[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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[2952] | 17 | #include <iostream>
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[805] | 18 |
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[130] | 19 | #include <casa/aips.h>
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[2177] | 20 | #include <casa/Arrays/Vector.h>
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| 21 | #include <casa/BasicSL/String.h>
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[81] | 22 | #include <casa/Utilities/CountedPtr.h>
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[2177] | 23 |
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[805] | 24 | #include <scimath/Mathematics/InterpolateArray1D.h>
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[294] | 25 |
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[805] | 26 | #include "Scantable.h"
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[834] | 27 | #include "STDefs.h"
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[896] | 28 | #include "STPol.h"
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[2] | 29 |
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[83] | 30 | namespace asap {
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[2] | 31 |
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[805] | 32 | /**
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[1106] | 33 | * Mathmatical operations on Scantable objects
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| 34 | * @author Malte Marquarding
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[805] | 35 | */
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[2658] | 36 | class STMath {
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[716] | 37 | public:
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[1106] | 38 | // typedef for long method name
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[3106] | 39 | typedef casacore::InterpolateArray1D<casacore::Double,
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| 40 | casacore::Float>::InterpolationMethod imethod;
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[299] | 41 |
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[1106] | 42 | // typedef for std::map
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[805] | 43 | typedef std::map<std::string, imethod> imap;
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[177] | 44 |
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[1106] | 45 | /**
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| 46 | * whether to operate on the given Scantable or return a new one
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| 47 | * @param insitu the toggle for this behaviour
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| 48 | */
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[1353] | 49 | explicit STMath(bool insitu=true);
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[221] | 50 |
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[995] | 51 | virtual ~STMath();
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[227] | 52 |
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[805] | 53 | /**
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[1295] | 54 | * get the currnt @attr inistu_ state
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[805] | 55 | */
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| 56 | bool insitu() const { return insitu_;};
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[1143] | 57 |
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[1106] | 58 | /**
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| 59 | * set the currnt @attr inistu state
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| 60 | * @param b the new state
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| 61 | */
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[805] | 62 | void setInsitu(bool b) { insitu_ = b; };
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[262] | 63 |
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[1106] | 64 |
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[1140] | 65 | /**
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| 66 | * average a vector of Scantables
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| 67 | * @param in the vector of Scantables to average
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[1295] | 68 | * @param mask an optional mask to apply on specific weights
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[1140] | 69 | * @param weight weighting scheme
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| 70 | * @param avmode the mode ov averaging. Per "SCAN" or "ALL".
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[3106] | 71 | * @return a casacore::CountedPtr<Scantable> which either holds a new Scantable
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[1140] | 72 | * or returns the imput pointer.
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| 73 | */
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[3106] | 74 | casacore::CountedPtr<Scantable>
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| 75 | average( const std::vector<casacore::CountedPtr<Scantable> >& in,
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[858] | 76 | const std::vector<bool>& mask = std::vector<bool>(),
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| 77 | const std::string& weight = "NONE",
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[977] | 78 | const std::string& avmode = "SCAN");
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[1066] | 79 |
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[1140] | 80 | /**
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| 81 | * median average a vector of Scantables. See also STMath::average
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| 82 | * @param in the Scantable to average
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| 83 | * @param mode the averaging mode. Currently only "MEDIAN"
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| 84 | * @param avmode the mode ov averaging. Per "SCAN" or "ALL".
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[3106] | 85 | * @return a casacore::CountedPtr<Scantable> which either holds a new Scantable
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[1140] | 86 | * or returns the imput pointer.
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| 87 | */
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[3106] | 88 | casacore::CountedPtr<Scantable>
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| 89 | averageChannel( const casacore::CountedPtr<Scantable> & in,
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[1078] | 90 | const std::string& mode = "MEDIAN",
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| 91 | const std::string& avmode = "SCAN");
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[1069] | 92 |
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[1140] | 93 | /**
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[1145] | 94 | * Average polarisations together. really only useful if only linears are
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| 95 | * available.
