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