[805] | 1 | // |
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| 2 | // C++ Implementation: 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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[206] | 12 | #include <map> |
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[1819] | 13 | #include <fstream> |
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[206] | 14 | |
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[125] | 15 | #include <casa/aips.h> |
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[80] | 16 | #include <casa/iostream.h> |
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| 17 | #include <casa/iomanip.h> |
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[805] | 18 | #include <casa/OS/Path.h> |
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| 19 | #include <casa/OS/File.h> |
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[80] | 20 | #include <casa/Arrays/Array.h> |
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| 21 | #include <casa/Arrays/ArrayMath.h> |
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| 22 | #include <casa/Arrays/MaskArrMath.h> |
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| 23 | #include <casa/Arrays/ArrayLogical.h> |
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| 24 | #include <casa/Arrays/ArrayAccessor.h> |
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[1325] | 25 | #include <casa/Arrays/Vector.h> |
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[455] | 26 | #include <casa/Arrays/VectorSTLIterator.h> |
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[1819] | 27 | #include <casa/Arrays/Slice.h> |
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[418] | 28 | #include <casa/BasicMath/Math.h> |
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[504] | 29 | #include <casa/BasicSL/Constants.h> |
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[286] | 30 | #include <casa/Quanta/MVAngle.h> |
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[805] | 31 | #include <casa/Containers/RecordField.h> |
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[902] | 32 | #include <casa/Utilities/GenSort.h> |
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[1819] | 33 | #include <casa/Logging/LogIO.h> |
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[2] | 34 | |
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[80] | 35 | #include <tables/Tables/TableParse.h> |
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| 36 | #include <tables/Tables/TableDesc.h> |
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[488] | 37 | #include <tables/Tables/TableCopy.h> |
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[80] | 38 | #include <tables/Tables/SetupNewTab.h> |
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| 39 | #include <tables/Tables/ScaColDesc.h> |
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| 40 | #include <tables/Tables/ArrColDesc.h> |
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[805] | 41 | #include <tables/Tables/TableRow.h> |
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| 42 | #include <tables/Tables/TableVector.h> |
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| 43 | #include <tables/Tables/TableIter.h> |
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[2] | 44 | |
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[80] | 45 | #include <tables/Tables/ExprNode.h> |
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| 46 | #include <tables/Tables/TableRecord.h> |
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[1325] | 47 | #include <casa/Quanta/MVTime.h> |
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| 48 | #include <casa/Quanta/MVAngle.h> |
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| 49 | #include <measures/Measures/MeasRef.h> |
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| 50 | #include <measures/Measures/MeasTable.h> |
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| 51 | // needed to avoid error in .tcc |
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| 52 | #include <measures/Measures/MCDirection.h> |
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| 53 | // |
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| 54 | #include <measures/Measures/MDirection.h> |
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[80] | 55 | #include <measures/Measures/MFrequency.h> |
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[805] | 56 | #include <measures/Measures/MEpoch.h> |
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| 57 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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| 58 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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| 59 | #include <measures/TableMeasures/TableMeasDesc.h> |
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| 60 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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[105] | 61 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[2] | 62 | |
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[2005] | 63 | #include <atnf/PKSIO/SrcType.h> |
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[805] | 64 | #include "Scantable.h" |
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[896] | 65 | #include "STPolLinear.h" |
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[1189] | 66 | #include "STPolCircular.h" |
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[913] | 67 | #include "STPolStokes.h" |
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[878] | 68 | #include "STAttr.h" |
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[2012] | 69 | #include "STLineFinder.h" |
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[902] | 70 | #include "MathUtils.h" |
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[2] | 71 | |
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[125] | 72 | using namespace casa; |
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[2] | 73 | |
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[805] | 74 | namespace asap { |
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| 75 | |
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[896] | 76 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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| 77 | |
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| 78 | void Scantable::initFactories() { |
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| 79 | if ( factories_.empty() ) { |
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| 80 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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[1323] | 81 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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[913] | 82 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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[896] | 83 | } |
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| 84 | } |
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| 85 | |
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[805] | 86 | Scantable::Scantable(Table::TableType ttype) : |
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[852] | 87 | type_(ttype) |
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[206] | 88 | { |
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[896] | 89 | initFactories(); |
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[805] | 90 | setupMainTable(); |
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[852] | 91 | freqTable_ = STFrequencies(*this); |
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[805] | 92 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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[852] | 93 | weatherTable_ = STWeather(*this); |
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[805] | 94 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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[852] | 95 | focusTable_ = STFocus(*this); |
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[805] | 96 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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[852] | 97 | tcalTable_ = STTcal(*this); |
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[805] | 98 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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[852] | 99 | moleculeTable_ = STMolecules(*this); |
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[805] | 100 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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[860] | 101 | historyTable_ = STHistory(*this); |
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| 102 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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[959] | 103 | fitTable_ = STFit(*this); |
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| 104 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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[1881] | 105 | table_.tableInfo().setType( "Scantable" ) ; |
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[805] | 106 | originalTable_ = table_; |
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[322] | 107 | attach(); |
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[18] | 108 | } |
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[206] | 109 | |
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[805] | 110 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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[852] | 111 | type_(ttype) |
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[206] | 112 | { |
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[896] | 113 | initFactories(); |
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[1819] | 114 | |
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[865] | 115 | Table tab(name, Table::Update); |
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[1009] | 116 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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[483] | 117 | if (version != version_) { |
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| 118 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 119 | } |
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[1009] | 120 | if ( type_ == Table::Memory ) { |
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[852] | 121 | table_ = tab.copyToMemoryTable(generateName()); |
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[1009] | 122 | } else { |
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[805] | 123 | table_ = tab; |
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[1009] | 124 | } |
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[1881] | 125 | table_.tableInfo().setType( "Scantable" ) ; |
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[1009] | 126 | |
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[859] | 127 | attachSubtables(); |
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[805] | 128 | originalTable_ = table_; |
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[329] | 129 | attach(); |
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[2] | 130 | } |
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[1819] | 131 | /* |
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| 132 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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| 133 | type_(ttype) |
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| 134 | { |
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| 135 | initFactories(); |
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| 136 | Table tab(name, Table::Update); |
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| 137 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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| 138 | if (version != version_) { |
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| 139 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 140 | } |
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| 141 | if ( type_ == Table::Memory ) { |
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| 142 | table_ = tab.copyToMemoryTable(generateName()); |
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| 143 | } else { |
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| 144 | table_ = tab; |
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| 145 | } |
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[2] | 146 | |
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[1819] | 147 | attachSubtables(); |
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| 148 | originalTable_ = table_; |
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| 149 | attach(); |
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| 150 | } |
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| 151 | */ |
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| 152 | |
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[805] | 153 | Scantable::Scantable( const Scantable& other, bool clear ) |
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[206] | 154 | { |
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[805] | 155 | // with or without data |
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[859] | 156 | String newname = String(generateName()); |
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[865] | 157 | type_ = other.table_.tableType(); |
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[859] | 158 | if ( other.table_.tableType() == Table::Memory ) { |
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| 159 | if ( clear ) { |
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| 160 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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| 161 | other.table_, True); |
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| 162 | } else |
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| 163 | table_ = other.table_.copyToMemoryTable(newname); |
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[16] | 164 | } else { |
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[915] | 165 | other.table_.deepCopy(newname, Table::New, False, |
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| 166 | other.table_.endianFormat(), |
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[865] | 167 | Bool(clear)); |
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| 168 | table_ = Table(newname, Table::Update); |
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| 169 | table_.markForDelete(); |
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| 170 | } |
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[1881] | 171 | table_.tableInfo().setType( "Scantable" ) ; |
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[1111] | 172 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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[915] | 173 | if ( clear ) copySubtables(other); |
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[859] | 174 | attachSubtables(); |
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[805] | 175 | originalTable_ = table_; |
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[322] | 176 | attach(); |
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[2] | 177 | } |
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| 178 | |
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[865] | 179 | void Scantable::copySubtables(const Scantable& other) { |
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| 180 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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| 181 | TableCopy::copyRows(t, other.freqTable_.table()); |
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| 182 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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| 183 | TableCopy::copyRows(t, other.focusTable_.table()); |
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| 184 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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| 185 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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| 186 | t = table_.rwKeywordSet().asTable("TCAL"); |
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| 187 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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| 188 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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| 189 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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| 190 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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| 191 | TableCopy::copyRows(t, other.historyTable_.table()); |
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[972] | 192 | t = table_.rwKeywordSet().asTable("FIT"); |
