[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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| 13 | |
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[2186] | 14 | #include <atnf/PKSIO/SrcType.h> |
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| 15 | |
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[125] | 16 | #include <casa/aips.h> |
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[2186] | 17 | #include <casa/iomanip.h> |
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[80] | 18 | #include <casa/iostream.h> |
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[2186] | 19 | #include <casa/OS/File.h> |
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[805] | 20 | #include <casa/OS/Path.h> |
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[80] | 21 | #include <casa/Arrays/Array.h> |
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[2186] | 22 | #include <casa/Arrays/ArrayAccessor.h> |
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| 23 | #include <casa/Arrays/ArrayLogical.h> |
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[80] | 24 | #include <casa/Arrays/ArrayMath.h> |
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| 25 | #include <casa/Arrays/MaskArrMath.h> |
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[2186] | 26 | #include <casa/Arrays/Slice.h> |
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[1325] | 27 | #include <casa/Arrays/Vector.h> |
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[455] | 28 | #include <casa/Arrays/VectorSTLIterator.h> |
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[418] | 29 | #include <casa/BasicMath/Math.h> |
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[504] | 30 | #include <casa/BasicSL/Constants.h> |
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[2186] | 31 | #include <casa/Containers/RecordField.h> |
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| 32 | #include <casa/Logging/LogIO.h> |
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[286] | 33 | #include <casa/Quanta/MVAngle.h> |
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[2186] | 34 | #include <casa/Quanta/MVTime.h> |
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[902] | 35 | #include <casa/Utilities/GenSort.h> |
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[2] | 36 | |
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[2186] | 37 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[2] | 38 | |
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[1325] | 39 | // needed to avoid error in .tcc |
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| 40 | #include <measures/Measures/MCDirection.h> |
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| 41 | // |
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| 42 | #include <measures/Measures/MDirection.h> |
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[2186] | 43 | #include <measures/Measures/MEpoch.h> |
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[80] | 44 | #include <measures/Measures/MFrequency.h> |
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[2186] | 45 | #include <measures/Measures/MeasRef.h> |
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| 46 | #include <measures/Measures/MeasTable.h> |
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| 47 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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| 48 | #include <measures/TableMeasures/TableMeasDesc.h> |
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[805] | 49 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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| 50 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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[2] | 51 | |
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[2186] | 52 | #include <tables/Tables/ArrColDesc.h> |
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| 53 | #include <tables/Tables/ExprNode.h> |
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| 54 | #include <tables/Tables/ScaColDesc.h> |
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| 55 | #include <tables/Tables/SetupNewTab.h> |
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| 56 | #include <tables/Tables/TableCopy.h> |
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| 57 | #include <tables/Tables/TableDesc.h> |
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| 58 | #include <tables/Tables/TableIter.h> |
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| 59 | #include <tables/Tables/TableParse.h> |
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| 60 | #include <tables/Tables/TableRecord.h> |
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| 61 | #include <tables/Tables/TableRow.h> |
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| 62 | #include <tables/Tables/TableVector.h> |
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| 63 | |
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| 64 | #include "MathUtils.h" |
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| 65 | #include "STAttr.h" |
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| 66 | #include "STLineFinder.h" |
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| 67 | #include "STPolCircular.h" |
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[896] | 68 | #include "STPolLinear.h" |
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[913] | 69 | #include "STPolStokes.h" |
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[2321] | 70 | #include "STUpgrade.h" |
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[2186] | 71 | #include "Scantable.h" |
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[2] | 72 | |
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[125] | 73 | using namespace casa; |
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[2] | 74 | |
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[805] | 75 | namespace asap { |
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| 76 | |
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[896] | 77 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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| 78 | |
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| 79 | void Scantable::initFactories() { |
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| 80 | if ( factories_.empty() ) { |
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| 81 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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[1323] | 82 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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[913] | 83 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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[896] | 84 | } |
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| 85 | } |
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| 86 | |
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[805] | 87 | Scantable::Scantable(Table::TableType ttype) : |
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[852] | 88 | type_(ttype) |
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[206] | 89 | { |
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[896] | 90 | initFactories(); |
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[805] | 91 | setupMainTable(); |
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[2346] | 92 | freqTable_ = STFrequencies(*this); |
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| 93 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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[852] | 94 | weatherTable_ = STWeather(*this); |
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[805] | 95 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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[852] | 96 | focusTable_ = STFocus(*this); |
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[805] | 97 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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[852] | 98 | tcalTable_ = STTcal(*this); |
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[805] | 99 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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[852] | 100 | moleculeTable_ = STMolecules(*this); |
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[805] | 101 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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[860] | 102 | historyTable_ = STHistory(*this); |
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| 103 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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[959] | 104 | fitTable_ = STFit(*this); |
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| 105 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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[1881] | 106 | table_.tableInfo().setType( "Scantable" ) ; |
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[805] | 107 | originalTable_ = table_; |
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[322] | 108 | attach(); |
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[18] | 109 | } |
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[206] | 110 | |
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[805] | 111 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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[852] | 112 | type_(ttype) |
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[206] | 113 | { |
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[896] | 114 | initFactories(); |
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[1819] | 115 | |
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[865] | 116 | Table tab(name, Table::Update); |
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[1009] | 117 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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[483] | 118 | if (version != version_) { |
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[2321] | 119 | STUpgrade upgrader(version_); |
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[2162] | 120 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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| 121 | os << LogIO::WARN |
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[2321] | 122 | << name << " data format version " << version |
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| 123 | << " is deprecated" << endl |
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| 124 | << "Running upgrade."<< endl |
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[2162] | 125 | << LogIO::POST ; |
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[2321] | 126 | std::string outname = upgrader.upgrade(name); |
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[2332] | 127 | if ( outname != name ) { |
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| 128 | os << LogIO::WARN |
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| 129 | << "Data will be loaded from " << outname << " instead of " |
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| 130 | << name << LogIO::POST ; |
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| 131 | tab = Table(outname, Table::Update ) ; |
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| 132 | } |
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[483] | 133 | } |
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[1009] | 134 | if ( type_ == Table::Memory ) { |
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[852] | 135 | table_ = tab.copyToMemoryTable(generateName()); |
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[1009] | 136 | } else { |
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[805] | 137 | table_ = tab; |
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[1009] | 138 | } |
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[1881] | 139 | table_.tableInfo().setType( "Scantable" ) ; |
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[1009] | 140 | |
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[859] | 141 | attachSubtables(); |
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[805] | 142 | originalTable_ = table_; |
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[329] | 143 | attach(); |
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[2] | 144 | } |
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[1819] | 145 | /* |
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| 146 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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| 147 | type_(ttype) |
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| 148 | { |
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| 149 | initFactories(); |
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| 150 | Table tab(name, Table::Update); |
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| 151 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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| 152 | if (version != version_) { |
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| 153 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 154 | } |
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| 155 | if ( type_ == Table::Memory ) { |
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| 156 | table_ = tab.copyToMemoryTable(generateName()); |
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| 157 | } else { |
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| 158 | table_ = tab; |
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| 159 | } |
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[2] | 160 | |
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[1819] | 161 | attachSubtables(); |
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| 162 | originalTable_ = table_; |
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| 163 | attach(); |
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| 164 | } |
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| 165 | */ |
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| 166 | |
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[2163] | 167 | Scantable::Scantable( const Scantable& other, bool clear ): |
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| 168 | Logger() |
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[206] | 169 | { |
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[805] | 170 | // with or without data |
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[859] | 171 | String newname = String(generateName()); |
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[865] | 172 | type_ = other.table_.tableType(); |
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[859] | 173 | if ( other.table_.tableType() == Table::Memory ) { |
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| 174 | if ( clear ) { |
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| 175 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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| 176 | other.table_, True); |
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| 177 | } else |
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| 178 | table_ = other.table_.copyToMemoryTable(newname); |
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[16] | 179 | } else { |
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[915] | 180 | other.table_.deepCopy(newname, Table::New, False, |
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| 181 | other.table_.endianFormat(), |
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[865] | 182 | Bool(clear)); |
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| 183 | table_ = Table(newname, Table::Update); |
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| 184 | table_.markForDelete(); |
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| 185 | } |
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[1881] | 186 | table_.tableInfo().setType( "Scantable" ) ; |
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[1111] | 187 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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[915] | 188 | if ( clear ) copySubtables(other); |
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[859] | 189 | attachSubtables(); |
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[805] | 190 | originalTable_ = table_; |
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[322] | 191 | attach(); |
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[2] | 192 | } |
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| 193 | |
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[865] | 194 | void Scantable::copySubtables(const Scantable& other) { |
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| 195 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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[2346] | 196 | TableCopy::copyRows(t, other.freqTable_.table()); |
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[865] | 197 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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| 198 | TableCopy::copyRows(t, other.focusTable_.table()); |
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| 199 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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| 200 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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| 201 | t = table_.rwKeywordSet().asTable("TCAL"); |
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| 202 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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| 203 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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| 204 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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| 205 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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| 206 | TableCopy::copyRows(t, other.historyTable_.table()); |
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[972] | 207 | t = table_.rwKeywordSet().asTable("FIT"); |
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| 208 | TableCopy::copyRows(t, other.fitTable_.table()); |
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[865] | 209 | } |
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| 210 | |
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[859] | 211 | void Scantable::attachSubtables() |
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| 212 | { |
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[2346] | 213 | freqTable_ = STFrequencies(table_); |
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[859] | 214 | focusTable_ = STFocus(table_); |
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| 215 | weatherTable_ = STWeather(table_); |
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| 216 | tcalTable_ = STTcal(table_); |
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| 217 | moleculeTable_ = STMolecules(table_); |
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[860] | 218 | historyTable_ = STHistory(table_); |
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[972] | 219 | fitTable_ = STFit(table_); |
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[859] | 220 | } |
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| 221 | |
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[805] | 222 | Scantable::~Scantable() |
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[206] | 223 | { |
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[2] | 224 | } |
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| 225 | |
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[805] | 226 | void Scantable::setupMainTable() |
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[206] | 227 | { |
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[805] | 228 | TableDesc td("", "1", TableDesc::Scratch); |
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| 229 | td.comment() = "An ASAP Scantable"; |
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[1009] | 230 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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[2] | 231 | |
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[805] | 232 | // n Cycles |
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| 233 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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| 234 | // new index every nBeam x nIF x nPol |
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| 235 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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[2] | 236 | |
