| 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 choffset2 = 0.0 );
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| 265 |
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| 266 | /**
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| 267 | * ALMA calibration
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| 268 | **/
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| 269 | casa::CountedPtr<Scantable> almacal( const casa::CountedPtr<Scantable>& s,
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| 270 | const casa::String calmode ) ;
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| 271 | casa::CountedPtr<Scantable> almacalfs( const casa::CountedPtr<Scantable>& s ) ;
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| 272 |
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| 273 | casa::CountedPtr<Scantable>
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| 274 | freqSwitch( const casa::CountedPtr<Scantable>& in );
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| 275 |
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| 276 | std::vector<float> statistic(const casa::CountedPtr<Scantable>& in,
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| 277 | const std::vector<bool>& mask,
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| 278 | const std::string& which);
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| 279 |
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| 280 | std::vector<float> statisticRow(const casa::CountedPtr<Scantable>& in,
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| 281 | const std::vector<bool>& mask,
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| 282 | const std::string& which,
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| 283 | int row);
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| 284 |
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| 285 | std::vector< int > minMaxChan(const casa::CountedPtr<Scantable>& in,
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| 286 | const std::vector<bool>& mask,
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| 287 | const std::string& which);
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| 288 |
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| 289 | casa::CountedPtr<Scantable> bin( const casa::CountedPtr<Scantable>& in,
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| 290 | int width=5);
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| 291 | casa::CountedPtr<Scantable>
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| 292 | resample(const casa::CountedPtr<Scantable>& in,
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| 293 | const std::string& method, float width);
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| 294 |
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| 295 | casa::CountedPtr<Scantable>
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| 296 | smooth(const casa::CountedPtr<Scantable>& in, const std::string& kernel,
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| 297 | float width, int order=2);
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| 298 |
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| 299 | casa::CountedPtr<Scantable>
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| 300 | gainElevation(const casa::CountedPtr<Scantable>& in,
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| 301 | const std::vector<float>& coeff,
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| 302 | const std::string& fileName,
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| 303 | const std::string& method);
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| 304 | casa::CountedPtr<Scantable>
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| 305 | convertFlux(const casa::CountedPtr<Scantable>& in, float d,
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| 306 | float etaap, float jyperk);
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| 307 |
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| 308 | casa::CountedPtr<Scantable> opacity(const casa::CountedPtr<Scantable>& in,
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| 309 | const std::vector<float>& tau);
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| 310 |
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| 311 | casa::CountedPtr<Scantable>
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| 312 | merge(const std::vector<casa::CountedPtr<Scantable> >& in);
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| 313 |
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| 314 | casa::CountedPtr<Scantable>
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| 315 | invertPhase( const casa::CountedPtr<Scantable>& in);
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| 316 |
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| 317 | casa::CountedPtr<Scantable>
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| 318 | rotateXYPhase( const casa::CountedPtr<Scantable>& in, float phase);
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| 319 |
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| 320 | casa::CountedPtr<Scantable>
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| 321 | rotateLinPolPhase( const casa::CountedPtr<Scantable>& in, float phase);
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| 322 |
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| 323 | casa::CountedPtr<Scantable>
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| 324 | swapPolarisations(const casa::CountedPtr<Scantable>& in);
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| 325 |
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| 326 | casa::CountedPtr<Scantable>
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| 327 | frequencyAlign( const casa::CountedPtr<Scantable>& in,
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| 328 | const std::string& refTime = "",
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| 329 | const std::string& method = "cubic" );
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| 330 |
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| 331 | casa::CountedPtr<Scantable>
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| 332 | convertPolarisation( const casa::CountedPtr<Scantable>& in,
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| 333 | const std::string& newtype);
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| 334 |
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| 335 | casa::CountedPtr<Scantable>
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| 336 | mxExtract( const casa::CountedPtr<Scantable>& in,
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| 337 | const std::string& srctype = "on");
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| 338 |
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| 339 | /**
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| 340 | * "hard" flag the data, this flags everything selected in setSelection()
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| 341 | * @param frequency the frequency to remove
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| 342 | * @param width the number of lags to flag left to the side of the frequency
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| 343 | */
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| 344 | casa::CountedPtr<Scantable>
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| 345 | lagFlag( const casa::CountedPtr<Scantable>& in, double start,
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| 346 | double end, const std::string& mode="frequency");
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| 347 |
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| 348 | // test for average spectra with different channel/resolution
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| 349 | casa::CountedPtr<Scantable>
