[824] | 1 | // |
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| 2 | // C++ Interface: Scantable |
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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) 2005 |
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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 ASAPSCANTABLE_H |
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| 13 | #define ASAPSCANTABLE_H |
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[2] | 14 | |
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| 15 | // STL |
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[2186] | 16 | #include <fstream> |
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| 17 | #include <iostream> |
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| 18 | #include <sstream> |
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[2] | 19 | #include <string> |
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| 20 | #include <vector> |
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| 21 | // AIPS++ |
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[455] | 22 | #include <casa/aips.h> |
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[322] | 23 | #include <casa/Arrays/MaskedArray.h> |
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[2186] | 24 | #include <casa/Arrays/Vector.h> |
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[80] | 25 | #include <casa/BasicSL/String.h> |
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[2186] | 26 | #include <casa/Containers/Record.h> |
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| 27 | #include <casa/Exceptions/Error.h> |
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| 28 | #include <casa/Quanta/Quantum.h> |
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[824] | 29 | #include <casa/Utilities/CountedPtr.h> |
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| 30 | |
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[2186] | 31 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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[322] | 32 | |
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[824] | 33 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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| 34 | |
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[2186] | 35 | #include <scimath/Mathematics/FFTServer.h> |
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[1598] | 36 | |
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[2186] | 37 | #include <tables/Tables/ArrayColumn.h> |
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| 38 | #include <tables/Tables/ScalarColumn.h> |
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| 39 | #include <tables/Tables/Table.h> |
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[1819] | 40 | |
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[2658] | 41 | |
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[2186] | 42 | #include "MathUtils.h" |
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| 43 | #include "STFit.h" |
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| 44 | #include "STFitEntry.h" |
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[2666] | 45 | //#include "STFitter.h" |
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[2186] | 46 | #include "STFocus.h" |
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| 47 | #include "STFrequencies.h" |
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[901] | 48 | #include "STHeader.h" |
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[2186] | 49 | #include "STHistory.h" |
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[824] | 50 | #include "STMolecules.h" |
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[2186] | 51 | #include "STPol.h" |
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[824] | 52 | #include "STSelector.h" |
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[2186] | 53 | #include "STTcal.h" |
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| 54 | #include "STWeather.h" |
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[2] | 55 | |
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[824] | 56 | namespace asap { |
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[2] | 57 | |
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[2666] | 58 | class Fitter; |
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| 59 | |
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[824] | 60 | /** |
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| 61 | * This class contains and wraps a casa::Table, which is used to store |
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| 62 | * all the information. This can be either a MemoryTable or a |
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| 63 | * disk based Table. |
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| 64 | * It provides access functions to the underlying table |
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| 65 | * It contains n subtables: |
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| 66 | * @li weather |
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| 67 | * @li frequencies |
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| 68 | * @li molecules |
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| 69 | * @li tcal |
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| 70 | * @li focus |
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| 71 | * @li fits |
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| 72 | * |
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| 73 | * @brief The main ASAP data container |
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| 74 | * @author Malte Marquarding |
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| 75 | * @date |
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| 76 | * @version |
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| 77 | */ |
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[2658] | 78 | class Scantable |
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[824] | 79 | { |
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[902] | 80 | |
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| 81 | friend class STMath; |
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| 82 | |
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[2] | 83 | public: |
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[824] | 84 | /** |
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| 85 | * Default constructor |
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| 86 | */ |
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[1350] | 87 | explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory); |
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[19] | 88 | |
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[824] | 89 | /** |
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[2321] | 90 | * Create a Scantable object from an existing table on disk |
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[824] | 91 | * @param[in] name the name of the existing Scantable |
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| 92 | */ |
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[2321] | 93 | explicit Scantable(const std::string& name, |
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| 94 | casa::Table::TableType ttype = casa::Table::Memory); |
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[2] | 95 | |
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[824] | 96 | /// @fixme this is only sensible for MemoryTables.... |
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| 97 | Scantable(const Scantable& other, bool clear=true); |
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[161] | 98 | |
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[824] | 99 | /** |