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[1140] | 96 | * @param in the input Scantable
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| 97 | * @param mask an optional mask if weight allows one
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| 98 | * @param weight weighting scheme
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[1143] | 99 | * @return
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[1140] | 100 | */
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[3106] | 101 | casacore::CountedPtr< Scantable >
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| 102 | averagePolarisations( const casacore::CountedPtr< Scantable > & in,
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[1140] | 103 | const std::vector<bool>& mask,
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| 104 | const std::string& weight );
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[234] | 105 |
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[1145] | 106 | /**
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| 107 | * Average beams together.
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| 108 | * @param in the input Scantable
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| 109 | * @param mask an optional mask if weight allows one
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| 110 | * @param weight weighting scheme
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| 111 | * @return
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| 112 | */
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[3106] | 113 | casacore::CountedPtr< Scantable >
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| 114 | averageBeams( const casacore::CountedPtr< Scantable > & in,
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[1145] | 115 | const std::vector<bool>& mask,
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| 116 | const std::string& weight );
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| 117 |
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[3106] | 118 | casacore::CountedPtr<Scantable>
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| 119 | unaryOperate( const casacore::CountedPtr<Scantable>& in, float val,
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[2952] | 120 | const std::string& mode, bool tsys=false,
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| 121 | bool skip_flaggedrow=false );
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[169] | 122 |
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[1819] | 123 | // array operation
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[3106] | 124 | casacore::CountedPtr<Scantable>
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| 125 | arrayOperate( const casacore::CountedPtr<Scantable>& in,
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[1819] | 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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[2952] | 129 | bool tsys=false,
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| 130 | bool skip_flaggedrow=false );
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[1819] | 131 |
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| 132 | // channel operation
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[3106] | 133 | casacore::CountedPtr<Scantable>
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| 134 | arrayOperateChannel( const casacore::CountedPtr<Scantable>& in,
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[1819] | 135 | const std::vector<float> val,
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[2952] | 136 | const std::string& mode, bool tsys=false,
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| 137 | bool skip_flaggedrow=false );
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[1819] | 138 |
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| 139 | // row operation
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[3106] | 140 | casacore::CountedPtr<Scantable>
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| 141 | arrayOperateRow( const casacore::CountedPtr<Scantable>& in,
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[1819] | 142 | const std::vector<float> val,
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[2952] | 143 | const std::string& mode, bool tsys=false,
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| 144 | bool skip_flaggedrow=false );
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[1819] | 145 |
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| 146 | // 2d array operation
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[3106] | 147 | casacore::CountedPtr<Scantable>
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| 148 | array2dOperate( const casacore::CountedPtr<Scantable>& in,
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[1819] | 149 | const std::vector< std::vector<float> > val,
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| 150 | const std::string& mode, bool tsys=false );
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| 151 |
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[3106] | 152 | casacore::CountedPtr<Scantable>
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| 153 | binaryOperate( const casacore::CountedPtr<Scantable>& left,
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| 154 | const casacore::CountedPtr<Scantable>& right,
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[1308] | 155 | const std::string& mode);
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| 156 |
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[3106] | 157 | casacore::CountedPtr<Scantable> autoQuotient(const casacore::CountedPtr<Scantable>& in,
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[1066] | 158 | const std::string& mode = "NEAREST",
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| 159 | bool preserve = true);
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| 160 |
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[3106] | 161 | casacore::CountedPtr<Scantable> quotient( const casacore::CountedPtr<Scantable>& on,
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| 162 | const casacore::CountedPtr<Scantable>& off,
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[805] | 163 | bool preserve = true );
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[169] | 164 |
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[1391] | 165 | /**
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| 166 | * Calibrate total power scans (translated from GBTIDL)
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[1819] | 167 | * @param calon uncalibrated Scantable with CAL noise signal
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[1391] | 168 | * @param caloff uncalibrated Scantable with no CAL signal
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| 169 | * @param tcal optional scalar Tcal, CAL temperature (K)
