[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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[894] | 41 | #include "Logger.h" |
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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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| 45 | #include "STFitter.h" |
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| 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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[824] | 58 | /** |
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| 59 | * This class contains and wraps a casa::Table, which is used to store |
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| 60 | * all the information. This can be either a MemoryTable or a |
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| 61 | * disk based Table. |
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| 62 | * It provides access functions to the underlying table |
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| 63 | * It contains n subtables: |
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| 64 | * @li weather |
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| 65 | * @li frequencies |
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| 66 | * @li molecules |
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| 67 | * @li tcal |
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| 68 | * @li focus |
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| 69 | * @li fits |
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| 70 | * |
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| 71 | * @brief The main ASAP data container |
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| 72 | * @author Malte Marquarding |
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| 73 | * @date |
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| 74 | * @version |
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| 75 | */ |
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[890] | 76 | class Scantable : private Logger |
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[824] | 77 | { |
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[902] | 78 | |
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| 79 | friend class STMath; |
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| 80 | |
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[2] | 81 | public: |
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[824] | 82 | /** |
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| 83 | * Default constructor |
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| 84 | */ |
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[1350] | 85 | explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory); |
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[19] | 86 | |
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[824] | 87 | /** |
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[2321] | 88 | * Create a Scantable object from an existing table on disk |
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[824] | 89 | * @param[in] name the name of the existing Scantable |
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| 90 | */ |
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[2321] | 91 | explicit Scantable(const std::string& name, |
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| 92 | casa::Table::TableType ttype = casa::Table::Memory); |
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[2] | 93 | |
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[824] | 94 | /// @fixme this is only sensible for MemoryTables.... |
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| 95 | Scantable(const Scantable& other, bool clear=true); |
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[161] | 96 | |
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[824] | 97 | /** |
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| 98 | * Destructor |
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| 99 | */ |
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| 100 | virtual ~Scantable(); |
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[745] | 101 | |
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[824] | 102 | /** |
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| 103 | * get a const reference to the underlying casa::Table |
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[1104] | 104 | * @return const \ref casa::Table reference |
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[824] | 105 | */ |
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| 106 | const casa::Table& table() const; |
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[19] | 107 | |
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[824] | 108 | /** |
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| 109 | * get a reference to the underlying casa::Table with the Selection |
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| 110 | * object applied if set |
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| 111 | * @return casa::Table reference |
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| 112 | */ |
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| 113 | casa::Table& table(); |
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[21] | 114 | |
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[845] | 115 | |
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| 116 | /** |
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| 117 | * Get a handle to the selection object |
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| 118 | * @return constant STSelector reference |
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| 119 | */ |
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| 120 | const STSelector& getSelection() const { return selector_; } |
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| 121 | |
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| 122 | /** |
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| 123 | * Set the data to be a subset as defined by the STSelector |
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| 124 | * @param selection a STSelector object |
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| 125 | */ |
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[824] | 126 | void setSelection(const STSelector& selection); |
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[845] | 127 | |
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| 128 | /** |
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| 129 | * unset the selection of the data |
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| 130 | */ |
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[824] | 131 | void unsetSelection(); |
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| 132 | /** |
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| 133 | * set the header |
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[1295] | 134 | * @param[in] sth an STHeader object |
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[824] | 135 | */ |
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[901] | 136 | void setHeader( const STHeader& sth ); |
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[386] | 137 | |
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[824] | 138 | /** |