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| 100 | * Destructor |
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| 101 | */ |
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| 102 | virtual ~Scantable(); |
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[745] | 103 | |
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[824] | 104 | /** |
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| 105 | * get a const reference to the underlying casa::Table |
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[1104] | 106 | * @return const \ref casa::Table reference |
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[824] | 107 | */ |
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| 108 | const casa::Table& table() const; |
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[19] | 109 | |
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[824] | 110 | /** |
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| 111 | * get a reference to the underlying casa::Table with the Selection |
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| 112 | * object applied if set |
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| 113 | * @return casa::Table reference |
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| 114 | */ |
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| 115 | casa::Table& table(); |
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[21] | 116 | |
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[845] | 117 | |
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| 118 | /** |
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| 119 | * Get a handle to the selection object |
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| 120 | * @return constant STSelector reference |
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| 121 | */ |
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| 122 | const STSelector& getSelection() const { return selector_; } |
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| 123 | |
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| 124 | /** |
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| 125 | * Set the data to be a subset as defined by the STSelector |
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| 126 | * @param selection a STSelector object |
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| 127 | */ |
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[824] | 128 | void setSelection(const STSelector& selection); |
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[845] | 129 | |
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| 130 | /** |
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| 131 | * unset the selection of the data |
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| 132 | */ |
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[824] | 133 | void unsetSelection(); |
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| 134 | /** |
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| 135 | * set the header |
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[1295] | 136 | * @param[in] sth an STHeader object |
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[824] | 137 | */ |
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[901] | 138 | void setHeader( const STHeader& sth ); |
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[386] | 139 | |
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[824] | 140 | /** |
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| 141 | * get the header information |
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[901] | 142 | * @return an STHeader object |
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[824] | 143 | */ |
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[901] | 144 | STHeader getHeader( ) const; |
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[1068] | 145 | |
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[824] | 146 | /** |
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| 147 | * Checks if the "other" Scantable is conformant with this, |
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| 148 | * i.e. if header values are the same. |
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| 149 | * @param[in] other another Scantable |
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| 150 | * @return true or false |
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| 151 | */ |
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| 152 | bool conformant( const Scantable& other); |
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[430] | 153 | |
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[824] | 154 | /** |
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[1068] | 155 | * |
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| 156 | * @param stype The type of the source, 0 = on, 1 = off |
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| 157 | */ |
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| 158 | void setSourceType(int stype); |
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| 159 | |
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| 160 | |
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| 161 | /** |
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[1104] | 162 | * The number of scans in the table |
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[824] | 163 | * @return number of scans in the table |
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| 164 | */ |
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[845] | 165 | int nscan() const; |
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[490] | 166 | |
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[915] | 167 | casa::MEpoch::Types getTimeReference() const; |
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[21] | 168 | |
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[1411] | 169 | |
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| 170 | casa::MEpoch getEpoch(int whichrow) const; |
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| 171 | |
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[824] | 172 | /** |
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| 173 | * Get global antenna position |
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[845] | 174 | * @return casa::MPosition |
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[824] | 175 | */ |
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| 176 | casa::MPosition getAntennaPosition() const; |
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[490] | 177 | |
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[1441] | 178 | /** |
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| 179 | * the @ref casa::MDirection for a specific row |
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| 180 | * @param[in] whichrow the row number |
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| 181 | * return casa::MDirection |
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| 182 | */ |
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[987] | 183 | casa::MDirection getDirection( int whichrow ) const; |
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[1598] | 184 | |
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[1441] | 185 | /** |
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| 186 | * get the direction type as a string, e.g. "J2000" |
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| 187 | * @param[in] whichrow the row number |
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| 188 | * return the direction string |
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| 189 | */ |
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[1068] | 190 | std::string getDirectionString( int whichrow ) const; |
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| 191 | |
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[1441] | 192 | /** |
