[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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[2791] | 7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005-2013 |
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[805] | 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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[2591] | 13 | #include <sys/time.h> |
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[3048] | 14 | #include <iostream> |
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[206] | 15 | |
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[2186] | 16 | #include <atnf/PKSIO/SrcType.h> |
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| 17 | |
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[125] | 18 | #include <casa/aips.h> |
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[2186] | 19 | #include <casa/iomanip.h> |
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[80] | 20 | #include <casa/iostream.h> |
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[2186] | 21 | #include <casa/OS/File.h> |
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[805] | 22 | #include <casa/OS/Path.h> |
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[2658] | 23 | #include <casa/Logging/LogIO.h> |
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[80] | 24 | #include <casa/Arrays/Array.h> |
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[2186] | 25 | #include <casa/Arrays/ArrayAccessor.h> |
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| 26 | #include <casa/Arrays/ArrayLogical.h> |
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[80] | 27 | #include <casa/Arrays/ArrayMath.h> |
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| 28 | #include <casa/Arrays/MaskArrMath.h> |
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[2186] | 29 | #include <casa/Arrays/Slice.h> |
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[1325] | 30 | #include <casa/Arrays/Vector.h> |
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[455] | 31 | #include <casa/Arrays/VectorSTLIterator.h> |
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[418] | 32 | #include <casa/BasicMath/Math.h> |
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[504] | 33 | #include <casa/BasicSL/Constants.h> |
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[2186] | 34 | #include <casa/Containers/RecordField.h> |
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| 35 | #include <casa/Logging/LogIO.h> |
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[286] | 36 | #include <casa/Quanta/MVAngle.h> |
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[2186] | 37 | #include <casa/Quanta/MVTime.h> |
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[902] | 38 | #include <casa/Utilities/GenSort.h> |
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[3026] | 39 | #include <casa/Utilities/Assert.h> |
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[2] | 40 | |
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[2186] | 41 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[2] | 42 | |
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[1325] | 43 | // needed to avoid error in .tcc |
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| 44 | #include <measures/Measures/MCDirection.h> |
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| 45 | // |
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| 46 | #include <measures/Measures/MDirection.h> |
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[2186] | 47 | #include <measures/Measures/MEpoch.h> |
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[80] | 48 | #include <measures/Measures/MFrequency.h> |
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[2186] | 49 | #include <measures/Measures/MeasRef.h> |
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| 50 | #include <measures/Measures/MeasTable.h> |
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| 51 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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| 52 | #include <measures/TableMeasures/TableMeasDesc.h> |
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[805] | 53 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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| 54 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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[2] | 55 | |
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[2186] | 56 | #include <tables/Tables/ArrColDesc.h> |
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| 57 | #include <tables/Tables/ExprNode.h> |
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| 58 | #include <tables/Tables/ScaColDesc.h> |
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| 59 | #include <tables/Tables/SetupNewTab.h> |
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| 60 | #include <tables/Tables/TableCopy.h> |
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| 61 | #include <tables/Tables/TableDesc.h> |
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| 62 | #include <tables/Tables/TableIter.h> |
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| 63 | #include <tables/Tables/TableParse.h> |
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| 64 | #include <tables/Tables/TableRecord.h> |
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| 65 | #include <tables/Tables/TableRow.h> |
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| 66 | #include <tables/Tables/TableVector.h> |
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| 67 | |
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| 68 | #include "MathUtils.h" |
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| 69 | #include "STAttr.h" |
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[2737] | 70 | #include "STBaselineTable.h" |
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[2186] | 71 | #include "STLineFinder.h" |
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| 72 | #include "STPolCircular.h" |
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[896] | 73 | #include "STPolLinear.h" |
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[913] | 74 | #include "STPolStokes.h" |
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[2321] | 75 | #include "STUpgrade.h" |
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[2666] | 76 | #include "STFitter.h" |
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[2186] | 77 | #include "Scantable.h" |
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[2] | 78 | |
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[2462] | 79 | #define debug 1 |
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| 80 | |
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[125] | 81 | using namespace casa; |
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[2] | 82 | |
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[805] | 83 | namespace asap { |
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| 84 | |
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[896] | 85 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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| 86 | |
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| 87 | void Scantable::initFactories() { |
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| 88 | if ( factories_.empty() ) { |
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| 89 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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[1323] | 90 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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[913] | 91 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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[896] | 92 | } |
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| 93 | } |
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| 94 | |
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[805] | 95 | Scantable::Scantable(Table::TableType ttype) : |
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[3045] | 96 | type_(ttype), |
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| 97 | cubicSplineModelPool_() |
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[206] | 98 | { |
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[896] | 99 | initFactories(); |
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[805] | 100 | setupMainTable(); |
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[2346] | 101 | freqTable_ = STFrequencies(*this); |
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| 102 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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[852] | 103 | weatherTable_ = STWeather(*this); |
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[805] | 104 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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[852] | 105 | focusTable_ = STFocus(*this); |
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[805] | 106 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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[852] | 107 | tcalTable_ = STTcal(*this); |
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[805] | 108 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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[852] | 109 | moleculeTable_ = STMolecules(*this); |
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[805] | 110 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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[860] | 111 | historyTable_ = STHistory(*this); |
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| 112 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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[959] | 113 | fitTable_ = STFit(*this); |