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[805] | 237 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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| 238 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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[972] | 239 | // linear, circular, stokes |
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[805] | 240 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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| 241 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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[138] | 242 | |
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[805] | 243 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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| 244 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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[80] | 245 | |
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[1819] | 246 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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| 247 | refbeamnoColumn.setDefault(Int(-1)); |
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| 248 | td.addColumn(refbeamnoColumn); |
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| 249 | |
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| 250 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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| 251 | flagrowColumn.setDefault(uInt(0)); |
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| 252 | td.addColumn(flagrowColumn); |
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| 253 | |
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[805] | 254 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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| 255 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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| 256 | TableMeasValueDesc measVal(td, "TIME"); |
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| 257 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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| 258 | mepochCol.write(td); |
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[483] | 259 | |
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[805] | 260 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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| 261 | |
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[2] | 262 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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[805] | 263 | // Type of source (on=0, off=1, other=-1) |
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[1503] | 264 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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| 265 | stypeColumn.setDefault(Int(-1)); |
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| 266 | td.addColumn(stypeColumn); |
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[805] | 267 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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| 268 | |
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| 269 | //The actual Data Vectors |
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[2] | 270 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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| 271 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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[89] | 272 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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[805] | 273 | |
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| 274 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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| 275 | IPosition(1,2), |
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| 276 | ColumnDesc::Direct)); |
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| 277 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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| 278 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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| 279 | // the TableMeasDesc gives the column a type |
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| 280 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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[987] | 281 | // a uder set table type e.g. GALCTIC, B1950 ... |
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| 282 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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[805] | 283 | // writing create the measure column |
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| 284 | mdirCol.write(td); |
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[923] | 285 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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| 286 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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[1047] | 287 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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[105] | 288 | |
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[805] | 289 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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[972] | 290 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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[973] | 291 | fitColumn.setDefault(Int(-1)); |
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[972] | 292 | td.addColumn(fitColumn); |
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[805] | 293 | |
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| 294 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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| 295 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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| 296 | |
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[999] | 297 | // columns which just get dragged along, as they aren't used in asap |
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| 298 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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| 299 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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| 300 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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| 301 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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| 302 | |
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[805] | 303 | td.rwKeywordSet().define("OBSMODE", String("")); |
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| 304 | |
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[418] | 305 | // Now create Table SetUp from the description. |
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[859] | 306 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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[852] | 307 | table_ = Table(aNewTab, type_, 0); |
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[805] | 308 | originalTable_ = table_; |
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| 309 | } |
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[418] | 310 | |
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[805] | 311 | void Scantable::attach() |
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[455] | 312 | { |
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[805] | 313 | timeCol_.attach(table_, "TIME"); |
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| 314 | srcnCol_.attach(table_, "SRCNAME"); |
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[1068] | 315 | srctCol_.attach(table_, "SRCTYPE"); |
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[805] | 316 | specCol_.attach(table_, "SPECTRA"); |
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| 317 | flagsCol_.attach(table_, "FLAGTRA"); |
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[865] | 318 | tsysCol_.attach(table_, "TSYS"); |
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[805] | 319 | cycleCol_.attach(table_,"CYCLENO"); |
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| 320 | scanCol_.attach(table_, "SCANNO"); |
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| 321 | beamCol_.attach(table_, "BEAMNO"); |
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[847] | 322 | ifCol_.attach(table_, "IFNO"); |
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| 323 | polCol_.attach(table_, "POLNO"); |
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[805] | 324 | integrCol_.attach(table_, "INTERVAL"); |
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| 325 | azCol_.attach(table_, "AZIMUTH"); |
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| 326 | elCol_.attach(table_, "ELEVATION"); |
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| 327 | dirCol_.attach(table_, "DIRECTION"); |
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| 328 | fldnCol_.attach(table_, "FIELDNAME"); |
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| 329 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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[455] | 330 | |
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[1730] | 331 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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[805] | 332 | mfitidCol_.attach(table_,"FIT_ID"); |
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| 333 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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| 334 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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| 335 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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| 336 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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[1819] | 337 | |
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| 338 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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| 339 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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| 340 | |
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[455] | 341 | } |
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| 342 | |
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[1819] | 343 | template<class T, class T2> |
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| 344 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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| 345 | const String& colName, |
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| 346 | const T2& defValue) |
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| 347 | { |
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| 348 | try { |
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| 349 | col.attach(table_, colName); |
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| 350 | } catch (TableError& err) { |
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| 351 | String errMesg = err.getMesg(); |
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| 352 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 353 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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| 354 | col.attach(table_, colName); |
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| 355 | col.fillColumn(static_cast<T>(defValue)); |
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| 356 | } else { |
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| 357 | throw; |
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| 358 | } |
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| 359 | } catch (...) { |
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| 360 | throw; |
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| 361 | } |
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| 362 | } |
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| 363 | |
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| 364 | template<class T, class T2> |
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| 365 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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| 366 | const String& colName, |
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| 367 | const Array<T2>& defValue) |
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| 368 | { |
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| 369 | try { |
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| 370 | col.attach(table_, colName); |
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| 371 | } catch (TableError& err) { |
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| 372 | String errMesg = err.getMesg(); |
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| 373 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 374 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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| 375 | col.attach(table_, colName); |
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| 376 | |
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| 377 | int size = 0; |
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| 378 | ArrayIterator<T2>& it = defValue.begin(); |
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| 379 | while (it != defValue.end()) { |
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| 380 | ++size; |
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| 381 | ++it; |
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| 382 | } |
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| 383 | IPosition ip(1, size); |
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| 384 | Array<T>& arr(ip); |
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| 385 | for (int i = 0; i < size; ++i) |
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| 386 | arr[i] = static_cast<T>(defValue[i]); |
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| 387 | |
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| 388 | col.fillColumn(arr); |
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| 389 | } else { |
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| 390 | throw; |
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| 391 | } |
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| 392 | } catch (...) { |
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| 393 | throw; |
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| 394 | } |
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| 395 | } |
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| 396 | |
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[901] | 397 | void Scantable::setHeader(const STHeader& sdh) |
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[206] | 398 | { |
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[18] | 399 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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| 400 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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| 401 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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| 402 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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| 403 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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| 404 | table_.rwKeywordSet().define("Project", sdh.project); |
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| 405 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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| 406 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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| 407 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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| 408 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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| 409 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
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| 410 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
---|
| 411 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
---|
| 412 | table_.rwKeywordSet().define("UTC", sdh.utc); |
---|
[206] | 413 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
---|
| 414 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
---|
[905] | 415 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
---|
[50] | 416 | } |
---|
[21] | 417 | |
---|
[901] | 418 | STHeader Scantable::getHeader() const |
---|
[206] | 419 | { |
---|
[901] | 420 | STHeader sdh; |
---|
[21] | 421 | table_.keywordSet().get("nBeam",sdh.nbeam); |
---|
| 422 | table_.keywordSet().get("nIF",sdh.nif); |
---|
| 423 | table_.keywordSet().get("nPol",sdh.npol); |
---|
| 424 | table_.keywordSet().get("nChan",sdh.nchan); |
---|
| 425 | table_.keywordSet().get("Observer", sdh.observer); |
---|
| 426 | table_.keywordSet().get("Project", sdh.project); |
---|
| 427 | table_.keywordSet().get("Obstype", sdh.obstype); |
---|
| 428 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
---|
| 429 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
---|
| 430 | table_.keywordSet().get("Equinox", sdh.equinox); |
---|
| 431 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
---|
| 432 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
---|
| 433 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
---|
| 434 | table_.keywordSet().get("UTC", sdh.utc); |
---|
[206] | 435 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
---|
| 436 | table_.keywordSet().get("Epoch", sdh.epoch); |
---|
[905] | 437 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
---|
[21] | 438 | return sdh; |
---|
[18] | 439 | } |
---|
[805] | 440 | |
---|
[1360] | 441 | void Scantable::setSourceType( int stype ) |
---|
[1068] | 442 | { |
---|
| 443 | if ( stype < 0 || stype > 1 ) |
---|
| 444 | throw(AipsError("Illegal sourcetype.")); |
---|
| 445 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
---|
| 446 | tabvec = Int(stype); |
---|
| 447 | } |
---|
| 448 | |
---|
[845] | 449 | bool Scantable::conformant( const Scantable& other ) |
---|
| 450 | { |
---|
| 451 | return this->getHeader().conformant(other.getHeader()); |
---|
| 452 | } |
---|
| 453 | |
---|
| 454 | |
---|
[50] | 455 | |
---|
[805] | 456 | std::string Scantable::formatSec(Double x) const |
---|
[206] | 457 | { |
---|
[105] | 458 | Double xcop = x; |
---|
| 459 | MVTime mvt(xcop/24./3600.); // make days |
---|
[365] | 460 | |
---|
[105] | 461 | if (x < 59.95) |
---|
[281] | 462 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
[745] | 463 | else if (x < 3599.95) |
---|
[281] | 464 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
| 465 | else { |
---|
| 466 | ostringstream oss; |
---|
| 467 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
| 468 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
| 469 | return String(oss); |
---|
[745] | 470 | } |
---|
[105] | 471 | }; |
---|
| 472 | |
---|
[805] | 473 | std::string Scantable::formatDirection(const MDirection& md) const |
---|
[281] | 474 | { |
---|
| 475 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
| 476 | Int prec = 7; |
---|
| 477 | |
---|
| 478 | MVAngle mvLon(t[0]); |
---|
| 479 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
[987] | 480 | uInt tp = md.getRef().getType(); |
---|
| 481 | if (tp == MDirection::GALACTIC || |
---|
| 482 | tp == MDirection::SUPERGAL ) { |
---|
| 483 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
| 484 | } |
---|
[281] | 485 | MVAngle mvLat(t[1]); |
---|
| 486 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
[380] | 487 | return sLon + String(" ") + sLat; |
---|
[281] | 488 | } |
---|
| 489 | |
---|
| 490 | |
---|
[805] | 491 | std::string Scantable::getFluxUnit() const |
---|
[206] | 492 | { |
---|
[847] | 493 | return table_.keywordSet().asString("FluxUnit"); |
---|
[206] | 494 | } |
---|
| 495 | |
---|
[805] | 496 | void Scantable::setFluxUnit(const std::string& unit) |
---|
[218] | 497 | { |
---|
| 498 | String tmp(unit); |
---|
| 499 | Unit tU(tmp); |
---|
| 500 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
| 501 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
| 502 | } else { |
---|
| 503 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
| 504 | } |
---|
| 505 | } |
---|
| 506 | |
---|
[805] | 507 | void Scantable::setInstrument(const std::string& name) |
---|
[236] | 508 | { |
---|
[805] | 509 | bool throwIt = true; |
---|
[996] | 510 | // create an Instrument to see if this is valid |
---|
| 511 | STAttr::convertInstrument(name, throwIt); |
---|
[236] | 512 | String nameU(name); |
---|
| 513 | nameU.upcase(); |
---|