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| 193 | * set the direction type as a string, e.g. "J2000" |
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| 194 | * @param[in] refstr the direction type |
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| 195 | */ |
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[987] | 196 | void setDirectionRefString(const std::string& refstr=""); |
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[1441] | 197 | |
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[1104] | 198 | /** |
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| 199 | * get the direction reference string |
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| 200 | * @return a string describing the direction reference |
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| 201 | */ |
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[1598] | 202 | std::string getDirectionRefString() const; |
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[987] | 203 | |
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[824] | 204 | /** |
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[845] | 205 | * Return the Flux unit of the data, e.g. "Jy" or "K" |
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| 206 | * @return string |
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[824] | 207 | */ |
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| 208 | std::string getFluxUnit() const; |
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[472] | 209 | |
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[824] | 210 | /** |
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[845] | 211 | * Set the Flux unit of the data |
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| 212 | * @param unit a string representing the unit, e.g "Jy" or "K" |
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[824] | 213 | */ |
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| 214 | void setFluxUnit( const std::string& unit ); |
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[472] | 215 | |
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[824] | 216 | /** |
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[1189] | 217 | * Set the Stokes type of the data |
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[1295] | 218 | * @param feedtype a string representing the type, e.g "circular" or "linear" |
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[1189] | 219 | */ |
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| 220 | void setFeedType( const std::string& feedtype ); |
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| 221 | |
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| 222 | /** |
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[824] | 223 | * |
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[845] | 224 | * @param instrument a string representing an insturment. see xxx |
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[824] | 225 | */ |
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| 226 | void setInstrument( const std::string& instrument ); |
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[2] | 227 | |
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[845] | 228 | /** |
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| 229 | * (Re)calculate the azimuth and elevationnfor all rows |
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| 230 | */ |
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[824] | 231 | void calculateAZEL(); |
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[745] | 232 | |
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[824] | 233 | /** |
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[845] | 234 | * "hard" flag the data, this flags everything selected in setSelection() |
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[1104] | 235 | * param[in] msk a boolean mask of length nchan describing the points to |
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| 236 | * to be flagged |
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[824] | 237 | */ |
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[1430] | 238 | //void flag( const std::vector<bool>& msk = std::vector<bool>()); |
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[1994] | 239 | //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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[455] | 240 | |
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[1994] | 241 | void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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| 242 | |
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[852] | 243 | /** |
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[1819] | 244 | * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki) |
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| 245 | * param[in] rows list of row numbers to be flagged |
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| 246 | */ |
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| 247 | void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false); |
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| 248 | |
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| 249 | /** |
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| 250 | * Get flagRow info at the specified row. If true, the whole data |
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| 251 | * at the row should be flagged. |
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| 252 | */ |
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| 253 | bool getFlagRow(int whichrow) const |
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| 254 | { return (flagrowCol_(whichrow) > 0); } |
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| 255 | |
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| 256 | /** |
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| 257 | * Flag the data outside a specified range (in a channel-based manner). |
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| 258 | * (CAS-1807 Wataru Kawasaki) |
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| 259 | */ |
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| 260 | void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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| 261 | |
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| 262 | /** |
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| 263 | * Return a list of booleans with the size of nchan for a specified row, to get info |
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| 264 | * about which channel is clipped. |
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| 265 | */ |
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| 266 | std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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| 267 | void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag, |
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| 268 | casa::Vector<casa::uChar> flgs); |
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| 269 | |
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| 270 | /** |
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[852] | 271 | * Return a list of row numbers with respect to the original table. |
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[902] | 272 | * @return a list of unsigned ints |
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[852] | 273 | */ |
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| 274 | std::vector<unsigned int> rownumbers() const; |
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[845] | 275 | |
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[852] | 276 | |
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[845] | 277 | /** |