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[3106] | 170 | * @return casacore::CountedPtr<Scantable> which holds a calibrated Scantable
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[1391] | 171 | * (spectrum - average of the two CAL on and off spectra;
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| 172 | * tsys - mean Tsys = <caloff>*Tcal/<calon-caloff> + Tcal/2)
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[1819] | 173 | */
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[3106] | 174 | casacore::CountedPtr<Scantable> dototalpower( const casacore::CountedPtr<Scantable>& calon,
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| 175 | const casacore::CountedPtr<Scantable>& caloff,
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| 176 | casacore::Float tcal=1.0 );
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[1391] | 177 |
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| 178 | /**
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| 179 | * Combine signal and reference scans (translated from GBTIDL)
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| 180 | * @param sig Scantable which contains signal scans
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| 181 | * @param ref Scantable which contains reference scans
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| 182 | * @param smoothref optional Boxcar smooth width of the reference scans
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| 183 | * default: no smoothing (=1)
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[1819] | 184 | * @param tsysv optional scalar Tsys value at the zenith, required to
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| 185 | * set tau, as well
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[1391] | 186 | * @param tau optional scalar Tau value
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[3106] | 187 | * @return casacore::CountedPtr<Scantable> which holds combined scans
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[1391] | 188 | * (spectrum = (sig-ref)/ref * Tsys )
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| 189 | */
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[3106] | 190 | casacore::CountedPtr<Scantable> dosigref( const casacore::CountedPtr<Scantable>& sig,
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| 191 | const casacore::CountedPtr<Scantable>& ref,
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[1391] | 192 | int smoothref=1,
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[3106] | 193 | casacore::Float tsysv=0.0,
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| 194 | casacore::Float tau=0.0 );
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[1391] | 195 |
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[1819] | 196 | /**
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[1391] | 197 | * Calibrate GBT Nod scan pairs (translated from GBTIDL)
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| 198 | * @param s Scantable which contains Nod scans
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| 199 | * @param scans Vector of scan numbers
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| 200 | * @param smoothref optional Boxcar smooth width of the reference scans
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| 201 | * @param tsysv optional scalar Tsys value at the zenith, required to
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| 202 | * set tau, as well
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[1819] | 203 | * @param tau optional scalar Tau value
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[1391] | 204 | * @param tcal optional scalar Tcal, CAL temperature (K)
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[3106] | 205 | * @return casacore::CountedPtr<Scantable> which holds calibrated scans
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[1391] | 206 | */
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[3106] | 207 | casacore::CountedPtr<Scantable> donod( const casacore::CountedPtr<Scantable>& s,
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[1391] | 208 | const std::vector<int>& scans,
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| 209 | int smoothref=1,
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[3106] | 210 | casacore::Float tsysv=0.0,
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| 211 | casacore::Float tau=0.0,
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| 212 | casacore::Float tcal=0.0 );
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[1391] | 213 |
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| 214 | /**
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| 215 | * Calibrate frequency switched scans (translated from GBTIDL)
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| 216 | * @param s Scantable which contains frequency switched scans
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| 217 | * @param scans Vector of scan numbers
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| 218 | * @param smoothref optional Boxcar smooth width of the reference scans
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| 219 | * @param tsysv optional scalar Tsys value at the zenith, required to
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| 220 | * set tau, as well
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| 221 | * @param tau optional scalar Tau value
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| 222 | * @param tcal optional scalar Tcal, CAL temperature (K)
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[3106] | 223 | * @return casacore::CountedPtr<Scantable> which holds calibrated scans
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[1391] | 224 | */
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[3106] | 225 | casacore::CountedPtr<Scantable> dofs( const casacore::CountedPtr<Scantable>& s,
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[1391] | 226 | const std::vector<int>& scans,
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| 227 | int smoothref=1,
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[3106] | 228 | casacore::Float tsysv=0.0,
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| 229 | casacore::Float tau=0.0,
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| 230 | casacore::Float tcal=0.0 );
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[1391] | 231 |
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[1819] | 232 | /**
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| 233 | * Calibrate data with Chopper-Wheel like calibration method
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| 234 | * which adopts position switching by antenna motion,
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| 235 | * wobbler (nutator) switching and On-The-Fly observation.