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| 139 | * get the header information |
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[901] | 140 | * @return an STHeader object |
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[824] | 141 | */ |
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[901] | 142 | STHeader getHeader( ) const; |
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[1068] | 143 | |
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[824] | 144 | /** |
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| 145 | * Checks if the "other" Scantable is conformant with this, |
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| 146 | * i.e. if header values are the same. |
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| 147 | * @param[in] other another Scantable |
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| 148 | * @return true or false |
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| 149 | */ |
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| 150 | bool conformant( const Scantable& other); |
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[430] | 151 | |
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[824] | 152 | /** |
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[1068] | 153 | * |
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| 154 | * @param stype The type of the source, 0 = on, 1 = off |
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| 155 | */ |
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| 156 | void setSourceType(int stype); |
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| 157 | |
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| 158 | |
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| 159 | /** |
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[1104] | 160 | * The number of scans in the table |
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[824] | 161 | * @return number of scans in the table |
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| 162 | */ |
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[845] | 163 | int nscan() const; |
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[490] | 164 | |
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[915] | 165 | casa::MEpoch::Types getTimeReference() const; |
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[21] | 166 | |
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[1411] | 167 | |
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| 168 | casa::MEpoch getEpoch(int whichrow) const; |
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| 169 | |
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[824] | 170 | /** |
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| 171 | * Get global antenna position |
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[845] | 172 | * @return casa::MPosition |
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[824] | 173 | */ |
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| 174 | casa::MPosition getAntennaPosition() const; |
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[490] | 175 | |
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[1441] | 176 | /** |
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| 177 | * the @ref casa::MDirection for a specific row |
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| 178 | * @param[in] whichrow the row number |
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| 179 | * return casa::MDirection |
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| 180 | */ |
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[987] | 181 | casa::MDirection getDirection( int whichrow ) const; |
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[1598] | 182 | |
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[1441] | 183 | /** |
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| 184 | * get the direction type as a string, e.g. "J2000" |
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| 185 | * @param[in] whichrow the row number |
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| 186 | * return the direction string |
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| 187 | */ |
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[1068] | 188 | std::string getDirectionString( int whichrow ) const; |
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| 189 | |
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[1441] | 190 | /** |
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| 191 | * set the direction type as a string, e.g. "J2000" |
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| 192 | * @param[in] refstr the direction type |
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| 193 | */ |
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[987] | 194 | void setDirectionRefString(const std::string& refstr=""); |
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[1441] | 195 | |
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[1104] | 196 | /** |
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| 197 | * get the direction reference string |
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| 198 | * @return a string describing the direction reference |
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| 199 | */ |
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[1598] | 200 | std::string getDirectionRefString() const; |
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[987] | 201 | |
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[824] | 202 | /** |
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[845] | 203 | * Return the Flux unit of the data, e.g. "Jy" or "K" |
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| 204 | * @return string |
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[824] | 205 | */ |
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| 206 | std::string getFluxUnit() const; |
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[472] | 207 | |
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[824] | 208 | /** |
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[845] | 209 | * Set the Flux unit of the data |
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| 210 | * @param unit a string representing the unit, e.g "Jy" or "K" |
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[824] | 211 | */ |
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| 212 | void setFluxUnit( const std::string& unit ); |
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[472] | 213 | |
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[824] | 214 | /** |
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[1189] | 215 | * Set the Stokes type of the data |
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[1295] | 216 | * @param feedtype a string representing the type, e.g "circular" or "linear" |
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[1189] | 217 | */ |
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| 218 | void setFeedType( const std::string& feedtype ); |
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| 219 | |
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| 220 | /** |
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[824] | 221 | * |
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[845] | 222 | * @param instrument a string representing an insturment. see xxx |
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[824] | 223 | */ |