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| 193 | TableCopy::copyRows(t, other.fitTable_.table()); |
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[865] | 194 | } |
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| 195 | |
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[859] | 196 | void Scantable::attachSubtables() |
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| 197 | { |
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| 198 | freqTable_ = STFrequencies(table_); |
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| 199 | focusTable_ = STFocus(table_); |
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| 200 | weatherTable_ = STWeather(table_); |
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| 201 | tcalTable_ = STTcal(table_); |
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| 202 | moleculeTable_ = STMolecules(table_); |
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[860] | 203 | historyTable_ = STHistory(table_); |
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[972] | 204 | fitTable_ = STFit(table_); |
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[859] | 205 | } |
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| 206 | |
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[805] | 207 | Scantable::~Scantable() |
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[206] | 208 | { |
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[941] | 209 | //cout << "~Scantable() " << this << endl; |
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[2] | 210 | } |
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| 211 | |
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[805] | 212 | void Scantable::setupMainTable() |
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[206] | 213 | { |
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[805] | 214 | TableDesc td("", "1", TableDesc::Scratch); |
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| 215 | td.comment() = "An ASAP Scantable"; |
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[1009] | 216 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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[2] | 217 | |
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[805] | 218 | // n Cycles |
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| 219 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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| 220 | // new index every nBeam x nIF x nPol |
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| 221 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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[2] | 222 | |
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[805] | 223 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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| 224 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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[972] | 225 | // linear, circular, stokes |
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[805] | 226 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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| 227 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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[138] | 228 | |
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[805] | 229 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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| 230 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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[80] | 231 | |
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[1819] | 232 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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| 233 | refbeamnoColumn.setDefault(Int(-1)); |
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| 234 | td.addColumn(refbeamnoColumn); |
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| 235 | |
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| 236 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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| 237 | flagrowColumn.setDefault(uInt(0)); |
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| 238 | td.addColumn(flagrowColumn); |
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| 239 | |
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[805] | 240 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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| 241 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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| 242 | TableMeasValueDesc measVal(td, "TIME"); |
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| 243 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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| 244 | mepochCol.write(td); |
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[483] | 245 | |
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[805] | 246 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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| 247 | |
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[2] | 248 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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[805] | 249 | // Type of source (on=0, off=1, other=-1) |
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[1503] | 250 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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| 251 | stypeColumn.setDefault(Int(-1)); |
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| 252 | td.addColumn(stypeColumn); |
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[805] | 253 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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| 254 | |
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| 255 | //The actual Data Vectors |
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[2] | 256 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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| 257 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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[89] | 258 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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[805] | 259 | |
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| 260 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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| 261 | IPosition(1,2), |
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| 262 | ColumnDesc::Direct)); |
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| 263 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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| 264 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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| 265 | // the TableMeasDesc gives the column a type |
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| 266 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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[987] | 267 | // a uder set table type e.g. GALCTIC, B1950 ... |
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| 268 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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[805] | 269 | // writing create the measure column |
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| 270 | mdirCol.write(td); |
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[923] | 271 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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| 272 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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[1047] | 273 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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[105] | 274 | |
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[805] | 275 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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[972] | 276 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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[973] | 277 | fitColumn.setDefault(Int(-1)); |
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[972] | 278 | td.addColumn(fitColumn); |
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[805] | 279 | |
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| 280 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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| 281 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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| 282 | |
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[999] | 283 | // columns which just get dragged along, as they aren't used in asap |
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| 284 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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| 285 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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| 286 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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| 287 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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| 288 | |
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[805] | 289 | td.rwKeywordSet().define("OBSMODE", String("")); |
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| 290 | |
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[418] | 291 | // Now create Table SetUp from the description. |
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[859] | 292 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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[852] | 293 | table_ = Table(aNewTab, type_, 0); |
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[805] | 294 | originalTable_ = table_; |
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| 295 | } |
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[418] | 296 | |
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[805] | 297 | void Scantable::attach() |
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[455] | 298 | { |
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[805] | 299 | timeCol_.attach(table_, "TIME"); |
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| 300 | srcnCol_.attach(table_, "SRCNAME"); |
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[1068] | 301 | srctCol_.attach(table_, "SRCTYPE"); |
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[805] | 302 | specCol_.attach(table_, "SPECTRA"); |
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| 303 | flagsCol_.attach(table_, "FLAGTRA"); |
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[865] | 304 | tsysCol_.attach(table_, "TSYS"); |
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[805] | 305 | cycleCol_.attach(table_,"CYCLENO"); |
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| 306 | scanCol_.attach(table_, "SCANNO"); |
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| 307 | beamCol_.attach(table_, "BEAMNO"); |
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[847] | 308 | ifCol_.attach(table_, "IFNO"); |
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| 309 | polCol_.attach(table_, "POLNO"); |
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[805] | 310 | integrCol_.attach(table_, "INTERVAL"); |
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| 311 | azCol_.attach(table_, "AZIMUTH"); |
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| 312 | elCol_.attach(table_, "ELEVATION"); |
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| 313 | dirCol_.attach(table_, "DIRECTION"); |
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| 314 | fldnCol_.attach(table_, "FIELDNAME"); |
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| 315 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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[455] | 316 | |
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[1730] | 317 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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[805] | 318 | mfitidCol_.attach(table_,"FIT_ID"); |
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| 319 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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| 320 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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| 321 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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| 322 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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[1819] | 323 | |
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| 324 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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| 325 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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| 326 | |
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[455] | 327 | } |
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| 328 | |
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[1819] | 329 | template<class T, class T2> |
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| 330 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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| 331 | const String& colName, |
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| 332 | const T2& defValue) |
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| 333 | { |
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| 334 | try { |
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| 335 | col.attach(table_, colName); |
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| 336 | } catch (TableError& err) { |
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| 337 | String errMesg = err.getMesg(); |
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| 338 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 339 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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| 340 | col.attach(table_, colName); |
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| 341 | col.fillColumn(static_cast<T>(defValue)); |
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| 342 | } else { |
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| 343 | throw; |
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| 344 | } |
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| 345 | } catch (...) { |
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| 346 | throw; |
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| 347 | } |
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| 348 | } |
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| 349 | |
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| 350 | template<class T, class T2> |
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| 351 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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| 352 | const String& colName, |
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| 353 | const Array<T2>& defValue) |
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| 354 | { |
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| 355 | try { |
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| 356 | col.attach(table_, colName); |
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| 357 | } catch (TableError& err) { |
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| 358 | String errMesg = err.getMesg(); |
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| 359 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 360 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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| 361 | col.attach(table_, colName); |
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| 362 | |
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| 363 | int size = 0; |
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| 364 | ArrayIterator<T2>& it = defValue.begin(); |
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| 365 | while (it != defValue.end()) { |
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| 366 | ++size; |
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| 367 | ++it; |
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| 368 | } |
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| 369 | IPosition ip(1, size); |
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| 370 | Array<T>& arr(ip); |
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| 371 | for (int i = 0; i < size; ++i) |
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| 372 | arr[i] = static_cast<T>(defValue[i]); |
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| 373 | |
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| 374 | col.fillColumn(arr); |
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| 375 | } else { |
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| 376 | throw; |
