[805] | 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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[2] | 14 | |
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[2177] | 15 | #include <map> |
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[38] | 16 | #include <string> |
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[805] | 17 | |
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[130] | 18 | #include <casa/aips.h> |
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[2177] | 19 | #include <casa/Arrays/Vector.h> |
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| 20 | #include <casa/BasicSL/String.h> |
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[81] | 21 | #include <casa/Utilities/CountedPtr.h> |
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[2177] | 22 | |
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| 23 | #include <scimath/Mathematics/FFTServer.h> |
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[805] | 24 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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[294] | 25 | |
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[2177] | 26 | #include "Logger.h" |
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[805] | 27 | #include "Scantable.h" |
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[834] | 28 | #include "STDefs.h" |
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[896] | 29 | #include "STPol.h" |
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[2] | 30 | |
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[83] | 31 | namespace asap { |
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[2] | 32 | |
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[805] | 33 | /** |
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[1106] | 34 | * Mathmatical operations on Scantable objects |
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| 35 | * @author Malte Marquarding |
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[805] | 36 | */ |
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[890] | 37 | class STMath : private Logger { |
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[716] | 38 | public: |
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[1106] | 39 | // typedef for long method name |
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[805] | 40 | typedef casa::InterpolateArray1D<casa::Double, |
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| 41 | casa::Float>::InterpolationMethod imethod; |
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[299] | 42 | |
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[1106] | 43 | // typedef for std::map |
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[805] | 44 | typedef std::map<std::string, imethod> imap; |
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[177] | 45 | |
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[1106] | 46 | /** |
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| 47 | * whether to operate on the given Scantable or return a new one |
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| 48 | * @param insitu the toggle for this behaviour |
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| 49 | */ |
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[1353] | 50 | explicit STMath(bool insitu=true); |
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[221] | 51 | |
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[995] | 52 | virtual ~STMath(); |
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[227] | 53 | |
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[805] | 54 | /** |
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[1295] | 55 | * get the currnt @attr inistu_ state |
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[805] | 56 | */ |
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| 57 | bool insitu() const { return insitu_;}; |
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[1143] | 58 | |
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[1106] | 59 | /** |
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| 60 | * set the currnt @attr inistu state |
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| 61 | * @param b the new state |
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| 62 | */ |
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[805] | 63 | void setInsitu(bool b) { insitu_ = b; }; |
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[262] | 64 | |
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[1106] | 65 | |
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[1140] | 66 | /** |
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| 67 | * average a vector of Scantables |
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| 68 | * @param in the vector of Scantables to average |
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[1295] | 69 | * @param mask an optional mask to apply on specific weights |
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[1140] | 70 | * @param weight weighting scheme |
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| 71 | * @param avmode the mode ov averaging. Per "SCAN" or "ALL". |
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| 72 | * @return a casa::CountedPtr<Scantable> which either holds a new Scantable |
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| 73 | * or returns the imput pointer. |
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| 74 | */ |
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[805] | 75 | casa::CountedPtr<Scantable> |
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| 76 | average( const std::vector<casa::CountedPtr<Scantable> >& in, |
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[858] | 77 | const std::vector<bool>& mask = std::vector<bool>(), |
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| 78 | const std::string& weight = "NONE", |
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[977] | 79 | const std::string& avmode = "SCAN"); |
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[1066] | 80 | |
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[1140] | 81 | /** |
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| 82 | * median average a vector of Scantables. See also STMath::average |
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| 83 | * @param in the Scantable to average |
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| 84 | * @param mode the averaging mode. Currently only "MEDIAN" |
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| 85 | * @param avmode the mode ov averaging. Per "SCAN" or "ALL". |
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| 86 | * @return a casa::CountedPtr<Scantable> which either holds a new Scantable |
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| 87 | * or returns the imput pointer. |
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| 88 | */ |
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[1069] | 89 | casa::CountedPtr<Scantable> |