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| 278 | * Get the number of beams in the data or a specific scan |
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| 279 | * @param scanno the scan number to get the number of beams for. |
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| 280 | * If scanno<0 the number is retrieved from the header. |
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| 281 | * @return an integer number |
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| 282 | */ |
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[824] | 283 | int nbeam(int scanno=-1) const; |
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[845] | 284 | /** |
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| 285 | * Get the number of IFs in the data or a specific scan |
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| 286 | * @param scanno the scan number to get the number of IFs for. |
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| 287 | * If scanno<0 the number is retrieved from the header. |
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| 288 | * @return an integer number |
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| 289 | */ |
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[824] | 290 | int nif(int scanno=-1) const; |
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[845] | 291 | /** |
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| 292 | * Get the number of polarizations in the data or a specific scan |
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| 293 | * @param scanno the scan number to get the number of polarizations for. |
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| 294 | * If scanno<0 the number is retrieved from the header. |
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| 295 | * @return an integer number |
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| 296 | */ |
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[824] | 297 | int npol(int scanno=-1) const; |
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[794] | 298 | |
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[896] | 299 | std::string getPolType() const; |
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| 300 | |
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[845] | 301 | |
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| 302 | /** |
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| 303 | * Get the number of integartion cycles |
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| 304 | * @param scanno the scan number to get the number of rows for. |
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| 305 | * If scanno<0 the number is retrieved from the header. |
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[1104] | 306 | * @return the number of rows (for the specified scanno) |
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[845] | 307 | */ |
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[824] | 308 | int nrow(int scanno=-1) const; |
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[794] | 309 | |
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[1111] | 310 | int getBeam(int whichrow) const; |
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[1694] | 311 | std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); } |
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[50] | 312 | |
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[847] | 313 | int getIF(int whichrow) const; |
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[1694] | 314 | std::vector<uint> getIFNos() const { return getNumbers(ifCol_); } |
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[1111] | 315 | |
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[847] | 316 | int getPol(int whichrow) const; |
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[1694] | 317 | std::vector<uint> getPolNos() const { return getNumbers(polCol_); } |
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[1111] | 318 | |
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[1694] | 319 | std::vector<uint> getScanNos() const { return getNumbers(scanCol_); } |
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[865] | 320 | int getScan(int whichrow) const { return scanCol_(whichrow); } |
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[1111] | 321 | |
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[2667] | 322 | std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); } |
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| 323 | int getCycle(int whichrow) const { return cycleCol_(whichrow); } |
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| 324 | |
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[1819] | 325 | //TT addition |
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| 326 | std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); } |
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| 327 | |
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[1111] | 328 | /** |
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| 329 | * Get the number of channels in the data or a specific IF. This currently |
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| 330 | * varies only with IF number |
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| 331 | * @param ifno the IF number to get the number of channels for. |
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| 332 | * If ifno<0 the number is retrieved from the header. |
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| 333 | * @return an integer number |
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| 334 | */ |
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| 335 | int nchan(int ifno=-1) const; |
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[923] | 336 | int getChannels(int whichrow) const; |
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[206] | 337 | |
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[1111] | 338 | int ncycle(int scanno=-1) const; |
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| 339 | |
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[2667] | 340 | |
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[847] | 341 | double getInterval(int whichrow) const |
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| 342 | { return integrCol_(whichrow); } |
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[845] | 343 | |
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[865] | 344 | float getTsys(int whichrow) const |
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| 345 | { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); } |
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[2161] | 346 | std::vector<float> getTsysSpectrum(int whichrow) const ; |
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[847] | 347 | float getElevation(int whichrow) const |
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| 348 | { return elCol_(whichrow); } |
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| 349 | float getAzimuth(int whichrow) const |
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| 350 | { return azCol_(whichrow); } |
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[865] | 351 | float getParAngle(int whichrow) const |
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[1819] | 352 | { return focus().getParAngle(mfocusidCol_(whichrow)); } |
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| 353 | int getTcalId(int whichrow) const |
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| 354 | { return mtcalidCol_(whichrow); } |
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[386] | 355 | |
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[865] | 356 | std::string getSourceName(int whichrow) const |
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| 357 | { return srcnCol_(whichrow); } |
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| 358 | |