| 514 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
| 515 | } |
---|
| 516 | |
---|
[1189] | 517 | void Scantable::setFeedType(const std::string& feedtype) |
---|
| 518 | { |
---|
| 519 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
| 520 | std::string msg = "Illegal feed type "+ feedtype; |
---|
| 521 | throw(casa::AipsError(msg)); |
---|
| 522 | } |
---|
| 523 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
| 524 | } |
---|
| 525 | |
---|
[1743] | 526 | MPosition Scantable::getAntennaPosition() const |
---|
[805] | 527 | { |
---|
| 528 | Vector<Double> antpos; |
---|
| 529 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
| 530 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
| 531 | return MPosition(mvpos); |
---|
| 532 | } |
---|
[281] | 533 | |
---|
[805] | 534 | void Scantable::makePersistent(const std::string& filename) |
---|
| 535 | { |
---|
| 536 | String inname(filename); |
---|
| 537 | Path path(inname); |
---|
[1111] | 538 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
[805] | 539 | inname = path.expandedName(); |
---|
[2030] | 540 | // 2011/03/04 TN |
---|
| 541 | // We can comment out this workaround since the essential bug is |
---|
| 542 | // fixed in casacore (r20889 in google code). |
---|
| 543 | table_.deepCopy(inname, Table::New); |
---|
| 544 | // // WORKAROUND !!! for Table bug |
---|
| 545 | // // Remove when fixed in casacore |
---|
| 546 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
| 547 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
| 548 | // tab.deepCopy(inname, Table::New); |
---|
| 549 | // tab.markForDelete(); |
---|
| 550 | // |
---|
| 551 | // } else { |
---|
| 552 | // table_.deepCopy(inname, Table::New); |
---|
| 553 | // } |
---|
[805] | 554 | } |
---|
| 555 | |
---|
[837] | 556 | int Scantable::nbeam( int scanno ) const |
---|
[805] | 557 | { |
---|
| 558 | if ( scanno < 0 ) { |
---|
| 559 | Int n; |
---|
| 560 | table_.keywordSet().get("nBeam",n); |
---|
| 561 | return int(n); |
---|
[105] | 562 | } else { |
---|
[805] | 563 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 564 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 565 | ROTableRow row(t); |
---|
| 566 | const TableRecord& rec = row.get(0); |
---|
| 567 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 568 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 569 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 570 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
[805] | 571 | return int(v.nelements()); |
---|
[105] | 572 | } |
---|
[805] | 573 | return 0; |
---|
| 574 | } |
---|
[455] | 575 | |
---|
[837] | 576 | int Scantable::nif( int scanno ) const |
---|
[805] | 577 | { |
---|
| 578 | if ( scanno < 0 ) { |
---|
| 579 | Int n; |
---|
| 580 | table_.keywordSet().get("nIF",n); |
---|
| 581 | return int(n); |
---|
| 582 | } else { |
---|
| 583 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 584 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 585 | ROTableRow row(t); |
---|
| 586 | const TableRecord& rec = row.get(0); |
---|
| 587 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 588 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 589 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 590 | if ( subt.nrow() == 0 ) return 0; |
---|
| 591 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
[805] | 592 | return int(v.nelements()); |
---|
[2] | 593 | } |
---|
[805] | 594 | return 0; |
---|
| 595 | } |
---|
[321] | 596 | |
---|
[837] | 597 | int Scantable::npol( int scanno ) const |
---|
[805] | 598 | { |
---|
| 599 | if ( scanno < 0 ) { |
---|
| 600 | Int n; |
---|
| 601 | table_.keywordSet().get("nPol",n); |
---|
| 602 | return n; |
---|
| 603 | } else { |
---|
| 604 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 605 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 606 | ROTableRow row(t); |
---|
| 607 | const TableRecord& rec = row.get(0); |
---|
| 608 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 609 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 610 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 611 | if ( subt.nrow() == 0 ) return 0; |
---|
| 612 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
[805] | 613 | return int(v.nelements()); |
---|
[321] | 614 | } |
---|
[805] | 615 | return 0; |
---|
[2] | 616 | } |
---|
[805] | 617 | |
---|
[845] | 618 | int Scantable::ncycle( int scanno ) const |
---|
[206] | 619 | { |
---|
[805] | 620 | if ( scanno < 0 ) { |
---|
[837] | 621 | Block<String> cols(2); |
---|
| 622 | cols[0] = "SCANNO"; |
---|
| 623 | cols[1] = "CYCLENO"; |
---|
| 624 | TableIterator it(table_, cols); |
---|
| 625 | int n = 0; |
---|
| 626 | while ( !it.pastEnd() ) { |
---|
| 627 | ++n; |
---|
[902] | 628 | ++it; |
---|
[837] | 629 | } |
---|
| 630 | return n; |
---|
[805] | 631 | } else { |
---|
[888] | 632 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 633 | ROTableRow row(t); |
---|
| 634 | const TableRecord& rec = row.get(0); |
---|
| 635 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 636 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 637 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
| 638 | if ( subt.nrow() == 0 ) return 0; |
---|
| 639 | return int(subt.nrow()); |
---|
[805] | 640 | } |
---|
| 641 | return 0; |
---|
[18] | 642 | } |
---|
[455] | 643 | |
---|
| 644 | |
---|
[845] | 645 | int Scantable::nrow( int scanno ) const |
---|
[805] | 646 | { |
---|
[845] | 647 | return int(table_.nrow()); |
---|
| 648 | } |
---|
| 649 | |
---|
| 650 | int Scantable::nchan( int ifno ) const |
---|
| 651 | { |
---|
| 652 | if ( ifno < 0 ) { |
---|
[805] | 653 | Int n; |
---|
| 654 | table_.keywordSet().get("nChan",n); |
---|
| 655 | return int(n); |
---|
| 656 | } else { |
---|
[1360] | 657 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
| 658 | // vary with these |
---|
[2244] | 659 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
[888] | 660 | if ( t.nrow() == 0 ) return 0; |
---|
| 661 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
[923] | 662 | return v.shape(0)(0); |
---|
[805] | 663 | } |
---|
| 664 | return 0; |
---|
[18] | 665 | } |
---|
[455] | 666 | |
---|
[1111] | 667 | int Scantable::nscan() const { |
---|
| 668 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
[1148] | 669 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
[1111] | 670 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 671 | return int(nout); |
---|
| 672 | } |
---|
| 673 | |
---|
[923] | 674 | int Scantable::getChannels(int whichrow) const |
---|
| 675 | { |
---|
| 676 | return specCol_.shape(whichrow)(0); |
---|
| 677 | } |
---|
[847] | 678 | |
---|
| 679 | int Scantable::getBeam(int whichrow) const |
---|
| 680 | { |
---|
| 681 | return beamCol_(whichrow); |
---|
| 682 | } |
---|
| 683 | |
---|
[1694] | 684 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
[1111] | 685 | { |
---|
| 686 | Vector<uInt> nos(col.getColumn()); |
---|
[1148] | 687 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 688 | nos.resize(n, True); |
---|
[1111] | 689 | std::vector<uint> stlout; |
---|
| 690 | nos.tovector(stlout); |
---|
| 691 | return stlout; |
---|
| 692 | } |
---|
| 693 | |
---|
[847] | 694 | int Scantable::getIF(int whichrow) const |
---|
| 695 | { |
---|
| 696 | return ifCol_(whichrow); |
---|
| 697 | } |
---|
| 698 | |
---|
| 699 | int Scantable::getPol(int whichrow) const |
---|
| 700 | { |
---|
| 701 | return polCol_(whichrow); |
---|
| 702 | } |
---|
| 703 | |
---|
[805] | 704 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
| 705 | { |
---|
[1947] | 706 | return formatTime(me, showdate, 0); |
---|
| 707 | } |
---|
| 708 | |
---|
| 709 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
| 710 | { |
---|
[805] | 711 | MVTime mvt(me.getValue()); |
---|
| 712 | if (showdate) |
---|
[1947] | 713 | //mvt.setFormat(MVTime::YMD); |
---|
| 714 | mvt.setFormat(MVTime::YMD, prec); |
---|
[805] | 715 | else |
---|
[1947] | 716 | //mvt.setFormat(MVTime::TIME); |
---|
| 717 | mvt.setFormat(MVTime::TIME, prec); |
---|
[805] | 718 | ostringstream oss; |
---|
| 719 | oss << mvt; |
---|
| 720 | return String(oss); |
---|
| 721 | } |
---|
[488] | 722 | |
---|
[805] | 723 | void Scantable::calculateAZEL() |
---|
| 724 | { |
---|
| 725 | MPosition mp = getAntennaPosition(); |
---|
| 726 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 727 | ostringstream oss; |
---|
| 728 | oss << "Computed azimuth/elevation using " << endl |
---|
| 729 | << mp << endl; |
---|
[996] | 730 | for (Int i=0; i<nrow(); ++i) { |
---|
[805] | 731 | MEpoch me = timeCol(i); |
---|
[987] | 732 | MDirection md = getDirection(i); |
---|
[805] | 733 | oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md) |
---|
| 734 | << endl << " => "; |
---|
| 735 | MeasFrame frame(mp, me); |
---|
| 736 | Vector<Double> azel = |
---|
| 737 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
| 738 | frame) |
---|
| 739 | )().getAngle("rad").getValue(); |
---|
[923] | 740 | azCol_.put(i,Float(azel[0])); |
---|
| 741 | elCol_.put(i,Float(azel[1])); |
---|
[805] | 742 | oss << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
| 743 | << azel[1]/C::pi*180.0 << " (deg)" << endl; |
---|
[16] | 744 | } |
---|
[805] | 745 | pushLog(String(oss)); |
---|
| 746 | } |
---|
[89] | 747 | |
---|
[1819] | 748 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 749 | { |
---|
| 750 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
| 751 | Vector<uChar> flgs = flagsCol_(i); |
---|
| 752 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
| 753 | flagsCol_.put(i, flgs); |
---|
| 754 | } |
---|
| 755 | } |
---|
| 756 | |
---|
| 757 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 758 | { |
---|
| 759 | Vector<uChar> flags; |
---|
| 760 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 761 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
| 762 | Vector<Bool> bflag(flags.shape()); |
---|
| 763 | convertArray(bflag, flags); |
---|
| 764 | //bflag = !bflag; |
---|
| 765 | |
---|
| 766 | std::vector<bool> mask; |
---|
| 767 | bflag.tovector(mask); |
---|
| 768 | return mask; |
---|
| 769 | } |
---|
| 770 | |
---|
| 771 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
| 772 | Vector<uChar> flgs) |
---|
| 773 | { |
---|
| 774 | Vector<Float> spcs = specCol_(whichrow); |
---|
[2348] | 775 | uInt nchannel = spcs.nelements(); |
---|
[1819] | 776 | if (spcs.nelements() != nchannel) { |
---|
| 777 | throw(AipsError("Data has incorrect number of channels")); |
---|
| 778 | } |
---|
| 779 | uChar userflag = 1 << 7; |
---|
| 780 | if (unflag) { |
---|
| 781 | userflag = 0 << 7; |
---|
| 782 | } |
---|
| 783 | if (clipoutside) { |
---|
| 784 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 785 | Float spc = spcs(j); |
---|
| 786 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
| 787 | flgs(j) = userflag; |
---|
| 788 | } |
---|
| 789 | } |
---|
| 790 | } else { |
---|
| 791 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 792 | Float spc = spcs(j); |
---|
| 793 | if ((spc < uthres) && (spc > dthres)) { |
---|
| 794 | flgs(j) = userflag; |
---|
| 795 | } |
---|
| 796 | } |
---|
| 797 | } |
---|
| 798 | } |
---|
| 799 | |
---|
[1994] | 800 | |
---|
| 801 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
[1333] | 802 | std::vector<bool>::const_iterator it; |
---|
| 803 | uInt ntrue = 0; |
---|
[1994] | 804 | if (whichrow >= int(table_.nrow()) ) { |
---|
| 805 | throw(AipsError("Invalid row number")); |
---|
| 806 | } |
---|
[1333] | 807 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 808 | if ( *it ) { |
---|
| 809 | ntrue++; |
---|
| 810 | } |
---|
| 811 | } |
---|
[1994] | 812 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
| 813 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
[1000] | 814 | throw(AipsError("Trying to flag whole scantable.")); |
---|
[1994] | 815 | uChar userflag = 1 << 7; |
---|
| 816 | if ( unflag ) { |
---|
| 817 | userflag = 0 << 7; |
---|
| 818 | } |
---|
| 819 | if (whichrow > -1 ) { |
---|
| 820 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
| 821 | } else { |
---|
[1000] | 822 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
[1994] | 823 | applyChanFlag(i, msk, userflag); |
---|
[1000] | 824 | } |
---|
[1994] | 825 | } |
---|
| 826 | } |
---|
| 827 | |
---|
| 828 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
| 829 | { |
---|
| 830 | if (whichrow >= table_.nrow() ) { |
---|
| 831 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
| 832 | } |
---|
| 833 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
| 834 | if ( msk.size() == 0 ) { |
---|
| 835 | flgs = flagval; |
---|
| 836 | flagsCol_.put(whichrow, flgs); |
---|
[1000] | 837 | return; |
---|
| 838 | } |
---|
[2348] | 839 | if ( int(msk.size()) != nchan( getIF(whichrow) ) ) { |
---|
[1000] | 840 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
| 841 | } |
---|
[1994] | 842 | if ( flgs.nelements() != msk.size() ) { |
---|
| 843 | throw(AipsError("Mask has incorrect number of channels." |
---|
| 844 | " Probably varying with IF. Please flag per IF")); |
---|
| 845 | } |
---|
| 846 | std::vector<bool>::const_iterator it; |
---|
| 847 | uInt j = 0; |
---|
| 848 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 849 | if ( *it ) { |
---|
| 850 | flgs(j) = flagval; |
---|
[1000] | 851 | } |
---|
[1994] | 852 | ++j; |
---|
[1000] | 853 | } |
---|
[1994] | 854 | flagsCol_.put(whichrow, flgs); |
---|
[865] | 855 | } |
---|
| 856 | |
---|
[1819] | 857 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
| 858 | { |
---|
| 859 | if ( selector_.empty() && (rows.size() == table_.nrow()) ) |
---|
| 860 | throw(AipsError("Trying to flag whole scantable.")); |
---|
| 861 | |
---|
| 862 | uInt rowflag = (unflag ? 0 : 1); |
---|
| 863 | std::vector<uInt>::const_iterator it; |
---|
| 864 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
| 865 | flagrowCol_.put(*it, rowflag); |
---|
| 866 | } |
---|
| 867 | |
---|
[805] | 868 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
| 869 | { |
---|
| 870 | Vector<uChar> flags; |
---|
| 871 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 872 | Vector<Bool> bflag(flags.shape()); |
---|
| 873 | convertArray(bflag, flags); |
---|
| 874 | bflag = !bflag; |
---|
| 875 | std::vector<bool> mask; |
---|
| 876 | bflag.tovector(mask); |
---|
| 877 | return mask; |
---|
| 878 | } |
---|
[89] | 879 | |
---|
[896] | 880 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
[902] | 881 | const std::string& poltype ) const |
---|
[805] | 882 | { |
---|
[905] | 883 | String ptype = poltype; |
---|
| 884 | if (poltype == "" ) ptype = getPolType(); |
---|
[902] | 885 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
| 886 | throw(AipsError("Illegal row number.")); |
---|
[896] | 887 | std::vector<float> out; |
---|
[805] | 888 | Vector<Float> arr; |
---|
[896] | 889 | uInt requestedpol = polCol_(whichrow); |
---|
| 890 | String basetype = getPolType(); |
---|
[905] | 891 | if ( ptype == basetype ) { |
---|
[896] | 892 | specCol_.get(whichrow, arr); |
---|
| 893 | } else { |
---|
[1598] | 894 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
[1586] | 895 | basetype)); |
---|
[1334] | 896 | uInt row = uInt(whichrow); |
---|
| 897 | stpol->setSpectra(getPolMatrix(row)); |
---|
[2047] | 898 | Float fang,fhand; |
---|
[1586] | 899 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
[1334] | 900 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
[1586] | 901 | stpol->setPhaseCorrections(fang, fhand); |
---|
[1334] | 902 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
[896] | 903 | } |
---|
[902] | 904 | if ( arr.nelements() == 0 ) |
---|
| 905 | pushLog("Not enough polarisations present to do the conversion."); |
---|
[805] | 906 | arr.tovector(out); |
---|
| 907 | return out; |
---|
[89] | 908 | } |
---|
[212] | 909 | |
---|
[1360] | 910 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
[884] | 911 | int whichrow ) |
---|
| 912 | { |
---|
| 913 | Vector<Float> spectrum(spec); |
---|
| 914 | Vector<Float> arr; |
---|
| 915 | specCol_.get(whichrow, arr); |
---|
| 916 | if ( spectrum.nelements() != arr.nelements() ) |
---|
[896] | 917 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
[884] | 918 | specCol_.put(whichrow, spectrum); |
---|
| 919 | } |
---|
| 920 | |
---|
| 921 | |
---|
[805] | 922 | String Scantable::generateName() |
---|
[745] | 923 | { |
---|
[805] | 924 | return (File::newUniqueName("./","temp")).baseName(); |
---|
[212] | 925 | } |
---|
| 926 | |
---|
[805] | 927 | const casa::Table& Scantable::table( ) const |
---|
[212] | 928 | { |
---|
[805] | 929 | return table_; |
---|
[212] | 930 | } |
---|
| 931 | |
---|
[805] | 932 | casa::Table& Scantable::table( ) |
---|
[386] | 933 | { |
---|
[805] | 934 | return table_; |
---|
[386] | 935 | } |
---|
| 936 | |
---|
[896] | 937 | std::string Scantable::getPolType() const |
---|
| 938 | { |
---|
| 939 | return table_.keywordSet().asString("POLTYPE"); |
---|
| 940 | } |
---|
| 941 | |
---|
[805] | 942 | void Scantable::unsetSelection() |
---|
[380] | 943 | { |
---|
[805] | 944 | table_ = originalTable_; |
---|
[847] | 945 | attach(); |
---|
[805] | 946 | selector_.reset(); |
---|
[380] | 947 | } |
---|
[386] | 948 | |
---|
[805] | 949 | void Scantable::setSelection( const STSelector& selection ) |
---|
[430] | 950 | { |
---|
[805] | 951 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
| 952 | if ( tab.nrow() == 0 ) { |
---|
| 953 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
| 954 | } |
---|
| 955 | table_ = tab; |
---|
[847] | 956 | attach(); |
---|
[2084] | 957 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
| 958 | // vector<uint> selectedIFs = getIFNos() ; |
---|
| 959 | // Int newnIF = selectedIFs.size() ; |
---|
| 960 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
| 961 | // if ( newnIF != 0 ) { |
---|
| 962 | // Int newnChan = 0 ; |
---|
| 963 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
| 964 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
| 965 | // if ( newnChan > nChan ) |
---|
| 966 | // newnChan = nChan ; |
---|
| 967 | // } |
---|
| 968 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
| 969 | // } |
---|
| 970 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
[805] | 971 | selector_ = selection; |
---|
[430] | 972 | } |
---|
| 973 | |
---|
[2111] | 974 | |
---|
[2163] | 975 | std::string Scantable::headerSummary() |
---|
[447] | 976 | { |
---|
[805] | 977 | // Format header info |
---|
[2111] | 978 | // STHeader sdh; |
---|
| 979 | // sdh = getHeader(); |
---|
| 980 | // sdh.print(); |
---|
[805] | 981 | ostringstream oss; |
---|
| 982 | oss.flags(std::ios_base::left); |
---|
[2290] | 983 | String tmp; |
---|
| 984 | // Project |
---|
| 985 | table_.keywordSet().get("Project", tmp); |
---|
| 986 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 987 | // Observation date |
---|
| 988 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 989 | // Observer |
---|
| 990 | oss << setw(15) << "Observer:" |
---|
| 991 | << table_.keywordSet().asString("Observer") << endl; |
---|
| 992 | // Antenna Name |
---|
| 993 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 994 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 995 | // Obs type |
---|
| 996 | table_.keywordSet().get("Obstype", tmp); |
---|
| 997 | // Records (nrow) |
---|
| 998 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
| 999 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1000 | // Beams, IFs, Polarizations, and Channels |
---|
[805] | 1001 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1002 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
[896] | 1003 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1004 | << "(" << getPolType() << ")" << endl |
---|
[1694] | 1005 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[2290] | 1006 | // Flux unit |
---|
| 1007 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1008 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
| 1009 | // Abscissa Unit |
---|
| 1010 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
| 1011 | // Selection |
---|
| 1012 | oss << selector_.print() << endl; |
---|
| 1013 | |
---|
| 1014 | return String(oss); |
---|
| 1015 | } |
---|
| 1016 | |
---|
| 1017 | void Scantable::summary( const std::string& filename ) |
---|
| 1018 | { |
---|
| 1019 | ostringstream oss; |
---|
| 1020 | ofstream ofs; |
---|
| 1021 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1022 | |
---|
| 1023 | if (filename != "") |
---|
| 1024 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1025 | |
---|
| 1026 | oss << endl; |
---|
| 1027 | oss << asap::SEPERATOR << endl; |
---|
| 1028 | oss << " Scan Table Summary" << endl; |
---|
| 1029 | oss << asap::SEPERATOR << endl; |
---|
| 1030 | |
---|
| 1031 | // Format header info |
---|
| 1032 | oss << headerSummary(); |
---|
| 1033 | oss << endl; |
---|
| 1034 | |
---|
| 1035 | if (table_.nrow() <= 0){ |
---|