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| 224 | void setInstrument( const std::string& instrument ); |
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[2] | 225 | |
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[845] | 226 | /** |
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| 227 | * (Re)calculate the azimuth and elevationnfor all rows |
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| 228 | */ |
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[824] | 229 | void calculateAZEL(); |
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[745] | 230 | |
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[824] | 231 | /** |
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[845] | 232 | * "hard" flag the data, this flags everything selected in setSelection() |
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[1104] | 233 | * param[in] msk a boolean mask of length nchan describing the points to |
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| 234 | * to be flagged |
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[824] | 235 | */ |
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[1430] | 236 | //void flag( const std::vector<bool>& msk = std::vector<bool>()); |
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[1994] | 237 | //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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[455] | 238 | |
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[1994] | 239 | void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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| 240 | |
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[852] | 241 | /** |
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[1819] | 242 | * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki) |
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| 243 | * param[in] rows list of row numbers to be flagged |
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| 244 | */ |
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| 245 | void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false); |
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| 246 | |
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| 247 | /** |
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| 248 | * Get flagRow info at the specified row. If true, the whole data |
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| 249 | * at the row should be flagged. |
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| 250 | */ |
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| 251 | bool getFlagRow(int whichrow) const |
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| 252 | { return (flagrowCol_(whichrow) > 0); } |
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| 253 | |
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| 254 | /** |
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| 255 | * Flag the data outside a specified range (in a channel-based manner). |
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| 256 | * (CAS-1807 Wataru Kawasaki) |
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| 257 | */ |
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| 258 | void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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| 259 | |
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| 260 | /** |
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| 261 | * Return a list of booleans with the size of nchan for a specified row, to get info |
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| 262 | * about which channel is clipped. |
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| 263 | */ |
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| 264 | std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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| 265 | void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag, |
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| 266 | casa::Vector<casa::uChar> flgs); |
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| 267 | |
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| 268 | /** |
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[852] | 269 | * Return a list of row numbers with respect to the original table. |
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[902] | 270 | * @return a list of unsigned ints |
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[852] | 271 | */ |
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| 272 | std::vector<unsigned int> rownumbers() const; |
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[845] | 273 | |
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[852] | 274 | |
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[845] | 275 | /** |
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| 276 | * Get the number of beams in the data or a specific scan |
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| 277 | * @param scanno the scan number to get the number of beams for. |
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| 278 | * If scanno<0 the number is retrieved from the header. |
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| 279 | * @return an integer number |
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| 280 | */ |
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[824] | 281 | int nbeam(int scanno=-1) const; |
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[845] | 282 | /** |
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| 283 | * Get the number of IFs in the data or a specific scan |
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| 284 | * @param scanno the scan number to get the number of IFs for. |
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| 285 | * If scanno<0 the number is retrieved from the header. |
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| 286 | * @return an integer number |
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| 287 | */ |
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[824] | 288 | int nif(int scanno=-1) const; |
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[845] | 289 | /** |
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| 290 | * Get the number of polarizations in the data or a specific scan |
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| 291 | * @param scanno the scan number to get the number of polarizations for. |
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| 292 | * If scanno<0 the number is retrieved from the header. |
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| 293 | * @return an integer number |
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| 294 | */ |
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[824] | 295 | int npol(int scanno=-1) const; |
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[794] | 296 | |
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[896] | 297 | std::string getPolType() const; |
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| 298 | |
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[845] | 299 | |
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| 300 | /** |
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| 301 | * Get the number of integartion cycles |