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[847] | 359 | std::vector<bool> getMask(int whichrow) const; |
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[896] | 360 | std::vector<float> getSpectrum(int whichrow, |
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[905] | 361 | const std::string& poltype = "" ) const; |
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[847] | 362 | |
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[884] | 363 | void setSpectrum(const std::vector<float>& spec, int whichrow); |
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| 364 | |
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[902] | 365 | std::string getPolarizationLabel(int index, const std::string& ptype) const |
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| 366 | { return STPol::getPolLabel(index, ptype ); } |
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[401] | 367 | |
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[845] | 368 | /** |
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| 369 | * Write the Scantable to disk |
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| 370 | * @param filename the output file name |
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| 371 | */ |
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[824] | 372 | void makePersistent(const std::string& filename); |
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[745] | 373 | |
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[860] | 374 | std::vector<std::string> getHistory() const |
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| 375 | { return historyTable_.getHistory(); }; |
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[483] | 376 | |
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[860] | 377 | void addHistory(const std::string& hist) { historyTable_.addEntry(hist); } |
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[488] | 378 | |
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[860] | 379 | void appendToHistoryTable(const STHistory& otherhist) |
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| 380 | { historyTable_.append(otherhist); } |
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| 381 | |
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[2163] | 382 | std::string headerSummary(); |
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[2290] | 383 | void summary(const std::string& filename=""); |
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| 384 | std::string oldheaderSummary(); |
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[2286] | 385 | // std::string summary(); |
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[2290] | 386 | void oldsummary(const std::string& filename=""); |
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| 387 | |
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[1947] | 388 | //std::string getTime(int whichrow=-1, bool showdate=true) const; |
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| 389 | std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const; |
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[1350] | 390 | double getIntTime(int whichrow) const { return integrCol_(whichrow); } |
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[19] | 391 | |
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[847] | 392 | // returns unit, conversion frame, doppler, base-frame |
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[18] | 393 | |
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[847] | 394 | /** |
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| 395 | * Get the frequency set up |
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| 396 | * This is forwarded to the STFrequencies subtable |
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| 397 | * @return unit, frame, doppler |
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| 398 | */ |
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| 399 | std::vector<std::string> getCoordInfo() const |
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| 400 | { return freqTable_.getInfo(); }; |
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| 401 | |
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| 402 | void setCoordInfo(std::vector<string> theinfo) |
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| 403 | { return freqTable_.setInfo(theinfo); }; |
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| 404 | |
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[865] | 405 | |
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| 406 | std::vector<double> getAbcissa(int whichrow) const; |
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| 407 | |
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[1730] | 408 | std::vector<float> getWeather(int whichrow) const; |
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| 409 | |
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[847] | 410 | std::string getAbcissaLabel(int whichrow) const; |
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| 411 | std::vector<double> getRestFrequencies() const |
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| 412 | { return moleculeTable_.getRestFrequencies(); } |
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[1819] | 413 | std::vector<double> getRestFrequency(int id) const |
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| 414 | { return moleculeTable_.getRestFrequency(id); } |
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[847] | 415 | |
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[1819] | 416 | /** |
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[1170] | 417 | void setRestFrequencies(double rf, const std::string& name = "", |
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| 418 | const std::string& = "Hz"); |
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[1819] | 419 | **/ |
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| 420 | // Modified by Takeshi Nakazato 05/09/2008 |
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| 421 | /*** |
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| 422 | void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "", |
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| 423 | const std::string& = "Hz"); |
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| 424 | ***/ |
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| 425 | void setRestFrequencies(vector<double> rf, |
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| 426 | const vector<std::string>& name = vector<std::string>(1,""), |
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| 427 | const std::string& = "Hz"); |
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[847] | 428 | |
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[1819] | 429 | //void setRestFrequencies(const std::string& name); |
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| 430 | void setRestFrequencies(const vector<std::string>& name); |
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| 431 | |
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[1360] | 432 | void shift(int npix); |
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| 433 | |
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[1598] | 434 | casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const; |
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| 435 | |
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[987] | 436 | void convertDirection(const std::string& newframe); |
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| 437 | |
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[824] | 438 | STFrequencies& frequencies() { return freqTable_; } |
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[1375] | 439 | const STFrequencies& frequencies() const { return freqTable_; } |