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| 90 | averageChannel( const casa::CountedPtr<Scantable> & in, |
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[1078] | 91 | const std::string& mode = "MEDIAN", |
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| 92 | const std::string& avmode = "SCAN"); |
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[1069] | 93 | |
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[1140] | 94 | /** |
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[1145] | 95 | * Average polarisations together. really only useful if only linears are |
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| 96 | * available. |
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[1140] | 97 | * @param in the input Scantable |
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| 98 | * @param mask an optional mask if weight allows one |
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| 99 | * @param weight weighting scheme |
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[1143] | 100 | * @return |
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[1140] | 101 | */ |
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[940] | 102 | casa::CountedPtr< Scantable > |
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| 103 | averagePolarisations( const casa::CountedPtr< Scantable > & in, |
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[1140] | 104 | const std::vector<bool>& mask, |
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| 105 | const std::string& weight ); |
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[234] | 106 | |
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[1145] | 107 | /** |
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| 108 | * Average beams together. |
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| 109 | * @param in the input Scantable |
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| 110 | * @param mask an optional mask if weight allows one |
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| 111 | * @param weight weighting scheme |
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| 112 | * @return |
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| 113 | */ |
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| 114 | casa::CountedPtr< Scantable > |
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| 115 | averageBeams( const casa::CountedPtr< Scantable > & in, |
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| 116 | const std::vector<bool>& mask, |
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| 117 | const std::string& weight ); |
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| 118 | |
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[805] | 119 | casa::CountedPtr<Scantable> |
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| 120 | unaryOperate( const casa::CountedPtr<Scantable>& in, float val, |
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| 121 | const std::string& mode, bool tsys=false ); |
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[169] | 122 | |
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[1819] | 123 | // array operation |
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[1308] | 124 | casa::CountedPtr<Scantable> |
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[1819] | 125 | arrayOperate( const casa::CountedPtr<Scantable>& in, |
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| 126 | const std::vector<float> val, |
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| 127 | const std::string& mode, |
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| 128 | const std::string& opmode="channel", |
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| 129 | bool tsys=false ); |
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| 130 | |
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| 131 | // channel operation |
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| 132 | casa::CountedPtr<Scantable> |
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| 133 | arrayOperateChannel( const casa::CountedPtr<Scantable>& in, |
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| 134 | const std::vector<float> val, |
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| 135 | const std::string& mode, bool tsys=false ); |
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| 136 | |
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| 137 | // row operation |
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| 138 | casa::CountedPtr<Scantable> |
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| 139 | arrayOperateRow( const casa::CountedPtr<Scantable>& in, |
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| 140 | const std::vector<float> val, |
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| 141 | const std::string& mode, bool tsys=false ); |
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| 142 | |
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| 143 | // 2d array operation |
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| 144 | casa::CountedPtr<Scantable> |
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| 145 | array2dOperate( const casa::CountedPtr<Scantable>& in, |
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| 146 | const std::vector< std::vector<float> > val, |
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| 147 | const std::string& mode, bool tsys=false ); |
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| 148 | |
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| 149 | casa::CountedPtr<Scantable> |
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[1570] | 150 | binaryOperate( const casa::CountedPtr<Scantable>& left, |
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| 151 | const casa::CountedPtr<Scantable>& right, |
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[1308] | 152 | const std::string& mode); |
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| 153 | |
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[1066] | 154 | casa::CountedPtr<Scantable> autoQuotient(const casa::CountedPtr<Scantable>& in, |
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| 155 | const std::string& mode = "NEAREST", |
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| 156 | bool preserve = true); |
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| 157 | |
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| 158 | casa::CountedPtr<Scantable> quotient( const casa::CountedPtr<Scantable>& on, |
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| 159 | const casa::CountedPtr<Scantable>& off, |
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[805] | 160 | bool preserve = true ); |
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[169] | 161 | |
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[1391] | 162 | /** |
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| 163 | * Calibrate total power scans (translated from GBTIDL) |
