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< int > minMaxChan(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 |
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284 | casa::CountedPtr<Scantable> bin( const casa::CountedPtr<Scantable>& in,
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285 | int width=5);
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286 | casa::CountedPtr<Scantable>
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287 | resample(const casa::CountedPtr<Scantable>& in,
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288 | const std::string& method, float width);
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289 |
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290 | casa::CountedPtr<Scantable>
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291 | smooth(const casa::CountedPtr<Scantable>& in, const std::string& kernel,
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292 | float width);
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293 |
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294 | casa::CountedPtr<Scantable>
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295 | gainElevation(const casa::CountedPtr<Scantable>& in,
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296 | const std::vector<float>& coeff,
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297 | const std::string& fileName,
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298 | const std::string& method);
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299 | casa::CountedPtr<Scantable>
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300 | convertFlux(const casa::CountedPtr<Scantable>& in, float d,
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301 | float etaap, float jyperk);
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302 |
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303 | casa::CountedPtr<Scantable> opacity(const casa::CountedPtr<Scantable>& in,
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304 | float tau);
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305 |
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306 | casa::CountedPtr<Scantable>
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307 | merge(const std::vector<casa::CountedPtr<Scantable> >& in);
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308 |
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309 | casa::CountedPtr<Scantable>
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310 | invertPhase( const casa::CountedPtr<Scantable>& in);
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311 |
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312 | casa::CountedPtr<Scantable>
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313 | rotateXYPhase( const casa::CountedPtr<Scantable>& in, float phase);
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314 |
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315 | casa::CountedPtr<Scantable>
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316 | rotateLinPolPhase( const casa::CountedPtr<Scantable>& in, float phase);
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317 |
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318 | casa::CountedPtr<Scantable>
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319 | swapPolarisations(const casa::CountedPtr<Scantable>& in);
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320 |
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321 | casa::CountedPtr<Scantable>
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322 | frequencyAlign( const casa::CountedPtr<Scantable>& in,
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323 | const std::string& refTime = "",
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324 | const std::string& method = "cubic" );
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325 |
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326 | casa::CountedPtr<Scantable>
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327 | convertPolarisation( const casa::CountedPtr<Scantable>& in,
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328 | const std::string& newtype);
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329 |
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330 | casa::CountedPtr<Scantable>
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331 | mxExtract( const casa::CountedPtr<Scantable>& in,
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332 | const std::string& srctype = "on");
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333 |
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334 | /**
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335 | * "hard" flag the data, this flags everything selected in setSelection()
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336 | * @param frequency the frequency to remove
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337 | * @param width the number of lags to flag left to the side of the frequency
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338 | */
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339 | casa::CountedPtr<Scantable>
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340 | lagFlag( const casa::CountedPtr<Scantable>& in, double frequency,
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341 | double width);
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342 |
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343 | // test for average spectra with different channel/resolution
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344 | casa::CountedPtr<Scantable>
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345 | new_average( const std::vector<casa::CountedPtr<Scantable> >& in,
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346 | const bool& compel,
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347 | const std::vector<bool>& mask = std::vector<bool>(),
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348 | const std::string& weight = "NONE",
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349 | const std::string& avmode = "SCAN" )
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350 | throw (casa::AipsError) ;
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351 |
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352 | private:
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353 | casa::CountedPtr<Scantable> applyToPol( const casa::CountedPtr<Scantable>& in,
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354 | STPol::polOperation fptr,
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355 | casa::Float phase);
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356 |
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357 | static imethod stringToIMethod(const std::string& in);
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358 | static WeightType stringToWeight(const std::string& in);
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359 |
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360 | void scaleByVector(casa::Table& in,
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361 | const casa::Vector<casa::Float>& factor,
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362 | bool dotsys);
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363 |
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364 | void scaleFromAsciiTable(casa::Table& in, const std::string& filename,
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365 | const std::string& method,
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366 | const casa::Vector<casa::Float>& xout,
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367 | bool dotsys);
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368 |
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369 | void scaleFromTable(casa::Table& in, const casa::Table& table,
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370 | const std::string& method,
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371 | const casa::Vector<casa::Float>& xout, bool dotsys);
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372 |
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373 | void convertBrightnessUnits(casa::CountedPtr<Scantable>& in,
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374 | bool tokelvin, float cfac);
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375 |
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376 | casa::CountedPtr< Scantable >
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377 | smoothOther( const casa::CountedPtr< Scantable >& in,
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378 | const std::string& kernel,
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379 | float width );
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380 |
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381 | casa::CountedPtr< Scantable >
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382 | getScantable(const casa::CountedPtr< Scantable >& in, bool droprows);
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383 |
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384 | casa::MaskedArray<casa::Float>
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385 | maskedArray( const casa::Vector<casa::Float>& s,
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386 | const casa::Vector<casa::uChar>& f );
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387 | casa::MaskedArray<casa::Double>
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388 | maskedArray( const casa::Vector<casa::Double>& s,
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389 | const casa::Vector<casa::uChar>& f );
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390 | casa::Vector<casa::uChar>
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391 | flagsFromMA(const casa::MaskedArray<casa::Float>& ma);
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392 |
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393 | vector<float> getSpectrumFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode = "before" ) ;
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394 | vector<float> getTcalFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ;
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395 | vector<float> getTsysFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ;
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396 | vector<int> getRowIdFromTime( string reftime, casa::CountedPtr<Scantable>& s ) ;
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397 |
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398 | // Chopper-Wheel type calibration
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399 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on,
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400 | casa::CountedPtr<Scantable>& off,
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401 | casa::CountedPtr<Scantable>& sky,
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402 | casa::CountedPtr<Scantable>& hot,
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403 | casa::CountedPtr<Scantable>& cold,
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404 | int index,
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405 | string antname ) ;
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406 | // Tsys * (ON-OFF)/OFF
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407 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on,
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408 | casa::CountedPtr<Scantable>& off,
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409 | int index ) ;
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410 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig,
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411 | casa::CountedPtr<Scantable>& ref,
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412 | casa::CountedPtr<Scantable>& sky,
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413 | casa::CountedPtr<Scantable>& hot,
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414 | casa::CountedPtr<Scantable>& cold,
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415 | int index ) ;
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416 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig,
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417 | casa::CountedPtr<Scantable>& ref,
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418 | vector< casa::CountedPtr<Scantable> >& sky,
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419 | vector< casa::CountedPtr<Scantable> >& hot,
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420 | vector< casa::CountedPtr<Scantable> >& cold,
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421 | int index ) ;
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422 | double getMJD( string strtime ) ;
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423 |
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424 | bool insitu_;
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425 | };
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426 |
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427 | }
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428 | #endif
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