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| 302 | * @param scanno the scan number to get the number of rows for. |
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| 303 | * If scanno<0 the number is retrieved from the header. |
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[1104] | 304 | * @return the number of rows (for the specified scanno) |
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[845] | 305 | */ |
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[824] | 306 | int nrow(int scanno=-1) const; |
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[794] | 307 | |
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[1111] | 308 | int getBeam(int whichrow) const; |
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[1694] | 309 | std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); } |
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[50] | 310 | |
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[847] | 311 | int getIF(int whichrow) const; |
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[1694] | 312 | std::vector<uint> getIFNos() const { return getNumbers(ifCol_); } |
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[1111] | 313 | |
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[847] | 314 | int getPol(int whichrow) const; |
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[1694] | 315 | std::vector<uint> getPolNos() const { return getNumbers(polCol_); } |
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[1111] | 316 | |
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[1694] | 317 | std::vector<uint> getScanNos() const { return getNumbers(scanCol_); } |
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[865] | 318 | int getScan(int whichrow) const { return scanCol_(whichrow); } |
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[1111] | 319 | |
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[1819] | 320 | //TT addition |
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| 321 | std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); } |
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| 322 | |
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[1111] | 323 | /** |
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| 324 | * Get the number of channels in the data or a specific IF. This currently |
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| 325 | * varies only with IF number |
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| 326 | * @param ifno the IF number to get the number of channels for. |
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| 327 | * If ifno<0 the number is retrieved from the header. |
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| 328 | * @return an integer number |
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| 329 | */ |
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| 330 | int nchan(int ifno=-1) const; |
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[923] | 331 | int getChannels(int whichrow) const; |
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[206] | 332 | |
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[1111] | 333 | int ncycle(int scanno=-1) const; |
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| 334 | int getCycle(int whichrow) const { return cycleCol_(whichrow); } |
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| 335 | |
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[847] | 336 | double getInterval(int whichrow) const |
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| 337 | { return integrCol_(whichrow); } |
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[845] | 338 | |
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[865] | 339 | float getTsys(int whichrow) const |
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| 340 | { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); } |
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[2161] | 341 | std::vector<float> getTsysSpectrum(int whichrow) const ; |
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[847] | 342 | float getElevation(int whichrow) const |
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| 343 | { return elCol_(whichrow); } |
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| 344 | float getAzimuth(int whichrow) const |
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| 345 | { return azCol_(whichrow); } |
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[865] | 346 | float getParAngle(int whichrow) const |
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[1819] | 347 | { return focus().getParAngle(mfocusidCol_(whichrow)); } |
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| 348 | int getTcalId(int whichrow) const |
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| 349 | { return mtcalidCol_(whichrow); } |
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[386] | 350 | |
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[865] | 351 | std::string getSourceName(int whichrow) const |
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| 352 | { return srcnCol_(whichrow); } |
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| 353 | |
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[847] | 354 | std::vector<bool> getMask(int whichrow) const; |
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[896] | 355 | std::vector<float> getSpectrum(int whichrow, |
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[905] | 356 | const std::string& poltype = "" ) const; |
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[847] | 357 | |
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[884] | 358 | void setSpectrum(const std::vector<float>& spec, int whichrow); |
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| 359 | |
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[902] | 360 | std::string getPolarizationLabel(int index, const std::string& ptype) const |
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| 361 | { return STPol::getPolLabel(index, ptype ); } |
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[401] | 362 | |
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[845] | 363 | /** |
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| 364 | * Write the Scantable to disk |
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| 365 | * @param filename the output file name |
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| 366 | */ |
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[824] | 367 | void makePersistent(const std::string& filename); |
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[745] | 368 | |
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[860] | 369 | std::vector<std::string> getHistory() const |
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| 370 | { return historyTable_.getHistory(); }; |
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[483] | 371 | |
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[860] | 372 | void addHistory(const std::string& hist) { historyTable_.addEntry(hist); } |
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[488] | 373 | |
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[860] | 374 | void appendToHistoryTable(const STHistory& otherhist) |
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| 375 | { historyTable_.append(otherhist); } |
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| 376 | |
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[2163] | 377 | std::string headerSummary(); |