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[1819] | 164 | * @param calon uncalibrated Scantable with CAL noise signal |
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[1391] | 165 | * @param caloff uncalibrated Scantable with no CAL signal |
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| 166 | * @param tcal optional scalar Tcal, CAL temperature (K) |
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[1819] | 167 | * @return casa::CountedPtr<Scantable> which holds a calibrated Scantable |
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[1391] | 168 | * (spectrum - average of the two CAL on and off spectra; |
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| 169 | * tsys - mean Tsys = <caloff>*Tcal/<calon-caloff> + Tcal/2) |
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[1819] | 170 | */ |
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[1391] | 171 | casa::CountedPtr<Scantable> dototalpower( const casa::CountedPtr<Scantable>& calon, |
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| 172 | const casa::CountedPtr<Scantable>& caloff, |
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| 173 | casa::Float tcal=1.0 ); |
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| 174 | |
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| 175 | /** |
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| 176 | * Combine signal and reference scans (translated from GBTIDL) |
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| 177 | * @param sig Scantable which contains signal scans |
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| 178 | * @param ref Scantable which contains reference scans |
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| 179 | * @param smoothref optional Boxcar smooth width of the reference scans |
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| 180 | * default: no smoothing (=1) |
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[1819] | 181 | * @param tsysv optional scalar Tsys value at the zenith, required to |
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| 182 | * set tau, as well |
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[1391] | 183 | * @param tau optional scalar Tau value |
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| 184 | * @return casa::CountedPtr<Scantable> which holds combined scans |
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| 185 | * (spectrum = (sig-ref)/ref * Tsys ) |
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| 186 | */ |
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| 187 | casa::CountedPtr<Scantable> dosigref( const casa::CountedPtr<Scantable>& sig, |
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| 188 | const casa::CountedPtr<Scantable>& ref, |
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| 189 | int smoothref=1, |
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| 190 | casa::Float tsysv=0.0, |
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| 191 | casa::Float tau=0.0 ); |
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| 192 | |
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[1819] | 193 | /** |
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[1391] | 194 | * Calibrate GBT Nod scan pairs (translated from GBTIDL) |
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| 195 | * @param s Scantable which contains Nod scans |
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| 196 | * @param scans Vector of scan numbers |
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| 197 | * @param smoothref optional Boxcar smooth width of the reference scans |
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| 198 | * @param tsysv optional scalar Tsys value at the zenith, required to |
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| 199 | * set tau, as well |
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[1819] | 200 | * @param tau optional scalar Tau value |
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[1391] | 201 | * @param tcal optional scalar Tcal, CAL temperature (K) |
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| 202 | * @return casa::CountedPtr<Scantable> which holds calibrated scans |
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| 203 | */ |
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| 204 | casa::CountedPtr<Scantable> donod( const casa::CountedPtr<Scantable>& s, |
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| 205 | const std::vector<int>& scans, |
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| 206 | int smoothref=1, |
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| 207 | casa::Float tsysv=0.0, |
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| 208 | casa::Float tau=0.0, |
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| 209 | casa::Float tcal=0.0 ); |
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| 210 | |
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| 211 | /** |
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| 212 | * Calibrate frequency switched scans (translated from GBTIDL) |
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| 213 | * @param s Scantable which contains frequency switched scans |
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| 214 | * @param scans Vector of scan numbers |
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| 215 | * @param smoothref optional Boxcar smooth width of the reference scans |
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| 216 | * @param tsysv optional scalar Tsys value at the zenith, required to |
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| 217 | * set tau, as well |
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| 218 | * @param tau optional scalar Tau value |
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| 219 | * @param tcal optional scalar Tcal, CAL temperature (K) |
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| 220 | * @return casa::CountedPtr<Scantable> which holds calibrated scans |
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| 221 | */ |
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| 222 | casa::CountedPtr<Scantable> dofs( const casa::CountedPtr<Scantable>& s, |
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| 223 | const std::vector<int>& scans, |
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| 224 | int smoothref=1, |
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| 225 | casa::Float tsysv=0.0, |
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| 226 | casa::Float tau=0.0, |
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| 227 | casa::Float tcal=0.0 ); |
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| 228 | |
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[1819] | 229 | /** |
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| 230 | * Calibrate data with Chopper-Wheel like calibration method |
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| 231 | * which adopts position switching by antenna motion, |