| 1036 | oss << asap::SEPERATOR << endl; |
---|
| 1037 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
| 1038 | oss << asap::SEPERATOR << endl; |
---|
| 1039 | |
---|
| 1040 | ols << String(oss) << LogIO::POST; |
---|
| 1041 | if (ofs) { |
---|
| 1042 | ofs << String(oss) << flush; |
---|
| 1043 | ofs.close(); |
---|
| 1044 | } |
---|
| 1045 | return; |
---|
| 1046 | } |
---|
| 1047 | |
---|
| 1048 | |
---|
| 1049 | |
---|
| 1050 | // main table |
---|
| 1051 | String dirtype = "Position (" |
---|
| 1052 | + getDirectionRefString() |
---|
| 1053 | + ")"; |
---|
| 1054 | oss.flags(std::ios_base::left); |
---|
| 1055 | oss << setw(5) << "Scan" |
---|
| 1056 | << setw(15) << "Source" |
---|
| 1057 | << setw(35) << "Time range" |
---|
| 1058 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
| 1059 | << setw(7) << "Record" |
---|
| 1060 | << setw(8) << "SrcType" |
---|
| 1061 | << setw(8) << "FreqIDs" |
---|
| 1062 | << setw(7) << "MolIDs" << endl; |
---|
| 1063 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
| 1064 | << setw(23) << dirtype << endl; |
---|
| 1065 | |
---|
| 1066 | oss << asap::SEPERATOR << endl; |
---|
| 1067 | |
---|
| 1068 | // Flush summary and clear up the string |
---|
| 1069 | ols << String(oss) << LogIO::POST; |
---|
| 1070 | if (ofs) ofs << String(oss) << flush; |
---|
| 1071 | oss.str(""); |
---|
| 1072 | oss.clear(); |
---|
| 1073 | |
---|
| 1074 | |
---|
| 1075 | // Get Freq_ID map |
---|
| 1076 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
| 1077 | Int nfid = ftabIds.nrow(); |
---|
| 1078 | if (nfid <= 0){ |
---|
| 1079 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
| 1080 | oss << asap::SEPERATOR << endl; |
---|
| 1081 | |
---|
| 1082 | ols << String(oss) << LogIO::POST; |
---|
| 1083 | if (ofs) { |
---|
| 1084 | ofs << String(oss) << flush; |
---|
| 1085 | ofs.close(); |
---|
| 1086 | } |
---|
| 1087 | return; |
---|
| 1088 | } |
---|
| 1089 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
| 1090 | // the orders are identical to ID in FREQ subtable |
---|
| 1091 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
| 1092 | Vector<Int> fIdchans(nfid,-1); |
---|
| 1093 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
| 1094 | for (Int i=0; i < nfid; i++){ |
---|
| 1095 | // fidMap[freqId] returns row number in FREQ subtable |
---|
| 1096 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
| 1097 | ifNos[i] = Vector<uInt>(); |
---|
| 1098 | polNos[i] = Vector<uInt>(); |
---|
| 1099 | } |
---|
| 1100 | |
---|
| 1101 | TableIterator iter(table_, "SCANNO"); |
---|
| 1102 | |
---|
| 1103 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
| 1104 | Vector<uInt> freqids; |
---|
| 1105 | Vector<uInt> molids; |
---|
| 1106 | Vector<uInt> beamids(1,0); |
---|
| 1107 | Vector<MDirection> beamDirs; |
---|
| 1108 | Vector<Int> stypeids(1,0); |
---|
| 1109 | Vector<String> stypestrs; |
---|
| 1110 | Int nfreq(1); |
---|
| 1111 | Int nmol(1); |
---|
| 1112 | uInt nbeam(1); |
---|
| 1113 | uInt nstype(1); |
---|
| 1114 | |
---|
| 1115 | Double btime(0.0), etime(0.0); |
---|
| 1116 | Double meanIntTim(0.0); |
---|
| 1117 | |
---|
| 1118 | uInt currFreqId(0), ftabRow(0); |
---|
| 1119 | Int iflen(0), pollen(0); |
---|
| 1120 | |
---|
| 1121 | while (!iter.pastEnd()) { |
---|
| 1122 | Table subt = iter.table(); |
---|
| 1123 | uInt snrow = subt.nrow(); |
---|
| 1124 | ROTableRow row(subt); |
---|
| 1125 | const TableRecord& rec = row.get(0); |
---|
| 1126 | |
---|
| 1127 | // relevant columns |
---|
| 1128 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
| 1129 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
| 1130 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
| 1131 | |
---|
| 1132 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
| 1133 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
| 1134 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
| 1135 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
| 1136 | |
---|
| 1137 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
| 1138 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
| 1139 | |
---|
| 1140 | |
---|
| 1141 | // Times |
---|
| 1142 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
| 1143 | minMax(btime, etime, mjdCol.getColumn()); |
---|
| 1144 | etime += meanIntTim/C::day; |
---|
| 1145 | |
---|
| 1146 | // MOLECULE_ID and FREQ_ID |
---|
| 1147 | molids = getNumbers(molIdCol); |
---|
| 1148 | molids.shape(nmol); |
---|
| 1149 | |
---|
| 1150 | freqids = getNumbers(freqIdCol); |
---|
| 1151 | freqids.shape(nfreq); |
---|
| 1152 | |
---|
| 1153 | // Add first beamid, and srcNames |
---|
| 1154 | beamids.resize(1,False); |
---|
| 1155 | beamDirs.resize(1,False); |
---|
| 1156 | beamids(0)=beamCol(0); |
---|
| 1157 | beamDirs(0)=dirCol(0); |
---|
| 1158 | nbeam = 1; |
---|
| 1159 | |
---|
| 1160 | stypeids.resize(1,False); |
---|
| 1161 | stypeids(0)=stypeCol(0); |
---|
| 1162 | nstype = 1; |
---|
| 1163 | |
---|
| 1164 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1165 | currFreqId=freqIdCol(0); |
---|
| 1166 | ftabRow = fidMap[currFreqId]; |
---|
| 1167 | // Assumes an identical number of channels per FREQ_ID |
---|
| 1168 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1169 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1170 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
| 1171 | } |
---|
| 1172 | // Should keep ifNos and polNos form the previous SCANNO |
---|
| 1173 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
| 1174 | ifNos[ftabRow].shape(iflen); |
---|
| 1175 | iflen++; |
---|
| 1176 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1177 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
| 1178 | } |
---|
| 1179 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
| 1180 | polNos[ftabRow].shape(pollen); |
---|
| 1181 | pollen++; |
---|
| 1182 | polNos[ftabRow].resize(pollen,True); |
---|
| 1183 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
| 1184 | } |
---|
| 1185 | |
---|
| 1186 | for (uInt i=1; i < snrow; i++){ |
---|
| 1187 | // Need to list BEAMNO and DIRECTION in the same order |
---|
| 1188 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
| 1189 | nbeam++; |
---|
| 1190 | beamids.resize(nbeam,True); |
---|
| 1191 | beamids(nbeam-1)=beamCol(i); |
---|
| 1192 | beamDirs.resize(nbeam,True); |
---|
| 1193 | beamDirs(nbeam-1)=dirCol(i); |
---|
| 1194 | } |
---|
| 1195 | |
---|
| 1196 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
| 1197 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
| 1198 | nstype++; |
---|
| 1199 | stypeids.resize(nstype,True); |
---|
| 1200 | stypeids(nstype-1)=stypeCol(i); |
---|
| 1201 | } |
---|
| 1202 | |
---|
| 1203 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1204 | currFreqId=freqIdCol(i); |
---|
| 1205 | ftabRow = fidMap[currFreqId]; |
---|
| 1206 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1207 | const TableRecord& rec = row.get(i); |
---|
| 1208 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1209 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
| 1210 | } |
---|
| 1211 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
| 1212 | ifNos[ftabRow].shape(iflen); |
---|
| 1213 | iflen++; |
---|
| 1214 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1215 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
| 1216 | } |
---|
| 1217 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
| 1218 | polNos[ftabRow].shape(pollen); |
---|
| 1219 | pollen++; |
---|
| 1220 | polNos[ftabRow].resize(pollen,True); |
---|
| 1221 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
| 1222 | } |
---|
| 1223 | } // end of row iteration |
---|
| 1224 | |
---|
| 1225 | stypestrs.resize(nstype,False); |
---|
| 1226 | for (uInt j=0; j < nstype; j++) |
---|
| 1227 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
| 1228 | |
---|
| 1229 | // Format Scan summary |
---|
| 1230 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1231 | << std::left << setw(1) << "" |
---|
| 1232 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1233 | << setw(21) << MVTime(btime).string(MVTime::YMD,7) |
---|
| 1234 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7) |
---|
| 1235 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
| 1236 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
| 1237 | << std::left << stypestrs << setw(1) << "" |
---|
| 1238 | << freqids << setw(1) << "" |
---|
| 1239 | << molids << endl; |
---|
| 1240 | // Format Beam summary |
---|
| 1241 | for (uInt j=0; j < nbeam; j++) { |
---|
| 1242 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
| 1243 | << formatDirection(beamDirs(j)) << endl; |
---|
| 1244 | } |
---|
| 1245 | // Flush summary every scan and clear up the string |
---|
| 1246 | ols << String(oss) << LogIO::POST; |
---|
| 1247 | if (ofs) ofs << String(oss) << flush; |
---|
| 1248 | oss.str(""); |
---|
| 1249 | oss.clear(); |
---|
| 1250 | |
---|
| 1251 | ++iter; |
---|
| 1252 | } // end of scan iteration |
---|
| 1253 | oss << asap::SEPERATOR << endl; |
---|
| 1254 | |
---|
| 1255 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
| 1256 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
| 1257 | oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
| 1258 | << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
| 1259 | << setw(8) << "Frame" |
---|
| 1260 | << setw(16) << "RefVal" |
---|
| 1261 | << setw(7) << "RefPix" |
---|
| 1262 | << setw(15) << "Increment" |
---|
| 1263 | << setw(9) << "Channels" |
---|
| 1264 | << setw(6) << "POLNOs" << endl; |
---|
| 1265 | Int tmplen; |
---|
| 1266 | for (Int i=0; i < nfid; i++){ |
---|
| 1267 | // List row=i of FREQUENCIES subtable |
---|
| 1268 | ifNos[i].shape(tmplen); |
---|
| 1269 | if (tmplen == 1) { |
---|
| 1270 | oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
| 1271 | << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
| 1272 | << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
| 1273 | << setw(2) << "" |
---|
| 1274 | << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
| 1275 | << std::left << polNos[i] << endl; |
---|
| 1276 | } else if (tmplen > 0 ) { |
---|
| 1277 | // You shouldn't come here |
---|
| 1278 | oss << std::left |
---|
| 1279 | << "Multiple IFNOs in FREQ_ID = " << ftabIds(i) |
---|
| 1280 | << " !!!" << endl; |
---|
| 1281 | } |
---|
| 1282 | } |
---|
| 1283 | oss << asap::SEPERATOR << endl; |
---|
| 1284 | |
---|
| 1285 | // List MOLECULES Table (currently lists all rows) |
---|
| 1286 | oss << "MOLECULES: " << endl; |
---|
| 1287 | if (molecules().nrow() <= 0) { |
---|
| 1288 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
| 1289 | } else { |
---|
| 1290 | ROTableRow row(molecules().table()); |
---|
| 1291 | oss << std::right << setw(5) << "ID" |
---|
| 1292 | << std::left << setw(3) << "" |
---|
| 1293 | << setw(18) << "RestFreq" |
---|
| 1294 | << setw(15) << "Name" << endl; |
---|
| 1295 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
| 1296 | const TableRecord& rec=row.get(i); |
---|
| 1297 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
| 1298 | << std::left << setw(3) << "" |
---|
| 1299 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
| 1300 | << rec.asArrayString("NAME") << endl; |
---|
| 1301 | } |
---|
| 1302 | } |
---|
| 1303 | oss << asap::SEPERATOR << endl; |
---|
| 1304 | ols << String(oss) << LogIO::POST; |
---|
| 1305 | if (ofs) { |
---|
| 1306 | ofs << String(oss) << flush; |
---|
| 1307 | ofs.close(); |
---|
| 1308 | } |
---|
| 1309 | // return String(oss); |
---|
| 1310 | } |
---|
| 1311 | |
---|
| 1312 | |
---|
| 1313 | std::string Scantable::oldheaderSummary() |
---|
| 1314 | { |
---|
| 1315 | // Format header info |
---|
| 1316 | // STHeader sdh; |
---|
| 1317 | // sdh = getHeader(); |
---|
| 1318 | // sdh.print(); |
---|
| 1319 | ostringstream oss; |
---|
| 1320 | oss.flags(std::ios_base::left); |
---|
| 1321 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1322 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
| 1323 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1324 | << "(" << getPolType() << ")" << endl |
---|
| 1325 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[805] | 1326 | String tmp; |
---|
[860] | 1327 | oss << setw(15) << "Observer:" |
---|
| 1328 | << table_.keywordSet().asString("Observer") << endl; |
---|
[805] | 1329 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1330 | table_.keywordSet().get("Project", tmp); |
---|
| 1331 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1332 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1333 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1334 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1335 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1336 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1337 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
[1819] | 1338 | int nid = moleculeTable_.nrow(); |
---|
| 1339 | Bool firstline = True; |
---|
[805] | 1340 | oss << setw(15) << "Rest Freqs:"; |
---|
[1819] | 1341 | for (int i=0; i<nid; i++) { |
---|
[2244] | 1342 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
[1819] | 1343 | if (t.nrow() > 0) { |
---|
| 1344 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
| 1345 | if (vec.nelements() > 0) { |
---|
| 1346 | if (firstline) { |
---|
| 1347 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1348 | firstline=False; |
---|
| 1349 | } |
---|
| 1350 | else{ |
---|
| 1351 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1352 | } |
---|
| 1353 | } else { |
---|
| 1354 | oss << "none" << endl; |
---|
| 1355 | } |
---|
| 1356 | } |
---|
[805] | 1357 | } |
---|
[941] | 1358 | |
---|
| 1359 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
[805] | 1360 | oss << selector_.print() << endl; |
---|
[2111] | 1361 | return String(oss); |
---|
| 1362 | } |
---|
| 1363 | |
---|
[2286] | 1364 | //std::string Scantable::summary( const std::string& filename ) |
---|
[2290] | 1365 | void Scantable::oldsummary( const std::string& filename ) |
---|
[2111] | 1366 | { |
---|
| 1367 | ostringstream oss; |
---|
[2286] | 1368 | ofstream ofs; |
---|
| 1369 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1370 | |
---|
| 1371 | if (filename != "") |
---|
| 1372 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1373 | |
---|
[805] | 1374 | oss << endl; |
---|
[2111] | 1375 | oss << asap::SEPERATOR << endl; |
---|
| 1376 | oss << " Scan Table Summary" << endl; |
---|
| 1377 | oss << asap::SEPERATOR << endl; |
---|
| 1378 | |
---|
| 1379 | // Format header info |
---|
[2290] | 1380 | oss << oldheaderSummary(); |
---|
[2111] | 1381 | oss << endl; |
---|
| 1382 | |
---|
[805] | 1383 | // main table |
---|
| 1384 | String dirtype = "Position (" |
---|
[987] | 1385 | + getDirectionRefString() |
---|
[805] | 1386 | + ")"; |
---|
[2111] | 1387 | oss.flags(std::ios_base::left); |
---|
[941] | 1388 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
[2005] | 1389 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
| 1390 | << setw(15) << "Source Type" << endl; |
---|
[941] | 1391 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
[1694] | 1392 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
[805] | 1393 | << setw(8) << "Frame" << setw(16) |
---|
[1694] | 1394 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
| 1395 | << setw(7) << "Channels" |
---|
| 1396 | << endl; |
---|
[805] | 1397 | oss << asap::SEPERATOR << endl; |
---|
[2286] | 1398 | |
---|
| 1399 | // Flush summary and clear up the string |
---|
| 1400 | ols << String(oss) << LogIO::POST; |
---|
| 1401 | if (ofs) ofs << String(oss) << flush; |
---|
| 1402 | oss.str(""); |
---|
| 1403 | oss.clear(); |
---|
| 1404 | |
---|
[805] | 1405 | TableIterator iter(table_, "SCANNO"); |
---|
| 1406 | while (!iter.pastEnd()) { |
---|
| 1407 | Table subt = iter.table(); |
---|
| 1408 | ROTableRow row(subt); |
---|
| 1409 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
| 1410 | const TableRecord& rec = row.get(0); |
---|
| 1411 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1412 | << std::left << setw(1) << "" |
---|
| 1413 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1414 | << setw(10) << formatTime(timeCol(0), false); |
---|
| 1415 | // count the cycles in the scan |
---|
| 1416 | TableIterator cyciter(subt, "CYCLENO"); |
---|
| 1417 | int nint = 0; |
---|
| 1418 | while (!cyciter.pastEnd()) { |
---|
| 1419 | ++nint; |
---|
| 1420 | ++cyciter; |
---|
| 1421 | } |
---|
| 1422 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
[2005] | 1423 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
| 1424 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
[447] | 1425 | |
---|
[805] | 1426 | TableIterator biter(subt, "BEAMNO"); |
---|
| 1427 | while (!biter.pastEnd()) { |
---|
| 1428 | Table bsubt = biter.table(); |
---|
| 1429 | ROTableRow brow(bsubt); |
---|
| 1430 | const TableRecord& brec = brow.get(0); |
---|
[1000] | 1431 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
[941] | 1432 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
[987] | 1433 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
[805] | 1434 | TableIterator iiter(bsubt, "IFNO"); |
---|
| 1435 | while (!iiter.pastEnd()) { |
---|
| 1436 | Table isubt = iiter.table(); |
---|
| 1437 | ROTableRow irow(isubt); |
---|
| 1438 | const TableRecord& irec = irow.get(0); |
---|
[1694] | 1439 | oss << setw(9) << ""; |
---|
[941] | 1440 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
[1694] | 1441 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
| 1442 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
[1375] | 1443 | << endl; |
---|
[447] | 1444 | |
---|
[805] | 1445 | ++iiter; |
---|
| 1446 | } |
---|
| 1447 | ++biter; |
---|
| 1448 | } |
---|
[2286] | 1449 | // Flush summary every scan and clear up the string |
---|
| 1450 | ols << String(oss) << LogIO::POST; |
---|
| 1451 | if (ofs) ofs << String(oss) << flush; |
---|
| 1452 | oss.str(""); |
---|
| 1453 | oss.clear(); |
---|
| 1454 | |
---|
[805] | 1455 | ++iter; |
---|
[447] | 1456 | } |
---|
[2286] | 1457 | oss << asap::SEPERATOR << endl; |
---|
| 1458 | ols << String(oss) << LogIO::POST; |
---|
| 1459 | if (ofs) { |
---|
[2290] | 1460 | ofs << String(oss) << flush; |
---|
[2286] | 1461 | ofs.close(); |
---|
| 1462 | } |
---|
| 1463 | // return String(oss); |
---|
[447] | 1464 | } |
---|
| 1465 | |
---|
[1947] | 1466 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
| 1467 | // { |
---|
| 1468 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 1469 | // MEpoch me; |
---|
| 1470 | // if (whichrow > -1) { |
---|
| 1471 | // me = timeCol(uInt(whichrow)); |
---|
| 1472 | // } else { |
---|
| 1473 | // Double tm; |
---|
| 1474 | // table_.keywordSet().get("UTC",tm); |
---|
| 1475 | // me = MEpoch(MVEpoch(tm)); |
---|
| 1476 | // } |
---|
| 1477 | // return formatTime(me, showdate); |
---|
| 1478 | // } |
---|
| 1479 | |
---|
| 1480 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
[777] | 1481 | { |
---|
[805] | 1482 | MEpoch me; |
---|
[1947] | 1483 | me = getEpoch(whichrow); |
---|
| 1484 | return formatTime(me, showdate, prec); |
---|
[777] | 1485 | } |
---|
[805] | 1486 | |
---|
[1411] | 1487 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
| 1488 | { |
---|
| 1489 | if (whichrow > -1) { |
---|
| 1490 | return timeCol_(uInt(whichrow)); |
---|
| 1491 | } else { |
---|
| 1492 | Double tm; |
---|
| 1493 | table_.keywordSet().get("UTC",tm); |
---|
[1598] | 1494 | return MEpoch(MVEpoch(tm)); |
---|
[1411] | 1495 | } |
---|
| 1496 | } |
---|
| 1497 | |
---|
[1068] | 1498 | std::string Scantable::getDirectionString(int whichrow) const |
---|
| 1499 | { |
---|
| 1500 | return formatDirection(getDirection(uInt(whichrow))); |
---|
| 1501 | } |
---|
| 1502 | |
---|
[1598] | 1503 | |
---|
| 1504 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
| 1505 | const MPosition& mp = getAntennaPosition(); |
---|
| 1506 | const MDirection& md = getDirection(whichrow); |
---|
| 1507 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1508 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
| 1509 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[2346] | 1510 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
[1598] | 1511 | mfreqidCol_(whichrow)); |
---|
| 1512 | } |
---|
| 1513 | |
---|
[1360] | 1514 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
[865] | 1515 | { |
---|
[1507] | 1516 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
[865] | 1517 | std::vector<double> stlout; |
---|
| 1518 | int nchan = specCol_(whichrow).nelements(); |
---|
[2346] | 1519 | String us = freqTable_.getUnitString(); |
---|
[865] | 1520 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
| 1521 | for (int i=0; i<nchan; ++i) { |
---|
| 1522 | stlout.push_back(double(i)); |
---|
| 1523 | } |
---|
| 1524 | return stlout; |
---|
| 1525 | } |
---|
[1598] | 1526 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
[865] | 1527 | Vector<Double> pixel(nchan); |
---|
| 1528 | Vector<Double> world; |