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| 114 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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[1881] | 115 | table_.tableInfo().setType( "Scantable" ) ; |
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[805] | 116 | originalTable_ = table_; |
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[322] | 117 | attach(); |
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[18] | 118 | } |
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[206] | 119 | |
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[805] | 120 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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[3045] | 121 | type_(ttype), |
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| 122 | cubicSplineModelPool_() |
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[206] | 123 | { |
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[896] | 124 | initFactories(); |
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[1819] | 125 | |
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[865] | 126 | Table tab(name, Table::Update); |
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[1009] | 127 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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[483] | 128 | if (version != version_) { |
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[2321] | 129 | STUpgrade upgrader(version_); |
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[2162] | 130 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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| 131 | os << LogIO::WARN |
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[2321] | 132 | << name << " data format version " << version |
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| 133 | << " is deprecated" << endl |
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| 134 | << "Running upgrade."<< endl |
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[2162] | 135 | << LogIO::POST ; |
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[2321] | 136 | std::string outname = upgrader.upgrade(name); |
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[2332] | 137 | if ( outname != name ) { |
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| 138 | os << LogIO::WARN |
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| 139 | << "Data will be loaded from " << outname << " instead of " |
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| 140 | << name << LogIO::POST ; |
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| 141 | tab = Table(outname, Table::Update ) ; |
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| 142 | } |
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[483] | 143 | } |
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[1009] | 144 | if ( type_ == Table::Memory ) { |
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[852] | 145 | table_ = tab.copyToMemoryTable(generateName()); |
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[1009] | 146 | } else { |
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[805] | 147 | table_ = tab; |
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[1009] | 148 | } |
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[1881] | 149 | table_.tableInfo().setType( "Scantable" ) ; |
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[1009] | 150 | |
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[859] | 151 | attachSubtables(); |
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[805] | 152 | originalTable_ = table_; |
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[329] | 153 | attach(); |
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[2] | 154 | } |
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[1819] | 155 | /* |
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| 156 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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| 157 | type_(ttype) |
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| 158 | { |
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| 159 | initFactories(); |
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| 160 | Table tab(name, Table::Update); |
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| 161 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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| 162 | if (version != version_) { |
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| 163 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 164 | } |
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| 165 | if ( type_ == Table::Memory ) { |
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| 166 | table_ = tab.copyToMemoryTable(generateName()); |
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| 167 | } else { |
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| 168 | table_ = tab; |
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| 169 | } |
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[2] | 170 | |
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[1819] | 171 | attachSubtables(); |
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| 172 | originalTable_ = table_; |
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| 173 | attach(); |
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| 174 | } |
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| 175 | */ |
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| 176 | |
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[2658] | 177 | Scantable::Scantable( const Scantable& other, bool clear ) |
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[206] | 178 | { |
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[805] | 179 | // with or without data |
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[859] | 180 | String newname = String(generateName()); |
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[865] | 181 | type_ = other.table_.tableType(); |
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[859] | 182 | if ( other.table_.tableType() == Table::Memory ) { |
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| 183 | if ( clear ) { |
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| 184 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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| 185 | other.table_, True); |
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[2818] | 186 | } else { |
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[859] | 187 | table_ = other.table_.copyToMemoryTable(newname); |
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[2818] | 188 | } |
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[16] | 189 | } else { |
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[915] | 190 | other.table_.deepCopy(newname, Table::New, False, |
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| 191 | other.table_.endianFormat(), |
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[865] | 192 | Bool(clear)); |
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| 193 | table_ = Table(newname, Table::Update); |
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| 194 | table_.markForDelete(); |
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| 195 | } |
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[1881] | 196 | table_.tableInfo().setType( "Scantable" ) ; |
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[1111] | 197 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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[2846] | 198 | if ( clear ) copySubtables(other); |
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[859] | 199 | attachSubtables(); |
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[805] | 200 | originalTable_ = table_; |
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[322] | 201 | attach(); |
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[2] | 202 | } |
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| 203 | |
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[865] | 204 | void Scantable::copySubtables(const Scantable& other) { |
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| 205 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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[2346] | 206 | TableCopy::copyRows(t, other.freqTable_.table()); |
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[865] | 207 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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| 208 | TableCopy::copyRows(t, other.focusTable_.table()); |
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| 209 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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| 210 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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| 211 | t = table_.rwKeywordSet().asTable("TCAL"); |
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| 212 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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| 213 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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| 214 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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| 215 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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| 216 | TableCopy::copyRows(t, other.historyTable_.table()); |
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[972] | 217 | t = table_.rwKeywordSet().asTable("FIT"); |
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| 218 | TableCopy::copyRows(t, other.fitTable_.table()); |
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[865] | 219 | } |
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| 220 | |
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[859] | 221 | void Scantable::attachSubtables() |