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| 232 | * wobbler (nutator) switching and On-The-Fly observation. |
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| 233 | * |
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| 234 | * The method is applicable to APEX, and other telescopes other than GBT. |
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| 235 | * |
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| 236 | * @param a Scantable which contains ON and OFF scans |
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| 237 | * @param a string that indicates calibration mode |
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| 238 | * @param a string that indicates antenna name |
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| 239 | **/ |
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| 240 | casa::CountedPtr<Scantable> cwcal( const casa::CountedPtr<Scantable>& s, |
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| 241 | const casa::String calmode, |
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| 242 | const casa::String antname ); |
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[1391] | 243 | |
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[1819] | 244 | /** |
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| 245 | * Calibrate frequency switched scans with Chopper-Wheel like |
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| 246 | * calibration method. |
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| 247 | * |
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| 248 | * The method is applicable to APEX, and other telescopes other than GBT. |
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| 249 | * |
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| 250 | * @param a Scantable which contains ON and OFF scans |
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| 251 | * @param a string that indicates antenna name |
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| 252 | **/ |
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| 253 | casa::CountedPtr<Scantable> cwcalfs( const casa::CountedPtr<Scantable>& s, |
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| 254 | const casa::String antname ); |
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| 255 | |
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| 256 | |
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| 257 | /** |
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| 258 | * Folding frequency-switch data |
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| 259 | * @param sig |
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| 260 | * @param ref |
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| 261 | * @param choffset |
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| 262 | **/ |
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| 263 | casa::CountedPtr<Scantable> dofold( const casa::CountedPtr<Scantable> &sig, |
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| 264 | const casa::CountedPtr<Scantable> &ref, |
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| 265 | casa::Double choffset, |
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[1937] | 266 | casa::Double choffset2 = 0.0 ); |
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[1819] | 267 | |
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| 268 | /** |
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| 269 | * ALMA calibration |
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| 270 | **/ |
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| 271 | casa::CountedPtr<Scantable> almacal( const casa::CountedPtr<Scantable>& s, |
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| 272 | const casa::String calmode ) ; |
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| 273 | casa::CountedPtr<Scantable> almacalfs( const casa::CountedPtr<Scantable>& s ) ; |
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| 274 | |
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[805] | 275 | casa::CountedPtr<Scantable> |
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| 276 | freqSwitch( const casa::CountedPtr<Scantable>& in ); |
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[716] | 277 | |
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[805] | 278 | std::vector<float> statistic(const casa::CountedPtr<Scantable>& in, |
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| 279 | const std::vector<bool>& mask, |
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| 280 | const std::string& which); |
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[457] | 281 | |
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[1907] | 282 | std::vector<float> statisticRow(const casa::CountedPtr<Scantable>& in, |
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| 283 | const std::vector<bool>& mask, |
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| 284 | const std::string& which, |
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| 285 | int row); |
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| 286 | |
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[1819] | 287 | std::vector< int > minMaxChan(const casa::CountedPtr<Scantable>& in, |
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| 288 | const std::vector<bool>& mask, |
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| 289 | const std::string& which); |
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| 290 | |
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[805] | 291 | casa::CountedPtr<Scantable> bin( const casa::CountedPtr<Scantable>& in, |
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| 292 | int width=5); |
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| 293 | casa::CountedPtr<Scantable> |
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| 294 | resample(const casa::CountedPtr<Scantable>& in, |
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| 295 | const std::string& method, float width); |
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[457] | 296 | |
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[805] | 297 | casa::CountedPtr<Scantable> |
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| 298 | smooth(const casa::CountedPtr<Scantable>& in, const std::string& kernel, |
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[1570] | 299 | float width, int order=2); |
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[169] | 300 | |
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[805] | 301 | casa::CountedPtr<Scantable> |
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| 302 | gainElevation(const casa::CountedPtr<Scantable>& in, |
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[867] | 303 | const std::vector<float>& coeff, |
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[805] | 304 | const std::string& fileName, |