---|
| 1529 | indgen(pixel); |
---|
| 1530 | if ( Unit(us) == Unit("Hz") ) { |
---|
| 1531 | for ( int i=0; i < nchan; ++i) { |
---|
| 1532 | Double world; |
---|
| 1533 | spc.toWorld(world, pixel[i]); |
---|
| 1534 | stlout.push_back(double(world)); |
---|
| 1535 | } |
---|
| 1536 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
| 1537 | Vector<Double> world; |
---|
| 1538 | spc.pixelToVelocity(world, pixel); |
---|
| 1539 | world.tovector(stlout); |
---|
| 1540 | } |
---|
| 1541 | return stlout; |
---|
| 1542 | } |
---|
[1360] | 1543 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
[987] | 1544 | { |
---|
| 1545 | MDirection::Types mdt; |
---|
| 1546 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
| 1547 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1548 | } |
---|
| 1549 | if ( refstr == "" ) { |
---|
| 1550 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1551 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
| 1552 | } else { |
---|
| 1553 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
| 1554 | } |
---|
| 1555 | } |
---|
[865] | 1556 | |
---|
[1360] | 1557 | std::string Scantable::getDirectionRefString( ) const |
---|
[987] | 1558 | { |
---|
| 1559 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1560 | } |
---|
| 1561 | |
---|
| 1562 | MDirection Scantable::getDirection(int whichrow ) const |
---|
| 1563 | { |
---|
| 1564 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1565 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1566 | if ( usertype != type ) { |
---|
| 1567 | MDirection::Types mdt; |
---|
| 1568 | if (!MDirection::getType(mdt, usertype)) { |
---|
| 1569 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1570 | } |
---|
| 1571 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
| 1572 | } else { |
---|
| 1573 | return dirCol_(uInt(whichrow)); |
---|
| 1574 | } |
---|
| 1575 | } |
---|
| 1576 | |
---|
[847] | 1577 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
| 1578 | { |
---|
[996] | 1579 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
[847] | 1580 | const MPosition& mp = getAntennaPosition(); |
---|
[987] | 1581 | const MDirection& md = getDirection(whichrow); |
---|
[847] | 1582 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1583 | //const Double& rf = mmolidCol_(whichrow); |
---|
| 1584 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[847] | 1585 | SpectralCoordinate spc = |
---|
[2346] | 1586 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
[847] | 1587 | |
---|
| 1588 | String s = "Channel"; |
---|
[2346] | 1589 | Unit u = Unit(freqTable_.getUnitString()); |
---|
[847] | 1590 | if (u == Unit("km/s")) { |
---|
[1170] | 1591 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
[847] | 1592 | } else if (u == Unit("Hz")) { |
---|
| 1593 | Vector<String> wau(1);wau = u.getName(); |
---|
| 1594 | spc.setWorldAxisUnits(wau); |
---|
[1170] | 1595 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
[847] | 1596 | } |
---|
| 1597 | return s; |
---|
| 1598 | |
---|
| 1599 | } |
---|
| 1600 | |
---|
[1819] | 1601 | /** |
---|
| 1602 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
[1170] | 1603 | const std::string& unit ) |
---|
[1819] | 1604 | **/ |
---|
| 1605 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
| 1606 | const std::string& unit ) |
---|
| 1607 | |
---|
[847] | 1608 | { |
---|
[923] | 1609 | ///@todo lookup in line table to fill in name and formattedname |
---|
[847] | 1610 | Unit u(unit); |
---|
[1819] | 1611 | //Quantum<Double> urf(rf, u); |
---|
| 1612 | Quantum<Vector<Double> >urf(rf, u); |
---|
| 1613 | Vector<String> formattedname(0); |
---|
| 1614 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
| 1615 | |
---|
| 1616 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
| 1617 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
[847] | 1618 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
| 1619 | tabvec = id; |
---|
| 1620 | } |
---|
| 1621 | |
---|
[1819] | 1622 | /** |
---|
| 1623 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
[847] | 1624 | { |
---|
| 1625 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
| 1626 | ///@todo implement |
---|
| 1627 | } |
---|
[1819] | 1628 | **/ |
---|
[2012] | 1629 | |
---|
[1819] | 1630 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
| 1631 | { |
---|
[2163] | 1632 | (void) name; // suppress unused warning |
---|
[1819] | 1633 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
| 1634 | ///@todo implement |
---|
| 1635 | } |
---|
[847] | 1636 | |
---|
[1360] | 1637 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
[852] | 1638 | { |
---|
| 1639 | std::vector<unsigned int> stlout; |
---|
| 1640 | Vector<uInt> vec = table_.rowNumbers(); |
---|
| 1641 | vec.tovector(stlout); |
---|
| 1642 | return stlout; |
---|
| 1643 | } |
---|
| 1644 | |
---|
[865] | 1645 | |
---|
[1360] | 1646 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
[896] | 1647 | { |
---|
| 1648 | ROTableRow row(table_); |
---|
| 1649 | const TableRecord& rec = row.get(whichrow); |
---|
| 1650 | Table t = |
---|
| 1651 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
| 1652 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 1653 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 1654 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 1655 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 1656 | return speccol.getColumn(); |
---|
| 1657 | } |
---|
[865] | 1658 | |
---|
[1360] | 1659 | std::vector< std::string > Scantable::columnNames( ) const |
---|
[902] | 1660 | { |
---|
| 1661 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
| 1662 | return mathutil::tovectorstring(vec); |
---|
| 1663 | } |
---|
[896] | 1664 | |
---|
[1360] | 1665 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
[915] | 1666 | { |
---|
| 1667 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
[972] | 1668 | } |
---|
[915] | 1669 | |
---|
[1360] | 1670 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
[972] | 1671 | { |
---|
[1819] | 1672 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
| 1673 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
| 1674 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
[972] | 1675 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
| 1676 | mfitidCol_.put(uInt(row), id); |
---|
| 1677 | } |
---|
[915] | 1678 | |
---|
[1360] | 1679 | void Scantable::shift(int npix) |
---|
| 1680 | { |
---|
| 1681 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
| 1682 | genSort( fids, Sort::Ascending, |
---|
| 1683 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 1684 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
[1567] | 1685 | frequencies().shiftRefPix(npix, fids[i]); |
---|
[1360] | 1686 | } |
---|
| 1687 | } |
---|
[987] | 1688 | |
---|
[1819] | 1689 | String Scantable::getAntennaName() const |
---|
[1391] | 1690 | { |
---|
| 1691 | String out; |
---|
| 1692 | table_.keywordSet().get("AntennaName", out); |
---|
[1987] | 1693 | String::size_type pos1 = out.find("@") ; |
---|
| 1694 | String::size_type pos2 = out.find("//") ; |
---|
| 1695 | if ( pos2 != String::npos ) |
---|
[2036] | 1696 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
[1987] | 1697 | else if ( pos1 != String::npos ) |
---|
| 1698 | out = out.substr(0,pos1) ; |
---|
[1391] | 1699 | return out; |
---|
[987] | 1700 | } |
---|
[1391] | 1701 | |
---|
[1730] | 1702 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
[1391] | 1703 | { |
---|
| 1704 | String tbpath; |
---|
| 1705 | int ret = 0; |
---|
| 1706 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
| 1707 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
| 1708 | Table t(tbpath,Table::Old); |
---|
| 1709 | // check each scan if other scan of the pair exist |
---|
| 1710 | int nscan = scanlist.size(); |
---|
| 1711 | for (int i = 0; i < nscan; i++) { |
---|
| 1712 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
| 1713 | if (subt.nrow()==0) { |
---|
[1819] | 1714 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
| 1715 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1716 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1717 | ret = 1; |
---|
| 1718 | break; |
---|
| 1719 | } |
---|
| 1720 | ROTableRow row(subt); |
---|
| 1721 | const TableRecord& rec = row.get(0); |
---|
| 1722 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
| 1723 | int laston1 = rec.asuInt("LASTON"); |
---|
| 1724 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
| 1725 | if ( i < nscan-1 ) { |
---|
| 1726 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
| 1727 | if ( subt2.nrow() == 0) { |
---|
[1819] | 1728 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1729 | |
---|
| 1730 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
| 1731 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1732 | ret = 1; |
---|
| 1733 | break; |
---|
| 1734 | } |
---|
| 1735 | ROTableRow row2(subt2); |
---|
| 1736 | const TableRecord& rec2 = row2.get(0); |
---|
| 1737 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
| 1738 | int laston2 = rec2.asuInt("LASTON"); |
---|
| 1739 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
| 1740 | if (laston1 == laston2) { |
---|
[1819] | 1741 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1742 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1743 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1744 | i +=1; |
---|
| 1745 | } |
---|
| 1746 | else { |
---|
[1819] | 1747 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1748 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1749 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1750 | } |
---|
| 1751 | } |
---|
| 1752 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
| 1753 | if (laston1 == laston2) { |
---|
[1819] | 1754 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1755 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
| 1756 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
[1391] | 1757 | ret = 1; |
---|
| 1758 | break; |
---|
| 1759 | } |
---|
| 1760 | } |
---|
| 1761 | else { |
---|
[1819] | 1762 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1763 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
| 1764 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
[1391] | 1765 | ret = 1; |
---|
| 1766 | break; |
---|
| 1767 | } |
---|
| 1768 | } |
---|
| 1769 | } |
---|
| 1770 | else { |
---|
[1819] | 1771 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1772 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
| 1773 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
[1391] | 1774 | } |
---|
| 1775 | //if ( i >= nscan ) break; |
---|
| 1776 | } |
---|
| 1777 | } |
---|
| 1778 | else { |
---|
[1819] | 1779 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1780 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
| 1781 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
[1391] | 1782 | ret = 1; |
---|
| 1783 | } |
---|
| 1784 | return ret; |
---|
| 1785 | } |
---|
| 1786 | |
---|
[1730] | 1787 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
[1391] | 1788 | { |
---|
| 1789 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
| 1790 | std::vector<double> dir; |
---|
| 1791 | Dir.tovector(dir); |
---|
| 1792 | return dir; |
---|
| 1793 | } |
---|
| 1794 | |
---|
[1819] | 1795 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
| 1796 | throw( casa::AipsError ) |
---|
| 1797 | { |
---|
| 1798 | // assumed that all rows have same nChan |
---|
| 1799 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1800 | int nChan = arr.nelements() ; |
---|
| 1801 | |
---|
| 1802 | // if nmin < 0 or nmax < 0, nothing to do |
---|
| 1803 | if ( nmin < 0 ) { |
---|
| 1804 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1805 | } |
---|
| 1806 | if ( nmax < 0 ) { |
---|
| 1807 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1808 | } |
---|
| 1809 | |
---|
| 1810 | // if nmin > nmax, exchange values |
---|
| 1811 | if ( nmin > nmax ) { |
---|
| 1812 | int tmp = nmax ; |
---|
| 1813 | nmax = nmin ; |
---|
| 1814 | nmin = tmp ; |
---|
| 1815 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1816 | os << "Swap values. Applied range is [" |
---|
| 1817 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
| 1818 | } |
---|
| 1819 | |
---|
| 1820 | // if nmin exceeds nChan, nothing to do |
---|
| 1821 | if ( nmin >= nChan ) { |
---|
| 1822 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
| 1823 | } |
---|
| 1824 | |
---|
| 1825 | // if nmax exceeds nChan, reset nmax to nChan |
---|
| 1826 | if ( nmax >= nChan ) { |
---|
| 1827 | if ( nmin == 0 ) { |
---|
| 1828 | // nothing to do |
---|
| 1829 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1830 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
| 1831 | return ; |
---|
| 1832 | } |
---|
| 1833 | else { |
---|
| 1834 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1835 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
| 1836 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
| 1837 | nmax = nChan - 1 ; |
---|
| 1838 | } |
---|
| 1839 | } |
---|
| 1840 | |
---|
| 1841 | // reshape specCol_ and flagCol_ |
---|
| 1842 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1843 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
| 1844 | } |
---|
| 1845 | |
---|
| 1846 | // update FREQUENCIES subtable |
---|
| 1847 | Double refpix ; |
---|
| 1848 | Double refval ; |
---|
| 1849 | Double increment ; |
---|
[2346] | 1850 | int freqnrow = freqTable_.table().nrow() ; |
---|
[1819] | 1851 | Vector<uInt> oldId( freqnrow ) ; |
---|
| 1852 | Vector<uInt> newId( freqnrow ) ; |
---|
| 1853 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
[2346] | 1854 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
[1819] | 1855 | /*** |
---|
| 1856 | * need to shift refpix to nmin |
---|
| 1857 | * note that channel nmin in old index will be channel 0 in new one |
---|
| 1858 | ***/ |
---|
| 1859 | refval = refval - ( refpix - nmin ) * increment ; |
---|
| 1860 | refpix = 0 ; |
---|
[2346] | 1861 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
[1819] | 1862 | } |
---|
| 1863 | |
---|
| 1864 | // update nchan |
---|
| 1865 | int newsize = nmax - nmin + 1 ; |
---|
| 1866 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
| 1867 | |
---|
| 1868 | // update bandwidth |
---|
| 1869 | // assumed all spectra in the scantable have same bandwidth |
---|
| 1870 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
| 1871 | |
---|
| 1872 | return ; |
---|
| 1873 | } |
---|
| 1874 | |
---|
| 1875 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
| 1876 | { |
---|
| 1877 | // reshape specCol_ and flagCol_ |
---|
| 1878 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1879 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 1880 | uInt newsize = nmax - nmin + 1 ; |
---|
| 1881 | specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ; |
---|
| 1882 | flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ; |
---|
| 1883 | |
---|
| 1884 | return ; |
---|
| 1885 | } |
---|
| 1886 | |
---|
| 1887 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
| 1888 | { |
---|
| 1889 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1890 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
| 1891 | // assumed that all rows have same nChan |
---|
| 1892 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1893 | int oldsize = arr.nelements() ; |
---|
| 1894 | |
---|
| 1895 | // if oldsize == nChan, nothing to do |
---|
| 1896 | if ( oldsize == nChan ) { |
---|
| 1897 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
| 1898 | return ; |
---|
| 1899 | } |
---|
| 1900 | |
---|
| 1901 | // if oldChan < nChan, unphysical operation |
---|
| 1902 | if ( oldsize < nChan ) { |
---|
| 1903 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
| 1904 | return ; |
---|
| 1905 | } |
---|
| 1906 | |
---|
| 1907 | // change channel number for specCol_ and flagCol_ |
---|
| 1908 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 1909 | Vector<uChar> newflag( nChan, false ) ; |
---|
| 1910 | vector<string> coordinfo = getCoordInfo() ; |
---|
| 1911 | string oldinfo = coordinfo[0] ; |
---|
| 1912 | coordinfo[0] = "Hz" ; |
---|
| 1913 | setCoordInfo( coordinfo ) ; |
---|
| 1914 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1915 | regridChannel( nChan, dnu, irow ) ; |
---|
| 1916 | } |
---|
| 1917 | coordinfo[0] = oldinfo ; |
---|
| 1918 | setCoordInfo( coordinfo ) ; |
---|
| 1919 | |
---|
| 1920 | |
---|
| 1921 | // NOTE: this method does not update metadata such as |
---|
| 1922 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
| 1923 | |
---|
| 1924 | return ; |
---|
| 1925 | } |
---|
| 1926 | |
---|
| 1927 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
| 1928 | { |
---|
| 1929 | // logging |
---|
| 1930 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
| 1931 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
| 1932 | |
---|
| 1933 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1934 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 1935 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 1936 | Vector<uChar> newflag( nChan, false ) ; |
---|
| 1937 | |
---|
| 1938 | // regrid |
---|
| 1939 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1940 | int oldsize = abcissa.size() ; |
---|
| 1941 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
| 1942 | //int refChan = 0 ; |
---|
| 1943 | //double frac = 0.0 ; |
---|
| 1944 | //double wedge = 0.0 ; |
---|
| 1945 | //double pile = 0.0 ; |
---|
| 1946 | int ichan = 0 ; |
---|
| 1947 | double wsum = 0.0 ; |
---|
| 1948 | Vector<Float> zi( nChan+1 ) ; |
---|
| 1949 | Vector<Float> yi( oldsize + 1 ) ; |
---|
[2133] | 1950 | zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 1951 | zi[1] = zi[1] + dnu ; |
---|
[1819] | 1952 | for ( int ii = 2 ; ii < nChan ; ii++ ) |
---|
[2133] | 1953 | zi[ii] = zi[0] + dnu * ii ; |
---|
| 1954 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
[1819] | 1955 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 1956 | yi[1] = abcissa[1] + 0.5 * olddnu ; |
---|
| 1957 | for ( int ii = 2 ; ii < oldsize ; ii++ ) |
---|
| 1958 | yi[ii] = abcissa[ii-1] + olddnu ; |
---|
| 1959 | yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ; |
---|
| 1960 | if ( dnu > 0.0 ) { |
---|
| 1961 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 1962 | double zl = zi[ii] ; |
---|
| 1963 | double zr = zi[ii+1] ; |
---|
| 1964 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 1965 | double yl = yi[j] ; |
---|
| 1966 | double yr = yi[j+1] ; |
---|
| 1967 | if ( yl <= zl ) { |
---|
| 1968 | if ( yr <= zl ) { |
---|
| 1969 | continue ; |
---|
| 1970 | } |
---|
| 1971 | else if ( yr <= zr ) { |
---|
| 1972 | newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
| 1973 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1974 | wsum += ( yr - zl ) ; |
---|
| 1975 | } |
---|
| 1976 | else { |
---|
| 1977 | newspec[ii] += oldspec[j] * dnu ; |
---|
| 1978 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1979 | wsum += dnu ; |
---|
| 1980 | ichan = j ; |
---|
| 1981 | break ; |
---|
| 1982 | } |
---|
| 1983 | } |
---|
| 1984 | else if ( yl < zr ) { |
---|
| 1985 | if ( yr <= zr ) { |
---|
| 1986 | newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
| 1987 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1988 | wsum += ( yr - yl ) ; |
---|
| 1989 | } |
---|
| 1990 | else { |
---|
| 1991 | newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
| 1992 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1993 | wsum += ( zr - yl ) ; |
---|
| 1994 | ichan = j ; |
---|
| 1995 | break ; |
---|
| 1996 | } |
---|
| 1997 | } |
---|
| 1998 | else { |
---|
| 1999 | ichan = j - 1 ; |
---|
| 2000 | break ; |
---|
| 2001 | } |
---|
| 2002 | } |
---|
[2133] | 2003 | if ( wsum != 0.0 ) |
---|
| 2004 | newspec[ii] /= wsum ; |
---|
[1819] | 2005 | wsum = 0.0 ; |
---|
| 2006 | } |
---|
| 2007 | } |
---|
| 2008 | else if ( dnu < 0.0 ) { |
---|
| 2009 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 2010 | double zl = zi[ii] ; |
---|
| 2011 | double zr = zi[ii+1] ; |
---|
| 2012 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 2013 | double yl = yi[j] ; |
---|
| 2014 | double yr = yi[j+1] ; |
---|
| 2015 | if ( yl >= zl ) { |
---|
| 2016 | if ( yr >= zl ) { |
---|
| 2017 | continue ; |
---|
| 2018 | } |
---|
| 2019 | else if ( yr >= zr ) { |
---|
| 2020 | newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
| 2021 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2022 | wsum += abs( yr - zl ) ; |
---|
| 2023 | } |
---|
| 2024 | else { |
---|
| 2025 | newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
| 2026 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2027 | wsum += abs( dnu ) ; |
---|
| 2028 | ichan = j ; |
---|
| 2029 | break ; |
---|
| 2030 | } |
---|
| 2031 | } |
---|
| 2032 | else if ( yl > zr ) { |
---|
| 2033 | if ( yr >= zr ) { |
---|
| 2034 | newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