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[824] | 440 | STWeather& weather() { return weatherTable_; } |
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[1375] | 441 | const STWeather& weather() const { return weatherTable_; } |
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[824] | 442 | STFocus& focus() { return focusTable_; } |
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[1375] | 443 | const STFocus& focus() const { return focusTable_; } |
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[824] | 444 | STTcal& tcal() { return tcalTable_; } |
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[1375] | 445 | const STTcal& tcal() const { return tcalTable_; } |
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[824] | 446 | STMolecules& molecules() { return moleculeTable_; } |
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[1375] | 447 | const STMolecules& molecules() const { return moleculeTable_; } |
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[860] | 448 | STHistory& history() { return historyTable_; } |
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[1375] | 449 | const STHistory& history() const { return historyTable_; } |
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[972] | 450 | STFit& fit() { return fitTable_; } |
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[1375] | 451 | const STFit& fit() const { return fitTable_; } |
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[2] | 452 | |
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[902] | 453 | std::vector<std::string> columnNames() const; |
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[896] | 454 | |
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[972] | 455 | void addFit(const STFitEntry& fit, int row); |
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| 456 | STFitEntry getFit(int row) const |
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| 457 | { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; } |
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| 458 | |
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[1391] | 459 | //Added by TT |
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| 460 | /** |
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| 461 | * Get the antenna name |
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| 462 | * @return antenna name string |
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| 463 | */ |
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[1819] | 464 | casa::String getAntennaName() const; |
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[1391] | 465 | |
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| 466 | /** |
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| 467 | * For GBT MS data only. check a scan list |
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| 468 | * against the information found in GBT_GO table for |
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| 469 | * scan number orders to get correct pairs. |
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| 470 | * @param[in] scan list |
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| 471 | * @return status |
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| 472 | */ |
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| 473 | int checkScanInfo(const std::vector<int>& scanlist) const; |
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| 474 | |
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| 475 | /** |
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| 476 | * Get the direction as a vector, for a specific row |
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| 477 | * @param[in] whichrow the row numbyyer |
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| 478 | * @return the direction in a vector |
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| 479 | */ |
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| 480 | std::vector<double> getDirectionVector(int whichrow) const; |
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| 481 | |
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[1586] | 482 | /** |
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| 483 | * Set a flag indicating whether the data was parallactified |
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| 484 | * @param[in] flag true or false |
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| 485 | */ |
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[1598] | 486 | void parallactify(bool flag) |
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[2357] | 487 | { focusTable_.setParallactify(flag); } |
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[1727] | 488 | |
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[1819] | 489 | /** |
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| 490 | * Reshape spectrum |
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| 491 | * @param[in] nmin, nmax minimum and maximum channel |
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| 492 | * @param[in] irow row number |
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| 493 | * |
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| 494 | * 30/07/2008 Takeshi Nakazato |
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| 495 | **/ |
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| 496 | void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError ); |
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| 497 | void reshapeSpectrum( int nmin, int nmax, int irow ) ; |
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| 498 | |
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| 499 | /** |
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| 500 | * Change channel number under fixed bandwidth |
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| 501 | * @param[in] nchan, dnu new channel number and spectral resolution |
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| 502 | * @param[in] irow row number |
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| 503 | * |
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| 504 | * 27/08/2008 Takeshi Nakazato |
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| 505 | **/ |
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| 506 | void regridChannel( int nchan, double dnu ) ; |
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| 507 | void regridChannel( int nchan, double dnu, int irow ) ; |
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[2595] | 508 | void regridChannel( int nchan, double dnu, double fmin, int irow ) ; |
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[1819] | 509 | |
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[2435] | 510 | void regridSpecChannel( double dnu, int nchan=-1 ) ; |
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| 511 | |
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[2047] | 512 | bool getFlagtraFast(casa::uInt whichrow); |
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[1819] | 513 | |
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[2012] | 514 | void polyBaseline(const std::vector<bool>& mask, |
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| 515 | int order, |
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[2094] | 516 | bool getResidual=true, |
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[2189] | 517 | const std::string& progressInfo="true,1000", |
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| 518 | const bool outLogger=false, |
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[2012] | 519 | const std::string& blfile=""); |
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| 520 | void autoPolyBaseline(const std::vector<bool>& mask, |
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| 521 | int order, |
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| 522 | const std::vector<int>& edge, |