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| 377 | } |
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| 378 | } catch (...) { |
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| 379 | throw; |
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| 380 | } |
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| 381 | } |
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| 382 | |
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[901] | 383 | void Scantable::setHeader(const STHeader& sdh) |
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[206] | 384 | { |
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[18] | 385 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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| 386 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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| 387 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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| 388 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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| 389 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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| 390 | table_.rwKeywordSet().define("Project", sdh.project); |
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| 391 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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| 392 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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| 393 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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| 394 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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| 395 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
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| 396 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
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| 397 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
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| 398 | table_.rwKeywordSet().define("UTC", sdh.utc); |
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[206] | 399 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
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| 400 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
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[905] | 401 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
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[50] | 402 | } |
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[21] | 403 | |
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[901] | 404 | STHeader Scantable::getHeader() const |
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[206] | 405 | { |
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[901] | 406 | STHeader sdh; |
---|
[21] | 407 | table_.keywordSet().get("nBeam",sdh.nbeam); |
---|
| 408 | table_.keywordSet().get("nIF",sdh.nif); |
---|
| 409 | table_.keywordSet().get("nPol",sdh.npol); |
---|
| 410 | table_.keywordSet().get("nChan",sdh.nchan); |
---|
| 411 | table_.keywordSet().get("Observer", sdh.observer); |
---|
| 412 | table_.keywordSet().get("Project", sdh.project); |
---|
| 413 | table_.keywordSet().get("Obstype", sdh.obstype); |
---|
| 414 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
---|
| 415 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
---|
| 416 | table_.keywordSet().get("Equinox", sdh.equinox); |
---|
| 417 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
---|
| 418 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
---|
| 419 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
---|
| 420 | table_.keywordSet().get("UTC", sdh.utc); |
---|
[206] | 421 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
---|
| 422 | table_.keywordSet().get("Epoch", sdh.epoch); |
---|
[905] | 423 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
---|
[21] | 424 | return sdh; |
---|
[18] | 425 | } |
---|
[805] | 426 | |
---|
[1360] | 427 | void Scantable::setSourceType( int stype ) |
---|
[1068] | 428 | { |
---|
| 429 | if ( stype < 0 || stype > 1 ) |
---|
| 430 | throw(AipsError("Illegal sourcetype.")); |
---|
| 431 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
---|
| 432 | tabvec = Int(stype); |
---|
| 433 | } |
---|
| 434 | |
---|
[845] | 435 | bool Scantable::conformant( const Scantable& other ) |
---|
| 436 | { |
---|
| 437 | return this->getHeader().conformant(other.getHeader()); |
---|
| 438 | } |
---|
| 439 | |
---|
| 440 | |
---|
[50] | 441 | |
---|
[805] | 442 | std::string Scantable::formatSec(Double x) const |
---|
[206] | 443 | { |
---|
[105] | 444 | Double xcop = x; |
---|
| 445 | MVTime mvt(xcop/24./3600.); // make days |
---|
[365] | 446 | |
---|
[105] | 447 | if (x < 59.95) |
---|
[281] | 448 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
[745] | 449 | else if (x < 3599.95) |
---|
[281] | 450 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
| 451 | else { |
---|
| 452 | ostringstream oss; |
---|
| 453 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
| 454 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
| 455 | return String(oss); |
---|
[745] | 456 | } |
---|
[105] | 457 | }; |
---|
| 458 | |
---|
[805] | 459 | std::string Scantable::formatDirection(const MDirection& md) const |
---|
[281] | 460 | { |
---|
| 461 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
| 462 | Int prec = 7; |
---|
| 463 | |
---|
| 464 | MVAngle mvLon(t[0]); |
---|
| 465 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
[987] | 466 | uInt tp = md.getRef().getType(); |
---|
| 467 | if (tp == MDirection::GALACTIC || |
---|
| 468 | tp == MDirection::SUPERGAL ) { |
---|
| 469 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
| 470 | } |
---|
[281] | 471 | MVAngle mvLat(t[1]); |
---|
| 472 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
[380] | 473 | return sLon + String(" ") + sLat; |
---|
[281] | 474 | } |
---|
| 475 | |
---|
| 476 | |
---|
[805] | 477 | std::string Scantable::getFluxUnit() const |
---|
[206] | 478 | { |
---|
[847] | 479 | return table_.keywordSet().asString("FluxUnit"); |
---|
[206] | 480 | } |
---|
| 481 | |
---|
[805] | 482 | void Scantable::setFluxUnit(const std::string& unit) |
---|
[218] | 483 | { |
---|
| 484 | String tmp(unit); |
---|
| 485 | Unit tU(tmp); |
---|
| 486 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
| 487 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
| 488 | } else { |
---|
| 489 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
| 490 | } |
---|
| 491 | } |
---|
| 492 | |
---|
[805] | 493 | void Scantable::setInstrument(const std::string& name) |
---|
[236] | 494 | { |
---|
[805] | 495 | bool throwIt = true; |
---|
[996] | 496 | // create an Instrument to see if this is valid |
---|
| 497 | STAttr::convertInstrument(name, throwIt); |
---|
[236] | 498 | String nameU(name); |
---|
| 499 | nameU.upcase(); |
---|
| 500 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
| 501 | } |
---|
| 502 | |
---|
[1189] | 503 | void Scantable::setFeedType(const std::string& feedtype) |
---|
| 504 | { |
---|
| 505 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
| 506 | std::string msg = "Illegal feed type "+ feedtype; |
---|
| 507 | throw(casa::AipsError(msg)); |
---|
| 508 | } |
---|
| 509 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
| 510 | } |
---|
| 511 | |
---|
[1743] | 512 | MPosition Scantable::getAntennaPosition() const |
---|
[805] | 513 | { |
---|
| 514 | Vector<Double> antpos; |
---|
| 515 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
| 516 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
| 517 | return MPosition(mvpos); |
---|
| 518 | } |
---|
[281] | 519 | |
---|
[805] | 520 | void Scantable::makePersistent(const std::string& filename) |
---|
| 521 | { |
---|
| 522 | String inname(filename); |
---|
| 523 | Path path(inname); |
---|
[1111] | 524 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
[805] | 525 | inname = path.expandedName(); |
---|
[2030] | 526 | // 2011/03/04 TN |
---|
| 527 | // We can comment out this workaround since the essential bug is |
---|
| 528 | // fixed in casacore (r20889 in google code). |
---|
| 529 | table_.deepCopy(inname, Table::New); |
---|
| 530 | // // WORKAROUND !!! for Table bug |
---|
| 531 | // // Remove when fixed in casacore |
---|
| 532 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
| 533 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
| 534 | // tab.deepCopy(inname, Table::New); |
---|
| 535 | // tab.markForDelete(); |
---|
| 536 | // |
---|
| 537 | // } else { |
---|
| 538 | // table_.deepCopy(inname, Table::New); |
---|
| 539 | // } |
---|
[805] | 540 | } |
---|
| 541 | |
---|
[837] | 542 | int Scantable::nbeam( int scanno ) const |
---|
[805] | 543 | { |
---|
| 544 | if ( scanno < 0 ) { |
---|
| 545 | Int n; |
---|
| 546 | table_.keywordSet().get("nBeam",n); |
---|
| 547 | return int(n); |
---|
[105] | 548 | } else { |
---|
[805] | 549 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 550 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 551 | ROTableRow row(t); |
---|
| 552 | const TableRecord& rec = row.get(0); |
---|
| 553 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 554 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 555 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 556 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
[805] | 557 | return int(v.nelements()); |
---|
[105] | 558 | } |
---|
[805] | 559 | return 0; |
---|
| 560 | } |
---|
[455] | 561 | |
---|
[837] | 562 | int Scantable::nif( int scanno ) const |
---|
[805] | 563 | { |
---|
| 564 | if ( scanno < 0 ) { |
---|
| 565 | Int n; |
---|
| 566 | table_.keywordSet().get("nIF",n); |
---|
| 567 | return int(n); |
---|
| 568 | } else { |
---|
| 569 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 570 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 571 | ROTableRow row(t); |
---|
| 572 | const TableRecord& rec = row.get(0); |
---|
| 573 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 574 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 575 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 576 | if ( subt.nrow() == 0 ) return 0; |
---|
| 577 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
[805] | 578 | return int(v.nelements()); |
---|
[2] | 579 | } |
---|
[805] | 580 | return 0; |
---|
| 581 | } |
---|
[321] | 582 | |
---|
[837] | 583 | int Scantable::npol( int scanno ) const |
---|
[805] | 584 | { |
---|
| 585 | if ( scanno < 0 ) { |
---|
| 586 | Int n; |
---|
| 587 | table_.keywordSet().get("nPol",n); |
---|
| 588 | return n; |
---|
| 589 | } else { |
---|
| 590 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 591 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 592 | ROTableRow row(t); |
---|
| 593 | const TableRecord& rec = row.get(0); |
---|
| 594 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 595 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 596 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 597 | if ( subt.nrow() == 0 ) return 0; |
---|
| 598 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
[805] | 599 | return int(v.nelements()); |
---|
[321] | 600 | } |
---|
[805] | 601 | return 0; |
---|
[2] | 602 | } |
---|
[805] | 603 | |
---|
[845] | 604 | int Scantable::ncycle( int scanno ) const |
---|
[206] | 605 | { |
---|
[805] | 606 | if ( scanno < 0 ) { |
---|
[837] | 607 | Block<String> cols(2); |
---|
| 608 | cols[0] = "SCANNO"; |
---|
| 609 | cols[1] = "CYCLENO"; |
---|
| 610 | TableIterator it(table_, cols); |
---|
| 611 | int n = 0; |
---|
| 612 | while ( !it.pastEnd() ) { |
---|
| 613 | ++n; |
---|
[902] | 614 | ++it; |
---|
[837] | 615 | } |
---|
| 616 | return n; |
---|
[805] | 617 | } else { |
---|
[888] | 618 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 619 | ROTableRow row(t); |
---|
| 620 | const TableRecord& rec = row.get(0); |
---|
| 621 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 622 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 623 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
| 624 | if ( subt.nrow() == 0 ) return 0; |
---|
| 625 | return int(subt.nrow()); |
---|
[805] | 626 | } |
---|
| 627 | return 0; |
---|
[18] | 628 | } |
---|
[455] | 629 | |
---|
| 630 | |
---|
[845] | 631 | int Scantable::nrow( int scanno ) const |
---|
[805] | 632 | { |
---|
[845] | 633 | return int(table_.nrow()); |
---|
| 634 | } |
---|
| 635 | |
---|
| 636 | int Scantable::nchan( int ifno ) const |
---|
| 637 | { |
---|
| 638 | if ( ifno < 0 ) { |
---|
[805] | 639 | Int n; |
---|
| 640 | table_.keywordSet().get("nChan",n); |
---|
| 641 | return int(n); |
---|
| 642 | } else { |
---|
[1360] | 643 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
| 644 | // vary with these |
---|
[888] | 645 | Table t = table_(table_.col("IFNO") == ifno); |
---|
| 646 | if ( t.nrow() == 0 ) return 0; |
---|
| 647 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
[923] | 648 | return v.shape(0)(0); |
---|
[805] | 649 | } |
---|
| 650 | return 0; |
---|
[18] | 651 | } |
---|
[455] | 652 | |
---|
[1111] | 653 | int Scantable::nscan() const { |
---|
| 654 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
[1148] | 655 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
[1111] | 656 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 657 | return int(nout); |
---|
| 658 | } |
---|
| 659 | |
---|
[923] | 660 | int Scantable::getChannels(int whichrow) const |
---|
| 661 | { |
---|
| 662 | return specCol_.shape(whichrow)(0); |
---|
| 663 | } |
---|
[847] | 664 | |
---|
| 665 | int Scantable::getBeam(int whichrow) const |
---|
| 666 | { |
---|
| 667 | return beamCol_(whichrow); |
---|
| 668 | } |
---|
| 669 | |
---|
[1694] | 670 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
[1111] | 671 | { |
---|
| 672 | Vector<uInt> nos(col.getColumn()); |
---|
[1148] | 673 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 674 | nos.resize(n, True); |
---|
[1111] | 675 | std::vector<uint> stlout; |
---|
| 676 | nos.tovector(stlout); |
---|
| 677 | return stlout; |
---|
| 678 | } |
---|
| 679 | |
---|
[847] | 680 | int Scantable::getIF(int whichrow) const |
---|
| 681 | { |
---|
| 682 | return ifCol_(whichrow); |
---|
| 683 | } |
---|
| 684 | |
---|
| 685 | int Scantable::getPol(int whichrow) const |
---|
| 686 | { |
---|
| 687 | return polCol_(whichrow); |
---|
| 688 | } |
---|
| 689 | |
---|
[805] | 690 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
| 691 | { |
---|
[1947] | 692 | return formatTime(me, showdate, 0); |
---|
| 693 | } |
---|
| 694 | |
---|
| 695 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
| 696 | { |
---|
[805] | 697 | MVTime mvt(me.getValue()); |
---|
| 698 | if (showdate) |
---|
[1947] | 699 | //mvt.setFormat(MVTime::YMD); |
---|
| 700 | mvt.setFormat(MVTime::YMD, prec); |
---|
[805] | 701 | else |
---|
[1947] | 702 | //mvt.setFormat(MVTime::TIME); |
---|
| 703 | mvt.setFormat(MVTime::TIME, prec); |
---|
[805] | 704 | ostringstream oss; |
---|
| 705 | oss << mvt; |
---|
| 706 | return String(oss); |
---|
| 707 | } |
---|
[488] | 708 | |
---|
[805] | 709 | void Scantable::calculateAZEL() |
---|
| 710 | { |
---|
| 711 | MPosition mp = getAntennaPosition(); |
---|
| 712 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 713 | ostringstream oss; |
---|
| 714 | oss << "Computed azimuth/elevation using " << endl |
---|
| 715 | << mp << endl; |
---|
[996] | 716 | for (Int i=0; i<nrow(); ++i) { |
---|
[805] | 717 | MEpoch me = timeCol(i); |
---|
[987] | 718 | MDirection md = getDirection(i); |
---|
[805] | 719 | oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md) |
---|
| 720 | << endl << " => "; |
---|
| 721 | MeasFrame frame(mp, me); |
---|
| 722 | Vector<Double> azel = |
---|
| 723 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
| 724 | frame) |
---|
| 725 | )().getAngle("rad").getValue(); |
---|
[923] | 726 | azCol_.put(i,Float(azel[0])); |
---|
| 727 | elCol_.put(i,Float(azel[1])); |
---|
[805] | 728 | oss << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
| 729 | << azel[1]/C::pi*180.0 << " (deg)" << endl; |
---|
[16] | 730 | } |
---|
[805] | 731 | pushLog(String(oss)); |
---|
| 732 | } |
---|
[89] | 733 | |
---|
[1819] | 734 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 735 | { |
---|
| 736 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
| 737 | Vector<uChar> flgs = flagsCol_(i); |
---|
| 738 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
| 739 | flagsCol_.put(i, flgs); |
---|
| 740 | } |
---|
| 741 | } |
---|
| 742 | |
---|
| 743 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 744 | { |
---|
| 745 | Vector<uChar> flags; |
---|
| 746 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 747 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
| 748 | Vector<Bool> bflag(flags.shape()); |
---|
| 749 | convertArray(bflag, flags); |
---|
| 750 | //bflag = !bflag; |
---|
| 751 | |
---|
| 752 | std::vector<bool> mask; |
---|
| 753 | bflag.tovector(mask); |
---|
| 754 | return mask; |
---|
| 755 | } |
---|
| 756 | |
