[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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[2186] | 30 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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[824] | 31 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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[2186] | 32 | #include <scimath/Mathematics/FFTServer.h> |
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| 33 | #include <tables/Tables/ArrayColumn.h> |
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| 34 | #include <tables/Tables/ScalarColumn.h> |
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| 35 | #include <tables/Tables/Table.h> |
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[1819] | 36 | |
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[2186] | 37 | #include "MathUtils.h" |
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[2767] | 38 | #include "STBaselineEnum.h" |
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[2186] | 39 | #include "STFit.h" |
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| 40 | #include "STFitEntry.h" |
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[2666] | 41 | //#include "STFitter.h" |
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[2186] | 42 | #include "STFocus.h" |
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| 43 | #include "STFrequencies.h" |
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[901] | 44 | #include "STHeader.h" |
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[2186] | 45 | #include "STHistory.h" |
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[824] | 46 | #include "STMolecules.h" |
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[2186] | 47 | #include "STPol.h" |
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[824] | 48 | #include "STSelector.h" |
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[2186] | 49 | #include "STTcal.h" |
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| 50 | #include "STWeather.h" |
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[2] | 51 | |
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[824] | 52 | namespace asap { |
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[2] | 53 | |
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[2666] | 54 | class Fitter; |
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| 55 | |
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[824] | 56 | /** |
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| 57 | * This class contains and wraps a casa::Table, which is used to store |
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| 58 | * all the information. This can be either a MemoryTable or a |
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| 59 | * disk based Table. |
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| 60 | * It provides access functions to the underlying table |
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| 61 | * It contains n subtables: |
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| 62 | * @li weather |
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| 63 | * @li frequencies |
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| 64 | * @li molecules |
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| 65 | * @li tcal |
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| 66 | * @li focus |
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| 67 | * @li fits |
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| 68 | * |
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| 69 | * @brief The main ASAP data container |
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| 70 | * @author Malte Marquarding |
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| 71 | * @date |
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| 72 | * @version |
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| 73 | */ |
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[2658] | 74 | class Scantable |
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[824] | 75 | { |
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[902] | 76 | |
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| 77 | friend class STMath; |
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| 78 | |
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[2] | 79 | public: |
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[824] | 80 | /** |
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| 81 | * Default constructor |
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| 82 | */ |
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[1350] | 83 | explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory); |
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[19] | 84 | |
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[824] | 85 | /** |
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[2321] | 86 | * Create a Scantable object from an existing table on disk |
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[824] | 87 | * @param[in] name the name of the existing Scantable |
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| 88 | */ |
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[2321] | 89 | explicit Scantable(const std::string& name, |
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| 90 | casa::Table::TableType ttype = casa::Table::Memory); |
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[2] | 91 | |
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[824] | 92 | /// @fixme this is only sensible for MemoryTables.... |
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| 93 | Scantable(const Scantable& other, bool clear=true); |
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[161] | 94 | |
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[824] | 95 | /** |
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| 96 | * Destructor |
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| 97 | */ |
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| 98 | virtual ~Scantable(); |
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[745] | 99 | |
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[824] | 100 | /** |
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| 101 | * get a const reference to the underlying casa::Table |
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[1104] | 102 | * @return const \ref casa::Table reference |
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[824] | 103 | */ |
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| 104 | const casa::Table& table() const; |
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[19] | 105 | |
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[824] | 106 | /** |
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| 107 | * get a reference to the underlying casa::Table with the Selection |
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| 108 | * object applied if set |
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| 109 | * @return casa::Table reference |
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| 110 | */ |
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| 111 | casa::Table& table(); |
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[21] | 112 | |
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[845] | 113 | |
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| 114 | /** |
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| 115 | * Get a handle to the selection object |
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| 116 | * @return constant STSelector reference |
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| 117 | */ |
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| 118 | const STSelector& getSelection() const { return selector_; } |
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| 119 | |