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[2290] | 378 | void summary(const std::string& filename=""); |
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| 379 | std::string oldheaderSummary(); |
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[2286] | 380 | // std::string summary(); |
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[2290] | 381 | void oldsummary(const std::string& filename=""); |
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| 382 | |
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[1947] | 383 | //std::string getTime(int whichrow=-1, bool showdate=true) const; |
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| 384 | std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const; |
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[1350] | 385 | double getIntTime(int whichrow) const { return integrCol_(whichrow); } |
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[19] | 386 | |
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[847] | 387 | // returns unit, conversion frame, doppler, base-frame |
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[18] | 388 | |
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[847] | 389 | /** |
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| 390 | * Get the frequency set up |
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| 391 | * This is forwarded to the STFrequencies subtable |
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| 392 | * @return unit, frame, doppler |
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| 393 | */ |
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| 394 | std::vector<std::string> getCoordInfo() const |
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| 395 | { return freqTable_.getInfo(); }; |
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| 396 | |
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| 397 | void setCoordInfo(std::vector<string> theinfo) |
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| 398 | { return freqTable_.setInfo(theinfo); }; |
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| 399 | |
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[865] | 400 | |
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| 401 | std::vector<double> getAbcissa(int whichrow) const; |
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| 402 | |
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[1730] | 403 | std::vector<float> getWeather(int whichrow) const; |
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| 404 | |
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[847] | 405 | std::string getAbcissaLabel(int whichrow) const; |
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| 406 | std::vector<double> getRestFrequencies() const |
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| 407 | { return moleculeTable_.getRestFrequencies(); } |
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[1819] | 408 | std::vector<double> getRestFrequency(int id) const |
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| 409 | { return moleculeTable_.getRestFrequency(id); } |
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[847] | 410 | |
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[1819] | 411 | /** |
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[1170] | 412 | void setRestFrequencies(double rf, const std::string& name = "", |
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| 413 | const std::string& = "Hz"); |
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[1819] | 414 | **/ |
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| 415 | // Modified by Takeshi Nakazato 05/09/2008 |
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| 416 | /*** |
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| 417 | void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "", |
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| 418 | const std::string& = "Hz"); |
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| 419 | ***/ |
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| 420 | void setRestFrequencies(vector<double> rf, |
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| 421 | const vector<std::string>& name = vector<std::string>(1,""), |
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| 422 | const std::string& = "Hz"); |
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[847] | 423 | |
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[1819] | 424 | //void setRestFrequencies(const std::string& name); |
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| 425 | void setRestFrequencies(const vector<std::string>& name); |
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| 426 | |
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[1360] | 427 | void shift(int npix); |
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| 428 | |
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[1598] | 429 | casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const; |
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| 430 | |
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[987] | 431 | void convertDirection(const std::string& newframe); |
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| 432 | |
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[824] | 433 | STFrequencies& frequencies() { return freqTable_; } |
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[1375] | 434 | const STFrequencies& frequencies() const { return freqTable_; } |
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[824] | 435 | STWeather& weather() { return weatherTable_; } |
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[1375] | 436 | const STWeather& weather() const { return weatherTable_; } |
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[824] | 437 | STFocus& focus() { return focusTable_; } |
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[1375] | 438 | const STFocus& focus() const { return focusTable_; } |
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[824] | 439 | STTcal& tcal() { return tcalTable_; } |
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[1375] | 440 | const STTcal& tcal() const { return tcalTable_; } |
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[824] | 441 | STMolecules& molecules() { return moleculeTable_; } |
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[1375] | 442 | const STMolecules& molecules() const { return moleculeTable_; } |
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[860] | 443 | STHistory& history() { return historyTable_; } |
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[1375] | 444 | const STHistory& history() const { return historyTable_; } |
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[972] | 445 | STFit& fit() { return fitTable_; } |
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[1375] | 446 | const STFit& fit() const { return fitTable_; } |
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[2] | 447 | |
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[902] | 448 | std::vector<std::string> columnNames() const; |
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[896] | 449 | |
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[972] | 450 | void addFit(const STFitEntry& fit, int row); |
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| 451 | STFitEntry getFit(int row) const |