---|
| 757 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
| 758 | Vector<uChar> flgs) |
---|
| 759 | { |
---|
| 760 | Vector<Float> spcs = specCol_(whichrow); |
---|
| 761 | uInt nchannel = nchan(); |
---|
| 762 | if (spcs.nelements() != nchannel) { |
---|
| 763 | throw(AipsError("Data has incorrect number of channels")); |
---|
| 764 | } |
---|
| 765 | uChar userflag = 1 << 7; |
---|
| 766 | if (unflag) { |
---|
| 767 | userflag = 0 << 7; |
---|
| 768 | } |
---|
| 769 | if (clipoutside) { |
---|
| 770 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 771 | Float spc = spcs(j); |
---|
| 772 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
| 773 | flgs(j) = userflag; |
---|
| 774 | } |
---|
| 775 | } |
---|
| 776 | } else { |
---|
| 777 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 778 | Float spc = spcs(j); |
---|
| 779 | if ((spc < uthres) && (spc > dthres)) { |
---|
| 780 | flgs(j) = userflag; |
---|
| 781 | } |
---|
| 782 | } |
---|
| 783 | } |
---|
| 784 | } |
---|
| 785 | |
---|
[1994] | 786 | |
---|
| 787 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
[1333] | 788 | std::vector<bool>::const_iterator it; |
---|
| 789 | uInt ntrue = 0; |
---|
[1994] | 790 | if (whichrow >= int(table_.nrow()) ) { |
---|
| 791 | throw(AipsError("Invalid row number")); |
---|
| 792 | } |
---|
[1333] | 793 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 794 | if ( *it ) { |
---|
| 795 | ntrue++; |
---|
| 796 | } |
---|
| 797 | } |
---|
[1994] | 798 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
| 799 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
[1000] | 800 | throw(AipsError("Trying to flag whole scantable.")); |
---|
[1994] | 801 | uChar userflag = 1 << 7; |
---|
| 802 | if ( unflag ) { |
---|
| 803 | userflag = 0 << 7; |
---|
| 804 | } |
---|
| 805 | if (whichrow > -1 ) { |
---|
| 806 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
| 807 | } else { |
---|
[1000] | 808 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
[1994] | 809 | applyChanFlag(i, msk, userflag); |
---|
[1000] | 810 | } |
---|
[1994] | 811 | } |
---|
| 812 | } |
---|
| 813 | |
---|
| 814 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
| 815 | { |
---|
| 816 | if (whichrow >= table_.nrow() ) { |
---|
| 817 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
| 818 | } |
---|
| 819 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
| 820 | if ( msk.size() == 0 ) { |
---|
| 821 | flgs = flagval; |
---|
| 822 | flagsCol_.put(whichrow, flgs); |
---|
[1000] | 823 | return; |
---|
| 824 | } |
---|
| 825 | if ( int(msk.size()) != nchan() ) { |
---|
| 826 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
| 827 | } |
---|
[1994] | 828 | if ( flgs.nelements() != msk.size() ) { |
---|
| 829 | throw(AipsError("Mask has incorrect number of channels." |
---|
| 830 | " Probably varying with IF. Please flag per IF")); |
---|
| 831 | } |
---|
| 832 | std::vector<bool>::const_iterator it; |
---|
| 833 | uInt j = 0; |
---|
| 834 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 835 | if ( *it ) { |
---|
| 836 | flgs(j) = flagval; |
---|
[1000] | 837 | } |
---|
[1994] | 838 | ++j; |
---|
[1000] | 839 | } |
---|
[1994] | 840 | flagsCol_.put(whichrow, flgs); |
---|
[865] | 841 | } |
---|
| 842 | |
---|
[1819] | 843 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
| 844 | { |
---|
| 845 | if ( selector_.empty() && (rows.size() == table_.nrow()) ) |
---|
| 846 | throw(AipsError("Trying to flag whole scantable.")); |
---|
| 847 | |
---|
| 848 | uInt rowflag = (unflag ? 0 : 1); |
---|
| 849 | std::vector<uInt>::const_iterator it; |
---|
| 850 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
| 851 | flagrowCol_.put(*it, rowflag); |
---|
| 852 | } |
---|
| 853 | |
---|
[805] | 854 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
| 855 | { |
---|
| 856 | Vector<uChar> flags; |
---|
| 857 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 858 | Vector<Bool> bflag(flags.shape()); |
---|
| 859 | convertArray(bflag, flags); |
---|
| 860 | bflag = !bflag; |
---|
| 861 | std::vector<bool> mask; |
---|
| 862 | bflag.tovector(mask); |
---|
| 863 | return mask; |
---|
| 864 | } |
---|
[89] | 865 | |
---|
[896] | 866 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
[902] | 867 | const std::string& poltype ) const |
---|
[805] | 868 | { |
---|
[905] | 869 | String ptype = poltype; |
---|
| 870 | if (poltype == "" ) ptype = getPolType(); |
---|
[902] | 871 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
| 872 | throw(AipsError("Illegal row number.")); |
---|
[896] | 873 | std::vector<float> out; |
---|
[805] | 874 | Vector<Float> arr; |
---|
[896] | 875 | uInt requestedpol = polCol_(whichrow); |
---|
| 876 | String basetype = getPolType(); |
---|
[905] | 877 | if ( ptype == basetype ) { |
---|
[896] | 878 | specCol_.get(whichrow, arr); |
---|
| 879 | } else { |
---|
[1598] | 880 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
[1586] | 881 | basetype)); |
---|
[1334] | 882 | uInt row = uInt(whichrow); |
---|
| 883 | stpol->setSpectra(getPolMatrix(row)); |
---|
[2047] | 884 | Float fang,fhand; |
---|
[1586] | 885 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
[1334] | 886 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
[1586] | 887 | stpol->setPhaseCorrections(fang, fhand); |
---|
[1334] | 888 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
[896] | 889 | } |
---|
[902] | 890 | if ( arr.nelements() == 0 ) |
---|
| 891 | pushLog("Not enough polarisations present to do the conversion."); |
---|
[805] | 892 | arr.tovector(out); |
---|
| 893 | return out; |
---|
[89] | 894 | } |
---|
[212] | 895 | |
---|
[1360] | 896 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
[884] | 897 | int whichrow ) |
---|
| 898 | { |
---|
| 899 | Vector<Float> spectrum(spec); |
---|
| 900 | Vector<Float> arr; |
---|
| 901 | specCol_.get(whichrow, arr); |
---|
| 902 | if ( spectrum.nelements() != arr.nelements() ) |
---|
[896] | 903 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
[884] | 904 | specCol_.put(whichrow, spectrum); |
---|
| 905 | } |
---|
| 906 | |
---|
| 907 | |
---|
[805] | 908 | String Scantable::generateName() |
---|
[745] | 909 | { |
---|
[805] | 910 | return (File::newUniqueName("./","temp")).baseName(); |
---|
[212] | 911 | } |
---|
| 912 | |
---|
[805] | 913 | const casa::Table& Scantable::table( ) const |
---|
[212] | 914 | { |
---|
[805] | 915 | return table_; |
---|
[212] | 916 | } |
---|
| 917 | |
---|
[805] | 918 | casa::Table& Scantable::table( ) |
---|
[386] | 919 | { |
---|
[805] | 920 | return table_; |
---|
[386] | 921 | } |
---|
| 922 | |
---|
[896] | 923 | std::string Scantable::getPolType() const |
---|
| 924 | { |
---|
| 925 | return table_.keywordSet().asString("POLTYPE"); |
---|
| 926 | } |
---|
| 927 | |
---|
[805] | 928 | void Scantable::unsetSelection() |
---|
[380] | 929 | { |
---|
[805] | 930 | table_ = originalTable_; |
---|
[847] | 931 | attach(); |
---|
[805] | 932 | selector_.reset(); |
---|
[380] | 933 | } |
---|
[386] | 934 | |
---|
[805] | 935 | void Scantable::setSelection( const STSelector& selection ) |
---|
[430] | 936 | { |
---|
[805] | 937 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
| 938 | if ( tab.nrow() == 0 ) { |
---|
| 939 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
| 940 | } |
---|
| 941 | table_ = tab; |
---|
[847] | 942 | attach(); |
---|
[805] | 943 | selector_ = selection; |
---|
[430] | 944 | } |
---|
| 945 | |
---|
[837] | 946 | std::string Scantable::summary( bool verbose ) |
---|
[447] | 947 | { |
---|
[805] | 948 | // Format header info |
---|
| 949 | ostringstream oss; |
---|
| 950 | oss << endl; |
---|
| 951 | oss << asap::SEPERATOR << endl; |
---|
| 952 | oss << " Scan Table Summary" << endl; |
---|
| 953 | oss << asap::SEPERATOR << endl; |
---|
| 954 | oss.flags(std::ios_base::left); |
---|
| 955 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 956 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
[896] | 957 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 958 | << "(" << getPolType() << ")" << endl |
---|
[1694] | 959 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[805] | 960 | String tmp; |
---|
[860] | 961 | oss << setw(15) << "Observer:" |
---|
| 962 | << table_.keywordSet().asString("Observer") << endl; |
---|
[805] | 963 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 964 | table_.keywordSet().get("Project", tmp); |
---|
| 965 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 966 | table_.keywordSet().get("Obstype", tmp); |
---|
| 967 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 968 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 969 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 970 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 971 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
[1819] | 972 | //Vector<Double> vec(moleculeTable_.getRestFrequencies()); |
---|
| 973 | int nid = moleculeTable_.nrow(); |
---|
| 974 | Bool firstline = True; |
---|
[805] | 975 | oss << setw(15) << "Rest Freqs:"; |
---|
[1819] | 976 | for (int i=0; i<nid; i++) { |
---|
| 977 | Table t = table_(table_.col("MOLECULE_ID") == i); |
---|
| 978 | if (t.nrow() > 0) { |
---|
| 979 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
| 980 | if (vec.nelements() > 0) { |
---|
| 981 | if (firstline) { |
---|
| 982 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 983 | firstline=False; |
---|
| 984 | } |
---|
| 985 | else{ |
---|
| 986 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 987 | } |
---|
| 988 | } else { |
---|
| 989 | oss << "none" << endl; |
---|
| 990 | } |
---|
| 991 | } |
---|
[805] | 992 | } |
---|
[941] | 993 | |
---|
| 994 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
[805] | 995 | oss << selector_.print() << endl; |
---|
| 996 | oss << endl; |
---|
| 997 | // main table |
---|
| 998 | String dirtype = "Position (" |
---|
[987] | 999 | + getDirectionRefString() |
---|
[805] | 1000 | + ")"; |
---|
[941] | 1001 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
[2005] | 1002 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
| 1003 | << setw(15) << "Source Type" << endl; |
---|
[941] | 1004 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
[1694] | 1005 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
[805] | 1006 | << setw(8) << "Frame" << setw(16) |
---|
[1694] | 1007 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
| 1008 | << setw(7) << "Channels" |
---|
| 1009 | << endl; |
---|
[805] | 1010 | oss << asap::SEPERATOR << endl; |
---|
| 1011 | TableIterator iter(table_, "SCANNO"); |
---|
| 1012 | while (!iter.pastEnd()) { |
---|
| 1013 | Table subt = iter.table(); |
---|
| 1014 | ROTableRow row(subt); |
---|
| 1015 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
| 1016 | const TableRecord& rec = row.get(0); |
---|
| 1017 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1018 | << std::left << setw(1) << "" |
---|
| 1019 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1020 | << setw(10) << formatTime(timeCol(0), false); |
---|
| 1021 | // count the cycles in the scan |
---|
| 1022 | TableIterator cyciter(subt, "CYCLENO"); |
---|
| 1023 | int nint = 0; |
---|
| 1024 | while (!cyciter.pastEnd()) { |
---|
| 1025 | ++nint; |
---|
| 1026 | ++cyciter; |
---|
| 1027 | } |
---|
| 1028 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
[2005] | 1029 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
| 1030 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
[447] | 1031 | |
---|
[805] | 1032 | TableIterator biter(subt, "BEAMNO"); |
---|
| 1033 | while (!biter.pastEnd()) { |
---|
| 1034 | Table bsubt = biter.table(); |
---|
| 1035 | ROTableRow brow(bsubt); |
---|
| 1036 | const TableRecord& brec = brow.get(0); |
---|
[1000] | 1037 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
[941] | 1038 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
[987] | 1039 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
[805] | 1040 | TableIterator iiter(bsubt, "IFNO"); |
---|
| 1041 | while (!iiter.pastEnd()) { |
---|
| 1042 | Table isubt = iiter.table(); |
---|
| 1043 | ROTableRow irow(isubt); |
---|
| 1044 | const TableRecord& irec = irow.get(0); |
---|
[1694] | 1045 | oss << setw(9) << ""; |
---|
[941] | 1046 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
[1694] | 1047 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
| 1048 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
[1375] | 1049 | << endl; |
---|
[447] | 1050 | |
---|
[805] | 1051 | ++iiter; |
---|
| 1052 | } |
---|
| 1053 | ++biter; |
---|
| 1054 | } |
---|
| 1055 | ++iter; |
---|
[447] | 1056 | } |
---|
[805] | 1057 | /// @todo implement verbose mode |
---|
| 1058 | return String(oss); |
---|
[447] | 1059 | } |
---|
| 1060 | |
---|
[1947] | 1061 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
| 1062 | // { |
---|
| 1063 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 1064 | // MEpoch me; |
---|
| 1065 | // if (whichrow > -1) { |
---|
| 1066 | // me = timeCol(uInt(whichrow)); |
---|
| 1067 | // } else { |
---|
| 1068 | // Double tm; |
---|
| 1069 | // table_.keywordSet().get("UTC",tm); |
---|
| 1070 | // me = MEpoch(MVEpoch(tm)); |
---|
| 1071 | // } |
---|
| 1072 | // return formatTime(me, showdate); |
---|
| 1073 | // } |
---|
| 1074 | |
---|
| 1075 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
[777] | 1076 | { |
---|
[805] | 1077 | MEpoch me; |
---|
[1947] | 1078 | me = getEpoch(whichrow); |
---|
| 1079 | return formatTime(me, showdate, prec); |
---|
[777] | 1080 | } |
---|
[805] | 1081 | |
---|
[1411] | 1082 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
| 1083 | { |
---|
| 1084 | if (whichrow > -1) { |
---|
| 1085 | return timeCol_(uInt(whichrow)); |
---|
| 1086 | } else { |
---|
| 1087 | Double tm; |
---|
| 1088 | table_.keywordSet().get("UTC",tm); |
---|
[1598] | 1089 | return MEpoch(MVEpoch(tm)); |
---|
[1411] | 1090 | } |
---|
| 1091 | } |
---|
| 1092 | |
---|
[1068] | 1093 | std::string Scantable::getDirectionString(int whichrow) const |
---|
| 1094 | { |
---|
| 1095 | return formatDirection(getDirection(uInt(whichrow))); |
---|
| 1096 | } |
---|
| 1097 | |
---|
[1598] | 1098 | |
---|
| 1099 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
| 1100 | const MPosition& mp = getAntennaPosition(); |
---|
| 1101 | const MDirection& md = getDirection(whichrow); |
---|
| 1102 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1103 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
| 1104 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[1598] | 1105 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
| 1106 | mfreqidCol_(whichrow)); |
---|
| 1107 | } |
---|
| 1108 | |
---|
[1360] | 1109 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
[865] | 1110 | { |
---|
[1507] | 1111 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
[865] | 1112 | std::vector<double> stlout; |
---|
| 1113 | int nchan = specCol_(whichrow).nelements(); |
---|
| 1114 | String us = freqTable_.getUnitString(); |
---|
| 1115 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
| 1116 | for (int i=0; i<nchan; ++i) { |
---|
| 1117 | stlout.push_back(double(i)); |
---|
| 1118 | } |
---|
| 1119 | return stlout; |
---|
| 1120 | } |
---|
[1598] | 1121 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
[865] | 1122 | Vector<Double> pixel(nchan); |
---|
| 1123 | Vector<Double> world; |
---|
| 1124 | indgen(pixel); |
---|
| 1125 | if ( Unit(us) == Unit("Hz") ) { |
---|
| 1126 | for ( int i=0; i < nchan; ++i) { |
---|
| 1127 | Double world; |
---|
| 1128 | spc.toWorld(world, pixel[i]); |
---|
| 1129 | stlout.push_back(double(world)); |
---|
| 1130 | } |
---|
| 1131 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
| 1132 | Vector<Double> world; |
---|
| 1133 | spc.pixelToVelocity(world, pixel); |
---|
| 1134 | world.tovector(stlout); |
---|
| 1135 | } |
---|
| 1136 | return stlout; |
---|
| 1137 | } |
---|
[1360] | 1138 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
[987] | 1139 | { |
---|
| 1140 | MDirection::Types mdt; |
---|
| 1141 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
| 1142 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1143 | } |
---|
| 1144 | if ( refstr == "" ) { |
---|
| 1145 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1146 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
| 1147 | } else { |
---|
| 1148 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
| 1149 | } |
---|
| 1150 | } |
---|
[865] | 1151 | |
---|
[1360] | 1152 | std::string Scantable::getDirectionRefString( ) const |
---|
[987] | 1153 | { |
---|
| 1154 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1155 | } |
---|
| 1156 | |
---|
| 1157 | MDirection Scantable::getDirection(int whichrow ) const |
---|
| 1158 | { |
---|
| 1159 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1160 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1161 | if ( usertype != type ) { |
---|
| 1162 | MDirection::Types mdt; |
---|
| 1163 | if (!MDirection::getType(mdt, usertype)) { |
---|
| 1164 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1165 | } |
---|