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| 120 | /** |
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| 121 | * Set the data to be a subset as defined by the STSelector |
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| 122 | * @param selection a STSelector object |
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| 123 | */ |
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[824] | 124 | void setSelection(const STSelector& selection); |
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[845] | 125 | |
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| 126 | /** |
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| 127 | * unset the selection of the data |
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| 128 | */ |
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[824] | 129 | void unsetSelection(); |
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| 130 | /** |
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| 131 | * set the header |
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[1295] | 132 | * @param[in] sth an STHeader object |
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[824] | 133 | */ |
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[901] | 134 | void setHeader( const STHeader& sth ); |
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[386] | 135 | |
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[824] | 136 | /** |
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| 137 | * get the header information |
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[901] | 138 | * @return an STHeader object |
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[824] | 139 | */ |
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[901] | 140 | STHeader getHeader( ) const; |
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[1068] | 141 | |
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[824] | 142 | /** |
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| 143 | * Checks if the "other" Scantable is conformant with this, |
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| 144 | * i.e. if header values are the same. |
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| 145 | * @param[in] other another Scantable |
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| 146 | * @return true or false |
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| 147 | */ |
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| 148 | bool conformant( const Scantable& other); |
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[430] | 149 | |
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[824] | 150 | /** |
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[1068] | 151 | * |
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| 152 | * @param stype The type of the source, 0 = on, 1 = off |
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| 153 | */ |
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| 154 | void setSourceType(int stype); |
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| 155 | |
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| 156 | |
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| 157 | /** |
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[1104] | 158 | * The number of scans in the table |
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[824] | 159 | * @return number of scans in the table |
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| 160 | */ |
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[845] | 161 | int nscan() const; |
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[490] | 162 | |
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[915] | 163 | casa::MEpoch::Types getTimeReference() const; |
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[21] | 164 | |
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[1411] | 165 | |
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| 166 | casa::MEpoch getEpoch(int whichrow) const; |
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| 167 | |
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[824] | 168 | /** |
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| 169 | * Get global antenna position |
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[845] | 170 | * @return casa::MPosition |
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[824] | 171 | */ |
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| 172 | casa::MPosition getAntennaPosition() const; |
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[490] | 173 | |
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[1441] | 174 | /** |
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| 175 | * the @ref casa::MDirection for a specific row |
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| 176 | * @param[in] whichrow the row number |
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| 177 | * return casa::MDirection |
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| 178 | */ |
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[987] | 179 | casa::MDirection getDirection( int whichrow ) const; |
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[1598] | 180 | |
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[1441] | 181 | /** |
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| 182 | * get the direction type as a string, e.g. "J2000" |
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| 183 | * @param[in] whichrow the row number |
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| 184 | * return the direction string |
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| 185 | */ |
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[1068] | 186 | std::string getDirectionString( int whichrow ) const; |
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| 187 | |
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[1441] | 188 | /** |
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| 189 | * set the direction type as a string, e.g. "J2000" |
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| 190 | * @param[in] refstr the direction type |
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| 191 | */ |
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[987] | 192 | void setDirectionRefString(const std::string& refstr=""); |
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[1441] | 193 | |
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[1104] | 194 | /** |
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| 195 | * get the direction reference string |
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| 196 | * @return a string describing the direction reference |
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| 197 | */ |
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[1598] | 198 | std::string getDirectionRefString() const; |
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[987] | 199 | |
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[824] | 200 | /** |
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[845] | 201 | * Return the Flux unit of the data, e.g. "Jy" or "K" |
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| 202 | * @return string |
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[824] | 203 | */ |
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| 204 | std::string getFluxUnit() const; |
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[472] | 205 | |
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[824] | 206 | /** |
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[845] | 207 | * Set the Flux unit of the data |
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| 208 | * @param unit a string representing the unit, e.g "Jy" or "K" |
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[824] | 209 | */ |
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| 210 | void setFluxUnit( const std::string& unit ); |