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| 523 | float threshold=3.0, |
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| 524 | int chanAvgLimit=1, |
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[2094] | 525 | bool getResidual=true, |
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[2189] | 526 | const std::string& progressInfo="true,1000", |
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| 527 | const bool outLogger=false, |
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[2012] | 528 | const std::string& blfile=""); |
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[2645] | 529 | void chebyshevBaseline(const std::vector<bool>& mask, |
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| 530 | int order, |
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| 531 | float thresClip, |
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| 532 | int nIterClip, |
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| 533 | bool getResidual=true, |
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| 534 | const std::string& progressInfo="true,1000", |
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| 535 | const bool outLogger=false, |
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| 536 | const std::string& blfile=""); |
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| 537 | void autoChebyshevBaseline(const std::vector<bool>& mask, |
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| 538 | int order, |
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| 539 | float thresClip, |
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| 540 | int nIterClip, |
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| 541 | const std::vector<int>& edge, |
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| 542 | float threshold=3.0, |
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| 543 | int chanAvgLimit=1, |
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| 544 | bool getResidual=true, |
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| 545 | const std::string& progressInfo="true,1000", |
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| 546 | const bool outLogger=false, |
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| 547 | const std::string& blfile=""); |
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[2012] | 548 | void cubicSplineBaseline(const std::vector<bool>& mask, |
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| 549 | int nPiece, |
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| 550 | float thresClip, |
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| 551 | int nIterClip, |
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[2094] | 552 | bool getResidual=true, |
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[2189] | 553 | const std::string& progressInfo="true,1000", |
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| 554 | const bool outLogger=false, |
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[2012] | 555 | const std::string& blfile=""); |
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| 556 | void autoCubicSplineBaseline(const std::vector<bool>& mask, |
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| 557 | int nPiece, |
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| 558 | float thresClip, |
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| 559 | int nIterClip, |
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| 560 | const std::vector<int>& edge, |
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| 561 | float threshold=3.0, |
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| 562 | int chanAvgLimit=1, |
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[2094] | 563 | bool getResidual=true, |
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[2189] | 564 | const std::string& progressInfo="true,1000", |
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| 565 | const bool outLogger=false, |
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[2012] | 566 | const std::string& blfile=""); |
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[2047] | 567 | void sinusoidBaseline(const std::vector<bool>& mask, |
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[2186] | 568 | const bool applyFFT, |
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| 569 | const std::string& fftMethod, |
---|
| 570 | const std::string& fftThresh, |
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| 571 | const std::vector<int>& addNWaves, |
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| 572 | const std::vector<int>& rejectNWaves, |
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[2047] | 573 | float thresClip, |
---|
| 574 | int nIterClip, |
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[2081] | 575 | bool getResidual=true, |
---|
[2189] | 576 | const std::string& progressInfo="true,1000", |
---|
| 577 | const bool outLogger=false, |
---|
[2047] | 578 | const std::string& blfile=""); |
---|
| 579 | void autoSinusoidBaseline(const std::vector<bool>& mask, |
---|
[2186] | 580 | const bool applyFFT, |
---|
| 581 | const std::string& fftMethod, |
---|
| 582 | const std::string& fftThresh, |
---|
| 583 | const std::vector<int>& addNWaves, |
---|
| 584 | const std::vector<int>& rejectNWaves, |
---|
[2047] | 585 | float thresClip, |
---|
| 586 | int nIterClip, |
---|
| 587 | const std::vector<int>& edge, |
---|
| 588 | float threshold=3.0, |
---|
| 589 | int chanAvgLimit=1, |
---|
[2081] | 590 | bool getResidual=true, |
---|
[2189] | 591 | const std::string& progressInfo="true,1000", |
---|
| 592 | const bool outLogger=false, |
---|
[2047] | 593 | const std::string& blfile=""); |
---|
[2186] | 594 | std::vector<float> execFFT(const int whichrow, |
---|
| 595 | const std::vector<bool>& inMask, |
---|
| 596 | bool getRealImag=false, |
---|
| 597 | bool getAmplitudeOnly=false); |
---|
[2012] | 598 | float getRms(const std::vector<bool>& mask, int whichrow); |
---|
| 599 | std::string formatBaselineParams(const std::vector<float>& params, |
---|
| 600 | const std::vector<bool>& fixed, |
---|
| 601 | float rms, |
---|
[2193] | 602 | int nClipped, |
---|
[2012] | 603 | const std::string& masklist, |
---|
| 604 | int whichrow, |
---|
[2064] | 605 | bool verbose=false, |
---|
[2641] | 606 | bool csvformat=false, |
---|
[2064] | 607 | int start=-1, |
---|
| 608 | int count=-1, |
---|
| 609 | bool resetparamid=false) const; |
---|
[2012] | 610 | std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges, |
---|
| 611 | const std::vector<float>& params, |
---|
| 612 | const std::vector<bool>& fixed, |
---|
| 613 | float rms, |
---|
[2193] | 614 | int nClipped, |
---|
[2012] | 615 | const std::string& masklist, |
---|
| 616 | int whichrow, |
---|
[2641] | 617 | bool verbose=false, |
---|
| 618 | bool csvformat=false) const; |
---|
[2591] | 619 | std::vector<uint> getMoleculeIdColumnData() const; |
---|
| 620 | void setMoleculeIdColumnData(const std::vector<uint>& molids); |
---|
[1907] | 621 | |
---|
[2012] | 622 | |
---|
[824] | 623 | private: |
---|
[896] | 624 | |
---|
| 625 | casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const; |
---|
| 626 | |
---|
[824] | 627 | /** |
---|
[2005] | 628 | * Turns a time value into a formatted string |
---|
[824] | 629 | * @param x |
---|
| 630 | * @return |
---|
| 631 | */ |
---|
| 632 | std::string formatSec(casa::Double x) const; |
---|
[18] | 633 | |
---|
[824] | 634 | std::string formatTime(const casa::MEpoch& me, bool showdate)const; |
---|
[1947] | 635 | std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const; |
---|
[22] | 636 | |
---|
[824] | 637 | /** |
---|
| 638 | * Turns a casa::MDirection into a nicely formatted string |
---|
| 639 | * @param md an casa::MDirection |
---|
| 640 | * @return |
---|
| 641 | */ |
---|
| 642 | std::string formatDirection(const casa::MDirection& md) const; |