| 1166 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
| 1167 | } else { |
---|
| 1168 | return dirCol_(uInt(whichrow)); |
---|
| 1169 | } |
---|
| 1170 | } |
---|
| 1171 | |
---|
[847] | 1172 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
| 1173 | { |
---|
[996] | 1174 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
[847] | 1175 | const MPosition& mp = getAntennaPosition(); |
---|
[987] | 1176 | const MDirection& md = getDirection(whichrow); |
---|
[847] | 1177 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1178 | //const Double& rf = mmolidCol_(whichrow); |
---|
| 1179 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[847] | 1180 | SpectralCoordinate spc = |
---|
| 1181 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
| 1182 | |
---|
| 1183 | String s = "Channel"; |
---|
| 1184 | Unit u = Unit(freqTable_.getUnitString()); |
---|
| 1185 | if (u == Unit("km/s")) { |
---|
[1170] | 1186 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
[847] | 1187 | } else if (u == Unit("Hz")) { |
---|
| 1188 | Vector<String> wau(1);wau = u.getName(); |
---|
| 1189 | spc.setWorldAxisUnits(wau); |
---|
[1170] | 1190 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
[847] | 1191 | } |
---|
| 1192 | return s; |
---|
| 1193 | |
---|
| 1194 | } |
---|
| 1195 | |
---|
[1819] | 1196 | /** |
---|
| 1197 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
[1170] | 1198 | const std::string& unit ) |
---|
[1819] | 1199 | **/ |
---|
| 1200 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
| 1201 | const std::string& unit ) |
---|
| 1202 | |
---|
[847] | 1203 | { |
---|
[923] | 1204 | ///@todo lookup in line table to fill in name and formattedname |
---|
[847] | 1205 | Unit u(unit); |
---|
[1819] | 1206 | //Quantum<Double> urf(rf, u); |
---|
| 1207 | Quantum<Vector<Double> >urf(rf, u); |
---|
| 1208 | Vector<String> formattedname(0); |
---|
| 1209 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
| 1210 | |
---|
| 1211 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
| 1212 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
[847] | 1213 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
| 1214 | tabvec = id; |
---|
| 1215 | } |
---|
| 1216 | |
---|
[1819] | 1217 | /** |
---|
| 1218 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
[847] | 1219 | { |
---|
| 1220 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
| 1221 | ///@todo implement |
---|
| 1222 | } |
---|
[1819] | 1223 | **/ |
---|
[2012] | 1224 | |
---|
[1819] | 1225 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
| 1226 | { |
---|
| 1227 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
| 1228 | ///@todo implement |
---|
| 1229 | } |
---|
[847] | 1230 | |
---|
[1360] | 1231 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
[852] | 1232 | { |
---|
| 1233 | std::vector<unsigned int> stlout; |
---|
| 1234 | Vector<uInt> vec = table_.rowNumbers(); |
---|
| 1235 | vec.tovector(stlout); |
---|
| 1236 | return stlout; |
---|
| 1237 | } |
---|
| 1238 | |
---|
[865] | 1239 | |
---|
[1360] | 1240 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
[896] | 1241 | { |
---|
| 1242 | ROTableRow row(table_); |
---|
| 1243 | const TableRecord& rec = row.get(whichrow); |
---|
| 1244 | Table t = |
---|
| 1245 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
| 1246 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 1247 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 1248 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 1249 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 1250 | return speccol.getColumn(); |
---|
| 1251 | } |
---|
[865] | 1252 | |
---|
[1360] | 1253 | std::vector< std::string > Scantable::columnNames( ) const |
---|
[902] | 1254 | { |
---|
| 1255 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
| 1256 | return mathutil::tovectorstring(vec); |
---|
| 1257 | } |
---|
[896] | 1258 | |
---|
[1360] | 1259 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
[915] | 1260 | { |
---|
| 1261 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
[972] | 1262 | } |
---|
[915] | 1263 | |
---|
[1360] | 1264 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
[972] | 1265 | { |
---|
[1819] | 1266 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
| 1267 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
| 1268 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
[972] | 1269 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
| 1270 | mfitidCol_.put(uInt(row), id); |
---|
| 1271 | } |
---|
[915] | 1272 | |
---|
[1360] | 1273 | void Scantable::shift(int npix) |
---|
| 1274 | { |
---|
| 1275 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
| 1276 | genSort( fids, Sort::Ascending, |
---|
| 1277 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 1278 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
[1567] | 1279 | frequencies().shiftRefPix(npix, fids[i]); |
---|
[1360] | 1280 | } |
---|
| 1281 | } |
---|
[987] | 1282 | |
---|
[1819] | 1283 | String Scantable::getAntennaName() const |
---|
[1391] | 1284 | { |
---|
| 1285 | String out; |
---|
| 1286 | table_.keywordSet().get("AntennaName", out); |
---|
[1987] | 1287 | String::size_type pos1 = out.find("@") ; |
---|
| 1288 | String::size_type pos2 = out.find("//") ; |
---|
| 1289 | if ( pos2 != String::npos ) |
---|
[2036] | 1290 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
[1987] | 1291 | else if ( pos1 != String::npos ) |
---|
| 1292 | out = out.substr(0,pos1) ; |
---|
[1391] | 1293 | return out; |
---|
[987] | 1294 | } |
---|
[1391] | 1295 | |
---|
[1730] | 1296 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
[1391] | 1297 | { |
---|
| 1298 | String tbpath; |
---|
| 1299 | int ret = 0; |
---|
| 1300 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
| 1301 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
| 1302 | Table t(tbpath,Table::Old); |
---|
| 1303 | // check each scan if other scan of the pair exist |
---|
| 1304 | int nscan = scanlist.size(); |
---|
| 1305 | for (int i = 0; i < nscan; i++) { |
---|
| 1306 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
| 1307 | if (subt.nrow()==0) { |
---|
[1819] | 1308 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
| 1309 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1310 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1311 | ret = 1; |
---|
| 1312 | break; |
---|
| 1313 | } |
---|
| 1314 | ROTableRow row(subt); |
---|
| 1315 | const TableRecord& rec = row.get(0); |
---|
| 1316 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
| 1317 | int laston1 = rec.asuInt("LASTON"); |
---|
| 1318 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
| 1319 | if ( i < nscan-1 ) { |
---|
| 1320 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
| 1321 | if ( subt2.nrow() == 0) { |
---|
[1819] | 1322 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1323 | |
---|
| 1324 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
| 1325 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1326 | ret = 1; |
---|
| 1327 | break; |
---|
| 1328 | } |
---|
| 1329 | ROTableRow row2(subt2); |
---|
| 1330 | const TableRecord& rec2 = row2.get(0); |
---|
| 1331 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
| 1332 | int laston2 = rec2.asuInt("LASTON"); |
---|
| 1333 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
| 1334 | if (laston1 == laston2) { |
---|
[1819] | 1335 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1336 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1337 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1338 | i +=1; |
---|
| 1339 | } |
---|
| 1340 | else { |
---|
[1819] | 1341 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1342 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1343 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1344 | } |
---|
| 1345 | } |
---|
| 1346 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
| 1347 | if (laston1 == laston2) { |
---|
[1819] | 1348 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1349 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
| 1350 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
[1391] | 1351 | ret = 1; |
---|
| 1352 | break; |
---|
| 1353 | } |
---|
| 1354 | } |
---|
| 1355 | else { |
---|
[1819] | 1356 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1357 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
| 1358 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
[1391] | 1359 | ret = 1; |
---|
| 1360 | break; |
---|
| 1361 | } |
---|
| 1362 | } |
---|
| 1363 | } |
---|
| 1364 | else { |
---|
[1819] | 1365 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1366 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
| 1367 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
[1391] | 1368 | } |
---|
| 1369 | //if ( i >= nscan ) break; |
---|
| 1370 | } |
---|
| 1371 | } |
---|
| 1372 | else { |
---|
[1819] | 1373 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1374 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
| 1375 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
[1391] | 1376 | ret = 1; |
---|
| 1377 | } |
---|
| 1378 | return ret; |
---|
| 1379 | } |
---|
| 1380 | |
---|
[1730] | 1381 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
[1391] | 1382 | { |
---|
| 1383 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
| 1384 | std::vector<double> dir; |
---|
| 1385 | Dir.tovector(dir); |
---|
| 1386 | return dir; |
---|
| 1387 | } |
---|
| 1388 | |
---|
[1819] | 1389 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
| 1390 | throw( casa::AipsError ) |
---|
| 1391 | { |
---|
| 1392 | // assumed that all rows have same nChan |
---|
| 1393 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1394 | int nChan = arr.nelements() ; |
---|
| 1395 | |
---|
| 1396 | // if nmin < 0 or nmax < 0, nothing to do |
---|
| 1397 | if ( nmin < 0 ) { |
---|
| 1398 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1399 | } |
---|
| 1400 | if ( nmax < 0 ) { |
---|
| 1401 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1402 | } |
---|
| 1403 | |
---|
| 1404 | // if nmin > nmax, exchange values |
---|
| 1405 | if ( nmin > nmax ) { |
---|
| 1406 | int tmp = nmax ; |
---|
| 1407 | nmax = nmin ; |
---|
| 1408 | nmin = tmp ; |
---|
| 1409 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1410 | os << "Swap values. Applied range is [" |
---|
| 1411 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
| 1412 | } |
---|
| 1413 | |
---|
| 1414 | // if nmin exceeds nChan, nothing to do |
---|
| 1415 | if ( nmin >= nChan ) { |
---|
| 1416 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
| 1417 | } |
---|
| 1418 | |
---|
| 1419 | // if nmax exceeds nChan, reset nmax to nChan |
---|
| 1420 | if ( nmax >= nChan ) { |
---|
| 1421 | if ( nmin == 0 ) { |
---|
| 1422 | // nothing to do |
---|
| 1423 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1424 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
| 1425 | return ; |
---|
| 1426 | } |
---|
| 1427 | else { |
---|
| 1428 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1429 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
| 1430 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
| 1431 | nmax = nChan - 1 ; |
---|
| 1432 | } |
---|
| 1433 | } |
---|
| 1434 | |
---|
| 1435 | // reshape specCol_ and flagCol_ |
---|
| 1436 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1437 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
| 1438 | } |
---|
| 1439 | |
---|
| 1440 | // update FREQUENCIES subtable |
---|
| 1441 | Double refpix ; |
---|
| 1442 | Double refval ; |
---|
| 1443 | Double increment ; |
---|
| 1444 | int freqnrow = freqTable_.table().nrow() ; |
---|
| 1445 | Vector<uInt> oldId( freqnrow ) ; |
---|
| 1446 | Vector<uInt> newId( freqnrow ) ; |
---|
| 1447 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
| 1448 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
| 1449 | /*** |
---|
| 1450 | * need to shift refpix to nmin |
---|
| 1451 | * note that channel nmin in old index will be channel 0 in new one |
---|
| 1452 | ***/ |
---|
| 1453 | refval = refval - ( refpix - nmin ) * increment ; |
---|
| 1454 | refpix = 0 ; |
---|
| 1455 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
| 1456 | } |
---|
| 1457 | |
---|
| 1458 | // update nchan |
---|
| 1459 | int newsize = nmax - nmin + 1 ; |
---|
| 1460 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
| 1461 | |
---|
| 1462 | // update bandwidth |
---|
| 1463 | // assumed all spectra in the scantable have same bandwidth |
---|
| 1464 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
| 1465 | |
---|
| 1466 | return ; |
---|
| 1467 | } |
---|
| 1468 | |
---|
| 1469 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
| 1470 | { |
---|
| 1471 | // reshape specCol_ and flagCol_ |
---|
| 1472 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1473 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 1474 | uInt newsize = nmax - nmin + 1 ; |
---|
| 1475 | specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ; |
---|
| 1476 | flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ; |
---|
| 1477 | |
---|
| 1478 | return ; |
---|
| 1479 | } |
---|
| 1480 | |
---|
| 1481 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
| 1482 | { |
---|
| 1483 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1484 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
| 1485 | // assumed that all rows have same nChan |
---|
| 1486 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1487 | int oldsize = arr.nelements() ; |
---|
| 1488 | |
---|
| 1489 | // if oldsize == nChan, nothing to do |
---|
| 1490 | if ( oldsize == nChan ) { |
---|
| 1491 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
| 1492 | return ; |
---|
| 1493 | } |
---|
| 1494 | |
---|
| 1495 | // if oldChan < nChan, unphysical operation |
---|
| 1496 | if ( oldsize < nChan ) { |
---|
| 1497 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
| 1498 | return ; |
---|
| 1499 | } |
---|
| 1500 | |
---|
| 1501 | // change channel number for specCol_ and flagCol_ |
---|
| 1502 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 1503 | Vector<uChar> newflag( nChan, false ) ; |
---|
| 1504 | vector<string> coordinfo = getCoordInfo() ; |
---|
| 1505 | string oldinfo = coordinfo[0] ; |
---|
| 1506 | coordinfo[0] = "Hz" ; |
---|
| 1507 | setCoordInfo( coordinfo ) ; |
---|
| 1508 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1509 | regridChannel( nChan, dnu, irow ) ; |
---|
| 1510 | } |
---|
| 1511 | coordinfo[0] = oldinfo ; |
---|
| 1512 | setCoordInfo( coordinfo ) ; |
---|
| 1513 | |
---|
| 1514 | |
---|
| 1515 | // NOTE: this method does not update metadata such as |
---|
| 1516 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
| 1517 | |
---|
| 1518 | return ; |
---|
| 1519 | } |
---|
| 1520 | |
---|
| 1521 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
| 1522 | { |
---|
| 1523 | // logging |
---|
| 1524 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
| 1525 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
| 1526 | |
---|
| 1527 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1528 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 1529 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 1530 | Vector<uChar> newflag( nChan, false ) ; |
---|
| 1531 | |
---|
| 1532 | // regrid |
---|
| 1533 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1534 | int oldsize = abcissa.size() ; |
---|
| 1535 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
| 1536 | //int refChan = 0 ; |
---|
| 1537 | //double frac = 0.0 ; |
---|
| 1538 | //double wedge = 0.0 ; |
---|
| 1539 | //double pile = 0.0 ; |
---|
| 1540 | int ichan = 0 ; |
---|
| 1541 | double wsum = 0.0 ; |
---|
| 1542 | Vector<Float> z( nChan ) ; |
---|
| 1543 | z[0] = abcissa[0] - 0.5 * olddnu + 0.5 * dnu ; |
---|
| 1544 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
| 1545 | z[ii] = z[ii-1] + dnu ; |
---|
| 1546 | Vector<Float> zi( nChan+1 ) ; |
---|
| 1547 | Vector<Float> yi( oldsize + 1 ) ; |
---|
| 1548 | zi[0] = z[0] - 0.5 * dnu ; |
---|
| 1549 | zi[1] = z[0] + 0.5 * dnu ; |
---|
| 1550 | for ( int ii = 2 ; ii < nChan ; ii++ ) |
---|
| 1551 | zi[ii] = zi[ii-1] + dnu ; |
---|
| 1552 | zi[nChan] = z[nChan-1] + 0.5 * dnu ; |
---|
| 1553 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 1554 | yi[1] = abcissa[1] + 0.5 * olddnu ; |
---|
| 1555 | for ( int ii = 2 ; ii < oldsize ; ii++ ) |
---|
| 1556 | yi[ii] = abcissa[ii-1] + olddnu ; |
---|
| 1557 | yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ; |
---|
| 1558 | if ( dnu > 0.0 ) { |
---|
| 1559 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 1560 | double zl = zi[ii] ; |
---|
| 1561 | double zr = zi[ii+1] ; |
---|
| 1562 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 1563 | double yl = yi[j] ; |
---|
| 1564 | double yr = yi[j+1] ; |
---|
| 1565 | if ( yl <= zl ) { |
---|
| 1566 | if ( yr <= zl ) { |
---|
| 1567 | continue ; |
---|
| 1568 | } |
---|
| 1569 | else if ( yr <= zr ) { |
---|
| 1570 | newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
| 1571 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1572 | wsum += ( yr - zl ) ; |
---|