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[472] | 211 | |
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[824] | 212 | /** |
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[1189] | 213 | * Set the Stokes type of the data |
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[1295] | 214 | * @param feedtype a string representing the type, e.g "circular" or "linear" |
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[1189] | 215 | */ |
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| 216 | void setFeedType( const std::string& feedtype ); |
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| 217 | |
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| 218 | /** |
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[824] | 219 | * |
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[845] | 220 | * @param instrument a string representing an insturment. see xxx |
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[824] | 221 | */ |
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| 222 | void setInstrument( const std::string& instrument ); |
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[2] | 223 | |
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[845] | 224 | /** |
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| 225 | * (Re)calculate the azimuth and elevationnfor all rows |
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| 226 | */ |
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[824] | 227 | void calculateAZEL(); |
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[745] | 228 | |
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[824] | 229 | /** |
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[845] | 230 | * "hard" flag the data, this flags everything selected in setSelection() |
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[1104] | 231 | * param[in] msk a boolean mask of length nchan describing the points to |
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| 232 | * to be flagged |
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[824] | 233 | */ |
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[1430] | 234 | //void flag( const std::vector<bool>& msk = std::vector<bool>()); |
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[1994] | 235 | //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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[455] | 236 | |
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[1994] | 237 | void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false); |
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| 238 | |
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[852] | 239 | /** |
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[1819] | 240 | * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki) |
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| 241 | * param[in] rows list of row numbers to be flagged |
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| 242 | */ |
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| 243 | void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false); |
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| 244 | |
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| 245 | /** |
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| 246 | * Get flagRow info at the specified row. If true, the whole data |
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| 247 | * at the row should be flagged. |
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| 248 | */ |
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| 249 | bool getFlagRow(int whichrow) const |
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| 250 | { return (flagrowCol_(whichrow) > 0); } |
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| 251 | |
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| 252 | /** |
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| 253 | * Flag the data outside a specified range (in a channel-based manner). |
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| 254 | * (CAS-1807 Wataru Kawasaki) |
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| 255 | */ |
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| 256 | void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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| 257 | |
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| 258 | /** |
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| 259 | * Return a list of booleans with the size of nchan for a specified row, to get info |
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| 260 | * about which channel is clipped. |
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| 261 | */ |
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| 262 | std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag); |
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| 263 | void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag, |
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| 264 | casa::Vector<casa::uChar> flgs); |
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| 265 | |
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| 266 | /** |
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[852] | 267 | * Return a list of row numbers with respect to the original table. |
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[902] | 268 | * @return a list of unsigned ints |
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[852] | 269 | */ |
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| 270 | std::vector<unsigned int> rownumbers() const; |
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[845] | 271 | |
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[852] | 272 | |
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[845] | 273 | /** |
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| 274 | * Get the number of beams in the data or a specific scan |
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| 275 | * @param scanno the scan number to get the number of beams for. |
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| 276 | * If scanno<0 the number is retrieved from the header. |
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| 277 | * @return an integer number |
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| 278 | */ |
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[824] | 279 | int nbeam(int scanno=-1) const; |
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[845] | 280 | /** |
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| 281 | * Get the number of IFs in the data or a specific scan |
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| 282 | * @param scanno the scan number to get the number of IFs for. |
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| 283 | * If scanno<0 the number is retrieved from the header. |
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| 284 | * @return an integer number |
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| 285 | */ |
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[824] | 286 | int nif(int scanno=-1) const; |
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[845] | 287 | /** |
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| 288 | * Get the number of polarizations in the data or a specific scan |
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| 289 | * @param scanno the scan number to get the number of polarizations for. |
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| 290 | * If scanno<0 the number is retrieved from the header. |
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| 291 | * @return an integer number |
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| 292 | */ |
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[824] | 293 | int npol(int scanno=-1) const; |