---|
[19] | 643 | |
---|
[824] | 644 | /** |
---|
| 645 | * Create a unique file name for the paged (temporary) table |
---|
| 646 | * @return just the name |
---|
| 647 | */ |
---|
| 648 | static casa::String generateName(); |
---|
[286] | 649 | |
---|
[824] | 650 | /** |
---|
| 651 | * attach to cached columns |
---|
| 652 | */ |
---|
| 653 | void attach(); |
---|
[50] | 654 | |
---|
[824] | 655 | /** |
---|
| 656 | * Set up the main casa::Table |
---|
| 657 | */ |
---|
| 658 | void setupMainTable(); |
---|
[88] | 659 | |
---|
[859] | 660 | void attachSubtables(); |
---|
[865] | 661 | void copySubtables(const Scantable& other); |
---|
| 662 | |
---|
[824] | 663 | /** |
---|
| 664 | * Convert an "old" asap1 style row index into a new index |
---|
| 665 | * @param[in] therow |
---|
| 666 | * @return and index into @table_ |
---|
| 667 | */ |
---|
| 668 | int rowToScanIndex(int therow); |
---|
[212] | 669 | |
---|
[1694] | 670 | std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const; |
---|
[1111] | 671 | |
---|
[2321] | 672 | static const casa::uInt version_ = 4; |
---|
[286] | 673 | |
---|
[824] | 674 | STSelector selector_; |
---|
[236] | 675 | |
---|
[824] | 676 | casa::Table::TableType type_; |
---|
[465] | 677 | |
---|
[824] | 678 | // the actual data |
---|
| 679 | casa::Table table_; |
---|
| 680 | casa::Table originalTable_; |
---|
[745] | 681 | |
---|
[824] | 682 | STTcal tcalTable_; |
---|
| 683 | STFrequencies freqTable_; |
---|
| 684 | STWeather weatherTable_; |
---|
| 685 | STFocus focusTable_; |
---|
| 686 | STMolecules moleculeTable_; |
---|
[860] | 687 | STHistory historyTable_; |
---|
[960] | 688 | STFit fitTable_; |
---|
[860] | 689 | |
---|
[824] | 690 | // Cached Columns to avoid reconstructing them for each row get/put |
---|
[847] | 691 | casa::ScalarColumn<casa::Double> integrCol_; |
---|
[824] | 692 | casa::MDirection::ScalarColumn dirCol_; |
---|
[847] | 693 | casa::MEpoch::ScalarColumn timeCol_; |
---|
[923] | 694 | casa::ScalarColumn<casa::Float> azCol_; |
---|
| 695 | casa::ScalarColumn<casa::Float> elCol_; |
---|
[824] | 696 | casa::ScalarColumn<casa::String> srcnCol_, fldnCol_; |
---|
[1819] | 697 | casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_; |
---|
[1068] | 698 | casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_; |
---|
[865] | 699 | casa::ArrayColumn<casa::Float> specCol_, tsysCol_; |
---|
[824] | 700 | casa::ArrayColumn<casa::uChar> flagsCol_; |
---|
[430] | 701 | |
---|
[824] | 702 | // id in frequencies table |
---|
| 703 | casa::ScalarColumn<casa::uInt> mfreqidCol_; |
---|
| 704 | // id in tcal table |
---|
| 705 | casa::ScalarColumn<casa::uInt> mtcalidCol_; |
---|
[430] | 706 | |
---|
[824] | 707 | casa::ArrayColumn<casa::String> histitemCol_; |
---|
[972] | 708 | casa::ScalarColumn<casa::Int> mfitidCol_; |
---|
[824] | 709 | casa::ScalarColumn<casa::uInt> mweatheridCol_; |
---|
[322] | 710 | |
---|
[824] | 711 | casa::ScalarColumn<casa::uInt> mfocusidCol_; |
---|
| 712 | |
---|
| 713 | casa::ScalarColumn<casa::uInt> mmolidCol_; |
---|
| 714 | |
---|
[896] | 715 | static std::map<std::string, STPol::STPolFactory *> factories_; |
---|
| 716 | void initFactories(); |
---|
| 717 | |
---|
[1819] | 718 | /** |
---|
| 719 | * Add an auxiliary column to the main table and attach it to a |
---|
| 720 | * cached column. Use for adding new columns that the original asap2 |
---|
| 721 | * tables do not have. |
---|
| 722 | * @param[in] col reference to the cached column to be attached |
---|
| 723 | * @param[in] colName column name in asap table |
---|
| 724 | * @param[in] defValue default value to fill in the column |
---|
| 725 | * |
---|
| 726 | * 25/10/2009 Wataru Kawasaki |
---|
| 727 | */ |
---|
| 728 | template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&, |
---|
| 729 | const casa::String&, |
---|
| 730 | const T2&); |
---|
| 731 | template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&, |
---|
| 732 | const casa::String&, |
---|
| 733 | const casa::Array<T2>&); |
---|
[1907] | 734 | |
---|
[2012] | 735 | void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter); |
---|
[2645] | 736 | double getChebyshevPolynomial(int n, double x); |
---|
| 737 | std::vector<float> doChebyshevFitting(const std::vector<float>& data, |
---|
| 738 | const std::vector<bool>& mask, |
---|
| 739 | int order, |
---|
| 740 | std::vector<float>& params, |
---|
| 741 | int& nClipped, |
---|
| 742 | float thresClip=3.0, |
---|
| 743 | int nIterClip=1, |
---|
| 744 | bool getResidual=true); |
---|
[2012] | 745 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
| 746 | const std::vector<bool>& mask, |
---|
[2081] | 747 | int nPiece, |
---|
[2064] | 748 | std::vector<int>& idxEdge, |
---|
[2012] | 749 | std::vector<float>& params, |
---|
[2193] | 750 | int& nClipped, |
---|
[2012] | 751 | float thresClip=3.0, |
---|
[2058] | 752 | int nIterClip=1, |
---|
[2094] | 753 | bool getResidual=true); |
---|
[2047] | 754 | std::vector<float> doSinusoidFitting(const std::vector<float>& data, |
---|
| 755 | const std::vector<bool>& mask, |
---|
[2081] | 756 | const std::vector<int>& waveNumbers, |
---|
[2047] | 757 | std::vector<float>& params, |
---|
[2193] | 758 | int& nClipped, |
---|
[2047] | 759 | float thresClip=3.0, |
---|
[2058] | 760 | int nIterClip=1, |
---|
[2094] | 761 | bool getResidual=true); |
---|
[2186] | 762 | void selectWaveNumbers(const int whichrow, |
---|
| 763 | const std::vector<bool>& chanMask, |
---|
| 764 | const bool applyFFT, |
---|
| 765 | const std::string& fftMethod, |
---|
| 766 | const std::string& fftThresh, |
---|
| 767 | const std::vector<int>& addNWaves, |
---|
| 768 | const std::vector<int>& rejectNWaves, |
---|
| 769 | std::vector<int>& nWaves); |
---|
| 770 | void parseThresholdExpression(const std::string& fftThresh, |
---|
| 771 | std::string& fftThAttr, |
---|
| 772 | float& fftThSigma, |
---|
| 773 | int& fftThTop); |
---|
| 774 | void doSelectWaveNumbers(const int whichrow, |
---|
| 775 | const std::vector<bool>& chanMask, |
---|
| 776 | const std::string& fftMethod, |
---|
| 777 | const float fftThSigma, |
---|
| 778 | const int fftThTop, |
---|
| 779 | const std::string& fftThAttr, |
---|
| 780 | std::vector<int>& nWaves); |
---|
[2411] | 781 | void addAuxWaveNumbers(const int whichrow, |
---|
| 782 | const std::vector<int>& addNWaves, |
---|
[2186] | 783 | const std::vector<int>& rejectNWaves, |
---|
| 784 | std::vector<int>& nWaves); |
---|
[2411] | 785 | void setWaveNumberListUptoNyquistFreq(const int whichrow, |
---|
| 786 | std::vector<int>& nWaves); |
---|
[2012] | 787 | bool hasSameNchanOverIFs(); |
---|
| 788 | std::string getMaskRangeList(const std::vector<bool>& mask, |
---|
| 789 | int whichrow, |
---|
| 790 | const casa::String& coordInfo, |
---|
[2047] | 791 | bool hasSameNchan, |
---|
| 792 | bool verbose=false); |
---|
| 793 | std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask); |
---|
[2641] | 794 | std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const; |
---|
| 795 | std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const; |
---|
[2012] | 796 | std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask); |
---|
| 797 | //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder); |
---|
[2641] | 798 | void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, Fitter& fitter); |
---|
| 799 | void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped); |
---|
| 800 | void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped); |
---|
[2189] | 801 | void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow); |
---|
| 802 | void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000); |
---|
[1994] | 803 | |
---|
| 804 | void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval); |
---|
| 805 | |
---|
[2] | 806 | }; |
---|
| 807 | |
---|
[824] | 808 | } // namespace |
---|
| 809 | |
---|
[2] | 810 | #endif |
---|