| 1573 | } |
---|
| 1574 | else { |
---|
| 1575 | newspec[ii] += oldspec[j] * dnu ; |
---|
| 1576 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1577 | wsum += dnu ; |
---|
| 1578 | ichan = j ; |
---|
| 1579 | break ; |
---|
| 1580 | } |
---|
| 1581 | } |
---|
| 1582 | else if ( yl < zr ) { |
---|
| 1583 | if ( yr <= zr ) { |
---|
| 1584 | newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
| 1585 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1586 | wsum += ( yr - yl ) ; |
---|
| 1587 | } |
---|
| 1588 | else { |
---|
| 1589 | newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
| 1590 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1591 | wsum += ( zr - yl ) ; |
---|
| 1592 | ichan = j ; |
---|
| 1593 | break ; |
---|
| 1594 | } |
---|
| 1595 | } |
---|
| 1596 | else { |
---|
| 1597 | ichan = j - 1 ; |
---|
| 1598 | break ; |
---|
| 1599 | } |
---|
| 1600 | } |
---|
| 1601 | newspec[ii] /= wsum ; |
---|
| 1602 | wsum = 0.0 ; |
---|
| 1603 | } |
---|
| 1604 | } |
---|
| 1605 | else if ( dnu < 0.0 ) { |
---|
| 1606 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 1607 | double zl = zi[ii] ; |
---|
| 1608 | double zr = zi[ii+1] ; |
---|
| 1609 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 1610 | double yl = yi[j] ; |
---|
| 1611 | double yr = yi[j+1] ; |
---|
| 1612 | if ( yl >= zl ) { |
---|
| 1613 | if ( yr >= zl ) { |
---|
| 1614 | continue ; |
---|
| 1615 | } |
---|
| 1616 | else if ( yr >= zr ) { |
---|
| 1617 | newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
| 1618 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1619 | wsum += abs( yr - zl ) ; |
---|
| 1620 | } |
---|
| 1621 | else { |
---|
| 1622 | newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
| 1623 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1624 | wsum += abs( dnu ) ; |
---|
| 1625 | ichan = j ; |
---|
| 1626 | break ; |
---|
| 1627 | } |
---|
| 1628 | } |
---|
| 1629 | else if ( yl > zr ) { |
---|
| 1630 | if ( yr >= zr ) { |
---|
| 1631 | newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
| 1632 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1633 | wsum += abs( yr - yl ) ; |
---|
| 1634 | } |
---|
| 1635 | else { |
---|
| 1636 | newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
| 1637 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1638 | wsum += abs( zr - yl ) ; |
---|
| 1639 | ichan = j ; |
---|
| 1640 | break ; |
---|
| 1641 | } |
---|
| 1642 | } |
---|
| 1643 | else { |
---|
| 1644 | ichan = j - 1 ; |
---|
| 1645 | break ; |
---|
| 1646 | } |
---|
| 1647 | } |
---|
| 1648 | newspec[ii] /= wsum ; |
---|
| 1649 | wsum = 0.0 ; |
---|
| 1650 | } |
---|
| 1651 | } |
---|
| 1652 | // * ichan = 0 |
---|
| 1653 | // ***/ |
---|
| 1654 | // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
| 1655 | // pile += dnu ; |
---|
| 1656 | // wedge = olddnu * ( refChan + 1 ) ; |
---|
| 1657 | // while ( wedge < pile ) { |
---|
| 1658 | // newspec[0] += olddnu * oldspec[refChan] ; |
---|
| 1659 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 1660 | // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
| 1661 | // refChan++ ; |
---|
| 1662 | // wedge += olddnu ; |
---|
| 1663 | // wsum += olddnu ; |
---|
| 1664 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 1665 | // } |
---|
| 1666 | // frac = ( wedge - pile ) / olddnu ; |
---|
| 1667 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 1668 | // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 1669 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 1670 | // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 1671 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 1672 | // newspec[0] /= wsum ; |
---|
| 1673 | // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
| 1674 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 1675 | |
---|
| 1676 | // /*** |
---|
| 1677 | // * ichan = 1 - nChan-2 |
---|
| 1678 | // ***/ |
---|
| 1679 | // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
| 1680 | // pile += dnu ; |
---|
| 1681 | // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
| 1682 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 1683 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
| 1684 | // refChan++ ; |
---|
| 1685 | // wedge += olddnu ; |
---|
| 1686 | // wsum = frac * olddnu ; |
---|
| 1687 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 1688 | // while ( wedge < pile ) { |
---|
| 1689 | // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
| 1690 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 1691 | // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
| 1692 | // refChan++ ; |
---|
| 1693 | // wedge += olddnu ; |
---|
| 1694 | // wsum += olddnu ; |
---|
| 1695 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 1696 | // } |
---|
| 1697 | // frac = ( wedge - pile ) / olddnu ; |
---|
| 1698 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 1699 | // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 1700 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 1701 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 1702 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 1703 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 1704 | // newspec[ichan] /= wsum ; |
---|
| 1705 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
| 1706 | // } |
---|
| 1707 | |
---|
| 1708 | // /*** |
---|
| 1709 | // * ichan = nChan-1 |
---|
| 1710 | // ***/ |
---|
| 1711 | // // NOTE: Assumed that all spectra have the same bandwidth |
---|
| 1712 | // pile += dnu ; |
---|
| 1713 | // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
| 1714 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
| 1715 | // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 1716 | // refChan++ ; |
---|
| 1717 | // wedge += olddnu ; |
---|
| 1718 | // wsum = frac * olddnu ; |
---|
| 1719 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 1720 | // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
| 1721 | // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
| 1722 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
| 1723 | // wsum += olddnu ; |
---|
| 1724 | // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 1725 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 1726 | // } |
---|
| 1727 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 1728 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 1729 | // newspec[nChan-1] /= wsum ; |
---|
| 1730 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
| 1731 | |
---|
| 1732 | // // ofs.close() ; |
---|
| 1733 | |
---|
[2032] | 1734 | specCol_.put( irow, newspec ) ; |
---|
| 1735 | flagsCol_.put( irow, newflag ) ; |
---|
[1819] | 1736 | |
---|
| 1737 | return ; |
---|
| 1738 | } |
---|
| 1739 | |
---|
[1730] | 1740 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
| 1741 | { |
---|
| 1742 | std::vector<float> out(5); |
---|
| 1743 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
| 1744 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
| 1745 | mweatheridCol_(uInt(whichrow))); |
---|
| 1746 | |
---|
| 1747 | |
---|
| 1748 | return out; |
---|
[1391] | 1749 | } |
---|
[1730] | 1750 | |
---|
[2047] | 1751 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
[1907] | 1752 | { |
---|
| 1753 | uChar flag; |
---|
| 1754 | Vector<uChar> flags; |
---|
[2047] | 1755 | flagsCol_.get(whichrow, flags); |
---|
[2012] | 1756 | flag = flags[0]; |
---|
[2047] | 1757 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
[2012] | 1758 | flag &= flags[i]; |
---|
| 1759 | } |
---|
| 1760 | return ((flag >> 7) == 1); |
---|
| 1761 | } |
---|
| 1762 | |
---|
[2047] | 1763 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool outLogger, const std::string& blfile) |
---|
| 1764 | { |
---|
| 1765 | ofstream ofs; |
---|
| 1766 | String coordInfo; |
---|
| 1767 | bool hasSameNchan = true; |
---|
| 1768 | bool outTextFile = false; |
---|
| 1769 | |
---|
| 1770 | if (blfile != "") { |
---|
| 1771 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 1772 | if (ofs) outTextFile = true; |
---|
| 1773 | } |
---|
| 1774 | |
---|
| 1775 | if (outLogger || outTextFile) { |
---|
| 1776 | coordInfo = getCoordInfo()[0]; |
---|
| 1777 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 1778 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 1779 | } |
---|
| 1780 | |
---|
| 1781 | Fitter fitter = Fitter(); |
---|
| 1782 | fitter.setExpression("poly", order); |
---|
| 1783 | |
---|
| 1784 | int nRow = nrow(); |
---|
| 1785 | std::vector<bool> chanMask; |
---|
| 1786 | |
---|
| 1787 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 1788 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 1789 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 1790 | setSpectrum(fitter.getResidual(), whichrow); |
---|
| 1791 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
| 1792 | } |
---|
| 1793 | |
---|
| 1794 | if (outTextFile) ofs.close(); |
---|
| 1795 | } |
---|
| 1796 | |
---|
| 1797 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile) |
---|
| 1798 | { |
---|
| 1799 | ofstream ofs; |
---|
| 1800 | String coordInfo; |
---|
| 1801 | bool hasSameNchan = true; |
---|
| 1802 | bool outTextFile = false; |
---|
| 1803 | |
---|
| 1804 | if (blfile != "") { |
---|
| 1805 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 1806 | if (ofs) outTextFile = true; |
---|
| 1807 | } |
---|
| 1808 | |
---|
| 1809 | if (outLogger || outTextFile) { |
---|
| 1810 | coordInfo = getCoordInfo()[0]; |
---|
| 1811 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 1812 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 1813 | } |
---|
| 1814 | |
---|
| 1815 | Fitter fitter = Fitter(); |
---|
| 1816 | fitter.setExpression("poly", order); |
---|
| 1817 | |
---|
| 1818 | int nRow = nrow(); |
---|
| 1819 | std::vector<bool> chanMask; |
---|
| 1820 | int minEdgeSize = getIFNos().size()*2; |
---|
| 1821 | STLineFinder lineFinder = STLineFinder(); |
---|
| 1822 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
| 1823 | |
---|
| 1824 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 1825 | |
---|
| 1826 | //------------------------------------------------------- |
---|
| 1827 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 1828 | //------------------------------------------------------- |
---|
| 1829 | int edgeSize = edge.size(); |
---|
| 1830 | std::vector<int> currentEdge; |
---|
| 1831 | if (edgeSize >= 2) { |
---|
| 1832 | int idx = 0; |
---|
| 1833 | if (edgeSize > 2) { |
---|
| 1834 | if (edgeSize < minEdgeSize) { |
---|
| 1835 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 1836 | } |
---|
| 1837 | idx = 2 * getIF(whichrow); |
---|
| 1838 | } |
---|
| 1839 | currentEdge.push_back(edge[idx]); |
---|
| 1840 | currentEdge.push_back(edge[idx+1]); |
---|
| 1841 | } else { |
---|
| 1842 | throw(AipsError("Wrong length of edge element")); |
---|
| 1843 | } |
---|
| 1844 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 1845 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 1846 | chanMask = lineFinder.getMask(); |
---|
| 1847 | //------------------------------------------------------- |
---|
| 1848 | |
---|
| 1849 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 1850 | setSpectrum(fitter.getResidual(), whichrow); |
---|
| 1851 | |
---|
| 1852 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
| 1853 | } |
---|
| 1854 | |
---|
| 1855 | if (outTextFile) ofs.close(); |
---|
| 1856 | } |
---|
| 1857 | |
---|
[2012] | 1858 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool outLogger, const std::string& blfile) { |
---|
| 1859 | ofstream ofs; |
---|
| 1860 | String coordInfo; |
---|
[2047] | 1861 | bool hasSameNchan = true; |
---|
[2012] | 1862 | bool outTextFile = false; |
---|
| 1863 | |
---|
| 1864 | if (blfile != "") { |
---|
| 1865 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 1866 | if (ofs) outTextFile = true; |
---|
| 1867 | } |
---|
| 1868 | |
---|
| 1869 | if (outLogger || outTextFile) { |
---|
| 1870 | coordInfo = getCoordInfo()[0]; |
---|
| 1871 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 1872 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 1873 | } |
---|
| 1874 | |
---|
| 1875 | //Fitter fitter = Fitter(); |
---|
[2047] | 1876 | //fitter.setExpression("cspline", nPiece); |
---|
[2012] | 1877 | |
---|
| 1878 | int nRow = nrow(); |
---|
| 1879 | std::vector<bool> chanMask; |
---|
| 1880 | |
---|
| 1881 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 1882 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[2047] | 1883 | //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip); |
---|
[2012] | 1884 | //setSpectrum(fitter.getResidual(), whichrow); |
---|
| 1885 | std::vector<int> pieceRanges; |
---|
| 1886 | std::vector<float> params; |
---|
[2058] | 1887 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, pieceRanges, params, nPiece, thresClip, nIterClip, true); |
---|
[2012] | 1888 | setSpectrum(res, whichrow); |
---|
[2047] | 1889 | // |
---|
[2012] | 1890 | |
---|
[2047] | 1891 | std::vector<bool> fixed; |
---|
| 1892 | fixed.clear(); |
---|
| 1893 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceRanges, params, fixed); |
---|
[2012] | 1894 | } |
---|
| 1895 | |
---|
| 1896 | if (outTextFile) ofs.close(); |
---|
| 1897 | } |
---|
| 1898 | |
---|
| 1899 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile) |
---|
| 1900 | { |
---|
| 1901 | ofstream ofs; |
---|
| 1902 | String coordInfo; |
---|
[2047] | 1903 | bool hasSameNchan = true; |
---|
[2012] | 1904 | bool outTextFile = false; |
---|
| 1905 | |
---|
| 1906 | if (blfile != "") { |
---|
| 1907 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 1908 | if (ofs) outTextFile = true; |
---|
| 1909 | } |
---|
| 1910 | |
---|
| 1911 | if (outLogger || outTextFile) { |
---|
| 1912 | coordInfo = getCoordInfo()[0]; |
---|
| 1913 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 1914 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 1915 | } |
---|
| 1916 | |
---|
| 1917 | //Fitter fitter = Fitter(); |
---|
[2047] | 1918 | //fitter.setExpression("cspline", nPiece); |
---|
[2012] | 1919 | |
---|
| 1920 | int nRow = nrow(); |
---|
| 1921 | std::vector<bool> chanMask; |
---|
| 1922 | int minEdgeSize = getIFNos().size()*2; |
---|
| 1923 | STLineFinder lineFinder = STLineFinder(); |
---|
| 1924 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
| 1925 | |
---|
| 1926 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 1927 | |
---|
| 1928 | //------------------------------------------------------- |
---|
| 1929 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 1930 | //------------------------------------------------------- |
---|
| 1931 | int edgeSize = edge.size(); |
---|
| 1932 | std::vector<int> currentEdge; |
---|
| 1933 | if (edgeSize >= 2) { |
---|
| 1934 | int idx = 0; |
---|
| 1935 | if (edgeSize > 2) { |
---|
| 1936 | if (edgeSize < minEdgeSize) { |
---|
| 1937 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 1938 | } |
---|
| 1939 | idx = 2 * getIF(whichrow); |
---|
| 1940 | } |
---|
| 1941 | currentEdge.push_back(edge[idx]); |
---|
| 1942 | currentEdge.push_back(edge[idx+1]); |
---|
| 1943 | } else { |
---|
| 1944 | throw(AipsError("Wrong length of edge element")); |
---|
[1907] | 1945 | } |
---|
[2012] | 1946 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 1947 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 1948 | chanMask = lineFinder.getMask(); |
---|
| 1949 | //------------------------------------------------------- |
---|
| 1950 | |
---|
| 1951 | |
---|
[2047] | 1952 | //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip); |
---|
[2012] | 1953 | //setSpectrum(fitter.getResidual(), whichrow); |
---|
| 1954 | std::vector<int> pieceRanges; |
---|
| 1955 | std::vector<float> params; |
---|
[2058] | 1956 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, pieceRanges, params, nPiece, thresClip, nIterClip, true); |
---|
[2012] | 1957 | setSpectrum(res, whichrow); |
---|
[2047] | 1958 | // |
---|
[2012] | 1959 | |
---|
[2047] | 1960 | std::vector<bool> fixed; |
---|
| 1961 | fixed.clear(); |
---|
| 1962 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceRanges, params, fixed); |
---|
[2012] | 1963 | } |
---|
| 1964 | |
---|
| 1965 | if (outTextFile) ofs.close(); |
---|
[1730] | 1966 | } |
---|
[1907] | 1967 | |
---|
[2064] | 1968 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, std::vector<int>& idxEdge, std::vector<float>& params, int nPiece, float thresClip, int nIterClip, bool getResidual) { |
---|
[2012] | 1969 | if (nPiece < 1) { |
---|
| 1970 | throw(AipsError("wrong number of the sections for fitting")); |
---|
| 1971 | } |
---|
| 1972 | if (data.size() != mask.size()) { |
---|
| 1973 | throw(AipsError("data and mask have different size")); |
---|
| 1974 | } |
---|
| 1975 | |
---|
| 1976 | int nChan = data.size(); |
---|
| 1977 | std::vector<int> maskArray; |
---|
| 1978 | std::vector<int> x; |
---|
| 1979 | for (int i = 0; i < nChan; ++i) { |
---|
| 1980 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 1981 | if (mask[i]) { |
---|
| 1982 | x.push_back(i); |
---|
| 1983 | } |
---|
| 1984 | } |
---|
| 1985 | |
---|