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[794] | 294 | |
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[896] | 295 | std::string getPolType() const; |
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| 296 | |
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[845] | 297 | |
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| 298 | /** |
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| 299 | * Get the number of integartion cycles |
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| 300 | * @param scanno the scan number to get the number of rows for. |
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| 301 | * If scanno<0 the number is retrieved from the header. |
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[1104] | 302 | * @return the number of rows (for the specified scanno) |
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[845] | 303 | */ |
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[824] | 304 | int nrow(int scanno=-1) const; |
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[794] | 305 | |
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[1111] | 306 | int getBeam(int whichrow) const; |
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[1694] | 307 | std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); } |
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[50] | 308 | |
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[847] | 309 | int getIF(int whichrow) const; |
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[1694] | 310 | std::vector<uint> getIFNos() const { return getNumbers(ifCol_); } |
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[1111] | 311 | |
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[847] | 312 | int getPol(int whichrow) const; |
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[1694] | 313 | std::vector<uint> getPolNos() const { return getNumbers(polCol_); } |
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[1111] | 314 | |
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[1694] | 315 | std::vector<uint> getScanNos() const { return getNumbers(scanCol_); } |
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[865] | 316 | int getScan(int whichrow) const { return scanCol_(whichrow); } |
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[1111] | 317 | |
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[2667] | 318 | std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); } |
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| 319 | int getCycle(int whichrow) const { return cycleCol_(whichrow); } |
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| 320 | |
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[1819] | 321 | //TT addition |
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| 322 | std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); } |
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| 323 | |
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[1111] | 324 | /** |
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| 325 | * Get the number of channels in the data or a specific IF. This currently |
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| 326 | * varies only with IF number |
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| 327 | * @param ifno the IF number to get the number of channels for. |
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| 328 | * If ifno<0 the number is retrieved from the header. |
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| 329 | * @return an integer number |
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| 330 | */ |
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| 331 | int nchan(int ifno=-1) const; |
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[923] | 332 | int getChannels(int whichrow) const; |
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[206] | 333 | |
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[1111] | 334 | int ncycle(int scanno=-1) const; |
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| 335 | |
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[2667] | 336 | |
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[847] | 337 | double getInterval(int whichrow) const |
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| 338 | { return integrCol_(whichrow); } |
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[845] | 339 | |
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[865] | 340 | float getTsys(int whichrow) const |
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| 341 | { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); } |
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[2161] | 342 | std::vector<float> getTsysSpectrum(int whichrow) const ; |
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[847] | 343 | float getElevation(int whichrow) const |
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| 344 | { return elCol_(whichrow); } |
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| 345 | float getAzimuth(int whichrow) const |
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| 346 | { return azCol_(whichrow); } |
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[865] | 347 | float getParAngle(int whichrow) const |
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[1819] | 348 | { return focus().getParAngle(mfocusidCol_(whichrow)); } |
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| 349 | int getTcalId(int whichrow) const |
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| 350 | { return mtcalidCol_(whichrow); } |
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[386] | 351 | |
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[865] | 352 | std::string getSourceName(int whichrow) const |
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| 353 | { return srcnCol_(whichrow); } |
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| 354 | |
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[847] | 355 | std::vector<bool> getMask(int whichrow) const; |
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[896] | 356 | std::vector<float> getSpectrum(int whichrow, |
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[905] | 357 | const std::string& poltype = "" ) const; |
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[847] | 358 | |
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[884] | 359 | void setSpectrum(const std::vector<float>& spec, int whichrow); |
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| 360 | |
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[902] | 361 | std::string getPolarizationLabel(int index, const std::string& ptype) const |
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| 362 | { return STPol::getPolLabel(index, ptype ); } |
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[401] | 363 | |
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[845] | 364 | /** |
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| 365 | * Write the Scantable to disk |
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| 366 | * @param filename the output file name |
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| 367 | */ |
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[824] | 368 | void makePersistent(const std::string& filename); |
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[745] | 369 | |
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[860] | 370 | std::vector<std::string> getHistory() const |
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| 371 | { return historyTable_.getHistory(); }; |
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[483] | 372 | |
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[860] | 373 | void addHistory(const std::string& hist) { historyTable_.addEntry(hist); } |
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[488] | 374 | |