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| 236 | *
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| 237 | * The method is applicable to APEX, and other telescopes other than GBT.
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| 238 | *
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| 239 | * @param a Scantable which contains ON and OFF scans
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| 240 | * @param a string that indicates calibration mode
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| 241 | * @param a string that indicates antenna name
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| 242 | **/
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[3106] | 243 | casacore::CountedPtr<Scantable> cwcal( const casacore::CountedPtr<Scantable>& s,
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| 244 | const casacore::String calmode,
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| 245 | const casacore::String antname );
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[1391] | 246 |
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[1819] | 247 | /**
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| 248 | * Calibrate frequency switched scans with Chopper-Wheel like
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| 249 | * calibration method.
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| 250 | *
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| 251 | * The method is applicable to APEX, and other telescopes other than GBT.
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| 252 | *
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| 253 | * @param a Scantable which contains ON and OFF scans
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| 254 | * @param a string that indicates antenna name
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| 255 | **/
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[3106] | 256 | casacore::CountedPtr<Scantable> cwcalfs( const casacore::CountedPtr<Scantable>& s,
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| 257 | const casacore::String antname );
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[1819] | 258 |
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| 259 |
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| 260 | /**
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| 261 | * Folding frequency-switch data
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| 262 | * @param sig
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| 263 | * @param ref
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| 264 | * @param choffset
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| 265 | **/
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[3106] | 266 | casacore::CountedPtr<Scantable> dofold( const casacore::CountedPtr<Scantable> &sig,
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| 267 | const casacore::CountedPtr<Scantable> &ref,
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| 268 | casacore::Double choffset,
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| 269 | casacore::Double choffset2 = 0.0 );
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[1819] | 270 |
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| 271 | /**
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| 272 | * ALMA calibration
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| 273 | **/
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[3106] | 274 | casacore::CountedPtr<Scantable> almacal( const casacore::CountedPtr<Scantable>& s,
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| 275 | const casacore::String calmode ) ;
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| 276 | casacore::CountedPtr<Scantable> almacalfs( const casacore::CountedPtr<Scantable>& s ) ;
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[1819] | 277 |
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[3106] | 278 | casacore::CountedPtr<Scantable>
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| 279 | freqSwitch( const casacore::CountedPtr<Scantable>& in );
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[716] | 280 |
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[3106] | 281 | std::vector<float> statistic(const casacore::CountedPtr<Scantable>& in,
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[805] | 282 | const std::vector<bool>& mask,
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| 283 | const std::string& which);
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[457] | 284 |
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[3106] | 285 | std::vector<float> statisticRow(const casacore::CountedPtr<Scantable>& in,
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[1907] | 286 | const std::vector<bool>& mask,
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| 287 | const std::string& which,
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| 288 | int row);
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| 289 |
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[3106] | 290 | std::vector< int > minMaxChan(const casacore::CountedPtr<Scantable>& in,
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[1819] | 291 | const std::vector<bool>& mask,
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| 292 | const std::string& which);
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| 293 |
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[3106] | 294 | casacore::CountedPtr<Scantable> bin( const casacore::CountedPtr<Scantable>& in,
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[805] | 295 | int width=5);
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[3106] | 296 | casacore::CountedPtr<Scantable>
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| 297 | resample(const casacore::CountedPtr<Scantable>& in,
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[805] | 298 | const std::string& method, float width);
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[457] | 299 |
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[3106] | 300 | casacore::CountedPtr<Scantable>
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| 301 | smooth(const casacore::CountedPtr<Scantable>& in, const std::string& kernel,
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[1570] | 302 | float width, int order=2);
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[169] | 303 |
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[3106] | 304 | casacore::CountedPtr<Scantable>
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| 305 | gainElevation(const casacore::CountedPtr<Scantable>& in,
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[867] | 306 | const std::vector<float>& coeff,