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| 452 | { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; } |
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| 453 | |
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[1391] | 454 | //Added by TT |
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| 455 | /** |
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| 456 | * Get the antenna name |
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| 457 | * @return antenna name string |
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| 458 | */ |
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[1819] | 459 | casa::String getAntennaName() const; |
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[1391] | 460 | |
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| 461 | /** |
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| 462 | * For GBT MS data only. check a scan list |
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| 463 | * against the information found in GBT_GO table for |
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| 464 | * scan number orders to get correct pairs. |
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| 465 | * @param[in] scan list |
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| 466 | * @return status |
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| 467 | */ |
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| 468 | int checkScanInfo(const std::vector<int>& scanlist) const; |
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| 469 | |
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| 470 | /** |
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| 471 | * Get the direction as a vector, for a specific row |
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| 472 | * @param[in] whichrow the row numbyyer |
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| 473 | * @return the direction in a vector |
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| 474 | */ |
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| 475 | std::vector<double> getDirectionVector(int whichrow) const; |
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| 476 | |
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[1586] | 477 | /** |
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| 478 | * Set a flag indicating whether the data was parallactified |
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| 479 | * @param[in] flag true or false |
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| 480 | */ |
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[1598] | 481 | void parallactify(bool flag) |
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[2357] | 482 | { focusTable_.setParallactify(flag); } |
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[1727] | 483 | |
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[1819] | 484 | /** |
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| 485 | * Reshape spectrum |
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| 486 | * @param[in] nmin, nmax minimum and maximum channel |
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| 487 | * @param[in] irow row number |
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| 488 | * |
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| 489 | * 30/07/2008 Takeshi Nakazato |
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| 490 | **/ |
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| 491 | void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError ); |
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| 492 | void reshapeSpectrum( int nmin, int nmax, int irow ) ; |
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| 493 | |
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| 494 | /** |
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| 495 | * Change channel number under fixed bandwidth |
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| 496 | * @param[in] nchan, dnu new channel number and spectral resolution |
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| 497 | * @param[in] irow row number |
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| 498 | * |
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| 499 | * 27/08/2008 Takeshi Nakazato |
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| 500 | **/ |
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| 501 | void regridChannel( int nchan, double dnu ) ; |
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| 502 | void regridChannel( int nchan, double dnu, int irow ) ; |
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| 503 | |
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[2435] | 504 | void regridSpecChannel( double dnu, int nchan=-1 ) ; |
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| 505 | |
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[2047] | 506 | bool getFlagtraFast(casa::uInt whichrow); |
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[1819] | 507 | |
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[2012] | 508 | void polyBaseline(const std::vector<bool>& mask, |
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| 509 | int order, |
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[2094] | 510 | bool getResidual=true, |
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[2189] | 511 | const std::string& progressInfo="true,1000", |
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| 512 | const bool outLogger=false, |
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[2012] | 513 | const std::string& blfile=""); |
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| 514 | void autoPolyBaseline(const std::vector<bool>& mask, |
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| 515 | int order, |
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| 516 | const std::vector<int>& edge, |
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| 517 | float threshold=3.0, |
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| 518 | int chanAvgLimit=1, |
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[2094] | 519 | bool getResidual=true, |
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[2189] | 520 | const std::string& progressInfo="true,1000", |
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| 521 | const bool outLogger=false, |
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[2012] | 522 | const std::string& blfile=""); |
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| 523 | void cubicSplineBaseline(const std::vector<bool>& mask, |
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| 524 | int nPiece, |
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| 525 | float thresClip, |
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| 526 | int nIterClip, |
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[2094] | 527 | bool getResidual=true, |
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[2189] | 528 | const std::string& progressInfo="true,1000", |
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| 529 | const bool outLogger=false, |
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[2012] | 530 | const std::string& blfile=""); |
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| 531 | void autoCubicSplineBaseline(const std::vector<bool>& mask, |