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| 222 | { |
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[2346] | 223 | freqTable_ = STFrequencies(table_); |
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[859] | 224 | focusTable_ = STFocus(table_); |
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| 225 | weatherTable_ = STWeather(table_); |
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| 226 | tcalTable_ = STTcal(table_); |
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| 227 | moleculeTable_ = STMolecules(table_); |
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[860] | 228 | historyTable_ = STHistory(table_); |
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[972] | 229 | fitTable_ = STFit(table_); |
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[859] | 230 | } |
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| 231 | |
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[805] | 232 | Scantable::~Scantable() |
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[206] | 233 | { |
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[2] | 234 | } |
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| 235 | |
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[805] | 236 | void Scantable::setupMainTable() |
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[206] | 237 | { |
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[805] | 238 | TableDesc td("", "1", TableDesc::Scratch); |
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| 239 | td.comment() = "An ASAP Scantable"; |
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[1009] | 240 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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[2] | 241 | |
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[805] | 242 | // n Cycles |
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| 243 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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| 244 | // new index every nBeam x nIF x nPol |
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| 245 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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[2] | 246 | |
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[805] | 247 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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| 248 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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[972] | 249 | // linear, circular, stokes |
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[805] | 250 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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| 251 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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[138] | 252 | |
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[805] | 253 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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| 254 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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[80] | 255 | |
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[1819] | 256 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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| 257 | refbeamnoColumn.setDefault(Int(-1)); |
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| 258 | td.addColumn(refbeamnoColumn); |
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| 259 | |
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| 260 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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| 261 | flagrowColumn.setDefault(uInt(0)); |
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| 262 | td.addColumn(flagrowColumn); |
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| 263 | |
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[805] | 264 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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| 265 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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| 266 | TableMeasValueDesc measVal(td, "TIME"); |
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| 267 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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| 268 | mepochCol.write(td); |
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[483] | 269 | |
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[805] | 270 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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| 271 | |
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[2] | 272 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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[805] | 273 | // Type of source (on=0, off=1, other=-1) |
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[1503] | 274 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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| 275 | stypeColumn.setDefault(Int(-1)); |
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| 276 | td.addColumn(stypeColumn); |
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[805] | 277 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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| 278 | |
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| 279 | //The actual Data Vectors |
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[2] | 280 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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| 281 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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[89] | 282 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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[805] | 283 | |
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| 284 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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| 285 | IPosition(1,2), |
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| 286 | ColumnDesc::Direct)); |
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| 287 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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| 288 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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| 289 | // the TableMeasDesc gives the column a type |
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| 290 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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[987] | 291 | // a uder set table type e.g. GALCTIC, B1950 ... |
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| 292 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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[805] | 293 | // writing create the measure column |
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| 294 | mdirCol.write(td); |
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[923] | 295 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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| 296 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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[1047] | 297 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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[105] | 298 | |
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[805] | 299 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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[972] | 300 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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[973] | 301 | fitColumn.setDefault(Int(-1)); |
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[972] | 302 | td.addColumn(fitColumn); |
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[805] | 303 | |
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| 304 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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| 305 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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| 306 | |
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[999] | 307 | // columns which just get dragged along, as they aren't used in asap |
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| 308 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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| 309 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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| 310 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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| 311 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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| 312 | |
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[805] | 313 | td.rwKeywordSet().define("OBSMODE", String("")); |
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| 314 | |
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[418] | 315 | // Now create Table SetUp from the description. |
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[859] | 316 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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[852] | 317 | table_ = Table(aNewTab, type_, 0); |
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[805] | 318 | originalTable_ = table_; |
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| 319 | } |
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[418] | 320 | |
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[805] | 321 | void Scantable::attach() |
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[455] | 322 | { |
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[805] | 323 | timeCol_.attach(table_, "TIME"); |