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[860] | 375 | void appendToHistoryTable(const STHistory& otherhist) |
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| 376 | { historyTable_.append(otherhist); } |
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| 377 | |
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[2163] | 378 | std::string headerSummary(); |
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[2290] | 379 | void summary(const std::string& filename=""); |
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| 380 | std::string oldheaderSummary(); |
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[2286] | 381 | // std::string summary(); |
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[2290] | 382 | void oldsummary(const std::string& filename=""); |
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| 383 | |
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[1947] | 384 | //std::string getTime(int whichrow=-1, bool showdate=true) const; |
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| 385 | std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const; |
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[1350] | 386 | double getIntTime(int whichrow) const { return integrCol_(whichrow); } |
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[19] | 387 | |
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[847] | 388 | // returns unit, conversion frame, doppler, base-frame |
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[18] | 389 | |
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[847] | 390 | /** |
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| 391 | * Get the frequency set up |
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| 392 | * This is forwarded to the STFrequencies subtable |
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| 393 | * @return unit, frame, doppler |
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| 394 | */ |
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| 395 | std::vector<std::string> getCoordInfo() const |
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| 396 | { return freqTable_.getInfo(); }; |
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| 397 | |
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| 398 | void setCoordInfo(std::vector<string> theinfo) |
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| 399 | { return freqTable_.setInfo(theinfo); }; |
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| 400 | |
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[865] | 401 | |
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| 402 | std::vector<double> getAbcissa(int whichrow) const; |
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| 403 | |
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[1730] | 404 | std::vector<float> getWeather(int whichrow) const; |
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| 405 | |
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[847] | 406 | std::string getAbcissaLabel(int whichrow) const; |
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| 407 | std::vector<double> getRestFrequencies() const |
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| 408 | { return moleculeTable_.getRestFrequencies(); } |
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[1819] | 409 | std::vector<double> getRestFrequency(int id) const |
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| 410 | { return moleculeTable_.getRestFrequency(id); } |
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[847] | 411 | |
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[1819] | 412 | /** |
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[1170] | 413 | void setRestFrequencies(double rf, const std::string& name = "", |
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| 414 | const std::string& = "Hz"); |
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[1819] | 415 | **/ |
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| 416 | // Modified by Takeshi Nakazato 05/09/2008 |
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| 417 | /*** |
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| 418 | void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "", |
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| 419 | const std::string& = "Hz"); |
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| 420 | ***/ |
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| 421 | void setRestFrequencies(vector<double> rf, |
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| 422 | const vector<std::string>& name = vector<std::string>(1,""), |
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| 423 | const std::string& = "Hz"); |
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[847] | 424 | |
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[1819] | 425 | //void setRestFrequencies(const std::string& name); |
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| 426 | void setRestFrequencies(const vector<std::string>& name); |
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| 427 | |
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[1360] | 428 | void shift(int npix); |
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| 429 | |
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[1598] | 430 | casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const; |
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| 431 | |
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[987] | 432 | void convertDirection(const std::string& newframe); |
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| 433 | |
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[824] | 434 | STFrequencies& frequencies() { return freqTable_; } |
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[1375] | 435 | const STFrequencies& frequencies() const { return freqTable_; } |
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[824] | 436 | STWeather& weather() { return weatherTable_; } |
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[1375] | 437 | const STWeather& weather() const { return weatherTable_; } |
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[824] | 438 | STFocus& focus() { return focusTable_; } |
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[1375] | 439 | const STFocus& focus() const { return focusTable_; } |
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[824] | 440 | STTcal& tcal() { return tcalTable_; } |
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[1375] | 441 | const STTcal& tcal() const { return tcalTable_; } |
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[824] | 442 | STMolecules& molecules() { return moleculeTable_; } |
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[1375] | 443 | const STMolecules& molecules() const { return moleculeTable_; } |
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[860] | 444 | STHistory& history() { return historyTable_; } |
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[1375] | 445 | const STHistory& history() const { return historyTable_; } |
---|
[972] | 446 | STFit& fit() { return fitTable_; } |
---|
[1375] | 447 | const STFit& fit() const { return fitTable_; } |
---|
[2] | 448 | |
---|
[902] | 449 | std::vector<std::string> columnNames() const; |
---|
[896] | 450 | |
---|
[972] | 451 | void addFit(const STFitEntry& fit, int row); |
---|
| 452 | STFitEntry getFit(int row) const |
---|
| 453 | { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; } |
---|
| 454 | |
---|
[1391] | 455 | //Added by TT |
---|
| 456 | /** |
---|
| 457 | * Get the antenna name |
---|
| 458 | * @return antenna name string |
---|
| 459 | */ |
---|
[1819] | 460 | casa::String getAntennaName() const; |
---|
[1391] | 461 | |
---|
| 462 | /** |
---|
| 463 | * For GBT MS data only. check a scan list |
---|