| 1986 | int nData = x.size(); |
---|
| 1987 | int nElement = (int)(floor(floor((double)(nData/nPiece))+0.5)); |
---|
[2064] | 1988 | std::vector<double> invEdge; |
---|
[2012] | 1989 | |
---|
[2064] | 1990 | idxEdge.clear(); |
---|
| 1991 | idxEdge.push_back(x[0]); |
---|
| 1992 | |
---|
[2012] | 1993 | for (int i = 1; i < nPiece; ++i) { |
---|
[2047] | 1994 | int valX = x[nElement*i]; |
---|
[2064] | 1995 | idxEdge.push_back(valX); |
---|
| 1996 | invEdge.push_back(1.0/(double)valX); |
---|
[2012] | 1997 | } |
---|
| 1998 | |
---|
[2064] | 1999 | idxEdge.push_back(x[x.size()-1]+1); |
---|
| 2000 | |
---|
| 2001 | std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1; |
---|
[2012] | 2002 | for (int i = 0; i < nChan; ++i) { |
---|
[2064] | 2003 | double di = (double)i; |
---|
| 2004 | double dD = (double)data[i]; |
---|
| 2005 | x1.push_back(di); |
---|
| 2006 | x2.push_back(di*di); |
---|
| 2007 | x3.push_back(di*di*di); |
---|
| 2008 | z1.push_back(dD); |
---|
| 2009 | x1z1.push_back(dD*di); |
---|
| 2010 | x2z1.push_back(dD*di*di); |
---|
| 2011 | x3z1.push_back(dD*di*di*di); |
---|
[2012] | 2012 | r1.push_back(0.0); |
---|
| 2013 | } |
---|
| 2014 | |
---|
| 2015 | int currentNData = nData; |
---|
| 2016 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
| 2017 | |
---|
| 2018 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2064] | 2019 | // xMatrix : horizontal concatenation of |
---|
| 2020 | // the least-sq. matrix (left) and an |
---|
| 2021 | // identity matrix (right). |
---|
| 2022 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2012] | 2023 | double xMatrix[nDOF][2*nDOF]; |
---|
| 2024 | double zMatrix[nDOF]; |
---|
| 2025 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2026 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 2027 | xMatrix[i][j] = 0.0; |
---|
| 2028 | } |
---|
| 2029 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 2030 | zMatrix[i] = 0.0; |
---|
| 2031 | } |
---|
| 2032 | |
---|
| 2033 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 2034 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2035 | |
---|
[2012] | 2036 | if (maskArray[i] == 0) continue; |
---|
[2064] | 2037 | |
---|
[2012] | 2038 | xMatrix[0][0] += 1.0; |
---|
[2064] | 2039 | xMatrix[0][1] += x1[i]; |
---|
| 2040 | xMatrix[0][2] += x2[i]; |
---|
| 2041 | xMatrix[0][3] += x3[i]; |
---|
| 2042 | xMatrix[1][1] += x2[i]; |
---|
| 2043 | xMatrix[1][2] += x3[i]; |
---|
| 2044 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
| 2045 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
| 2046 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
| 2047 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
[2012] | 2048 | zMatrix[0] += z1[i]; |
---|
[2064] | 2049 | zMatrix[1] += x1z1[i]; |
---|
| 2050 | zMatrix[2] += x2z1[i]; |
---|
| 2051 | zMatrix[3] += x3z1[i]; |
---|
| 2052 | |
---|
[2012] | 2053 | for (int j = 0; j < n; ++j) { |
---|
[2064] | 2054 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
[2012] | 2055 | q = q*q*q; |
---|
| 2056 | xMatrix[0][j+4] += q; |
---|
[2064] | 2057 | xMatrix[1][j+4] += q*x1[i]; |
---|
| 2058 | xMatrix[2][j+4] += q*x2[i]; |
---|
| 2059 | xMatrix[3][j+4] += q*x3[i]; |
---|
[2012] | 2060 | for (int k = 0; k < j; ++k) { |
---|
[2064] | 2061 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
[2012] | 2062 | r = r*r*r; |
---|
| 2063 | xMatrix[k+4][j+4] += r*q; |
---|
| 2064 | } |
---|
| 2065 | xMatrix[j+4][j+4] += q*q; |
---|
| 2066 | zMatrix[j+4] += q*z1[i]; |
---|
| 2067 | } |
---|
[2064] | 2068 | |
---|
[2012] | 2069 | } |
---|
| 2070 | } |
---|
| 2071 | |
---|
| 2072 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2073 | for (int j = 0; j < i; ++j) { |
---|
| 2074 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 2075 | } |
---|
| 2076 | } |
---|
| 2077 | |
---|
| 2078 | std::vector<double> invDiag; |
---|
| 2079 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2080 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 2081 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2082 | xMatrix[i][j] *= invDiag[i]; |
---|
| 2083 | } |
---|
| 2084 | } |
---|
| 2085 | |
---|
| 2086 | for (int k = 0; k < nDOF; ++k) { |
---|
| 2087 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2088 | if (i != k) { |
---|
| 2089 | double factor1 = xMatrix[k][k]; |
---|
| 2090 | double factor2 = xMatrix[i][k]; |
---|
| 2091 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2092 | xMatrix[i][j] *= factor1; |
---|
| 2093 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 2094 | xMatrix[i][j] /= factor1; |
---|
| 2095 | } |
---|
| 2096 | } |
---|
| 2097 | } |
---|
| 2098 | double xDiag = xMatrix[k][k]; |
---|
| 2099 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2100 | xMatrix[k][j] /= xDiag; |
---|
| 2101 | } |
---|
| 2102 | } |
---|
| 2103 | |
---|
| 2104 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2105 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2106 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 2107 | } |
---|
| 2108 | } |
---|
| 2109 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
| 2110 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
| 2111 | //cubic terms for the other pieces (in case nPiece>1). |
---|
| 2112 | std::vector<double> y; |
---|
[2058] | 2113 | y.clear(); |
---|
[2012] | 2114 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2115 | y.push_back(0.0); |
---|
| 2116 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2117 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 2118 | } |
---|
| 2119 | } |
---|
| 2120 | |
---|
| 2121 | double a0 = y[0]; |
---|
| 2122 | double a1 = y[1]; |
---|
| 2123 | double a2 = y[2]; |
---|
| 2124 | double a3 = y[3]; |
---|
| 2125 | params.clear(); |
---|
| 2126 | |
---|
| 2127 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 2128 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2129 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
[2012] | 2130 | } |
---|
| 2131 | params.push_back(a0); |
---|
| 2132 | params.push_back(a1); |
---|
| 2133 | params.push_back(a2); |
---|
| 2134 | params.push_back(a3); |
---|
| 2135 | |
---|
| 2136 | if (n == nPiece-1) break; |
---|
| 2137 | |
---|
| 2138 | double d = y[4+n]; |
---|
[2064] | 2139 | double iE = invEdge[n]; |
---|
| 2140 | a0 += d; |
---|
| 2141 | a1 -= 3.0*d*iE; |
---|
| 2142 | a2 += 3.0*d*iE*iE; |
---|
| 2143 | a3 -= d*iE*iE*iE; |
---|
[2012] | 2144 | } |
---|
| 2145 | |
---|
| 2146 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 2147 | break; |
---|
| 2148 | } else { |
---|
| 2149 | std::vector<double> rz; |
---|
| 2150 | double stdDev = 0.0; |
---|
| 2151 | for (int i = 0; i < nChan; ++i) { |
---|
| 2152 | double val = abs(r1[i] - z1[i]); |
---|
| 2153 | rz.push_back(val); |
---|
| 2154 | stdDev += val*val*(double)maskArray[i]; |
---|
| 2155 | } |
---|
| 2156 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 2157 | |
---|
| 2158 | double thres = stdDev * thresClip; |
---|
| 2159 | int newNData = 0; |
---|
| 2160 | for (int i = 0; i < nChan; ++i) { |
---|
| 2161 | if (rz[i] >= thres) { |
---|
| 2162 | maskArray[i] = 0; |
---|
| 2163 | } |
---|
| 2164 | if (maskArray[i] > 0) { |
---|
| 2165 | newNData++; |
---|
| 2166 | } |
---|
| 2167 | } |
---|
| 2168 | if (newNData == currentNData) { |
---|
[2064] | 2169 | break; //no more flag to add. iteration stops. |
---|
[2012] | 2170 | } else { |
---|
| 2171 | currentNData = newNData; |
---|
| 2172 | } |
---|
| 2173 | } |
---|
| 2174 | } |
---|
| 2175 | |
---|
[2058] | 2176 | std::vector<float> result; |
---|
| 2177 | if (getResidual) { |
---|
| 2178 | for (int i = 0; i < nChan; ++i) { |
---|
| 2179 | result.push_back((float)(z1[i] - r1[i])); |
---|
| 2180 | } |
---|
| 2181 | } else { |
---|
| 2182 | for (int i = 0; i < nChan; ++i) { |
---|
| 2183 | result.push_back((float)r1[i]); |
---|
| 2184 | } |
---|
[2012] | 2185 | } |
---|
| 2186 | |
---|
[2058] | 2187 | return result; |
---|
[2012] | 2188 | } |
---|
| 2189 | |
---|
[2064] | 2190 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, int nMinWavesInSW, int nMaxWavesInSW, float thresClip, int nIterClip, bool outLogger, const std::string& blfile) { |
---|
[2012] | 2191 | ofstream ofs; |
---|
| 2192 | String coordInfo; |
---|
[2047] | 2193 | bool hasSameNchan = true; |
---|
[2012] | 2194 | bool outTextFile = false; |
---|
| 2195 | |
---|
| 2196 | if (blfile != "") { |
---|
| 2197 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2198 | if (ofs) outTextFile = true; |
---|
| 2199 | } |
---|
| 2200 | |
---|
| 2201 | if (outLogger || outTextFile) { |
---|
| 2202 | coordInfo = getCoordInfo()[0]; |
---|
| 2203 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2204 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2205 | } |
---|
| 2206 | |
---|
[2047] | 2207 | //Fitter fitter = Fitter(); |
---|
| 2208 | //fitter.setExpression("sinusoid", nMaxWavesInSW); |
---|
[2012] | 2209 | |
---|
| 2210 | int nRow = nrow(); |
---|
| 2211 | std::vector<bool> chanMask; |
---|
| 2212 | |
---|
| 2213 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2214 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[2047] | 2215 | //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip); |
---|
| 2216 | //setSpectrum(fitter.getResidual(), whichrow); |
---|
| 2217 | std::vector<int> pieceRanges; |
---|
| 2218 | std::vector<float> params; |
---|
[2058] | 2219 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nMinWavesInSW, nMaxWavesInSW, params, thresClip, nIterClip, true); |
---|
[2047] | 2220 | setSpectrum(res, whichrow); |
---|
| 2221 | // |
---|
[2012] | 2222 | |
---|
[2047] | 2223 | std::vector<bool> fixed; |
---|
| 2224 | fixed.clear(); |
---|
| 2225 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", pieceRanges, params, fixed); |
---|
[1931] | 2226 | } |
---|
[2012] | 2227 | |
---|
| 2228 | if (outTextFile) ofs.close(); |
---|
[1907] | 2229 | } |
---|
| 2230 | |
---|
[2047] | 2231 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, int nMinWavesInSW, int nMaxWavesInSW, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile) |
---|
[2012] | 2232 | { |
---|
| 2233 | ofstream ofs; |
---|
| 2234 | String coordInfo; |
---|
[2047] | 2235 | bool hasSameNchan = true; |
---|
[2012] | 2236 | bool outTextFile = false; |
---|
| 2237 | |
---|
| 2238 | if (blfile != "") { |
---|
| 2239 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2240 | if (ofs) outTextFile = true; |
---|
| 2241 | } |
---|
| 2242 | |
---|
| 2243 | if (outLogger || outTextFile) { |
---|
| 2244 | coordInfo = getCoordInfo()[0]; |
---|
| 2245 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2246 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2247 | } |
---|
| 2248 | |
---|
[2047] | 2249 | //Fitter fitter = Fitter(); |
---|
| 2250 | //fitter.setExpression("sinusoid", nMaxWavesInSW); |
---|
[2012] | 2251 | |
---|
| 2252 | int nRow = nrow(); |
---|
| 2253 | std::vector<bool> chanMask; |
---|
| 2254 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2255 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2256 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
| 2257 | |
---|
| 2258 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2259 | |
---|
| 2260 | //------------------------------------------------------- |
---|
| 2261 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2262 | //------------------------------------------------------- |
---|
| 2263 | int edgeSize = edge.size(); |
---|
| 2264 | std::vector<int> currentEdge; |
---|
| 2265 | if (edgeSize >= 2) { |
---|
| 2266 | int idx = 0; |
---|
| 2267 | if (edgeSize > 2) { |
---|
| 2268 | if (edgeSize < minEdgeSize) { |
---|
| 2269 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2270 | } |
---|
| 2271 | idx = 2 * getIF(whichrow); |
---|
| 2272 | } |
---|
| 2273 | currentEdge.push_back(edge[idx]); |
---|
| 2274 | currentEdge.push_back(edge[idx+1]); |
---|
| 2275 | } else { |
---|
| 2276 | throw(AipsError("Wrong length of edge element")); |
---|
| 2277 | } |
---|
| 2278 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2279 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2280 | chanMask = lineFinder.getMask(); |
---|
| 2281 | //------------------------------------------------------- |
---|
| 2282 | |
---|
| 2283 | |
---|
[2047] | 2284 | //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip); |
---|
| 2285 | //setSpectrum(fitter.getResidual(), whichrow); |
---|
| 2286 | std::vector<int> pieceRanges; |
---|
| 2287 | std::vector<float> params; |
---|
[2058] | 2288 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nMinWavesInSW, nMaxWavesInSW, params, thresClip, nIterClip, true); |
---|
[2047] | 2289 | setSpectrum(res, whichrow); |
---|
| 2290 | // |
---|
[2012] | 2291 | |
---|
[2047] | 2292 | std::vector<bool> fixed; |
---|
| 2293 | fixed.clear(); |
---|
| 2294 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", pieceRanges, params, fixed); |
---|
| 2295 | } |
---|
[2012] | 2296 | |
---|
[2047] | 2297 | if (outTextFile) ofs.close(); |
---|
| 2298 | } |
---|
| 2299 | |
---|
[2058] | 2300 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nMinWavesInSW, int nMaxWavesInSW, std::vector<float>& params, float thresClip, int nIterClip, bool getResidual) { |
---|
[2047] | 2301 | if (data.size() != mask.size()) { |
---|
| 2302 | throw(AipsError("data and mask have different size")); |
---|
| 2303 | } |
---|
[2058] | 2304 | if ((nMinWavesInSW < 0) || (nMaxWavesInSW < 0)) { |
---|
| 2305 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
| 2306 | } else { |
---|
| 2307 | if (nMaxWavesInSW < nMinWavesInSW) { |
---|
| 2308 | int temp = nMaxWavesInSW; |
---|
| 2309 | nMaxWavesInSW = nMinWavesInSW; |
---|
| 2310 | nMinWavesInSW = temp; |
---|
| 2311 | } |
---|
| 2312 | } |
---|
[2047] | 2313 | |
---|
| 2314 | int nChan = data.size(); |
---|
| 2315 | std::vector<int> maskArray; |
---|
| 2316 | std::vector<int> x; |
---|
| 2317 | for (int i = 0; i < nChan; ++i) { |
---|
| 2318 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 2319 | if (mask[i]) { |
---|
| 2320 | x.push_back(i); |
---|
| 2321 | } |
---|
| 2322 | } |
---|
| 2323 | |
---|
| 2324 | int nData = x.size(); |
---|
| 2325 | |
---|
| 2326 | std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1; |
---|
| 2327 | for (int i = 0; i < nChan; ++i) { |
---|
[2064] | 2328 | double di = (double)i; |
---|
| 2329 | double dD = (double)data[i]; |
---|
| 2330 | x1.push_back(di); |
---|
| 2331 | x2.push_back(di*di); |
---|
| 2332 | x3.push_back(di*di*di); |
---|
| 2333 | z1.push_back(dD); |
---|
| 2334 | x1z1.push_back(di*dD); |
---|
| 2335 | x2z1.push_back(di*di*dD); |
---|
| 2336 | x3z1.push_back(di*di*di*dD); |
---|
[2047] | 2337 | r1.push_back(0.0); |
---|
| 2338 | } |
---|
| 2339 | |
---|
| 2340 | int currentNData = nData; |
---|
| 2341 | int nDOF = nMaxWavesInSW + 1; //number of parameters to solve. |
---|
| 2342 | |
---|
| 2343 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
| 2344 | //xMatrix : horizontal concatenation of the least-sq. matrix (left) and an |
---|
| 2345 | //identity matrix (right). |
---|
| 2346 | //the right part is used to calculate the inverse matrix of the left part. |
---|
| 2347 | double xMatrix[nDOF][2*nDOF]; |
---|
| 2348 | double zMatrix[nDOF]; |
---|
| 2349 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2350 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 2351 | xMatrix[i][j] = 0.0; |
---|
[2012] | 2352 | } |
---|
[2047] | 2353 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 2354 | zMatrix[i] = 0.0; |
---|
| 2355 | } |
---|
| 2356 | |
---|
| 2357 | for (int i = 0; i < currentNData; ++i) { |
---|
| 2358 | if (maskArray[i] == 0) continue; |
---|
| 2359 | xMatrix[0][0] += 1.0; |
---|
| 2360 | xMatrix[0][1] += x1[i]; |
---|
| 2361 | xMatrix[0][2] += x2[i]; |
---|
| 2362 | xMatrix[0][3] += x3[i]; |
---|
| 2363 | xMatrix[1][1] += x2[i]; |
---|
| 2364 | xMatrix[1][2] += x3[i]; |
---|
| 2365 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
| 2366 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
| 2367 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
| 2368 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
| 2369 | zMatrix[0] += z1[i]; |
---|
| 2370 | zMatrix[1] += x1z1[i]; |
---|
| 2371 | zMatrix[2] += x2z1[i]; |
---|
| 2372 | zMatrix[3] += x3z1[i]; |
---|
| 2373 | } |
---|
| 2374 | |
---|
| 2375 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2376 | for (int j = 0; j < i; ++j) { |
---|
| 2377 | xMatrix[i][j] = xMatrix[j][i]; |
---|
[2012] | 2378 | } |
---|
| 2379 | } |
---|
| 2380 | |
---|
[2047] | 2381 | std::vector<double> invDiag; |
---|
| 2382 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2383 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 2384 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2385 | xMatrix[i][j] *= invDiag[i]; |
---|
| 2386 | } |
---|
| 2387 | } |
---|
| 2388 | |
---|
| 2389 | for (int k = 0; k < nDOF; ++k) { |
---|
| 2390 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2391 | if (i != k) { |
---|
| 2392 | double factor1 = xMatrix[k][k]; |
---|
| 2393 | double factor2 = xMatrix[i][k]; |
---|
| 2394 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2395 | xMatrix[i][j] *= factor1; |