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[805] | 307 | const std::string& fileName,
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[995] | 308 | const std::string& method);
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[3106] | 309 | casacore::CountedPtr<Scantable>
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| 310 | convertFlux(const casacore::CountedPtr<Scantable>& in, float d,
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[805] | 311 | float etaap, float jyperk);
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[152] | 312 |
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[3106] | 313 | casacore::CountedPtr<Scantable> opacity(const casacore::CountedPtr<Scantable>& in,
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[1689] | 314 | const std::vector<float>& tau);
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[144] | 315 |
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[3106] | 316 | casacore::CountedPtr<Scantable>
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| 317 | merge(const std::vector<casacore::CountedPtr<Scantable> >& in,
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[2900] | 318 | const std::string &freqTol = "");
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[841] | 319 |
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[3106] | 320 | casacore::CountedPtr<Scantable>
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| 321 | invertPhase( const casacore::CountedPtr<Scantable>& in);
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[912] | 322 |
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[3106] | 323 | casacore::CountedPtr<Scantable>
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| 324 | rotateXYPhase( const casacore::CountedPtr<Scantable>& in, float phase);
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[912] | 325 |
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[3106] | 326 | casacore::CountedPtr<Scantable>
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| 327 | rotateLinPolPhase( const casacore::CountedPtr<Scantable>& in, float phase);
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[896] | 328 |
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[3106] | 329 | casacore::CountedPtr<Scantable>
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| 330 | swapPolarisations(const casacore::CountedPtr<Scantable>& in);
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[896] | 331 |
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[3106] | 332 | casacore::CountedPtr<Scantable>
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| 333 | frequencyAlign( const casacore::CountedPtr<Scantable>& in,
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[927] | 334 | const std::string& refTime = "",
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| 335 | const std::string& method = "cubic" );
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[917] | 336 |
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[3106] | 337 | casacore::CountedPtr<Scantable>
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| 338 | convertPolarisation( const casacore::CountedPtr<Scantable>& in,
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[992] | 339 | const std::string& newtype);
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[1143] | 340 |
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[3106] | 341 | casacore::CountedPtr<Scantable>
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| 342 | mxExtract( const casacore::CountedPtr<Scantable>& in,
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[1143] | 343 | const std::string& srctype = "on");
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[992] | 344 |
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[1192] | 345 | /**
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| 346 | * "hard" flag the data, this flags everything selected in setSelection()
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| 347 | * @param frequency the frequency to remove
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| 348 | * @param width the number of lags to flag left to the side of the frequency
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| 349 | */
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[3106] | 350 | casacore::CountedPtr<Scantable>
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| 351 | lagFlag( const casacore::CountedPtr<Scantable>& in, double start,
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[1570] | 352 | double end, const std::string& mode="frequency");
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[1192] | 353 |
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[2177] | 354 | std::vector<float>
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[3106] | 355 | fft( const casacore::CountedPtr<Scantable>& in,
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[2177] | 356 | const std::vector<int>& whichrow,
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| 357 | bool getRealImag=false );
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| 358 |
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[1819] | 359 | // test for average spectra with different channel/resolution
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[3106] | 360 | casacore::CountedPtr<Scantable>
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| 361 | new_average( const std::vector<casacore::CountedPtr<Scantable> >& in,
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[1819] | 362 | const bool& compel,
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| 363 | const std::vector<bool>& mask = std::vector<bool>(),
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| 364 | const std::string& weight = "NONE",
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| 365 | const std::string& avmode = "SCAN" )
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[3106] | 366 | throw (casacore::AipsError) ;
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[1819] | 367 |
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[805] | 368 | private:
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[3106] | 369 | casacore::CountedPtr<Scantable> applyToPol( const casacore::CountedPtr<Scantable>& in,
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[896] | 370 | STPol::polOperation fptr,
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[3106] | 371 | casacore::Float phase);
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[896] | 372 |
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[805] | 373 | static imethod stringToIMethod(const std::string& in);