| 464 | * against the information found in GBT_GO table for |
---|
| 465 | * scan number orders to get correct pairs. |
---|
| 466 | * @param[in] scan list |
---|
| 467 | * @return status |
---|
| 468 | */ |
---|
| 469 | int checkScanInfo(const std::vector<int>& scanlist) const; |
---|
| 470 | |
---|
| 471 | /** |
---|
| 472 | * Get the direction as a vector, for a specific row |
---|
| 473 | * @param[in] whichrow the row numbyyer |
---|
| 474 | * @return the direction in a vector |
---|
| 475 | */ |
---|
| 476 | std::vector<double> getDirectionVector(int whichrow) const; |
---|
| 477 | |
---|
[1586] | 478 | /** |
---|
| 479 | * Set a flag indicating whether the data was parallactified |
---|
| 480 | * @param[in] flag true or false |
---|
| 481 | */ |
---|
[1598] | 482 | void parallactify(bool flag) |
---|
[2357] | 483 | { focusTable_.setParallactify(flag); } |
---|
[1727] | 484 | |
---|
[1819] | 485 | /** |
---|
| 486 | * Reshape spectrum |
---|
| 487 | * @param[in] nmin, nmax minimum and maximum channel |
---|
| 488 | * @param[in] irow row number |
---|
| 489 | * |
---|
| 490 | * 30/07/2008 Takeshi Nakazato |
---|
| 491 | **/ |
---|
| 492 | void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError ); |
---|
| 493 | void reshapeSpectrum( int nmin, int nmax, int irow ) ; |
---|
| 494 | |
---|
| 495 | /** |
---|
| 496 | * Change channel number under fixed bandwidth |
---|
| 497 | * @param[in] nchan, dnu new channel number and spectral resolution |
---|
| 498 | * @param[in] irow row number |
---|
| 499 | * |
---|
| 500 | * 27/08/2008 Takeshi Nakazato |
---|
| 501 | **/ |
---|
| 502 | void regridChannel( int nchan, double dnu ) ; |
---|
| 503 | void regridChannel( int nchan, double dnu, int irow ) ; |
---|
[2595] | 504 | void regridChannel( int nchan, double dnu, double fmin, int irow ) ; |
---|
[2435] | 505 | void regridSpecChannel( double dnu, int nchan=-1 ) ; |
---|
| 506 | |
---|
[2047] | 507 | bool getFlagtraFast(casa::uInt whichrow); |
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[1819] | 508 | |
---|
[2767] | 509 | std::vector<std::string> applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite); |
---|
| 510 | std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite); |
---|
| 511 | void polyBaseline(const std::vector<bool>& mask, |
---|
| 512 | int order, |
---|
| 513 | float thresClip, |
---|
| 514 | int nIterClip, |
---|
[2094] | 515 | bool getResidual=true, |
---|
[2189] | 516 | const std::string& progressInfo="true,1000", |
---|
[2767] | 517 | const bool outLogger=false, |
---|
| 518 | const std::string& blfile="", |
---|
| 519 | const std::string& bltable=""); |
---|
[2012] | 520 | void autoPolyBaseline(const std::vector<bool>& mask, |
---|
[2767] | 521 | int order, |
---|
| 522 | float thresClip, |
---|
| 523 | int nIterClip, |
---|
| 524 | const std::vector<int>& edge, |
---|
| 525 | float threshold=3.0, |
---|
| 526 | int chanAvgLimit=1, |
---|
| 527 | bool getResidual=true, |
---|
| 528 | const std::string& progressInfo="true,1000", |
---|
| 529 | const bool outLogger=false, |
---|
| 530 | const std::string& blfile="", |
---|
| 531 | const std::string& bltable=""); |
---|
[2645] | 532 | void chebyshevBaseline(const std::vector<bool>& mask, |
---|
| 533 | int order, |
---|
| 534 | float thresClip, |
---|
| 535 | int nIterClip, |
---|
| 536 | bool getResidual=true, |
---|
| 537 | const std::string& progressInfo="true,1000", |
---|
| 538 | const bool outLogger=false, |
---|
[2767] | 539 | const std::string& blfile="", |
---|
| 540 | const std::string& bltable=""); |
---|
[2645] | 541 | void autoChebyshevBaseline(const std::vector<bool>& mask, |
---|
| 542 | int order, |
---|
| 543 | float thresClip, |
---|
| 544 | int nIterClip, |
---|
| 545 | const std::vector<int>& edge, |
---|
| 546 | float threshold=3.0, |
---|
| 547 | int chanAvgLimit=1, |
---|
| 548 | bool getResidual=true, |
---|
| 549 | const std::string& progressInfo="true,1000", |
---|
| 550 | const bool outLogger=false, |
---|
[2767] | 551 | const std::string& blfile="", |
---|
| 552 | const std::string& bltable=""); |
---|
[2012] | 553 | void cubicSplineBaseline(const std::vector<bool>& mask, |
---|
| 554 | int nPiece, |
---|
| 555 | float thresClip, |
---|
| 556 | int nIterClip, |
---|
[2094] | 557 | bool getResidual=true, |
---|
[2189] | 558 | const std::string& progressInfo="true,1000", |
---|
| 559 | const bool outLogger=false, |
---|
[2767] | 560 | const std::string& blfile="", |
---|
| 561 | const std::string& bltable=""); |
---|
[2012] | 562 | void autoCubicSplineBaseline(const std::vector<bool>& mask, |
---|
| 563 | int nPiece, |
---|
| 564 | float thresClip, |
---|
| 565 | int nIterClip, |
---|
| 566 | const std::vector<int>& edge, |
---|
| 567 | float threshold=3.0, |
---|
| 568 | int chanAvgLimit=1, |
---|
[2094] | 569 | bool getResidual=true, |
---|
[2189] | 570 | const std::string& progressInfo="true,1000", |
---|
| 571 | const bool outLogger=false, |
---|
[2767] | 572 | const std::string& blfile="", |
---|
| 573 | const std::string& bltable=""); |
---|
[2047] | 574 | void sinusoidBaseline(const std::vector<bool>& mask, |
---|
[2767] | 575 | const std::string& fftInfo, |
---|
[2186] | 576 | const std::vector<int>& addNWaves, |
---|
| 577 | const std::vector<int>& rejectNWaves, |
---|
[2047] | 578 | float thresClip, |
---|
| 579 | int nIterClip, |
---|
[2081] | 580 | bool getResidual=true, |
---|
[2189] | 581 | const std::string& progressInfo="true,1000", |
---|
| 582 | const bool outLogger=false, |
---|
[2767] | 583 | const std::string& blfile="", |
---|
| 584 | const std::string& bltable=""); |
---|
[2047] | 585 | void autoSinusoidBaseline(const std::vector<bool>& mask, |
---|
[2767] | 586 | const std::string& fftInfo, |
---|
[2186] | 587 | const std::vector<int>& addNWaves, |
---|
| 588 | const std::vector<int>& rejectNWaves, |
---|
[2047] | 589 | float thresClip, |
---|
| 590 | int nIterClip, |
---|
| 591 | const std::vector<int>& edge, |
---|
| 592 | float threshold=3.0, |
---|
| 593 | int chanAvgLimit=1, |
---|
[2081] | 594 | bool getResidual=true, |
---|
[2189] | 595 | const std::string& progressInfo="true,1000", |
---|
| 596 | const bool outLogger=false, |
---|
[2767] | 597 | const std::string& blfile="", |
---|
| 598 | const std::string& bltable=""); |
---|
[2186] | 599 | std::vector<float> execFFT(const int whichrow, |
---|
| 600 | const std::vector<bool>& inMask, |
---|
| 601 | bool getRealImag=false, |
---|
| 602 | bool getAmplitudeOnly=false); |
---|
[2012] | 603 | float getRms(const std::vector<bool>& mask, int whichrow); |
---|
| 604 | std::string formatBaselineParams(const std::vector<float>& params, |
---|
| 605 | const std::vector<bool>& fixed, |
---|
| 606 | float rms, |
---|
[2193] | 607 | int nClipped, |
---|
[2012] | 608 | const std::string& masklist, |
---|
| 609 | int whichrow, |
---|
[2064] | 610 | bool verbose=false, |
---|
[2641] | 611 | bool csvformat=false, |
---|
[2064] | 612 | int start=-1, |
---|
| 613 | int count=-1, |
---|
| 614 | bool resetparamid=false) const; |
---|
[2012] | 615 | std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges, |
---|
| 616 | const std::vector<float>& params, |
---|
| 617 | const std::vector<bool>& fixed, |
---|
| 618 | float rms, |
---|
[2193] | 619 | int nClipped, |
---|
[2012] | 620 | const std::string& masklist, |
---|
| 621 | int whichrow, |
---|
[2641] | 622 | bool verbose=false, |
---|
| 623 | bool csvformat=false) const; |
---|
[2591] | 624 | std::vector<uint> getMoleculeIdColumnData() const; |
---|
| 625 | void setMoleculeIdColumnData(const std::vector<uint>& molids); |
---|
[2713] | 626 | double calculateModelSelectionCriteria(const std::string& valname, |
---|
| 627 | const std::string& blfunc, |
---|
| 628 | int order, |
---|
| 629 | const std::vector<bool>& inMask, |
---|
| 630 | int whichrow, |
---|
| 631 | bool useLineFinder, |
---|
| 632 | const std::vector<int>& edge, |