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| 532 | int nPiece, |
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| 533 | float thresClip, |
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| 534 | int nIterClip, |
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| 535 | const std::vector<int>& edge, |
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| 536 | float threshold=3.0, |
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| 537 | int chanAvgLimit=1, |
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[2094] | 538 | bool getResidual=true, |
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[2189] | 539 | const std::string& progressInfo="true,1000", |
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| 540 | const bool outLogger=false, |
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[2012] | 541 | const std::string& blfile=""); |
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[2047] | 542 | void sinusoidBaseline(const std::vector<bool>& mask, |
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[2186] | 543 | const bool applyFFT, |
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| 544 | const std::string& fftMethod, |
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| 545 | const std::string& fftThresh, |
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| 546 | const std::vector<int>& addNWaves, |
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| 547 | const std::vector<int>& rejectNWaves, |
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[2047] | 548 | float thresClip, |
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| 549 | int nIterClip, |
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[2081] | 550 | bool getResidual=true, |
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[2189] | 551 | const std::string& progressInfo="true,1000", |
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| 552 | const bool outLogger=false, |
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[2047] | 553 | const std::string& blfile=""); |
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| 554 | void autoSinusoidBaseline(const std::vector<bool>& mask, |
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[2186] | 555 | const bool applyFFT, |
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| 556 | const std::string& fftMethod, |
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| 557 | const std::string& fftThresh, |
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| 558 | const std::vector<int>& addNWaves, |
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| 559 | const std::vector<int>& rejectNWaves, |
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[2047] | 560 | float thresClip, |
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| 561 | int nIterClip, |
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| 562 | const std::vector<int>& edge, |
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| 563 | float threshold=3.0, |
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| 564 | int chanAvgLimit=1, |
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[2081] | 565 | bool getResidual=true, |
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[2189] | 566 | const std::string& progressInfo="true,1000", |
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| 567 | const bool outLogger=false, |
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[2047] | 568 | const std::string& blfile=""); |
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[2186] | 569 | std::vector<float> execFFT(const int whichrow, |
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| 570 | const std::vector<bool>& inMask, |
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| 571 | bool getRealImag=false, |
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| 572 | bool getAmplitudeOnly=false); |
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[2012] | 573 | float getRms(const std::vector<bool>& mask, int whichrow); |
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| 574 | std::string formatBaselineParams(const std::vector<float>& params, |
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| 575 | const std::vector<bool>& fixed, |
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| 576 | float rms, |
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[2193] | 577 | int nClipped, |
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[2012] | 578 | const std::string& masklist, |
---|
| 579 | int whichrow, |
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[2064] | 580 | bool verbose=false, |
---|
[2640] | 581 | bool csvformat=false, |
---|
[2064] | 582 | int start=-1, |
---|
| 583 | int count=-1, |
---|
| 584 | bool resetparamid=false) const; |
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[2012] | 585 | std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges, |
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| 586 | const std::vector<float>& params, |
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| 587 | const std::vector<bool>& fixed, |
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| 588 | float rms, |
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[2193] | 589 | int nClipped, |
---|
[2012] | 590 | const std::string& masklist, |
---|
| 591 | int whichrow, |
---|
[2640] | 592 | bool verbose=false, |
---|
| 593 | bool csvformat=false) const; |
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[1907] | 594 | |
---|
[2012] | 595 | |
---|
[824] | 596 | private: |
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[896] | 597 | |
---|
| 598 | casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const; |
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| 599 | |
---|
[824] | 600 | /** |
---|
[2005] | 601 | * Turns a time value into a formatted string |
---|
[824] | 602 | * @param x |
---|
| 603 | * @return |
---|
| 604 | */ |
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| 605 | std::string formatSec(casa::Double x) const; |
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[18] | 606 | |
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[824] | 607 | std::string formatTime(const casa::MEpoch& me, bool showdate)const; |
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[1947] | 608 | std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const; |
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[22] | 609 | |
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[824] | 610 | /** |
---|
| 611 | * Turns a casa::MDirection into a nicely formatted string |
---|
| 612 | * @param md an casa::MDirection |
---|
| 613 | * @return |
---|
| 614 | */ |
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| 615 | std::string formatDirection(const casa::MDirection& md) const; |
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[19] | 616 | |
---|
[824] | 617 | /** |
---|
| 618 | * Create a unique file name for the paged (temporary) table |
---|
| 619 | * @return just the name |
---|
| 620 | */ |
---|
| 621 | static casa::String generateName(); |
---|
[286] | 622 | |
---|
[824] | 623 | /** |
---|
| 624 | * attach to cached columns |
---|
| 625 | */ |
---|
| 626 | void attach(); |
---|
[50] | 627 | |
---|
[824] | 628 | /** |
---|
| 629 | * Set up the main casa::Table |
---|
| 630 | */ |
---|
| 631 | void setupMainTable(); |
---|
[88] | 632 | |
---|
[859] | 633 | void attachSubtables(); |
