CountedPtr<Scantable> |
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315 | invertPhase( const casa::CountedPtr<Scantable>& in); |
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316 | |
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317 | casa::CountedPtr<Scantable> |
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318 | rotateXYPhase( const casa::CountedPtr<Scantable>& in, float phase); |
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319 | |
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320 | casa::CountedPtr<Scantable> |
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321 | rotateLinPolPhase( const casa::CountedPtr<Scantable>& in, float phase); |
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322 | |
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323 | casa::CountedPtr<Scantable> |
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324 | swapPolarisations(const casa::CountedPtr<Scantable>& in); |
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325 | |
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326 | casa::CountedPtr<Scantable> |
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327 | frequencyAlign( const casa::CountedPtr<Scantable>& in, |
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328 | const std::string& refTime = "", |
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329 | const std::string& method = "cubic" ); |
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330 | |
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331 | casa::CountedPtr<Scantable> |
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332 | convertPolarisation( const casa::CountedPtr<Scantable>& in, |
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333 | const std::string& newtype); |
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334 | |
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335 | casa::CountedPtr<Scantable> |
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336 | mxExtract( const casa::CountedPtr<Scantable>& in, |
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337 | const std::string& srctype = "on"); |
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338 | |
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339 | /** |
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340 | * "hard" flag the data, this flags everything selected in setSelection() |
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341 | * @param frequency the frequency to remove |
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342 | * @param width the number of lags to flag left to the side of the frequency |
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343 | */ |
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344 | casa::CountedPtr<Scantable> |
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345 | lagFlag( const casa::CountedPtr<Scantable>& in, double start, |
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346 | double end, const std::string& mode="frequency"); |
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347 | |
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348 | // test for average spectra with different channel/resolution |
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349 | casa::CountedPtr<Scantable> |
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350 | new_average( const std::vector<casa::CountedPtr<Scantable> >& in, |
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351 | const bool& compel, |
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352 | const std::vector<bool>& mask = std::vector<bool>(), |
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353 | const std::string& weight = "NONE", |
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354 | const std::string& avmode = "SCAN" ) |
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355 | throw (casa::AipsError) ; |
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356 | |
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357 | private: |
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358 | casa::CountedPtr<Scantable> applyToPol( const casa::CountedPtr<Scantable>& in, |
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359 | STPol::polOperation fptr, |
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360 | casa::Float phase); |
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361 | |
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362 | static imethod stringToIMethod(const std::string& in); |
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363 | static WeightType stringToWeight(const std::string& in); |
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364 | |
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365 | void scaleByVector(casa::Table& in, |
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366 | const casa::Vector<casa::Float>& factor, |
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367 | bool dotsys); |
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368 | |
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369 | void scaleFromAsciiTable(casa::Table& in, const std::string& filename, |
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370 | const std::string& method, |
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371 | const casa::Vector<casa::Float>& xout, |
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372 | bool dotsys); |
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373 | |
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374 | void scaleFromTable(casa::Table& in, const casa::Table& table, |
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375 | const std::string& method, |
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376 | const casa::Vector<casa::Float>& xout, bool dotsys); |
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377 | |
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378 | void convertBrightnessUnits(casa::CountedPtr<Scantable>& in, |
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379 | bool tokelvin, float cfac); |
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380 | |
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381 | casa::CountedPtr< Scantable > |
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382 | smoothOther( const casa::CountedPtr< Scantable >& in, |
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383 | const std::string& kernel, |
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384 | float width, int order=2 ); |
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385 | |
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386 | casa::CountedPtr< Scantable > |
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387 | getScantable(const casa::CountedPtr< Scantable >& in, bool droprows); |
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388 | |
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389 | casa::MaskedArray<casa::Float> |
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390 | maskedArray( const casa::Vector<casa::Float>& s, |
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391 | const casa::Vector<casa::uChar>& f ); |
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392 | casa::MaskedArray<casa::Double> |
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393 | maskedArray( const casa::Vector<casa::Double>& s, |
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394 | const casa::Vector<casa::uChar>& f ); |
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395 | casa::Vector<casa::uChar> |
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396 | flagsFromMA(const casa::MaskedArray<casa::Float>& ma); |
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397 | |
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398 | vector<float> getSpectrumFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode = "before" ) ; |
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399 | vector<float> getTcalFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ; |
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400 | vector<float> getTsysFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ; |
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401 | vector<int> getRowIdFromTime( string reftime, casa::CountedPtr<Scantable>& s ) ; |
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402 | |
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403 | // Chopper-Wheel type calibration |
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404 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on, |
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405 | casa::CountedPtr<Scantable>& off, |
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406 | casa::CountedPtr<Scantable>& sky, |
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407 | casa::CountedPtr<Scantable>& hot, |
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408 | casa::CountedPtr<Scantable>& cold, |
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409 | int index, |
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410 | string antname ) ; |
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411 | // Tsys * (ON-OFF)/OFF |
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412 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on, |
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413 | casa::CountedPtr<Scantable>& off, |
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414 | int index ) ; |
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415 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig, |
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416 | casa::CountedPtr<Scantable>& ref, |
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417 | casa::CountedPtr<Scantable>& sky, |
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418 | casa::CountedPtr<Scantable>& hot, |
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419 | casa::CountedPtr<Scantable>& cold, |
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420 | int index ) ; |
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421 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig, |
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422 | casa::CountedPtr<Scantable>& ref, |
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423 | vector< casa::CountedPtr<Scantable> >& sky, |
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424 | vector< casa::CountedPtr<Scantable> >& hot, |
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425 | vector< casa::CountedPtr<Scantable> >& cold, |
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426 | int index ) ; |
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427 | double getMJD( string strtime ) ; |
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428 | |
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429 | bool insitu_; |
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430 | }; |
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431 | |
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432 | } |
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433 | #endif |
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