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[995] | 305 | const std::string& method); |
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[805] | 306 | casa::CountedPtr<Scantable> |
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| 307 | convertFlux(const casa::CountedPtr<Scantable>& in, float d, |
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| 308 | float etaap, float jyperk); |
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[152] | 309 | |
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[805] | 310 | casa::CountedPtr<Scantable> opacity(const casa::CountedPtr<Scantable>& in, |
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[1689] | 311 | const std::vector<float>& tau); |
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[144] | 312 | |
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[841] | 313 | casa::CountedPtr<Scantable> |
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| 314 | merge(const std::vector<casa::CountedPtr<Scantable> >& in); |
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| 315 | |
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[896] | 316 | casa::CountedPtr<Scantable> |
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| 317 | invertPhase( const casa::CountedPtr<Scantable>& in); |
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[912] | 318 | |
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[896] | 319 | casa::CountedPtr<Scantable> |
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| 320 | rotateXYPhase( const casa::CountedPtr<Scantable>& in, float phase); |
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[912] | 321 | |
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[896] | 322 | casa::CountedPtr<Scantable> |
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| 323 | rotateLinPolPhase( const casa::CountedPtr<Scantable>& in, float phase); |
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| 324 | |
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| 325 | casa::CountedPtr<Scantable> |
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| 326 | swapPolarisations(const casa::CountedPtr<Scantable>& in); |
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| 327 | |
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[917] | 328 | casa::CountedPtr<Scantable> |
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| 329 | frequencyAlign( const casa::CountedPtr<Scantable>& in, |
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[927] | 330 | const std::string& refTime = "", |
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| 331 | const std::string& method = "cubic" ); |
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[917] | 332 | |
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[992] | 333 | casa::CountedPtr<Scantable> |
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| 334 | convertPolarisation( const casa::CountedPtr<Scantable>& in, |
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| 335 | const std::string& newtype); |
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[1143] | 336 | |
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[1140] | 337 | casa::CountedPtr<Scantable> |
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[1143] | 338 | mxExtract( const casa::CountedPtr<Scantable>& in, |
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| 339 | const std::string& srctype = "on"); |
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[992] | 340 | |
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[1192] | 341 | /** |
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| 342 | * "hard" flag the data, this flags everything selected in setSelection() |
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| 343 | * @param frequency the frequency to remove |
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| 344 | * @param width the number of lags to flag left to the side of the frequency |
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| 345 | */ |
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| 346 | casa::CountedPtr<Scantable> |
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[1570] | 347 | lagFlag( const casa::CountedPtr<Scantable>& in, double start, |
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| 348 | double end, const std::string& mode="frequency"); |
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[1192] | 349 | |
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[2177] | 350 | std::vector<float> |
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| 351 | fft( const casa::CountedPtr<Scantable>& in, |
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| 352 | const std::vector<int>& whichrow, |
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| 353 | bool getRealImag=false ); |
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| 354 | |
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[1819] | 355 | // test for average spectra with different channel/resolution |
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| 356 | casa::CountedPtr<Scantable> |
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| 357 | new_average( const std::vector<casa::CountedPtr<Scantable> >& in, |
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| 358 | const bool& compel, |
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| 359 | const std::vector<bool>& mask = std::vector<bool>(), |
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| 360 | const std::string& weight = "NONE", |
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| 361 | const std::string& avmode = "SCAN" ) |
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| 362 | throw (casa::AipsError) ; |
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| 363 | |
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[805] | 364 | private: |
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[896] | 365 | casa::CountedPtr<Scantable> applyToPol( const casa::CountedPtr<Scantable>& in, |
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| 366 | STPol::polOperation fptr, |
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| 367 | casa::Float phase); |
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| 368 | |
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[805] | 369 | static imethod stringToIMethod(const std::string& in); |
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| 370 | static WeightType stringToWeight(const std::string& in); |
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[146] | 371 | |
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[805] | 372 | void scaleByVector(casa::Table& in, |
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| 373 | const casa::Vector<casa::Float>& factor, |
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| 374 | bool dotsys); |
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[152] | 375 | |
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[805] | 376 | void scaleFromAsciiTable(casa::Table& in, const std::string& filename, |