---|
| 633 | float threshold, |
---|
| 634 | int chanAvgLimit); |
---|
[2767] | 635 | static std::vector<bool> getMaskFromMaskList(const int nchan, |
---|
| 636 | const std::vector<int>& masklist); |
---|
| 637 | static std::vector<int> splitToIntList(const std::string& str, const char delim); |
---|
| 638 | static std::vector<string> splitToStringList(const std::string& str, const char delim); |
---|
[1907] | 639 | |
---|
[2012] | 640 | |
---|
[2767] | 641 | |
---|
[824] | 642 | private: |
---|
[896] | 643 | |
---|
| 644 | casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const; |
---|
| 645 | |
---|
[824] | 646 | /** |
---|
[2005] | 647 | * Turns a time value into a formatted string |
---|
[824] | 648 | * @param x |
---|
| 649 | * @return |
---|
| 650 | */ |
---|
| 651 | std::string formatSec(casa::Double x) const; |
---|
[18] | 652 | |
---|
[824] | 653 | std::string formatTime(const casa::MEpoch& me, bool showdate)const; |
---|
[1947] | 654 | std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const; |
---|
[22] | 655 | |
---|
[824] | 656 | /** |
---|
| 657 | * Turns a casa::MDirection into a nicely formatted string |
---|
| 658 | * @param md an casa::MDirection |
---|
| 659 | * @return |
---|
| 660 | */ |
---|
| 661 | std::string formatDirection(const casa::MDirection& md) const; |
---|
[19] | 662 | |
---|
[824] | 663 | /** |
---|
| 664 | * Create a unique file name for the paged (temporary) table |
---|
| 665 | * @return just the name |
---|
| 666 | */ |
---|
| 667 | static casa::String generateName(); |
---|
[286] | 668 | |
---|
[824] | 669 | /** |
---|
| 670 | * attach to cached columns |
---|
| 671 | */ |
---|
| 672 | void attach(); |
---|
[50] | 673 | |
---|
[824] | 674 | /** |
---|
| 675 | * Set up the main casa::Table |
---|
| 676 | */ |
---|
| 677 | void setupMainTable(); |
---|
[88] | 678 | |
---|
[859] | 679 | void attachSubtables(); |
---|
[865] | 680 | void copySubtables(const Scantable& other); |
---|
| 681 | |
---|
[824] | 682 | /** |
---|
| 683 | * Convert an "old" asap1 style row index into a new index |
---|
| 684 | * @param[in] therow |
---|
| 685 | * @return and index into @table_ |
---|
| 686 | */ |
---|
| 687 | int rowToScanIndex(int therow); |
---|
[212] | 688 | |
---|
[1694] | 689 | std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const; |
---|
[1111] | 690 | |
---|
[2321] | 691 | static const casa::uInt version_ = 4; |
---|
[286] | 692 | |
---|
[824] | 693 | STSelector selector_; |
---|
[236] | 694 | |
---|
[824] | 695 | casa::Table::TableType type_; |
---|
[465] | 696 | |
---|
[824] | 697 | // the actual data |
---|
| 698 | casa::Table table_; |
---|
| 699 | casa::Table originalTable_; |
---|
[745] | 700 | |
---|
[824] | 701 | STTcal tcalTable_; |
---|
| 702 | STFrequencies freqTable_; |
---|
| 703 | STWeather weatherTable_; |
---|
| 704 | STFocus focusTable_; |
---|
| 705 | STMolecules moleculeTable_; |
---|
[860] | 706 | STHistory historyTable_; |
---|
[960] | 707 | STFit fitTable_; |
---|
[860] | 708 | |
---|
[824] | 709 | // Cached Columns to avoid reconstructing them for each row get/put |
---|
[847] | 710 | casa::ScalarColumn<casa::Double> integrCol_; |
---|
[824] | 711 | casa::MDirection::ScalarColumn dirCol_; |
---|
[847] | 712 | casa::MEpoch::ScalarColumn timeCol_; |
---|
[923] | 713 | casa::ScalarColumn<casa::Float> azCol_; |
---|
| 714 | casa::ScalarColumn<casa::Float> elCol_; |
---|
[824] | 715 | casa::ScalarColumn<casa::String> srcnCol_, fldnCol_; |
---|
[1819] | 716 | casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_; |
---|
[1068] | 717 | casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_; |
---|
[865] | 718 | casa::ArrayColumn<casa::Float> specCol_, tsysCol_; |
---|
[824] | 719 | casa::ArrayColumn<casa::uChar> flagsCol_; |
---|
[430] | 720 | |
---|
[824] | 721 | // id in frequencies table |
---|
| 722 | casa::ScalarColumn<casa::uInt> mfreqidCol_; |
---|
| 723 | // id in tcal table |
---|
| 724 | casa::ScalarColumn<casa::uInt> mtcalidCol_; |
---|
[430] | 725 | |
---|
[824] | 726 | casa::ArrayColumn<casa::String> histitemCol_; |
---|
[972] | 727 | casa::ScalarColumn<casa::Int> mfitidCol_; |
---|
[824] | 728 | casa::ScalarColumn<casa::uInt> mweatheridCol_; |
---|
[322] | 729 | |
---|
[824] | 730 | casa::ScalarColumn<casa::uInt> mfocusidCol_; |
---|
| 731 | |
---|
| 732 | casa::ScalarColumn<casa::uInt> mmolidCol_; |
---|
| 733 | |
---|
[896] | 734 | static std::map<std::string, STPol::STPolFactory *> factories_; |
---|
| 735 | void initFactories(); |
---|
| 736 | |
---|
[1819] | 737 | /** |
---|
| 738 | * Add an auxiliary column to the main table and attach it to a |
---|
| 739 | * cached column. Use for adding new columns that the original asap2 |
---|
| 740 | * tables do not have. |
---|
| 741 | * @param[in] col reference to the cached column to be attached |
---|
| 742 | * @param[in] colName column name in asap table |
---|
| 743 | * @param[in] defValue default value to fill in the column |
---|
| 744 | * |
---|
| 745 | * 25/10/2009 Wataru Kawasaki |
---|
| 746 | */ |
---|
| 747 | template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&, |
---|
| 748 | const casa::String&, |
---|
| 749 | const T2&); |
---|
| 750 | template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&, |
---|
| 751 | const casa::String&, |
---|
| 752 | const casa::Array<T2>&); |
---|
[1907] | 753 | |
---|
[2012] | 754 | void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter); |
---|
[2767] | 755 | double getNormalPolynomial(int n, double x); |
---|
[2645] | 756 | double getChebyshevPolynomial(int n, double x); |
---|
[2767] | 757 | std::vector<float> doPolynomialFitting(const std::vector<float>& data, |
---|
| 758 | const std::vector<bool>& mask, |
---|
| 759 | int order, |
---|
| 760 | std::vector<float>& params, |
---|
| 761 | float& rms, |
---|
| 762 | std::vector<bool>& finalMask, |
---|
| 763 | float clipth, |
---|
| 764 | int clipn); |
---|
| 765 | std::vector<float> doPolynomialFitting(const std::vector<float>& data, |
---|
| 766 | const std::vector<bool>& mask, |
---|
| 767 | int order, |
---|
| 768 | std::vector<float>& params, |
---|
| 769 | float& rms, |
---|
| 770 | std::vector<bool>& finalMask, |
---|
| 771 | int& nClipped, |
---|
| 772 | float thresClip=3.0, |
---|
| 773 | int nIterClip=0, |
---|
| 774 | bool getResidual=true); |
---|
[2645] | 775 | std::vector<float> doChebyshevFitting(const std::vector<float>& data, |
---|
[2767] | 776 | const std::vector<bool>& mask, |
---|
| 777 | int order, |
---|
| 778 | std::vector<float>& params, |
---|
| 779 | float& rms, |
---|
| 780 | std::vector<bool>& finalMask, |
---|
| 781 | float clipth, |
---|
| 782 | int clipn); |
---|
| 783 | std::vector<float> doChebyshevFitting(const std::vector<float>& data, |
---|
| 784 | const std::vector<bool>& mask, |
---|
| 785 | int order, |
---|
| 786 | std::vector<float>& params, |
---|
| 787 | float& rms, |
---|
| 788 | std::vector<bool>& finalMask, |
---|
| 789 | int& nClipped, |
---|
| 790 | float thresClip=3.0, |
---|
| 791 | int nIterClip=0, |
---|
| 792 | bool getResidual=true); |
---|
| 793 | std::vector<float> doLeastSquareFitting(const std::vector<float>& data, |
---|
| 794 | const std::vector<bool>& mask, |
---|
| 795 | double (Scantable::*pfunc)(int, double), |
---|
| 796 | int order, |
---|
| 797 | std::vector<float>& params, |
---|
| 798 | float& rms, |
---|
| 799 | std::vector<bool>& finalMask, |
---|
| 800 | int& nClipped, |
---|
| 801 | float thresClip=3.0, |
---|
| 802 | int nIterClip=0, |
---|
| 803 | bool getResidual=true); |
---|
| 804 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
[2645] | 805 | const std::vector<bool>& mask, |
---|
[2767] | 806 | std::vector<int>& idxEdge, |
---|
[2645] | 807 | std::vector<float>& params, |
---|
[2767] | 808 | float& rms, |
---|
[2737] | 809 | std::vector<bool>& finalMask, |
---|
[2767] | 810 | float clipth, |
---|