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[865] | 634 | void copySubtables(const Scantable& other); |
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| 635 | |
---|
[824] | 636 | /** |
---|
| 637 | * Convert an "old" asap1 style row index into a new index |
---|
| 638 | * @param[in] therow |
---|
| 639 | * @return and index into @table_ |
---|
| 640 | */ |
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| 641 | int rowToScanIndex(int therow); |
---|
[212] | 642 | |
---|
[1694] | 643 | std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const; |
---|
[1111] | 644 | |
---|
[2321] | 645 | static const casa::uInt version_ = 4; |
---|
[286] | 646 | |
---|
[824] | 647 | STSelector selector_; |
---|
[236] | 648 | |
---|
[824] | 649 | casa::Table::TableType type_; |
---|
[465] | 650 | |
---|
[824] | 651 | // the actual data |
---|
| 652 | casa::Table table_; |
---|
| 653 | casa::Table originalTable_; |
---|
[745] | 654 | |
---|
[824] | 655 | STTcal tcalTable_; |
---|
| 656 | STFrequencies freqTable_; |
---|
| 657 | STWeather weatherTable_; |
---|
| 658 | STFocus focusTable_; |
---|
| 659 | STMolecules moleculeTable_; |
---|
[860] | 660 | STHistory historyTable_; |
---|
[960] | 661 | STFit fitTable_; |
---|
[860] | 662 | |
---|
[824] | 663 | // Cached Columns to avoid reconstructing them for each row get/put |
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[847] | 664 | casa::ScalarColumn<casa::Double> integrCol_; |
---|
[824] | 665 | casa::MDirection::ScalarColumn dirCol_; |
---|
[847] | 666 | casa::MEpoch::ScalarColumn timeCol_; |
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[923] | 667 | casa::ScalarColumn<casa::Float> azCol_; |
---|
| 668 | casa::ScalarColumn<casa::Float> elCol_; |
---|
[824] | 669 | casa::ScalarColumn<casa::String> srcnCol_, fldnCol_; |
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[1819] | 670 | casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_; |
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[1068] | 671 | casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_; |
---|
[865] | 672 | casa::ArrayColumn<casa::Float> specCol_, tsysCol_; |
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[824] | 673 | casa::ArrayColumn<casa::uChar> flagsCol_; |
---|
[430] | 674 | |
---|
[824] | 675 | // id in frequencies table |
---|
| 676 | casa::ScalarColumn<casa::uInt> mfreqidCol_; |
---|
| 677 | // id in tcal table |
---|
| 678 | casa::ScalarColumn<casa::uInt> mtcalidCol_; |
---|
[430] | 679 | |
---|
[824] | 680 | casa::ArrayColumn<casa::String> histitemCol_; |
---|
[972] | 681 | casa::ScalarColumn<casa::Int> mfitidCol_; |
---|
[824] | 682 | casa::ScalarColumn<casa::uInt> mweatheridCol_; |
---|
[322] | 683 | |
---|
[824] | 684 | casa::ScalarColumn<casa::uInt> mfocusidCol_; |
---|
| 685 | |
---|
| 686 | casa::ScalarColumn<casa::uInt> mmolidCol_; |
---|
| 687 | |
---|
[896] | 688 | static std::map<std::string, STPol::STPolFactory *> factories_; |
---|
| 689 | void initFactories(); |
---|
| 690 | |
---|
[1819] | 691 | /** |
---|
| 692 | * Add an auxiliary column to the main table and attach it to a |
---|
| 693 | * cached column. Use for adding new columns that the original asap2 |
---|
| 694 | * tables do not have. |
---|
| 695 | * @param[in] col reference to the cached column to be attached |
---|
| 696 | * @param[in] colName column name in asap table |
---|
| 697 | * @param[in] defValue default value to fill in the column |
---|
| 698 | * |
---|
| 699 | * 25/10/2009 Wataru Kawasaki |
---|
| 700 | */ |
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| 701 | template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&, |
---|
| 702 | const casa::String&, |
---|
| 703 | const T2&); |
---|
| 704 | template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&, |
---|
| 705 | const casa::String&, |
---|
| 706 | const casa::Array<T2>&); |
---|
[1907] | 707 | |
---|
[2012] | 708 | void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter); |
---|
| 709 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
| 710 | const std::vector<bool>& mask, |
---|
[2081] | 711 | int nPiece, |
---|
[2064] | 712 | std::vector<int>& idxEdge, |
---|
[2012] | 713 | std::vector<float>& params, |
---|
[2193] | 714 | int& nClipped, |
---|
[2012] | 715 | float thresClip=3.0, |
---|
[2058] | 716 | int nIterClip=1, |
---|
[2094] | 717 | bool getResidual=true); |
---|
[2047] | 718 | std::vector<float> doSinusoidFitting(const std::vector<float>& data, |
---|
| 719 | const std::vector<bool>& mask, |
---|
[2081] | 720 | const std::vector<int>& waveNumbers, |
---|
[2047] | 721 | std::vector<float>& params, |
---|
[2193] | 722 | int& nClipped, |
---|
[2047] | 723 | float thresClip=3.0, |
---|
[2058] | 724 | int nIterClip=1, |
---|
[2094] | 725 | bool getResidual=true); |
---|
[2186] | 726 | void selectWaveNumbers(const int whichrow, |
---|
| 727 | const std::vector<bool>& chanMask, |
---|
| 728 | const bool applyFFT, |
---|
| 729 | const std::string& fftMethod, |
---|
| 730 | const std::string& fftThresh, |
---|
| 731 | const std::vector<int>& addNWaves, |
---|
| 732 | const std::vector<int>& rejectNWaves, |
---|
| 733 | std::vector<int>& nWaves); |
---|
| 734 | void parseThresholdExpression(const std::string& fftThresh, |
---|
| 735 | std::string& fftThAttr, |
---|
| 736 | float& fftThSigma, |
---|
| 737 | int& fftThTop); |
---|
| 738 | void doSelectWaveNumbers(const int whichrow, |
---|
| 739 | const std::vector<bool>& chanMask, |
---|
| 740 | const std::string& fftMethod, |
---|
| 741 | const float fftThSigma, |
---|
| 742 | const int fftThTop, |
---|
| 743 | const std::string& fftThAttr, |
---|
| 744 | std::vector<int>& nWaves); |
---|
[2411] | 745 | void addAuxWaveNumbers(const int whichrow, |
---|
| 746 | const std::vector<int>& addNWaves, |
---|
[2186] | 747 | const std::vector<int>& rejectNWaves, |
---|
| 748 | std::vector<int>& nWaves); |
---|
[2411] | 749 | void setWaveNumberListUptoNyquistFreq(const int whichrow, |
---|
| 750 | std::vector<int>& nWaves); |
---|
[2012] | 751 | bool hasSameNchanOverIFs(); |
---|
| 752 | std::string getMaskRangeList(const std::vector<bool>& mask, |
---|
| 753 | int whichrow, |
---|
| 754 | const casa::String& coordInfo, |
---|
[2047] | 755 | bool hasSameNchan, |
---|
| 756 | bool verbose=false); |
---|
| 757 | std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask); |
---|
[2640] | 758 | std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const; |
---|
| 759 | std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const; |
---|
[2012] | 760 | std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask); |
---|
| 761 | //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder); |
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[2640] | 762 | 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); |
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| 763 | 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); |
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| 764 | 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] | 765 | void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow); |
---|
| 766 | void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000); |
---|
[1994] | 767 | |
---|
| 768 | void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval); |
---|
| 769 | |
---|
| 770 | |
---|
[2] | 771 | }; |
---|
| 772 | |
---|
[824] | 773 | } // namespace |
---|
| 774 | |
---|
[2] | 775 | #endif |
---|