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| 350 | new_average( const std::vector<casa::CountedPtr<Scantable> >& in,
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| 351 | const bool& compel,
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| 352 | const std::vector<bool>& mask = std::vector<bool>(),
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| 353 | const std::string& weight = "NONE",
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| 354 | const std::string& avmode = "SCAN" )
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| 355 | throw (casa::AipsError) ;
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| 356 |
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| 357 | private:
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| 358 | casa::CountedPtr<Scantable> applyToPol( const casa::CountedPtr<Scantable>& in,
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| 359 | STPol::polOperation fptr,
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| 360 | casa::Float phase);
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| 361 |
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| 362 | static imethod stringToIMethod(const std::string& in);
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| 363 | static WeightType stringToWeight(const std::string& in);
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| 364 |
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| 365 | void scaleByVector(casa::Table& in,
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| 366 | const casa::Vector<casa::Float>& factor,
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| 367 | bool dotsys);
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| 368 |
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| 369 | void scaleFromAsciiTable(casa::Table& in, const std::string& filename,
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| 370 | const std::string& method,
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| 371 | const casa::Vector<casa::Float>& xout,
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| 372 | bool dotsys);
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| 373 |
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| 374 | void scaleFromTable(casa::Table& in, const casa::Table& table,
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| 375 | const std::string& method,
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| 376 | const casa::Vector<casa::Float>& xout, bool dotsys);
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| 377 |
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| 378 | void convertBrightnessUnits(casa::CountedPtr<Scantable>& in,
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| 379 | bool tokelvin, float cfac);
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| 380 |
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| 381 | casa::CountedPtr< Scantable >
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| 382 | smoothOther( const casa::CountedPtr< Scantable >& in,
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| 383 | const std::string& kernel,
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| 384 | float width, int order=2 );
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| 385 |
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| 386 | casa::CountedPtr< Scantable >
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| 387 | getScantable(const casa::CountedPtr< Scantable >& in, bool droprows);
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| 388 |
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| 389 | casa::MaskedArray<casa::Float>
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| 390 | maskedArray( const casa::Vector<casa::Float>& s,
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| 391 | const casa::Vector<casa::uChar>& f );
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| 392 | casa::MaskedArray<casa::Double>
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| 393 | maskedArray( const casa::Vector<casa::Double>& s,
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| 394 | const casa::Vector<casa::uChar>& f );
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| 395 | casa::Vector<casa::uChar>
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| 396 | flagsFromMA(const casa::MaskedArray<casa::Float>& ma);
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| 397 |
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| 398 | vector<float> getSpectrumFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode = "before" ) ;
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| 399 | vector<float> getTcalFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ;
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| 400 | vector<float> getTsysFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ;
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| 401 | vector<int> getRowIdFromTime( string reftime, casa::CountedPtr<Scantable>& s ) ;
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| 402 |
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| 403 | // Chopper-Wheel type calibration
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| 404 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on,
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| 405 | casa::CountedPtr<Scantable>& off,
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| 406 | casa::CountedPtr<Scantable>& sky,
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| 407 | casa::CountedPtr<Scantable>& hot,
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| 408 | casa::CountedPtr<Scantable>& cold,
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| 409 | int index,
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| 410 | string antname ) ;
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| 411 | // Tsys * (ON-OFF)/OFF
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| 412 | vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on,
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| 413 | casa::CountedPtr<Scantable>& off,
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| 414 | int index ) ;
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| 415 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig,
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| 416 | casa::CountedPtr<Scantable>& ref,
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| 417 | casa::CountedPtr<Scantable>& sky,
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| 418 | casa::CountedPtr<Scantable>& hot,
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| 419 | casa::CountedPtr<Scantable>& cold,
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| 420 | int index ) ;
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| 421 | vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig,
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| 422 | casa::CountedPtr<Scantable>& ref,
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| 423 | vector< casa::CountedPtr<Scantable> >& sky,
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| 424 | vector< casa::CountedPtr<Scantable> >& hot,
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| 425 | vector< casa::CountedPtr<Scantable> >& cold,
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| 426 | int index ) ;
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| 427 | double getMJD( string strtime ) ;
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| 428 |
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| 429 | bool insitu_;
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| 430 | };
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| 431 |
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| 432 | }
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| 433 | #endif
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