| 811 | int clipn); |
---|
| 812 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
| 813 | const std::vector<bool>& mask, |
---|
| 814 | int nPiece, |
---|
| 815 | std::vector<int>& idxEdge, |
---|
| 816 | std::vector<float>& params, |
---|
[2737] | 817 | float& rms, |
---|
[2767] | 818 | std::vector<bool>& finalMask, |
---|
| 819 | float clipth, |
---|
| 820 | int clipn); |
---|
[2012] | 821 | std::vector<float> doCubicSplineFitting(const std::vector<float>& data, |
---|
| 822 | const std::vector<bool>& mask, |
---|
[2081] | 823 | int nPiece, |
---|
[2767] | 824 | bool useGivenPieceBoundary, |
---|
[2064] | 825 | std::vector<int>& idxEdge, |
---|
[2012] | 826 | std::vector<float>& params, |
---|
[2767] | 827 | float& rms, |
---|
| 828 | std::vector<bool>& finalMask, |
---|
[2193] | 829 | int& nClipped, |
---|
[2012] | 830 | float thresClip=3.0, |
---|
[2767] | 831 | int nIterClip=0, |
---|
[2094] | 832 | bool getResidual=true); |
---|
[2047] | 833 | std::vector<float> doSinusoidFitting(const std::vector<float>& data, |
---|
| 834 | const std::vector<bool>& mask, |
---|
[2081] | 835 | const std::vector<int>& waveNumbers, |
---|
[2047] | 836 | std::vector<float>& params, |
---|
[2767] | 837 | float& rms, |
---|
| 838 | std::vector<bool>& finalMask, |
---|
| 839 | float clipth, |
---|
| 840 | int clipn); |
---|
| 841 | std::vector<float> doSinusoidFitting(const std::vector<float>& data, |
---|
| 842 | const std::vector<bool>& mask, |
---|
| 843 | const std::vector<int>& waveNumbers, |
---|
| 844 | std::vector<float>& params, |
---|
| 845 | float& rms, |
---|
| 846 | std::vector<bool>& finalMask, |
---|
[2193] | 847 | int& nClipped, |
---|
[2047] | 848 | float thresClip=3.0, |
---|
[2767] | 849 | int nIterClip=0, |
---|
[2094] | 850 | bool getResidual=true); |
---|
[2186] | 851 | void selectWaveNumbers(const int whichrow, |
---|
| 852 | const std::vector<bool>& chanMask, |
---|
[2767] | 853 | const std::string& fftInfo, |
---|
| 854 | //const bool applyFFT, |
---|
| 855 | //const std::string& fftMethod, |
---|
| 856 | //const std::string& fftThresh, |
---|
[2186] | 857 | const std::vector<int>& addNWaves, |
---|
| 858 | const std::vector<int>& rejectNWaves, |
---|
| 859 | std::vector<int>& nWaves); |
---|
[2767] | 860 | void parseFFTInfo(const std::string& fftInfo, |
---|
| 861 | bool& applyFFT, |
---|
| 862 | std::string& fftMethod, |
---|
| 863 | std::string& fftThresh); |
---|
[2186] | 864 | void parseThresholdExpression(const std::string& fftThresh, |
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| 865 | std::string& fftThAttr, |
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| 866 | float& fftThSigma, |
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| 867 | int& fftThTop); |
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| 868 | void doSelectWaveNumbers(const int whichrow, |
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| 869 | const std::vector<bool>& chanMask, |
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| 870 | const std::string& fftMethod, |
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| 871 | const float fftThSigma, |
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| 872 | const int fftThTop, |
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| 873 | const std::string& fftThAttr, |
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| 874 | std::vector<int>& nWaves); |
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[2411] | 875 | void addAuxWaveNumbers(const int whichrow, |
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| 876 | const std::vector<int>& addNWaves, |
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[2186] | 877 | const std::vector<int>& rejectNWaves, |
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| 878 | std::vector<int>& nWaves); |
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[2411] | 879 | void setWaveNumberListUptoNyquistFreq(const int whichrow, |
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| 880 | std::vector<int>& nWaves); |
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[2012] | 881 | bool hasSameNchanOverIFs(); |
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| 882 | std::string getMaskRangeList(const std::vector<bool>& mask, |
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| 883 | int whichrow, |
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| 884 | const casa::String& coordInfo, |
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[2047] | 885 | bool hasSameNchan, |
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| 886 | bool verbose=false); |
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| 887 | std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask); |
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[2641] | 888 | std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const; |
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| 889 | std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const; |
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[2012] | 890 | std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask); |
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| 891 | //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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[2641] | 892 | 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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| 893 | 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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| 894 | 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); |
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[2189] | 895 | void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow); |
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| 896 | void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000); |
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[1994] | 897 | |
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| 898 | void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval); |
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| 899 | |
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[2713] | 900 | double doCalculateModelSelectionCriteria(const std::string& valname, |
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| 901 | const std::vector<float>& spec, |
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| 902 | const std::vector<bool>& mask, |
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| 903 | const std::string& blfunc, |
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| 904 | int order); |
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[2737] | 905 | double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec); |
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[2767] | 906 | std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms); |
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| 907 | void parseBlInfo(const std::string& blInfo, int& whichrow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF); |
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| 908 | std::vector<float> doApplyBaselineTable(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms); |
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| 909 | std::vector<float> doSubtractBaseline(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, std::vector<bool>& finalmask, float clipth, int clipn, bool uself, int irow, float lfth, std::vector<int>& lfedge, int lfavg); |
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[2713] | 910 | |
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[2] | 911 | }; |
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[824] | 912 | } // namespace |
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| 913 | |
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[2] | 914 | #endif |
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