| 2035 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2036 | wsum += abs( yr - yl ) ; |
---|
| 2037 | } |
---|
| 2038 | else { |
---|
| 2039 | newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
| 2040 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2041 | wsum += abs( zr - yl ) ; |
---|
| 2042 | ichan = j ; |
---|
| 2043 | break ; |
---|
| 2044 | } |
---|
| 2045 | } |
---|
| 2046 | else { |
---|
| 2047 | ichan = j - 1 ; |
---|
| 2048 | break ; |
---|
| 2049 | } |
---|
| 2050 | } |
---|
[2133] | 2051 | if ( wsum != 0.0 ) |
---|
| 2052 | newspec[ii] /= wsum ; |
---|
[1819] | 2053 | wsum = 0.0 ; |
---|
| 2054 | } |
---|
| 2055 | } |
---|
| 2056 | // * ichan = 0 |
---|
| 2057 | // ***/ |
---|
| 2058 | // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
| 2059 | // pile += dnu ; |
---|
| 2060 | // wedge = olddnu * ( refChan + 1 ) ; |
---|
| 2061 | // while ( wedge < pile ) { |
---|
| 2062 | // newspec[0] += olddnu * oldspec[refChan] ; |
---|
| 2063 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2064 | // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
| 2065 | // refChan++ ; |
---|
| 2066 | // wedge += olddnu ; |
---|
| 2067 | // wsum += olddnu ; |
---|
| 2068 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2069 | // } |
---|
| 2070 | // frac = ( wedge - pile ) / olddnu ; |
---|
| 2071 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2072 | // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2073 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2074 | // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2075 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2076 | // newspec[0] /= wsum ; |
---|
| 2077 | // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
| 2078 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2079 | |
---|
| 2080 | // /*** |
---|
| 2081 | // * ichan = 1 - nChan-2 |
---|
| 2082 | // ***/ |
---|
| 2083 | // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
| 2084 | // pile += dnu ; |
---|
| 2085 | // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
| 2086 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2087 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
| 2088 | // refChan++ ; |
---|
| 2089 | // wedge += olddnu ; |
---|
| 2090 | // wsum = frac * olddnu ; |
---|
| 2091 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2092 | // while ( wedge < pile ) { |
---|
| 2093 | // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
| 2094 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2095 | // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
| 2096 | // refChan++ ; |
---|
| 2097 | // wedge += olddnu ; |
---|
| 2098 | // wsum += olddnu ; |
---|
| 2099 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2100 | // } |
---|
| 2101 | // frac = ( wedge - pile ) / olddnu ; |
---|
| 2102 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2103 | // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2104 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2105 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2106 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2107 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2108 | // newspec[ichan] /= wsum ; |
---|
| 2109 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
| 2110 | // } |
---|
| 2111 | |
---|
| 2112 | // /*** |
---|
| 2113 | // * ichan = nChan-1 |
---|
| 2114 | // ***/ |
---|
| 2115 | // // NOTE: Assumed that all spectra have the same bandwidth |
---|
| 2116 | // pile += dnu ; |
---|
| 2117 | // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
| 2118 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
| 2119 | // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2120 | // refChan++ ; |
---|
| 2121 | // wedge += olddnu ; |
---|
| 2122 | // wsum = frac * olddnu ; |
---|
| 2123 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2124 | // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
| 2125 | // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
| 2126 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
| 2127 | // wsum += olddnu ; |
---|
| 2128 | // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2129 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2130 | // } |
---|
| 2131 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2132 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2133 | // newspec[nChan-1] /= wsum ; |
---|
| 2134 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
| 2135 | |
---|
| 2136 | // // ofs.close() ; |
---|
| 2137 | |
---|
[2032] | 2138 | specCol_.put( irow, newspec ) ; |
---|
| 2139 | flagsCol_.put( irow, newflag ) ; |
---|
[1819] | 2140 | |
---|
| 2141 | return ; |
---|
| 2142 | } |
---|
| 2143 | |
---|
[1730] | 2144 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
| 2145 | { |
---|
| 2146 | std::vector<float> out(5); |
---|
| 2147 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
| 2148 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
| 2149 | mweatheridCol_(uInt(whichrow))); |
---|
| 2150 | |
---|
| 2151 | |
---|
| 2152 | return out; |
---|
[1391] | 2153 | } |
---|
[1730] | 2154 | |
---|
[2047] | 2155 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
[1907] | 2156 | { |
---|
| 2157 | uChar flag; |
---|
| 2158 | Vector<uChar> flags; |
---|
[2047] | 2159 | flagsCol_.get(whichrow, flags); |
---|
[2012] | 2160 | flag = flags[0]; |
---|
[2047] | 2161 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
[2012] | 2162 | flag &= flags[i]; |
---|
| 2163 | } |
---|
| 2164 | return ((flag >> 7) == 1); |
---|
| 2165 | } |
---|
| 2166 | |
---|
[2277] | 2167 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2168 | { |
---|
[2193] | 2169 | try { |
---|
| 2170 | ofstream ofs; |
---|
| 2171 | String coordInfo = ""; |
---|
| 2172 | bool hasSameNchan = true; |
---|
| 2173 | bool outTextFile = false; |
---|
[2047] | 2174 | |
---|
[2193] | 2175 | if (blfile != "") { |
---|
| 2176 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2177 | if (ofs) outTextFile = true; |
---|
| 2178 | } |
---|
[2047] | 2179 | |
---|
[2193] | 2180 | if (outLogger || outTextFile) { |
---|
| 2181 | coordInfo = getCoordInfo()[0]; |
---|
| 2182 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2183 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2184 | } |
---|
[2047] | 2185 | |
---|
[2193] | 2186 | Fitter fitter = Fitter(); |
---|
| 2187 | fitter.setExpression("poly", order); |
---|
| 2188 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2189 | |
---|
[2193] | 2190 | int nRow = nrow(); |
---|
| 2191 | std::vector<bool> chanMask; |
---|
| 2192 | bool showProgress; |
---|
| 2193 | int minNRow; |
---|
| 2194 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2047] | 2195 | |
---|
[2193] | 2196 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2197 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2198 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2199 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2277] | 2200 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
[2193] | 2201 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2202 | } |
---|
| 2203 | |
---|
| 2204 | if (outTextFile) ofs.close(); |
---|
| 2205 | |
---|
| 2206 | } catch (...) { |
---|
| 2207 | throw; |
---|
[2047] | 2208 | } |
---|
| 2209 | } |
---|
| 2210 | |
---|
[2189] | 2211 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2212 | { |
---|
[2193] | 2213 | try { |
---|
| 2214 | ofstream ofs; |
---|
| 2215 | String coordInfo = ""; |
---|
| 2216 | bool hasSameNchan = true; |
---|
| 2217 | bool outTextFile = false; |
---|
[2047] | 2218 | |
---|
[2193] | 2219 | if (blfile != "") { |
---|
| 2220 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2221 | if (ofs) outTextFile = true; |
---|
| 2222 | } |
---|
[2047] | 2223 | |
---|
[2193] | 2224 | if (outLogger || outTextFile) { |
---|
| 2225 | coordInfo = getCoordInfo()[0]; |
---|
| 2226 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2227 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2228 | } |
---|
[2047] | 2229 | |
---|
[2193] | 2230 | Fitter fitter = Fitter(); |
---|
| 2231 | fitter.setExpression("poly", order); |
---|
| 2232 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2233 | |
---|
[2193] | 2234 | int nRow = nrow(); |
---|
| 2235 | std::vector<bool> chanMask; |
---|
| 2236 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2237 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2238 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2047] | 2239 | |
---|
[2193] | 2240 | bool showProgress; |
---|
| 2241 | int minNRow; |
---|
| 2242 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2243 | |
---|
[2193] | 2244 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2047] | 2245 | |
---|
[2193] | 2246 | //------------------------------------------------------- |
---|
| 2247 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2248 | //------------------------------------------------------- |
---|
| 2249 | int edgeSize = edge.size(); |
---|
| 2250 | std::vector<int> currentEdge; |
---|
| 2251 | if (edgeSize >= 2) { |
---|
| 2252 | int idx = 0; |
---|
| 2253 | if (edgeSize > 2) { |
---|
| 2254 | if (edgeSize < minEdgeSize) { |
---|
| 2255 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2256 | } |
---|
| 2257 | idx = 2 * getIF(whichrow); |
---|
[2047] | 2258 | } |
---|
[2193] | 2259 | currentEdge.push_back(edge[idx]); |
---|
| 2260 | currentEdge.push_back(edge[idx+1]); |
---|
| 2261 | } else { |
---|
| 2262 | throw(AipsError("Wrong length of edge element")); |
---|
[2047] | 2263 | } |
---|
[2193] | 2264 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2265 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2266 | chanMask = lineFinder.getMask(); |
---|
| 2267 | //------------------------------------------------------- |
---|
| 2268 | |
---|
| 2269 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2270 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2271 | |
---|
| 2272 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
| 2273 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2047] | 2274 | } |
---|
| 2275 | |
---|
[2193] | 2276 | if (outTextFile) ofs.close(); |
---|
[2047] | 2277 | |
---|
[2193] | 2278 | } catch (...) { |
---|
| 2279 | throw; |
---|
[2047] | 2280 | } |
---|
| 2281 | } |
---|
| 2282 | |
---|
[2189] | 2283 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2081] | 2284 | { |
---|
[2193] | 2285 | try { |
---|
| 2286 | ofstream ofs; |
---|
| 2287 | String coordInfo = ""; |
---|
| 2288 | bool hasSameNchan = true; |
---|
| 2289 | bool outTextFile = false; |
---|
[2012] | 2290 | |
---|
[2193] | 2291 | if (blfile != "") { |
---|
| 2292 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2293 | if (ofs) outTextFile = true; |
---|
| 2294 | } |
---|
[2012] | 2295 | |
---|
[2193] | 2296 | if (outLogger || outTextFile) { |
---|
| 2297 | coordInfo = getCoordInfo()[0]; |
---|
| 2298 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2299 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2300 | } |
---|
[2012] | 2301 | |
---|
[2193] | 2302 | //Fitter fitter = Fitter(); |
---|
| 2303 | //fitter.setExpression("cspline", nPiece); |
---|
| 2304 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2305 | |
---|
[2193] | 2306 | bool showProgress; |
---|
| 2307 | int minNRow; |
---|
| 2308 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2012] | 2309 | |
---|
[2344] | 2310 | int nRow = nrow(); |
---|
| 2311 | std::vector<bool> chanMask; |
---|
| 2312 | |
---|
| 2313 | //-------------------------------- |
---|
[2193] | 2314 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2315 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2316 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2317 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2344] | 2318 | std::vector<int> pieceEdges(nPiece+1); |
---|
| 2319 | std::vector<float> params(nPiece*4); |
---|
[2193] | 2320 | int nClipped = 0; |
---|
| 2321 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2322 | setSpectrum(res, whichrow); |
---|
| 2323 | // |
---|
[2012] | 2324 | |
---|
[2193] | 2325 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
| 2326 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2327 | } |
---|
[2344] | 2328 | //-------------------------------- |
---|
| 2329 | |
---|
[2193] | 2330 | if (outTextFile) ofs.close(); |
---|
| 2331 | |
---|
| 2332 | } catch (...) { |
---|
| 2333 | throw; |
---|
[2012] | 2334 | } |
---|
| 2335 | } |
---|
| 2336 | |
---|
[2189] | 2337 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 2338 | { |
---|
[2193] | 2339 | try { |
---|
| 2340 | ofstream ofs; |
---|
| 2341 | String coordInfo = ""; |
---|
| 2342 | bool hasSameNchan = true; |
---|
| 2343 | bool outTextFile = false; |
---|
[2012] | 2344 | |
---|
[2193] | 2345 | if (blfile != "") { |
---|
| 2346 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2347 | if (ofs) outTextFile = true; |
---|
| 2348 | } |
---|
[2012] | 2349 | |
---|
[2193] | 2350 | if (outLogger || outTextFile) { |
---|
| 2351 | coordInfo = getCoordInfo()[0]; |
---|
| 2352 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2353 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2354 | } |
---|
[2012] | 2355 | |
---|
[2193] | 2356 | //Fitter fitter = Fitter(); |
---|
| 2357 | //fitter.setExpression("cspline", nPiece); |
---|
| 2358 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2359 | |
---|
[2193] | 2360 | int nRow = nrow(); |
---|
| 2361 | std::vector<bool> chanMask; |
---|
| 2362 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2363 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2364 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 2365 | |
---|
[2193] | 2366 | bool showProgress; |
---|
| 2367 | int minNRow; |
---|
| 2368 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2369 | |
---|
[2193] | 2370 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 2371 | |
---|
[2193] | 2372 | //------------------------------------------------------- |
---|
| 2373 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2374 | //------------------------------------------------------- |
---|
| 2375 | int edgeSize = edge.size(); |
---|
| 2376 | std::vector<int> currentEdge; |
---|
| 2377 | if (edgeSize >= 2) { |
---|
| 2378 | int idx = 0; |
---|
| 2379 | if (edgeSize > 2) { |
---|
| 2380 | if (edgeSize < minEdgeSize) { |
---|
| 2381 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2382 | } |
---|
| 2383 | idx = 2 * getIF(whichrow); |
---|
[2012] | 2384 | } |
---|
[2193] | 2385 | currentEdge.push_back(edge[idx]); |
---|
| 2386 | currentEdge.push_back(edge[idx+1]); |
---|
| 2387 | } else { |
---|
| 2388 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 2389 | } |
---|
[2193] | 2390 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2391 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2392 | chanMask = lineFinder.getMask(); |
---|
| 2393 | //------------------------------------------------------- |
---|
| 2394 | |
---|
| 2395 | |
---|
| 2396 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2397 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2344] | 2398 | std::vector<int> pieceEdges(nPiece+1); |
---|
| 2399 | std::vector<float> params(nPiece*4); |
---|
[2193] | 2400 | int nClipped = 0; |
---|
| 2401 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2402 | setSpectrum(res, whichrow); |
---|
| 2403 | // |
---|
| 2404 | |
---|
| 2405 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
| 2406 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[1907] | 2407 | } |
---|
[2012] | 2408 | |
---|
[2193] | 2409 | if (outTextFile) ofs.close(); |
---|
[2012] | 2410 | |
---|
[2193] | 2411 | } catch (...) { |
---|
| 2412 | throw; |
---|
[2012] | 2413 | } |
---|
[1730] | 2414 | } |
---|
[1907] | 2415 | |
---|
[2193] | 2416 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 2417 | { |
---|
| 2418 | if (data.size() != mask.size()) { |
---|
| 2419 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 2420 | } |
---|
[2012] | 2421 | if (nPiece < 1) { |
---|
[2094] | 2422 | throw(AipsError("number of the sections must be one or more")); |
---|
[2012] | 2423 | } |
---|
| 2424 | |
---|
| 2425 | int nChan = data.size(); |
---|
[2344] | 2426 | std::vector<int> maskArray(nChan); |
---|
| 2427 | std::vector<int> x(nChan); |
---|
| 2428 | int j = 0; |
---|
[2012] | 2429 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 2430 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2012] | 2431 | if (mask[i]) { |
---|
[2344] | 2432 | x[j] = i; |
---|
| 2433 | j++; |
---|
[2012] | 2434 | } |
---|
| 2435 | } |
---|
[2344] | 2436 | int initNData = j; |
---|
[2012] | 2437 | |
---|
[2193] | 2438 | if (initNData < nPiece) { |
---|
| 2439 | throw(AipsError("too few non-flagged channels")); |
---|
| 2440 | } |
---|
[2081] | 2441 | |
---|
| 2442 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
[2344] | 2443 | std::vector<double> invEdge(nPiece-1); |
---|
| 2444 | idxEdge[0] = x[0]; |
---|
[2012] | 2445 | for (int i = 1; i < nPiece; ++i) { |
---|
[2047] | 2446 | int valX = x[nElement*i]; |
---|
[2344] | 2447 | idxEdge[i] = valX; |
---|
| 2448 | invEdge[i-1] = 1.0/(double)valX; |
---|
[2012] | 2449 | } |
---|
[2344] | 2450 | idxEdge[nPiece] = x[initNData-1]+1; |
---|
[2064] | 2451 | |
---|
[2081] | 2452 | int nData = initNData; |
---|
| 2453 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
| 2454 | |
---|
[2344] | 2455 | std::vector<double> x1(nChan), x2(nChan), x3(nChan); |
---|
| 2456 | std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan); |
---|
| 2457 | std::vector<double> r1(nChan), residual(nChan); |
---|
[2012] | 2458 | for (int i = 0; i < nChan; ++i) { |
---|
[2064] | 2459 | double di = (double)i; |
---|
| 2460 | double dD = (double)data[i]; |
---|
[2344] | 2461 | x1[i] = di; |
---|
| 2462 | x2[i] = di*di; |
---|
| 2463 | x3[i] = di*di*di; |
---|
| 2464 | z1[i] = dD; |
---|
| 2465 | x1z1[i] = dD*di; |
---|
| 2466 | x2z1[i] = dD*di*di; |
---|
| 2467 | x3z1[i] = dD*di*di*di; |
---|
| 2468 | r1[i] = 0.0; |
---|
| 2469 | residual[i] = 0.0; |
---|
[2012] | 2470 | } |
---|
| 2471 | |
---|
| 2472 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2064] | 2473 | // xMatrix : horizontal concatenation of |
---|
| 2474 | // the least-sq. matrix (left) and an |
---|
| 2475 | // identity matrix (right). |
---|
| 2476 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2012] | 2477 | double xMatrix[nDOF][2*nDOF]; |
---|
| 2478 | double zMatrix[nDOF]; |
---|
| 2479 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2480 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 2481 | xMatrix[i][j] = 0.0; |
---|
| 2482 | } |
---|
| 2483 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 2484 | zMatrix[i] = 0.0; |
---|
| 2485 | } |
---|
| 2486 | |
---|
| 2487 | for (int n = 0; n < nPiece; ++n) { |
---|
[2193] | 2488 | int nUseDataInPiece = 0; |
---|
[2064] | 2489 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2490 | |
---|
[2012] | 2491 | if (maskArray[i] == 0) continue; |
---|
[2064] | 2492 | |
---|
[2012] | 2493 | xMatrix[0][0] += 1.0; |
---|
[2064] | 2494 | xMatrix[0][1] += x1[i]; |
---|
| 2495 | xMatrix[0][2] += x2[i]; |
---|
| 2496 | xMatrix[0][3] += x3[i]; |
---|
| 2497 | xMatrix[1][1] += x2[i]; |
---|
| 2498 | xMatrix[1][2] += x3[i]; |
---|
| 2499 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
| 2500 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
| 2501 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
| 2502 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
[2012] | 2503 | zMatrix[0] += z1[i]; |
---|
[2064] | 2504 | zMatrix[1] += x1z1[i]; |
---|
| 2505 | zMatrix[2] += x2z1[i]; |
---|
| 2506 | zMatrix[3] += x3z1[i]; |
---|
| 2507 | |
---|
[2012] | 2508 | for (int j = 0; j < n; ++j) { |
---|
[2064] | 2509 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
[2012] | 2510 | q = q*q*q; |
---|
| 2511 | xMatrix[0][j+4] += q; |
---|
[2064] | 2512 | xMatrix[1][j+4] += q*x1[i]; |
---|
| 2513 | xMatrix[2][j+4] += q*x2[i]; |
---|
| 2514 | xMatrix[3][j+4] += q*x3[i]; |
---|
[2012] | 2515 | for (int k = 0; k < j; ++k) { |
---|
[2064] | 2516 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
[2012] | 2517 | r = r*r*r; |
---|
| 2518 | xMatrix[k+4][j+4] += r*q; |
---|
| 2519 | } |
---|
| 2520 | xMatrix[j+4][j+4] += q*q; |
---|
| 2521 | zMatrix[j+4] += q*z1[i]; |
---|
| 2522 | } |
---|
[2064] | 2523 | |
---|
[2193] | 2524 | nUseDataInPiece++; |
---|
[2012] | 2525 | } |
---|
[2193] | 2526 | |
---|
| 2527 | if (nUseDataInPiece < 1) { |
---|
| 2528 | std::vector<string> suffixOfPieceNumber(4); |
---|
| 2529 | suffixOfPieceNumber[0] = "th"; |
---|
| 2530 | suffixOfPieceNumber[1] = "st"; |
---|
| 2531 | suffixOfPieceNumber[2] = "nd"; |
---|
| 2532 | suffixOfPieceNumber[3] = "rd"; |
---|
| 2533 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
| 2534 | ostringstream oss; |
---|
| 2535 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
| 2536 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