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| 377 | const std::string& method, |
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| 378 | const casa::Vector<casa::Float>& xout, |
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| 379 | bool dotsys); |
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[162] | 380 | |
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[805] | 381 | void scaleFromTable(casa::Table& in, const casa::Table& table, |
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| 382 | const std::string& method, |
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| 383 | const casa::Vector<casa::Float>& xout, bool dotsys); |
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[227] | 384 | |
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[805] | 385 | void convertBrightnessUnits(casa::CountedPtr<Scantable>& in, |
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| 386 | bool tokelvin, float cfac); |
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[227] | 387 | |
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[1570] | 388 | casa::CountedPtr< Scantable > |
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[1374] | 389 | smoothOther( const casa::CountedPtr< Scantable >& in, |
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| 390 | const std::string& kernel, |
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[1570] | 391 | float width, int order=2 ); |
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[1374] | 392 | |
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[805] | 393 | casa::CountedPtr< Scantable > |
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| 394 | getScantable(const casa::CountedPtr< Scantable >& in, bool droprows); |
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[230] | 395 | |
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[805] | 396 | casa::MaskedArray<casa::Float> |
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| 397 | maskedArray( const casa::Vector<casa::Float>& s, |
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| 398 | const casa::Vector<casa::uChar>& f ); |
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[1819] | 399 | casa::MaskedArray<casa::Double> |
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| 400 | maskedArray( const casa::Vector<casa::Double>& s, |
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| 401 | const casa::Vector<casa::uChar>& f ); |
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[805] | 402 | casa::Vector<casa::uChar> |
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| 403 | flagsFromMA(const casa::MaskedArray<casa::Float>& ma); |
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[230] | 404 | |
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[1819] | 405 | vector<float> getSpectrumFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode = "before" ) ; |
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| 406 | vector<float> getTcalFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ; |
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| 407 | vector<float> getTsysFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ; |
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| 408 | vector<int> getRowIdFromTime( string reftime, casa::CountedPtr<Scantable>& s ) ; |
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| 409 | |
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| 410 | // Chopper-Wheel type calibration |
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| 411 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on, |
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| 412 | casa::CountedPtr<Scantable>& off, |
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| 413 | casa::CountedPtr<Scantable>& sky, |
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| 414 | casa::CountedPtr<Scantable>& hot, |
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| 415 | casa::CountedPtr<Scantable>& cold, |
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| 416 | int index, |
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| 417 | string antname ) ; |
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| 418 | // Tsys * (ON-OFF)/OFF |
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| 419 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on, |
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| 420 | casa::CountedPtr<Scantable>& off, |
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| 421 | int index ) ; |
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| 422 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig, |
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| 423 | casa::CountedPtr<Scantable>& ref, |
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| 424 | casa::CountedPtr<Scantable>& sky, |
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| 425 | casa::CountedPtr<Scantable>& hot, |
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| 426 | casa::CountedPtr<Scantable>& cold, |
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| 427 | int index ) ; |
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| 428 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig, |
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| 429 | casa::CountedPtr<Scantable>& ref, |
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| 430 | vector< casa::CountedPtr<Scantable> >& sky, |
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| 431 | vector< casa::CountedPtr<Scantable> >& hot, |
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| 432 | vector< casa::CountedPtr<Scantable> >& cold, |
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| 433 | int index ) ; |
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| 434 | double getMJD( string strtime ) ; |
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[2177] | 435 | void doFFT( std::vector<float>& out, |
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| 436 | casa::FFTServer< casa::Float, casa::Complex >& ffts, |
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| 437 | bool getRealImag, |
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| 438 | casa::Vector<casa::Float>& spec, |
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| 439 | casa::Vector<casa::uChar>& flag ) ; |
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| 440 | void doZeroOrderInterpolation( casa::Vector<casa::Float>& spec, |
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| 441 | casa::Vector<casa::uChar>& flag) ; |
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[1819] | 442 | |
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[805] | 443 | bool insitu_; |
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| 444 | }; |
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[234] | 445 | |
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[805] | 446 | } |
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[165] | 447 | #endif |
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