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| 374 | static WeightType stringToWeight(const std::string& in);
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[146] | 375 |
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[3106] | 376 | void scaleByVector(casacore::Table& in,
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| 377 | const casacore::Vector<casacore::Float>& factor,
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[805] | 378 | bool dotsys);
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[152] | 379 |
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[3106] | 380 | void scaleFromAsciiTable(casacore::Table& in, const std::string& filename,
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[805] | 381 | const std::string& method,
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[3106] | 382 | const casacore::Vector<casacore::Float>& xout,
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[805] | 383 | bool dotsys);
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[162] | 384 |
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[3106] | 385 | void scaleFromTable(casacore::Table& in, const casacore::Table& table,
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[805] | 386 | const std::string& method,
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[3106] | 387 | const casacore::Vector<casacore::Float>& xout, bool dotsys);
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[227] | 388 |
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[3106] | 389 | void convertBrightnessUnits(casacore::CountedPtr<Scantable>& in,
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[805] | 390 | bool tokelvin, float cfac);
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[227] | 391 |
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[3106] | 392 | casacore::CountedPtr< Scantable >
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| 393 | smoothOther( const casacore::CountedPtr< Scantable >& in,
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[1374] | 394 | const std::string& kernel,
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[1570] | 395 | float width, int order=2 );
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[1374] | 396 |
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[3106] | 397 | casacore::CountedPtr< Scantable >
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| 398 | getScantable(const casacore::CountedPtr< Scantable >& in, bool droprows);
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[230] | 399 |
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[3106] | 400 | casacore::MaskedArray<casacore::Float>
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| 401 | maskedArray( const casacore::Vector<casacore::Float>& s,
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| 402 | const casacore::Vector<casacore::uChar>& f );
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| 403 | casacore::MaskedArray<casacore::Double>
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| 404 | maskedArray( const casacore::Vector<casacore::Double>& s,
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| 405 | const casacore::Vector<casacore::uChar>& f );
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| 406 | casacore::Vector<casacore::uChar>
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| 407 | flagsFromMA(const casacore::MaskedArray<casacore::Float>& ma);
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[230] | 408 |
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[2580] | 409 | // Frequency switching
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[3106] | 410 | void calibrateFS( casacore::CountedPtr<Scantable> &sig,
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| 411 | casacore::CountedPtr<Scantable> &ref,
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| 412 | const casacore::CountedPtr<Scantable> &rsig,
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| 413 | const casacore::CountedPtr<Scantable> &rref,
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| 414 | const casacore::CountedPtr<Scantable> &sky,
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| 415 | const casacore::CountedPtr<Scantable> &hot,
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| 416 | const casacore::CountedPtr<Scantable> &cold,
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| 417 | const casacore::Vector<casacore::uInt> &rows ) ;
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| 418 | void calibrateAPEXFS( casacore::CountedPtr<Scantable> &sig,
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| 419 | casacore::CountedPtr<Scantable> &ref,
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| 420 | const vector< casacore::CountedPtr<Scantable> > &on,
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| 421 | const vector< casacore::CountedPtr<Scantable> > &sky,
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| 422 | const vector< casacore::CountedPtr<Scantable> > &hot,
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| 423 | const vector< casacore::CountedPtr<Scantable> > &cold,
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| 424 | const casacore::Vector<casacore::uInt> &rows ) ;
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| 425 | void copyRows( casacore::Table &out,
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| 426 | const casacore::Table &in,
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| 427 | casacore::uInt startout,
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| 428 | casacore::uInt startin,
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| 429 | casacore::uInt nrow,
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| 430 | casacore::Bool copySpectra=true,
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| 431 | casacore::Bool copyFlagtra=true,
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| 432 | casacore::Bool copyTsys=true ) ;
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| 433 | casacore::CountedPtr<Scantable> averageWithinSession( casacore::CountedPtr<Scantable> &s,
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[2580] | 434 | vector<bool> &mask,
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| 435 | string weight ) ;
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| 436 |
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[805] | 437 | bool insitu_;
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| 438 | };
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[234] | 439 |
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[805] | 440 | }
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[165] | 441 | #endif
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