---|
| 2396 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 2397 | xMatrix[i][j] /= factor1; |
---|
| 2398 | } |
---|
| 2399 | } |
---|
| 2400 | } |
---|
| 2401 | double xDiag = xMatrix[k][k]; |
---|
| 2402 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2403 | xMatrix[k][j] /= xDiag; |
---|
| 2404 | } |
---|
| 2405 | } |
---|
| 2406 | |
---|
| 2407 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2408 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2409 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 2410 | } |
---|
| 2411 | } |
---|
| 2412 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
| 2413 | //best-fit curves (a0,b0,a1,b1,...), namely, a* and b* are of sine and cosine functions, |
---|
| 2414 | //respectively. |
---|
| 2415 | std::vector<double> y; |
---|
| 2416 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2417 | y.push_back(0.0); |
---|
| 2418 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2419 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 2420 | } |
---|
| 2421 | } |
---|
| 2422 | |
---|
| 2423 | double a0 = y[0]; |
---|
| 2424 | double a1 = y[1]; |
---|
| 2425 | double a2 = y[2]; |
---|
| 2426 | double a3 = y[3]; |
---|
| 2427 | params.clear(); |
---|
| 2428 | |
---|
| 2429 | for (int i = 0; i < nChan; ++i) { |
---|
| 2430 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
| 2431 | } |
---|
| 2432 | params.push_back(a0); |
---|
| 2433 | params.push_back(a1); |
---|
| 2434 | params.push_back(a2); |
---|
| 2435 | params.push_back(a3); |
---|
| 2436 | |
---|
| 2437 | |
---|
| 2438 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 2439 | break; |
---|
| 2440 | } else { |
---|
| 2441 | std::vector<double> rz; |
---|
| 2442 | double stdDev = 0.0; |
---|
| 2443 | for (int i = 0; i < nChan; ++i) { |
---|
| 2444 | double val = abs(r1[i] - z1[i]); |
---|
| 2445 | rz.push_back(val); |
---|
| 2446 | stdDev += val*val*(double)maskArray[i]; |
---|
| 2447 | } |
---|
| 2448 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 2449 | |
---|
| 2450 | double thres = stdDev * thresClip; |
---|
| 2451 | int newNData = 0; |
---|
| 2452 | for (int i = 0; i < nChan; ++i) { |
---|
| 2453 | if (rz[i] >= thres) { |
---|
| 2454 | maskArray[i] = 0; |
---|
| 2455 | } |
---|
| 2456 | if (maskArray[i] > 0) { |
---|
| 2457 | newNData++; |
---|
| 2458 | } |
---|
| 2459 | } |
---|
| 2460 | if (newNData == currentNData) { |
---|
| 2461 | break; //no additional flag. finish iteration. |
---|
| 2462 | } else { |
---|
| 2463 | currentNData = newNData; |
---|
| 2464 | } |
---|
| 2465 | } |
---|
[2012] | 2466 | } |
---|
| 2467 | |
---|
[2058] | 2468 | std::vector<float> result; |
---|
| 2469 | if (getResidual) { |
---|
| 2470 | for (int i = 0; i < nChan; ++i) { |
---|
| 2471 | result.push_back((float)(z1[i] - r1[i])); |
---|
| 2472 | } |
---|
| 2473 | } else { |
---|
| 2474 | for (int i = 0; i < nChan; ++i) { |
---|
| 2475 | result.push_back((float)r1[i]); |
---|
| 2476 | } |
---|
[2047] | 2477 | } |
---|
| 2478 | |
---|
[2058] | 2479 | return result; |
---|
[2012] | 2480 | } |
---|
| 2481 | |
---|
[2047] | 2482 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
| 2483 | { |
---|
| 2484 | std::vector<double> abcsd = getAbcissa(whichrow); |
---|
| 2485 | std::vector<float> abcs; |
---|
| 2486 | for (uInt i = 0; i < abcsd.size(); ++i) { |
---|
| 2487 | abcs.push_back((float)abcsd[i]); |
---|
| 2488 | } |
---|
| 2489 | std::vector<float> spec = getSpectrum(whichrow); |
---|
[2012] | 2490 | |
---|
[2047] | 2491 | fitter.setData(abcs, spec, mask); |
---|
| 2492 | fitter.lfit(); |
---|
| 2493 | } |
---|
| 2494 | |
---|
| 2495 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
| 2496 | { |
---|
| 2497 | std::vector<bool> chanMask = getMask(whichrow); |
---|
| 2498 | uInt chanMaskSize = chanMask.size(); |
---|
| 2499 | if (chanMaskSize != inMask.size()) { |
---|
| 2500 | throw(AipsError("different mask sizes")); |
---|
| 2501 | } |
---|
| 2502 | for (uInt i = 0; i < chanMaskSize; ++i) { |
---|
| 2503 | chanMask[i] = chanMask[i] && inMask[i]; |
---|
| 2504 | } |
---|
| 2505 | |
---|
| 2506 | return chanMask; |
---|
| 2507 | } |
---|
| 2508 | |
---|
| 2509 | /* |
---|
| 2510 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
| 2511 | { |
---|
| 2512 | int edgeSize = edge.size(); |
---|
| 2513 | std::vector<int> currentEdge; |
---|
| 2514 | if (edgeSize >= 2) { |
---|
| 2515 | int idx = 0; |
---|
| 2516 | if (edgeSize > 2) { |
---|
| 2517 | if (edgeSize < minEdgeSize) { |
---|
| 2518 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2519 | } |
---|
| 2520 | idx = 2 * getIF(whichrow); |
---|
| 2521 | } |
---|
| 2522 | currentEdge.push_back(edge[idx]); |
---|
| 2523 | currentEdge.push_back(edge[idx+1]); |
---|
| 2524 | } else { |
---|
| 2525 | throw(AipsError("Wrong length of edge element")); |
---|
| 2526 | } |
---|
| 2527 | |
---|
| 2528 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2529 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
| 2530 | |
---|
| 2531 | return lineFinder.getMask(); |
---|
| 2532 | } |
---|
| 2533 | */ |
---|
| 2534 | |
---|
| 2535 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
| 2536 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter) { |
---|
| 2537 | if (outLogger || outTextFile) { |
---|
| 2538 | std::vector<float> params = fitter.getParameters(); |
---|
| 2539 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
| 2540 | float rms = getRms(chanMask, whichrow); |
---|
| 2541 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 2542 | |
---|
| 2543 | if (outLogger) { |
---|
| 2544 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
| 2545 | ols << formatBaselineParams(params, fixed, rms, masklist, whichrow, false) << LogIO::POST ; |
---|
| 2546 | } |
---|
| 2547 | if (outTextFile) { |
---|
| 2548 | ofs << formatBaselineParams(params, fixed, rms, masklist, whichrow, true) << flush; |
---|
| 2549 | } |
---|
| 2550 | } |
---|
| 2551 | } |
---|
| 2552 | |
---|
| 2553 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
[2064] | 2554 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const std::vector<bool>& fixed) { |
---|
[2047] | 2555 | if (outLogger || outTextFile) { |
---|
| 2556 | float rms = getRms(chanMask, whichrow); |
---|
| 2557 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 2558 | |
---|
| 2559 | if (outLogger) { |
---|
| 2560 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2064] | 2561 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 2562 | } |
---|
| 2563 | if (outTextFile) { |
---|
[2064] | 2564 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, masklist, whichrow, true) << flush; |
---|
[2047] | 2565 | } |
---|
| 2566 | } |
---|
| 2567 | } |
---|
| 2568 | |
---|
| 2569 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */ |
---|
| 2570 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const std::vector<bool>& fixed) { |
---|
| 2571 | if (outLogger || outTextFile) { |
---|
| 2572 | float rms = getRms(chanMask, whichrow); |
---|
| 2573 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 2574 | |
---|
| 2575 | if (outLogger) { |
---|
| 2576 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
| 2577 | ols << formatBaselineParams(params, fixed, rms, masklist, whichrow, false) << LogIO::POST ; |
---|
| 2578 | } |
---|
| 2579 | if (outTextFile) { |
---|
| 2580 | ofs << formatBaselineParams(params, fixed, rms, masklist, whichrow, true) << flush; |
---|
| 2581 | } |
---|
| 2582 | } |
---|
| 2583 | } |
---|
| 2584 | |
---|
[2012] | 2585 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) { |
---|
| 2586 | Vector<Float> spec; |
---|
| 2587 | specCol_.get(whichrow, spec); |
---|
| 2588 | |
---|
| 2589 | float mean = 0.0; |
---|
| 2590 | float smean = 0.0; |
---|
| 2591 | int n = 0; |
---|
[2047] | 2592 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
[2012] | 2593 | if (mask[i]) { |
---|
| 2594 | mean += spec[i]; |
---|
| 2595 | smean += spec[i]*spec[i]; |
---|
| 2596 | n++; |
---|
| 2597 | } |
---|
| 2598 | } |
---|
| 2599 | |
---|
| 2600 | mean /= (float)n; |
---|
| 2601 | smean /= (float)n; |
---|
| 2602 | |
---|
| 2603 | return sqrt(smean - mean*mean); |
---|
| 2604 | } |
---|
| 2605 | |
---|
| 2606 | |
---|
| 2607 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const |
---|
| 2608 | { |
---|
| 2609 | ostringstream oss; |
---|
| 2610 | |
---|
| 2611 | if (verbose) { |
---|
| 2612 | for (int i = 0; i < 60; ++i) { |
---|
| 2613 | oss << "-"; |
---|
| 2614 | } |
---|
| 2615 | oss << endl; |
---|
| 2616 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
| 2617 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
| 2618 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
| 2619 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
| 2620 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
| 2621 | oss << "Fitter range = " << masklist << endl; |
---|
| 2622 | oss << "Baseline parameters" << endl; |
---|
| 2623 | oss << flush; |
---|
| 2624 | } |
---|
| 2625 | |
---|
| 2626 | return String(oss); |
---|
| 2627 | } |
---|
| 2628 | |
---|
| 2629 | std::string Scantable::formatBaselineParamsFooter(float rms, bool verbose) const |
---|
| 2630 | { |
---|
| 2631 | ostringstream oss; |
---|
| 2632 | |
---|
| 2633 | if (verbose) { |
---|
| 2634 | oss << "Results of baseline fit" << endl; |
---|
| 2635 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
| 2636 | } |
---|
| 2637 | |
---|
| 2638 | return String(oss); |
---|
| 2639 | } |
---|
| 2640 | |
---|
[2064] | 2641 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, const std::vector<bool>& fixed, float rms, const std::string& masklist, int whichrow, bool verbose, int start, int count, bool resetparamid) const |
---|
[2047] | 2642 | { |
---|
[2064] | 2643 | int nParam = (int)(params.size()); |
---|
[2047] | 2644 | |
---|
[2064] | 2645 | if (nParam < 1) { |
---|
| 2646 | return(" Not fitted"); |
---|
| 2647 | } else { |
---|
| 2648 | |
---|
| 2649 | ostringstream oss; |
---|
| 2650 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
| 2651 | |
---|
| 2652 | if (start < 0) start = 0; |
---|
| 2653 | if (count < 0) count = nParam; |
---|
| 2654 | int end = start + count; |
---|
| 2655 | if (end > nParam) end = nParam; |
---|
| 2656 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
| 2657 | |
---|
| 2658 | for (int i = start; i < end; ++i) { |
---|
| 2659 | if (i > start) { |
---|
[2047] | 2660 | oss << ","; |
---|
| 2661 | } |
---|
[2064] | 2662 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
| 2663 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
[2047] | 2664 | } |
---|
[2064] | 2665 | |
---|
| 2666 | oss << endl; |
---|
| 2667 | oss << formatBaselineParamsFooter(rms, verbose); |
---|
| 2668 | |
---|
| 2669 | return String(oss); |
---|
[2047] | 2670 | } |
---|
| 2671 | |
---|
| 2672 | } |
---|
| 2673 | |
---|
[2012] | 2674 | std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, const std::string& masklist, int whichrow, bool verbose) const |
---|
| 2675 | { |
---|
[2064] | 2676 | int nOutParam = (int)(params.size()); |
---|
| 2677 | int nPiece = (int)(ranges.size()) - 1; |
---|
[2012] | 2678 | |
---|
[2064] | 2679 | if (nOutParam < 1) { |
---|
| 2680 | return(" Not fitted"); |
---|
| 2681 | } else if (nPiece < 0) { |
---|
| 2682 | return formatBaselineParams(params, fixed, rms, masklist, whichrow, verbose); |
---|
| 2683 | } else if (nPiece < 1) { |
---|
| 2684 | return(" Bad count of the piece edge info"); |
---|
| 2685 | } else if (nOutParam % nPiece != 0) { |
---|
| 2686 | return(" Bad count of the output baseline parameters"); |
---|
| 2687 | } else { |
---|
| 2688 | |
---|
| 2689 | int nParam = nOutParam / nPiece; |
---|
| 2690 | |
---|
| 2691 | ostringstream oss; |
---|
| 2692 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
| 2693 | |
---|
| 2694 | stringstream ss; |
---|
| 2695 | ss << ranges[nPiece] << flush; |
---|
| 2696 | int wRange = ss.str().size() * 2 + 5; |
---|
| 2697 | |
---|
| 2698 | for (int i = 0; i < nPiece; ++i) { |
---|
[2047] | 2699 | ss.str(""); |
---|
[2064] | 2700 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
| 2701 | oss << left << setw(wRange) << ss.str(); |
---|
| 2702 | oss << formatBaselineParams(params, fixed, rms, masklist, whichrow, false, i*nParam, nParam, true); |
---|
[2012] | 2703 | } |
---|
[2064] | 2704 | |
---|
| 2705 | oss << formatBaselineParamsFooter(rms, verbose); |
---|
| 2706 | |
---|
| 2707 | return String(oss); |
---|
[2012] | 2708 | } |
---|
| 2709 | |
---|
| 2710 | } |
---|
| 2711 | |
---|
[2047] | 2712 | bool Scantable::hasSameNchanOverIFs() |
---|
[2012] | 2713 | { |
---|
[2047] | 2714 | int nIF = nif(-1); |
---|
| 2715 | int nCh; |
---|
| 2716 | int totalPositiveNChan = 0; |
---|
| 2717 | int nPositiveNChan = 0; |
---|
[2012] | 2718 | |
---|
[2047] | 2719 | for (int i = 0; i < nIF; ++i) { |
---|
| 2720 | nCh = nchan(i); |
---|
| 2721 | if (nCh > 0) { |
---|
| 2722 | totalPositiveNChan += nCh; |
---|
| 2723 | nPositiveNChan++; |
---|
[2012] | 2724 | } |
---|
| 2725 | } |
---|
| 2726 | |
---|
[2047] | 2727 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
[2012] | 2728 | } |
---|
| 2729 | |
---|
[2047] | 2730 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
[2012] | 2731 | { |
---|
| 2732 | if (mask.size() < 2) { |
---|
| 2733 | throw(AipsError("The mask elements should be > 1")); |
---|
| 2734 | } |
---|
[2047] | 2735 | int IF = getIF(whichrow); |
---|
| 2736 | if (mask.size() != (uInt)nchan(IF)) { |
---|
[2012] | 2737 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
| 2738 | } |
---|
| 2739 | |
---|
[2047] | 2740 | if (verbose) { |
---|
[2012] | 2741 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
| 2742 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
| 2743 | if (!hasSameNchan) { |
---|
[2047] | 2744 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
[2012] | 2745 | } |
---|
| 2746 | logOs << LogIO::POST; |
---|
| 2747 | } |
---|
| 2748 | |
---|
| 2749 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
[2047] | 2750 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
| 2751 | |
---|
[2012] | 2752 | ostringstream oss; |
---|
| 2753 | oss.setf(ios::fixed); |
---|
| 2754 | oss << setprecision(1) << "["; |
---|
[2047] | 2755 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
[2012] | 2756 | if (i > 0) oss << ","; |
---|
[2047] | 2757 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
[2012] | 2758 | } |
---|
| 2759 | oss << "]" << flush; |
---|
| 2760 | |
---|
| 2761 | return String(oss); |
---|
| 2762 | } |
---|
| 2763 | |
---|
[2047] | 2764 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
[2012] | 2765 | { |
---|
[2047] | 2766 | if (mask.size() < 2) { |
---|
| 2767 | throw(AipsError("The mask elements should be > 1")); |
---|
[2012] | 2768 | } |
---|
| 2769 | |
---|
[2047] | 2770 | std::vector<int> out, startIndices, endIndices; |
---|
| 2771 | int maskSize = mask.size(); |
---|
[2012] | 2772 | |
---|
[2047] | 2773 | startIndices.clear(); |
---|
| 2774 | endIndices.clear(); |
---|
| 2775 | |
---|
| 2776 | if (mask[0]) { |
---|
| 2777 | startIndices.push_back(0); |
---|
[2012] | 2778 | } |
---|
[2047] | 2779 | for (int i = 1; i < maskSize; ++i) { |
---|
| 2780 | if ((!mask[i-1]) && mask[i]) { |
---|
| 2781 | startIndices.push_back(i); |
---|
| 2782 | } else if (mask[i-1] && (!mask[i])) { |
---|
| 2783 | endIndices.push_back(i-1); |
---|
| 2784 | } |
---|
[2012] | 2785 | } |
---|
[2047] | 2786 | if (mask[maskSize-1]) { |
---|
| 2787 | endIndices.push_back(maskSize-1); |
---|
| 2788 | } |
---|
[2012] | 2789 | |
---|
[2047] | 2790 | if (startIndices.size() != endIndices.size()) { |
---|
| 2791 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
| 2792 | } |
---|
| 2793 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 2794 | if (startIndices[i] > endIndices[i]) { |
---|
| 2795 | throw(AipsError("Mask start index > mask end index")); |
---|
[2012] | 2796 | } |
---|
| 2797 | } |
---|
| 2798 | |
---|
[2047] | 2799 | out.clear(); |
---|
| 2800 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 2801 | out.push_back(startIndices[i]); |
---|
| 2802 | out.push_back(endIndices[i]); |
---|
| 2803 | } |
---|
| 2804 | |
---|
[2012] | 2805 | return out; |
---|
| 2806 | } |
---|
| 2807 | |
---|
| 2808 | |
---|
| 2809 | /* |
---|
[1931] | 2810 | STFitEntry Scantable::polyBaseline(const std::vector<bool>& mask, int order, int rowno) |
---|
[1907] | 2811 | { |
---|
| 2812 | Fitter fitter = Fitter(); |
---|
[2012] | 2813 | fitter.setExpression("poly", order); |
---|
| 2814 | |
---|
| 2815 | std::vector<bool> fmask = getMask(rowno); |
---|
| 2816 | if (fmask.size() != mask.size()) { |
---|
| 2817 | throw(AipsError("different mask sizes")); |
---|
| 2818 | } |
---|
| 2819 | for (int i = 0; i < fmask.size(); ++i) { |
---|
| 2820 | fmask[i] = fmask[i] && mask[i]; |
---|
| 2821 | } |
---|
| 2822 | |
---|
| 2823 | fitBaseline(fmask, rowno, fitter); |
---|
[1907] | 2824 | setSpectrum(fitter.getResidual(), rowno); |
---|
[1931] | 2825 | return fitter.getFitEntry(); |
---|
[1907] | 2826 | } |
---|
[2012] | 2827 | */ |
---|
[1907] | 2828 | |
---|
| 2829 | } |
---|
[1819] | 2830 | //namespace asap |
---|