| 2537 | throw(AipsError(String(oss))); |
---|
| 2538 | } |
---|
[2012] | 2539 | } |
---|
| 2540 | |
---|
| 2541 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2542 | for (int j = 0; j < i; ++j) { |
---|
| 2543 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 2544 | } |
---|
| 2545 | } |
---|
| 2546 | |
---|
[2344] | 2547 | std::vector<double> invDiag(nDOF); |
---|
[2012] | 2548 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 2549 | invDiag[i] = 1.0/xMatrix[i][i]; |
---|
[2012] | 2550 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2551 | xMatrix[i][j] *= invDiag[i]; |
---|
| 2552 | } |
---|
| 2553 | } |
---|
| 2554 | |
---|
| 2555 | for (int k = 0; k < nDOF; ++k) { |
---|
| 2556 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2557 | if (i != k) { |
---|
| 2558 | double factor1 = xMatrix[k][k]; |
---|
| 2559 | double factor2 = xMatrix[i][k]; |
---|
| 2560 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2561 | xMatrix[i][j] *= factor1; |
---|
| 2562 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 2563 | xMatrix[i][j] /= factor1; |
---|
| 2564 | } |
---|
| 2565 | } |
---|
| 2566 | } |
---|
| 2567 | double xDiag = xMatrix[k][k]; |
---|
| 2568 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2569 | xMatrix[k][j] /= xDiag; |
---|
| 2570 | } |
---|
| 2571 | } |
---|
| 2572 | |
---|
| 2573 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2574 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2575 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 2576 | } |
---|
| 2577 | } |
---|
| 2578 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
| 2579 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
| 2580 | //cubic terms for the other pieces (in case nPiece>1). |
---|
[2344] | 2581 | std::vector<double> y(nDOF); |
---|
[2012] | 2582 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 2583 | y[i] = 0.0; |
---|
[2012] | 2584 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2585 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 2586 | } |
---|
| 2587 | } |
---|
| 2588 | |
---|
| 2589 | double a0 = y[0]; |
---|
| 2590 | double a1 = y[1]; |
---|
| 2591 | double a2 = y[2]; |
---|
| 2592 | double a3 = y[3]; |
---|
| 2593 | |
---|
[2344] | 2594 | int j = 0; |
---|
[2012] | 2595 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 2596 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2597 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
[2012] | 2598 | } |
---|
[2344] | 2599 | params[j] = a0; |
---|
| 2600 | params[j+1] = a1; |
---|
| 2601 | params[j+2] = a2; |
---|
| 2602 | params[j+3] = a3; |
---|
| 2603 | j += 4; |
---|
[2012] | 2604 | |
---|
| 2605 | if (n == nPiece-1) break; |
---|
| 2606 | |
---|
| 2607 | double d = y[4+n]; |
---|
[2064] | 2608 | double iE = invEdge[n]; |
---|
| 2609 | a0 += d; |
---|
| 2610 | a1 -= 3.0*d*iE; |
---|
| 2611 | a2 += 3.0*d*iE*iE; |
---|
| 2612 | a3 -= d*iE*iE*iE; |
---|
[2012] | 2613 | } |
---|
| 2614 | |
---|
[2344] | 2615 | //subtract constant value for masked regions at the edge of spectrum |
---|
| 2616 | if (idxEdge[0] > 0) { |
---|
| 2617 | int n = idxEdge[0]; |
---|
| 2618 | for (int i = 0; i < idxEdge[0]; ++i) { |
---|
| 2619 | //--cubic extrapolate-- |
---|
| 2620 | //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i]; |
---|
| 2621 | //--linear extrapolate-- |
---|
| 2622 | //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 2623 | //--constant-- |
---|
| 2624 | r1[i] = r1[n]; |
---|
| 2625 | } |
---|
| 2626 | } |
---|
| 2627 | if (idxEdge[nPiece] < nChan) { |
---|
| 2628 | int n = idxEdge[nPiece]-1; |
---|
| 2629 | for (int i = idxEdge[nPiece]; i < nChan; ++i) { |
---|
| 2630 | //--cubic extrapolate-- |
---|
| 2631 | //int m = 4*(nPiece-1); |
---|
| 2632 | //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i]; |
---|
| 2633 | //--linear extrapolate-- |
---|
| 2634 | //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 2635 | //--constant-- |
---|
| 2636 | r1[i] = r1[n]; |
---|
| 2637 | } |
---|
| 2638 | } |
---|
| 2639 | |
---|
| 2640 | for (int i = 0; i < nChan; ++i) { |
---|
| 2641 | residual[i] = z1[i] - r1[i]; |
---|
| 2642 | } |
---|
| 2643 | |
---|
[2012] | 2644 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 2645 | break; |
---|
| 2646 | } else { |
---|
| 2647 | double stdDev = 0.0; |
---|
| 2648 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2649 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2012] | 2650 | } |
---|
| 2651 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 2652 | |
---|
| 2653 | double thres = stdDev * thresClip; |
---|
| 2654 | int newNData = 0; |
---|
| 2655 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2656 | if (abs(residual[i]) >= thres) { |
---|
[2012] | 2657 | maskArray[i] = 0; |
---|
| 2658 | } |
---|
| 2659 | if (maskArray[i] > 0) { |
---|
| 2660 | newNData++; |
---|
| 2661 | } |
---|
| 2662 | } |
---|
[2081] | 2663 | if (newNData == nData) { |
---|
[2064] | 2664 | break; //no more flag to add. iteration stops. |
---|
[2012] | 2665 | } else { |
---|
[2081] | 2666 | nData = newNData; |
---|
[2012] | 2667 | } |
---|
| 2668 | } |
---|
| 2669 | } |
---|
| 2670 | |
---|
[2193] | 2671 | nClipped = initNData - nData; |
---|
| 2672 | |
---|
[2344] | 2673 | std::vector<float> result(nChan); |
---|
[2058] | 2674 | if (getResidual) { |
---|
| 2675 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 2676 | result[i] = (float)residual[i]; |
---|
[2058] | 2677 | } |
---|
| 2678 | } else { |
---|
| 2679 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 2680 | result[i] = (float)r1[i]; |
---|
[2058] | 2681 | } |
---|
[2012] | 2682 | } |
---|
| 2683 | |
---|
[2058] | 2684 | return result; |
---|
[2012] | 2685 | } |
---|
| 2686 | |
---|
[2344] | 2687 | void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2081] | 2688 | { |
---|
[2186] | 2689 | nWaves.clear(); |
---|
| 2690 | |
---|
| 2691 | if (applyFFT) { |
---|
| 2692 | string fftThAttr; |
---|
| 2693 | float fftThSigma; |
---|
| 2694 | int fftThTop; |
---|
| 2695 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
| 2696 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
| 2697 | } |
---|
| 2698 | |
---|
| 2699 | addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves); |
---|
| 2700 | } |
---|
| 2701 | |
---|
| 2702 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
| 2703 | { |
---|
| 2704 | uInt idxSigma = fftThresh.find("sigma"); |
---|
| 2705 | uInt idxTop = fftThresh.find("top"); |
---|
| 2706 | |
---|
| 2707 | if (idxSigma == fftThresh.size() - 5) { |
---|
| 2708 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
| 2709 | is >> fftThSigma; |
---|
| 2710 | fftThAttr = "sigma"; |
---|
| 2711 | } else if (idxTop == 0) { |
---|
| 2712 | std::istringstream is(fftThresh.substr(3)); |
---|
| 2713 | is >> fftThTop; |
---|
| 2714 | fftThAttr = "top"; |
---|
| 2715 | } else { |
---|
| 2716 | bool isNumber = true; |
---|
| 2717 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
| 2718 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
| 2719 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
| 2720 | isNumber = false; |
---|
| 2721 | break; |
---|
| 2722 | } |
---|
| 2723 | } |
---|
| 2724 | if (isNumber) { |
---|
| 2725 | std::istringstream is(fftThresh); |
---|
| 2726 | is >> fftThSigma; |
---|
| 2727 | fftThAttr = "sigma"; |
---|
| 2728 | } else { |
---|
| 2729 | throw(AipsError("fftthresh has a wrong value")); |
---|
| 2730 | } |
---|
| 2731 | } |
---|
| 2732 | } |
---|
| 2733 | |
---|
| 2734 | void Scantable::doSelectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftMethod, const float fftThSigma, const int fftThTop, const std::string& fftThAttr, std::vector<int>& nWaves) |
---|
| 2735 | { |
---|
| 2736 | std::vector<float> fspec; |
---|
| 2737 | if (fftMethod == "fft") { |
---|
| 2738 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
| 2739 | //} else if (fftMethod == "lsp") { |
---|
| 2740 | // fspec = lombScarglePeriodogram(whichrow); |
---|
| 2741 | } |
---|
| 2742 | |
---|
| 2743 | if (fftThAttr == "sigma") { |
---|
| 2744 | float mean = 0.0; |
---|
| 2745 | float mean2 = 0.0; |
---|
| 2746 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 2747 | mean += fspec[i]; |
---|
| 2748 | mean2 += fspec[i]*fspec[i]; |
---|
| 2749 | } |
---|
| 2750 | mean /= float(fspec.size()); |
---|
| 2751 | mean2 /= float(fspec.size()); |
---|
| 2752 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
| 2753 | |
---|
| 2754 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 2755 | if (fspec[i] >= thres) { |
---|
| 2756 | nWaves.push_back(i); |
---|
| 2757 | } |
---|
| 2758 | } |
---|
| 2759 | |
---|
| 2760 | } else if (fftThAttr == "top") { |
---|
| 2761 | for (int i = 0; i < fftThTop; ++i) { |
---|
| 2762 | float max = 0.0; |
---|
| 2763 | int maxIdx = 0; |
---|
| 2764 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
| 2765 | if (fspec[j] > max) { |
---|
| 2766 | max = fspec[j]; |
---|
| 2767 | maxIdx = j; |
---|
| 2768 | } |
---|
| 2769 | } |
---|
| 2770 | nWaves.push_back(maxIdx); |
---|
| 2771 | fspec[maxIdx] = 0.0; |
---|
| 2772 | } |
---|
| 2773 | |
---|
| 2774 | } |
---|
| 2775 | |
---|
| 2776 | if (nWaves.size() > 1) { |
---|
| 2777 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2778 | } |
---|
| 2779 | } |
---|
| 2780 | |
---|
| 2781 | void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
| 2782 | { |
---|
| 2783 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
| 2784 | bool found = false; |
---|
| 2785 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
| 2786 | if (nWaves[j] == addNWaves[i]) { |
---|
| 2787 | found = true; |
---|
| 2788 | break; |
---|
| 2789 | } |
---|
| 2790 | } |
---|
| 2791 | if (!found) nWaves.push_back(addNWaves[i]); |
---|
| 2792 | } |
---|
| 2793 | |
---|
| 2794 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
| 2795 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
| 2796 | if (*j == rejectNWaves[i]) { |
---|
| 2797 | j = nWaves.erase(j); |
---|
| 2798 | } else { |
---|
| 2799 | ++j; |
---|
| 2800 | } |
---|
| 2801 | } |
---|
| 2802 | } |
---|
| 2803 | |
---|
| 2804 | if (nWaves.size() > 1) { |
---|
| 2805 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2806 | unique(nWaves.begin(), nWaves.end()); |
---|
| 2807 | } |
---|
| 2808 | } |
---|
| 2809 | |
---|
[2189] | 2810 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2186] | 2811 | { |
---|
[2193] | 2812 | try { |
---|
| 2813 | ofstream ofs; |
---|
| 2814 | String coordInfo = ""; |
---|
| 2815 | bool hasSameNchan = true; |
---|
| 2816 | bool outTextFile = false; |
---|
[2012] | 2817 | |
---|
[2193] | 2818 | if (blfile != "") { |
---|
| 2819 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2820 | if (ofs) outTextFile = true; |
---|
| 2821 | } |
---|
[2012] | 2822 | |
---|
[2193] | 2823 | if (outLogger || outTextFile) { |
---|
| 2824 | coordInfo = getCoordInfo()[0]; |
---|
| 2825 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2826 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2827 | } |
---|
[2012] | 2828 | |
---|
[2193] | 2829 | //Fitter fitter = Fitter(); |
---|
| 2830 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 2831 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2832 | |
---|
[2193] | 2833 | int nRow = nrow(); |
---|
| 2834 | std::vector<bool> chanMask; |
---|
| 2835 | std::vector<int> nWaves; |
---|
[2012] | 2836 | |
---|
[2193] | 2837 | bool showProgress; |
---|
| 2838 | int minNRow; |
---|
| 2839 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2840 | |
---|
[2193] | 2841 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2842 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2843 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
[2186] | 2844 | |
---|
[2193] | 2845 | //FOR DEBUGGING------------ |
---|
| 2846 | if (whichrow < 0) {// == nRow -1) { |
---|
| 2847 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow); |
---|
| 2848 | if (applyFFT) { |
---|
[2186] | 2849 | cout << "[ "; |
---|
| 2850 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
| 2851 | cout << nWaves[j] << ", "; |
---|
| 2852 | } |
---|
| 2853 | cout << " ] " << endl; |
---|
[2193] | 2854 | } |
---|
| 2855 | cout << flush; |
---|
[2186] | 2856 | } |
---|
[2193] | 2857 | //------------------------- |
---|
| 2858 | |
---|
| 2859 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2860 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2861 | std::vector<float> params; |
---|
| 2862 | int nClipped = 0; |
---|
| 2863 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2864 | setSpectrum(res, whichrow); |
---|
| 2865 | // |
---|
| 2866 | |
---|
| 2867 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped); |
---|
| 2868 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2186] | 2869 | } |
---|
| 2870 | |
---|
[2193] | 2871 | if (outTextFile) ofs.close(); |
---|
[2012] | 2872 | |
---|
[2193] | 2873 | } catch (...) { |
---|
| 2874 | throw; |
---|
[1931] | 2875 | } |
---|
[1907] | 2876 | } |
---|
| 2877 | |
---|
[2189] | 2878 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 2879 | { |
---|
[2193] | 2880 | try { |
---|
| 2881 | ofstream ofs; |
---|
| 2882 | String coordInfo = ""; |
---|
| 2883 | bool hasSameNchan = true; |
---|
| 2884 | bool outTextFile = false; |
---|
[2012] | 2885 | |
---|
[2193] | 2886 | if (blfile != "") { |
---|
| 2887 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2888 | if (ofs) outTextFile = true; |
---|
| 2889 | } |
---|
[2012] | 2890 | |
---|
[2193] | 2891 | if (outLogger || outTextFile) { |
---|
| 2892 | coordInfo = getCoordInfo()[0]; |
---|
| 2893 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2894 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2895 | } |
---|
[2012] | 2896 | |
---|
[2193] | 2897 | //Fitter fitter = Fitter(); |
---|
| 2898 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 2899 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2900 | |
---|
[2193] | 2901 | int nRow = nrow(); |
---|
| 2902 | std::vector<bool> chanMask; |
---|
| 2903 | std::vector<int> nWaves; |
---|
[2186] | 2904 | |
---|
[2193] | 2905 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2906 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2907 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 2908 | |
---|
[2193] | 2909 | bool showProgress; |
---|
| 2910 | int minNRow; |
---|
| 2911 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2912 | |
---|
[2193] | 2913 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 2914 | |
---|
[2193] | 2915 | //------------------------------------------------------- |
---|
| 2916 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2917 | //------------------------------------------------------- |
---|
| 2918 | int edgeSize = edge.size(); |
---|
| 2919 | std::vector<int> currentEdge; |
---|
| 2920 | if (edgeSize >= 2) { |
---|
| 2921 | int idx = 0; |
---|
| 2922 | if (edgeSize > 2) { |
---|
| 2923 | if (edgeSize < minEdgeSize) { |
---|
| 2924 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2925 | } |
---|
| 2926 | idx = 2 * getIF(whichrow); |
---|
[2012] | 2927 | } |
---|
[2193] | 2928 | currentEdge.push_back(edge[idx]); |
---|
| 2929 | currentEdge.push_back(edge[idx+1]); |
---|
| 2930 | } else { |
---|
| 2931 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 2932 | } |
---|
[2193] | 2933 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2934 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2935 | chanMask = lineFinder.getMask(); |
---|
| 2936 | //------------------------------------------------------- |
---|
| 2937 | |
---|
| 2938 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
| 2939 | |
---|
| 2940 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2941 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2942 | std::vector<float> params; |
---|
| 2943 | int nClipped = 0; |
---|
| 2944 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2945 | setSpectrum(res, whichrow); |
---|
| 2946 | // |
---|
| 2947 | |
---|
| 2948 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped); |
---|
| 2949 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2012] | 2950 | } |
---|
| 2951 | |
---|
[2193] | 2952 | if (outTextFile) ofs.close(); |
---|
[2012] | 2953 | |
---|
[2193] | 2954 | } catch (...) { |
---|
| 2955 | throw; |
---|
[2047] | 2956 | } |
---|
| 2957 | } |
---|
| 2958 | |
---|
[2193] | 2959 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 2960 | { |
---|
[2047] | 2961 | if (data.size() != mask.size()) { |
---|
[2081] | 2962 | throw(AipsError("data and mask sizes are not identical")); |
---|
[2047] | 2963 | } |
---|
[2081] | 2964 | if (data.size() < 2) { |
---|
| 2965 | throw(AipsError("data size is too short")); |
---|
| 2966 | } |
---|
| 2967 | if (waveNumbers.size() == 0) { |
---|
[2186] | 2968 | throw(AipsError("no wave numbers given")); |
---|
[2081] | 2969 | } |
---|
| 2970 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
| 2971 | nWaves.reserve(waveNumbers.size()); |
---|
| 2972 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
| 2973 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2974 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
| 2975 | nWaves.erase(end_it, nWaves.end()); |
---|
| 2976 | |
---|
| 2977 | int minNWaves = nWaves[0]; |
---|
| 2978 | if (minNWaves < 0) { |
---|
[2058] | 2979 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
| 2980 | } |
---|
[2081] | 2981 | bool hasConstantTerm = (minNWaves == 0); |
---|
[2047] | 2982 | |
---|
| 2983 | int nChan = data.size(); |
---|
| 2984 | std::vector<int> maskArray; |
---|
| 2985 | std::vector<int> x; |
---|
| 2986 | for (int i = 0; i < nChan; ++i) { |
---|
| 2987 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 2988 | if (mask[i]) { |
---|
| 2989 | x.push_back(i); |
---|
| 2990 | } |
---|
| 2991 | } |
---|
| 2992 | |
---|
[2081] | 2993 | int initNData = x.size(); |
---|
[2047] | 2994 | |
---|
[2081] | 2995 | int nData = initNData; |
---|
| 2996 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
| 2997 | |
---|
| 2998 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
[2186] | 2999 | double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK) |
---|
[2081] | 3000 | |
---|
| 3001 | // xArray : contains elemental values for computing the least-square matrix. |
---|
| 3002 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
| 3003 | // Each xArray element are as follows: |
---|
| 3004 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
| 3005 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])}, |
---|
| 3006 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])}, |
---|
| 3007 | // where (1 <= n <= nMaxWavesInSW), |
---|
| 3008 | // or, |
---|
| 3009 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])}, |
---|
| 3010 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])}, |
---|
| 3011 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
| 3012 | std::vector<std::vector<double> > xArray; |
---|
| 3013 | if (hasConstantTerm) { |
---|
| 3014 | std::vector<double> xu; |
---|
| 3015 | for (int j = 0; j < nChan; ++j) { |
---|
| 3016 | xu.push_back(1.0); |
---|
| 3017 | } |
---|
| 3018 | xArray.push_back(xu); |
---|
| 3019 | } |
---|
| 3020 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
| 3021 | double xFactor = baseXFactor*(double)nWaves[i]; |
---|
| 3022 | std::vector<double> xs, xc; |
---|
| 3023 | xs.clear(); |
---|
| 3024 | xc.clear(); |
---|
| 3025 | for (int j = 0; j < nChan; ++j) { |
---|
| 3026 | xs.push_back(sin(xFactor*(double)j)); |
---|
| 3027 | xc.push_back(cos(xFactor*(double)j)); |
---|
| 3028 | } |
---|
| 3029 | xArray.push_back(xs); |
---|
| 3030 | xArray.push_back(xc); |
---|
| 3031 | } |
---|
| 3032 | |
---|
| 3033 | std::vector<double> z1, r1, residual; |
---|
[2047] | 3034 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3035 | z1.push_back((double)data[i]); |
---|
[2047] | 3036 | r1.push_back(0.0); |
---|
[2081] | 3037 | residual.push_back(0.0); |
---|
[2047] | 3038 | } |
---|
| 3039 | |
---|
| 3040 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2081] | 3041 | // xMatrix : horizontal concatenation of |
---|
| 3042 | // the least-sq. matrix (left) and an |
---|
| 3043 | // identity matrix (right). |
---|
| 3044 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2047] | 3045 | double xMatrix[nDOF][2*nDOF]; |
---|
| 3046 | double zMatrix[nDOF]; |
---|
| 3047 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3048 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 3049 | xMatrix[i][j] = 0.0; |
---|
[2012] | 3050 | } |
---|
[2047] | 3051 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 3052 | zMatrix[i] = 0.0; |
---|
| 3053 | } |
---|
| 3054 | |
---|
[2193] | 3055 | int nUseData = 0; |
---|
[2081] | 3056 | for (int k = 0; k < nChan; ++k) { |
---|
| 3057 | if (maskArray[k] == 0) continue; |
---|
| 3058 | |
---|
| 3059 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3060 | for (int j = i; j < nDOF; ++j) { |
---|
| 3061 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
| 3062 | } |
---|
| 3063 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
| 3064 | } |
---|
[2193] | 3065 | |
---|
| 3066 | nUseData++; |
---|
[2047] | 3067 | } |
---|
| 3068 | |
---|
[2193] | 3069 | if (nUseData < 1) { |
---|
| 3070 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
| 3071 | } |
---|
| 3072 | |
---|
[2047] | 3073 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3074 | for (int j = 0; j < i; ++j) { |
---|
| 3075 | xMatrix[i][j] = xMatrix[j][i]; |
---|
[2012] | 3076 | } |
---|
| 3077 | } |
---|
| 3078 | |
---|
[2047] | 3079 | std::vector<double> invDiag; |
---|
| 3080 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3081 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 3082 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3083 | xMatrix[i][j] *= invDiag[i]; |
---|
| 3084 | } |
---|
| 3085 | } |
---|
| 3086 | |
---|
| 3087 | for (int k = 0; k < nDOF; ++k) { |
---|
| 3088 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3089 | if (i != k) { |
---|
| 3090 | double factor1 = xMatrix[k][k]; |
---|
| 3091 | double factor2 = xMatrix[i][k]; |
---|
| 3092 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3093 | xMatrix[i][j] *= factor1; |
---|
| 3094 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 3095 | xMatrix[i][j] /= factor1; |
---|
| 3096 | } |
---|
| 3097 | } |
---|
| 3098 | } |
---|
| 3099 | double xDiag = xMatrix[k][k]; |
---|
| 3100 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3101 | xMatrix[k][j] /= xDiag; |
---|
| 3102 | } |
---|
| 3103 | } |
---|
| 3104 | |
---|
| 3105 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3106 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3107 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 3108 | } |
---|
| 3109 | } |
---|
| 3110 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
[2081] | 3111 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
| 3112 | //and cosine functions, respectively. |
---|
[2047] | 3113 | std::vector<double> y; |
---|
[2081] | 3114 | params.clear(); |
---|
[2047] | 3115 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3116 | y.push_back(0.0); |
---|
| 3117 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3118 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 3119 | } |
---|
[2081] | 3120 | params.push_back(y[i]); |
---|
[2047] | 3121 | } |
---|
| 3122 | |
---|
| 3123 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3124 | r1[i] = y[0]; |
---|
| 3125 | for (int j = 1; j < nDOF; ++j) { |
---|
| 3126 | r1[i] += y[j]*xArray[j][i]; |
---|
| 3127 | } |
---|
| 3128 | residual[i] = z1[i] - r1[i]; |
---|
[2047] | 3129 | } |
---|
| 3130 | |
---|
| 3131 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 3132 | break; |
---|
| 3133 | } else { |
---|
| 3134 | double stdDev = 0.0; |
---|
| 3135 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3136 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2047] | 3137 | } |
---|
| 3138 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 3139 | |
---|
| 3140 | double thres = stdDev * thresClip; |
---|
| 3141 | int newNData = 0; |
---|
| 3142 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3143 | if (abs(residual[i]) >= thres) { |
---|
[2047] | 3144 | maskArray[i] = 0; |
---|
| 3145 | } |
---|
| 3146 | if (maskArray[i] > 0) { |
---|
| 3147 | newNData++; |
---|
| 3148 | } |
---|
| 3149 | } |
---|
[2081] | 3150 | if (newNData == nData) { |
---|
| 3151 | break; //no more flag to add. iteration stops. |
---|
[2047] | 3152 | } else { |
---|
[2081] | 3153 | nData = newNData; |
---|
[2047] | 3154 | } |
---|
| 3155 | } |
---|
[2012] | 3156 | } |
---|
| 3157 | |
---|
[2193] | 3158 | nClipped = initNData - nData; |
---|
| 3159 | |
---|
[2058] | 3160 | std::vector<float> result; |
---|
| 3161 | if (getResidual) { |
---|
| 3162 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3163 | result.push_back((float)residual[i]); |
---|
[2058] | 3164 | } |
---|
| 3165 | } else { |
---|
| 3166 | for (int i = 0; i < nChan; ++i) { |
---|
| 3167 | result.push_back((float)r1[i]); |
---|
| 3168 | } |
---|
[2047] | 3169 | } |
---|
| 3170 | |
---|
[2058] | 3171 | return result; |
---|
[2012] | 3172 | } |
---|
| 3173 | |
---|
[2047] | 3174 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
| 3175 | { |
---|
[2081] | 3176 | std::vector<double> dAbcissa = getAbcissa(whichrow); |
---|
| 3177 | std::vector<float> abcissa; |
---|
| 3178 | for (uInt i = 0; i < dAbcissa.size(); ++i) { |
---|
| 3179 | abcissa.push_back((float)dAbcissa[i]); |
---|
[2047] | 3180 | } |
---|
| 3181 | std::vector<float> spec = getSpectrum(whichrow); |
---|
[2012] | 3182 | |
---|
[2081] | 3183 | fitter.setData(abcissa, spec, mask); |
---|
[2047] | 3184 | fitter.lfit(); |
---|
| 3185 | } |
---|
| 3186 | |
---|
| 3187 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
| 3188 | { |
---|
[2186] | 3189 | std::vector<bool> mask = getMask(whichrow); |
---|
| 3190 | uInt maskSize = mask.size(); |
---|
| 3191 | if (maskSize != inMask.size()) { |
---|
| 3192 | throw(AipsError("mask sizes are not the same.")); |
---|
[2047] | 3193 | } |
---|
[2186] | 3194 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 3195 | mask[i] = mask[i] && inMask[i]; |
---|
[2047] | 3196 | } |
---|
| 3197 | |
---|
[2186] | 3198 | return mask; |
---|
[2047] | 3199 | } |
---|
| 3200 | |
---|
| 3201 | /* |
---|
| 3202 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
| 3203 | { |
---|
| 3204 | int edgeSize = edge.size(); |
---|
| 3205 | std::vector<int> currentEdge; |
---|
| 3206 | if (edgeSize >= 2) { |
---|
| 3207 | int idx = 0; |
---|
| 3208 | if (edgeSize > 2) { |
---|
| 3209 | if (edgeSize < minEdgeSize) { |
---|
| 3210 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3211 | } |
---|
| 3212 | idx = 2 * getIF(whichrow); |
---|
| 3213 | } |
---|
| 3214 | currentEdge.push_back(edge[idx]); |
---|
| 3215 | currentEdge.push_back(edge[idx+1]); |
---|
| 3216 | } else { |
---|
| 3217 | throw(AipsError("Wrong length of edge element")); |
---|
| 3218 | } |
---|
| 3219 | |
---|
| 3220 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 3221 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
| 3222 | |
---|
| 3223 | return lineFinder.getMask(); |
---|
| 3224 | } |
---|
| 3225 | */ |
---|
| 3226 | |
---|
| 3227 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
[2186] | 3228 | 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) |
---|
| 3229 | { |
---|
[2047] | 3230 | if (outLogger || outTextFile) { |
---|
| 3231 | std::vector<float> params = fitter.getParameters(); |
---|
| 3232 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
| 3233 | float rms = getRms(chanMask, whichrow); |
---|
| 3234 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 3235 | |
---|
| 3236 | if (outLogger) { |
---|
| 3237 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2193] | 3238 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 3239 | } |
---|
| 3240 | if (outTextFile) { |
---|
[2193] | 3241 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush; |
---|
[2047] | 3242 | } |
---|
| 3243 | } |
---|
| 3244 | } |
---|
| 3245 | |
---|
| 3246 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
[2193] | 3247 | 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 int nClipped) |
---|
[2186] | 3248 | { |
---|
[2047] | 3249 | if (outLogger || outTextFile) { |
---|
| 3250 | float rms = getRms(chanMask, whichrow); |
---|
| 3251 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 3252 | std::vector<bool> fixed; |
---|
| 3253 | fixed.clear(); |
---|
[2047] | 3254 | |
---|
| 3255 | if (outLogger) { |
---|
| 3256 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2193] | 3257 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 3258 | } |
---|
| 3259 | if (outTextFile) { |
---|
[2193] | 3260 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush; |
---|
[2047] | 3261 | } |
---|
| 3262 | } |
---|
| 3263 | } |
---|
| 3264 | |
---|
| 3265 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */ |
---|
[2193] | 3266 | 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 int nClipped) |
---|
[2186] | 3267 | { |
---|
[2047] | 3268 | if (outLogger || outTextFile) { |
---|
| 3269 | float rms = getRms(chanMask, whichrow); |
---|
| 3270 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 3271 | std::vector<bool> fixed; |
---|
| 3272 | fixed.clear(); |
---|
[2047] | 3273 | |
---|
| 3274 | if (outLogger) { |
---|
| 3275 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2193] | 3276 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 3277 | } |
---|
| 3278 | if (outTextFile) { |
---|
[2193] | 3279 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush; |
---|
[2047] | 3280 | } |
---|
| 3281 | } |
---|
| 3282 | } |
---|
| 3283 | |
---|
[2189] | 3284 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
[2186] | 3285 | { |
---|
[2189] | 3286 | int idxDelimiter = progressInfo.find(","); |
---|
| 3287 | if (idxDelimiter < 0) { |
---|
| 3288 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
| 3289 | } |
---|
| 3290 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
| 3291 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
| 3292 | is >> minNRow; |
---|
| 3293 | } |
---|
| 3294 | |
---|
| 3295 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
| 3296 | { |
---|
| 3297 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
[2186] | 3298 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
| 3299 | if (nInterval == 0) nInterval++; |
---|
| 3300 | |
---|
[2193] | 3301 | if (nProcessed % nInterval == 0) { |
---|
[2189] | 3302 | printf("\r"); //go to the head of line |
---|
[2186] | 3303 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
[2189] | 3304 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
| 3305 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
[2186] | 3306 | fflush(NULL); |
---|
| 3307 | } |
---|
[2193] | 3308 | |
---|
[2186] | 3309 | if (nProcessed == nTotal - 1) { |
---|
| 3310 | printf("\r\x1b[K"); //clear |
---|
| 3311 | fflush(NULL); |
---|
| 3312 | } |
---|
[2193] | 3313 | |
---|
[2186] | 3314 | } |
---|
| 3315 | } |
---|
| 3316 | |
---|
| 3317 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
| 3318 | { |
---|
| 3319 | std::vector<bool> mask = getMask(whichrow); |
---|
| 3320 | |
---|
| 3321 | if (inMask.size() > 0) { |
---|
| 3322 | uInt maskSize = mask.size(); |
---|
| 3323 | if (maskSize != inMask.size()) { |
---|
| 3324 | throw(AipsError("mask sizes are not the same.")); |
---|
| 3325 | } |
---|
| 3326 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 3327 | mask[i] = mask[i] && inMask[i]; |
---|
| 3328 | } |
---|
| 3329 | } |
---|
| 3330 | |
---|
| 3331 | Vector<Float> spec = getSpectrum(whichrow); |
---|
| 3332 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
| 3333 | |
---|
| 3334 | FFTServer<Float,Complex> ffts; |
---|
| 3335 | Vector<Complex> fftres; |
---|
| 3336 | ffts.fft0(fftres, spec); |
---|
| 3337 | |
---|
| 3338 | std::vector<float> res; |
---|
| 3339 | float norm = float(2.0/double(spec.size())); |
---|
| 3340 | |
---|
| 3341 | if (getRealImag) { |
---|
| 3342 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 3343 | res.push_back(real(fftres[i])*norm); |
---|
| 3344 | res.push_back(imag(fftres[i])*norm); |
---|
| 3345 | } |
---|
| 3346 | } else { |
---|
| 3347 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 3348 | res.push_back(abs(fftres[i])*norm); |
---|
| 3349 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
| 3350 | } |
---|
| 3351 | } |
---|
| 3352 | |
---|
| 3353 | return res; |
---|
| 3354 | } |
---|
| 3355 | |
---|
| 3356 | |
---|
| 3357 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
| 3358 | { |
---|
[2012] | 3359 | Vector<Float> spec; |
---|
| 3360 | specCol_.get(whichrow, spec); |
---|
| 3361 | |
---|
| 3362 | float mean = 0.0; |
---|
| 3363 | float smean = 0.0; |
---|
| 3364 | int n = 0; |
---|
[2047] | 3365 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
[2012] | 3366 | if (mask[i]) { |
---|
| 3367 | mean += spec[i]; |
---|
| 3368 | smean += spec[i]*spec[i]; |
---|
| 3369 | n++; |
---|
| 3370 | } |
---|
| 3371 | } |
---|
| 3372 | |
---|
| 3373 | mean /= (float)n; |
---|
| 3374 | smean /= (float)n; |
---|
| 3375 | |
---|
| 3376 | return sqrt(smean - mean*mean); |
---|
| 3377 | } |
---|
| 3378 | |
---|
| 3379 | |
---|
[2186] | 3380 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const |
---|
[2012] | 3381 | { |
---|
| 3382 | ostringstream oss; |
---|
| 3383 | |
---|
| 3384 | if (verbose) { |
---|
| 3385 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
| 3386 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
| 3387 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
| 3388 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
| 3389 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
| 3390 | oss << "Fitter range = " << masklist << endl; |
---|
| 3391 | oss << "Baseline parameters" << endl; |
---|
| 3392 | oss << flush; |
---|
| 3393 | } |
---|
| 3394 | |
---|
| 3395 | return String(oss); |
---|
| 3396 | } |
---|
| 3397 | |
---|
[2193] | 3398 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const |
---|
[2012] | 3399 | { |
---|
| 3400 | ostringstream oss; |
---|
| 3401 | |
---|
| 3402 | if (verbose) { |
---|
| 3403 | oss << "Results of baseline fit" << endl; |
---|
| 3404 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
[2193] | 3405 | if (nClipped >= 0) { |
---|
| 3406 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
| 3407 | } |
---|
[2094] | 3408 | for (int i = 0; i < 60; ++i) { |
---|
| 3409 | oss << "-"; |
---|
| 3410 | } |
---|
[2131] | 3411 | oss << endl; |
---|
[2094] | 3412 | oss << flush; |
---|
[2012] | 3413 | } |
---|
| 3414 | |
---|
| 3415 | return String(oss); |
---|
| 3416 | } |
---|
| 3417 | |
---|
[2186] | 3418 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
| 3419 | const std::vector<bool>& fixed, |
---|
| 3420 | float rms, |
---|
[2193] | 3421 | int nClipped, |
---|
[2186] | 3422 | const std::string& masklist, |
---|
| 3423 | int whichrow, |
---|
| 3424 | bool verbose, |
---|
| 3425 | int start, int count, |
---|
| 3426 | bool resetparamid) const |
---|
[2047] | 3427 | { |
---|
[2064] | 3428 | int nParam = (int)(params.size()); |
---|
[2047] | 3429 | |
---|
[2064] | 3430 | if (nParam < 1) { |
---|
| 3431 | return(" Not fitted"); |
---|
| 3432 | } else { |
---|
| 3433 | |
---|
| 3434 | ostringstream oss; |
---|
| 3435 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
| 3436 | |
---|
| 3437 | if (start < 0) start = 0; |
---|
| 3438 | if (count < 0) count = nParam; |
---|
| 3439 | int end = start + count; |
---|
| 3440 | if (end > nParam) end = nParam; |
---|
| 3441 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
| 3442 | |
---|
| 3443 | for (int i = start; i < end; ++i) { |
---|
| 3444 | if (i > start) { |
---|
[2047] | 3445 | oss << ","; |
---|
| 3446 | } |
---|
[2064] | 3447 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
| 3448 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
[2047] | 3449 | } |
---|
[2064] | 3450 | |
---|
| 3451 | oss << endl; |
---|
[2193] | 3452 | oss << formatBaselineParamsFooter(rms, nClipped, verbose); |
---|
[2064] | 3453 | |
---|
| 3454 | return String(oss); |
---|
[2047] | 3455 | } |
---|
| 3456 | |
---|
| 3457 | } |
---|
| 3458 | |
---|
[2193] | 3459 | std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose) const |
---|
[2012] | 3460 | { |
---|
[2064] | 3461 | int nOutParam = (int)(params.size()); |
---|
| 3462 | int nPiece = (int)(ranges.size()) - 1; |
---|
[2012] | 3463 | |
---|
[2064] | 3464 | if (nOutParam < 1) { |
---|
| 3465 | return(" Not fitted"); |
---|
| 3466 | } else if (nPiece < 0) { |
---|
[2193] | 3467 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose); |
---|
[2064] | 3468 | } else if (nPiece < 1) { |
---|
| 3469 | return(" Bad count of the piece edge info"); |
---|
| 3470 | } else if (nOutParam % nPiece != 0) { |
---|
| 3471 | return(" Bad count of the output baseline parameters"); |
---|
| 3472 | } else { |
---|
| 3473 | |
---|
| 3474 | int nParam = nOutParam / nPiece; |
---|
| 3475 | |
---|
| 3476 | ostringstream oss; |
---|
| 3477 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
| 3478 | |
---|
| 3479 | stringstream ss; |
---|
| 3480 | ss << ranges[nPiece] << flush; |
---|
| 3481 | int wRange = ss.str().size() * 2 + 5; |
---|
| 3482 | |
---|
| 3483 | for (int i = 0; i < nPiece; ++i) { |
---|
[2047] | 3484 | ss.str(""); |
---|
[2064] | 3485 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
| 3486 | oss << left << setw(wRange) << ss.str(); |
---|
[2193] | 3487 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true); |
---|
[2012] | 3488 | } |
---|
[2064] | 3489 | |
---|
[2193] | 3490 | oss << formatBaselineParamsFooter(rms, nClipped, verbose); |
---|
[2064] | 3491 | |
---|
| 3492 | return String(oss); |
---|
[2012] | 3493 | } |
---|
| 3494 | |
---|
| 3495 | } |
---|
| 3496 | |
---|
[2047] | 3497 | bool Scantable::hasSameNchanOverIFs() |
---|
[2012] | 3498 | { |
---|
[2047] | 3499 | int nIF = nif(-1); |
---|
| 3500 | int nCh; |
---|
| 3501 | int totalPositiveNChan = 0; |
---|
| 3502 | int nPositiveNChan = 0; |
---|
[2012] | 3503 | |
---|
[2047] | 3504 | for (int i = 0; i < nIF; ++i) { |
---|
| 3505 | nCh = nchan(i); |
---|
| 3506 | if (nCh > 0) { |
---|
| 3507 | totalPositiveNChan += nCh; |
---|
| 3508 | nPositiveNChan++; |
---|
[2012] | 3509 | } |
---|
| 3510 | } |
---|
| 3511 | |
---|
[2047] | 3512 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
[2012] | 3513 | } |
---|
| 3514 | |
---|
[2047] | 3515 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
[2012] | 3516 | { |
---|
| 3517 | if (mask.size() < 2) { |
---|
| 3518 | throw(AipsError("The mask elements should be > 1")); |
---|
| 3519 | } |
---|
[2047] | 3520 | int IF = getIF(whichrow); |
---|
| 3521 | if (mask.size() != (uInt)nchan(IF)) { |
---|
[2012] | 3522 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
| 3523 | } |
---|
| 3524 | |
---|
[2047] | 3525 | if (verbose) { |
---|
[2012] | 3526 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
| 3527 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
| 3528 | if (!hasSameNchan) { |
---|
[2047] | 3529 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
[2012] | 3530 | } |
---|
| 3531 | logOs << LogIO::POST; |
---|
| 3532 | } |
---|
| 3533 | |
---|
| 3534 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
[2047] | 3535 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
| 3536 | |
---|
[2012] | 3537 | ostringstream oss; |
---|
| 3538 | oss.setf(ios::fixed); |
---|
| 3539 | oss << setprecision(1) << "["; |
---|
[2047] | 3540 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
[2012] | 3541 | if (i > 0) oss << ","; |
---|
[2047] | 3542 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
[2012] | 3543 | } |
---|
| 3544 | oss << "]" << flush; |
---|
| 3545 | |
---|
| 3546 | return String(oss); |
---|
| 3547 | } |
---|
| 3548 | |
---|
[2047] | 3549 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
[2012] | 3550 | { |
---|
[2047] | 3551 | if (mask.size() < 2) { |
---|
| 3552 | throw(AipsError("The mask elements should be > 1")); |
---|
[2012] | 3553 | } |
---|
| 3554 | |
---|
[2047] | 3555 | std::vector<int> out, startIndices, endIndices; |
---|
| 3556 | int maskSize = mask.size(); |
---|
[2012] | 3557 | |
---|
[2047] | 3558 | startIndices.clear(); |
---|
| 3559 | endIndices.clear(); |
---|
| 3560 | |
---|
| 3561 | if (mask[0]) { |
---|
| 3562 | startIndices.push_back(0); |
---|
[2012] | 3563 | } |
---|
[2047] | 3564 | for (int i = 1; i < maskSize; ++i) { |
---|
| 3565 | if ((!mask[i-1]) && mask[i]) { |
---|
| 3566 | startIndices.push_back(i); |
---|
| 3567 | } else if (mask[i-1] && (!mask[i])) { |
---|
| 3568 | endIndices.push_back(i-1); |
---|
| 3569 | } |
---|
[2012] | 3570 | } |
---|
[2047] | 3571 | if (mask[maskSize-1]) { |
---|
| 3572 | endIndices.push_back(maskSize-1); |
---|
| 3573 | } |
---|
[2012] | 3574 | |
---|
[2047] | 3575 | if (startIndices.size() != endIndices.size()) { |
---|
| 3576 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
| 3577 | } |
---|
| 3578 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 3579 | if (startIndices[i] > endIndices[i]) { |
---|
| 3580 | throw(AipsError("Mask start index > mask end index")); |
---|
[2012] | 3581 | } |
---|
| 3582 | } |
---|
| 3583 | |
---|
[2047] | 3584 | out.clear(); |
---|
| 3585 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 3586 | out.push_back(startIndices[i]); |
---|
| 3587 | out.push_back(endIndices[i]); |
---|
| 3588 | } |
---|
| 3589 | |
---|
[2012] | 3590 | return out; |
---|
| 3591 | } |
---|
| 3592 | |
---|
[2161] | 3593 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
| 3594 | { |
---|
| 3595 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
| 3596 | vector<float> stlTsys ; |
---|
| 3597 | tsys.tovector( stlTsys ) ; |
---|
| 3598 | return stlTsys ; |
---|
| 3599 | } |
---|
[2012] | 3600 | |
---|
| 3601 | |
---|
[1907] | 3602 | } |
---|
[1819] | 3603 | //namespace asap |
---|