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| 324 | srcnCol_.attach(table_, "SRCNAME"); |
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[1068] | 325 | srctCol_.attach(table_, "SRCTYPE"); |
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[805] | 326 | specCol_.attach(table_, "SPECTRA"); |
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| 327 | flagsCol_.attach(table_, "FLAGTRA"); |
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[865] | 328 | tsysCol_.attach(table_, "TSYS"); |
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[805] | 329 | cycleCol_.attach(table_,"CYCLENO"); |
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| 330 | scanCol_.attach(table_, "SCANNO"); |
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| 331 | beamCol_.attach(table_, "BEAMNO"); |
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[847] | 332 | ifCol_.attach(table_, "IFNO"); |
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| 333 | polCol_.attach(table_, "POLNO"); |
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[805] | 334 | integrCol_.attach(table_, "INTERVAL"); |
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| 335 | azCol_.attach(table_, "AZIMUTH"); |
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| 336 | elCol_.attach(table_, "ELEVATION"); |
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| 337 | dirCol_.attach(table_, "DIRECTION"); |
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| 338 | fldnCol_.attach(table_, "FIELDNAME"); |
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| 339 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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[455] | 340 | |
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[1730] | 341 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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[805] | 342 | mfitidCol_.attach(table_,"FIT_ID"); |
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| 343 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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| 344 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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| 345 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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| 346 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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[1819] | 347 | |
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| 348 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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| 349 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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| 350 | |
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[455] | 351 | } |
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| 352 | |
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[1819] | 353 | template<class T, class T2> |
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| 354 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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| 355 | const String& colName, |
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| 356 | const T2& defValue) |
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| 357 | { |
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| 358 | try { |
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| 359 | col.attach(table_, colName); |
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| 360 | } catch (TableError& err) { |
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| 361 | String errMesg = err.getMesg(); |
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| 362 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 363 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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| 364 | col.attach(table_, colName); |
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| 365 | col.fillColumn(static_cast<T>(defValue)); |
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| 366 | } else { |
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| 367 | throw; |
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| 368 | } |
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| 369 | } catch (...) { |
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| 370 | throw; |
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| 371 | } |
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| 372 | } |
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| 373 | |
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| 374 | template<class T, class T2> |
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| 375 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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| 376 | const String& colName, |
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| 377 | const Array<T2>& defValue) |
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| 378 | { |
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| 379 | try { |
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| 380 | col.attach(table_, colName); |
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| 381 | } catch (TableError& err) { |
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| 382 | String errMesg = err.getMesg(); |
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| 383 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 384 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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| 385 | col.attach(table_, colName); |
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| 386 | |
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| 387 | int size = 0; |
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| 388 | ArrayIterator<T2>& it = defValue.begin(); |
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| 389 | while (it != defValue.end()) { |
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| 390 | ++size; |
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| 391 | ++it; |
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| 392 | } |
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| 393 | IPosition ip(1, size); |
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| 394 | Array<T>& arr(ip); |
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| 395 | for (int i = 0; i < size; ++i) |
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| 396 | arr[i] = static_cast<T>(defValue[i]); |
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| 397 | |
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| 398 | col.fillColumn(arr); |
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| 399 | } else { |
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| 400 | throw; |
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| 401 | } |
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| 402 | } catch (...) { |
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| 403 | throw; |
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| 404 | } |
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| 405 | } |
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| 406 | |
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[901] | 407 | void Scantable::setHeader(const STHeader& sdh) |
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[206] | 408 | { |
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[18] | 409 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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| 410 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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| 411 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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| 412 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
---|
| 413 | table_.rwKeywordSet().define("Observer", sdh.observer); |
---|
| 414 | table_.rwKeywordSet().define("Project", sdh.project); |
---|
| 415 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
---|
| 416 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
---|
| 417 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
---|
| 418 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
---|
| 419 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
---|
| 420 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
---|
| 421 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
---|
| 422 | table_.rwKeywordSet().define("UTC", sdh.utc); |
---|
[206] | 423 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
---|
| 424 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
---|
[905] | 425 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
---|
[50] | 426 | } |
---|
[21] | 427 | |
---|
[901] | 428 | STHeader Scantable::getHeader() const |
---|
[206] | 429 | { |
---|
[901] | 430 | STHeader sdh; |
---|
[21] | 431 | table_.keywordSet().get("nBeam",sdh.nbeam); |
---|
| 432 | table_.keywordSet().get("nIF",sdh.nif); |
---|
| 433 | table_.keywordSet().get("nPol",sdh.npol); |
---|
| 434 | table_.keywordSet().get("nChan",sdh.nchan); |
---|
| 435 | table_.keywordSet().get("Observer", sdh.observer); |
---|
| 436 | table_.keywordSet().get("Project", sdh.project); |
---|
| 437 | table_.keywordSet().get("Obstype", sdh.obstype); |
---|
| 438 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
---|
| 439 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
---|
| 440 | table_.keywordSet().get("Equinox", sdh.equinox); |
---|
| 441 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
---|
| 442 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
---|
| 443 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
---|
| 444 | table_.keywordSet().get("UTC", sdh.utc); |
---|
[206] | 445 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
---|
| 446 | table_.keywordSet().get("Epoch", sdh.epoch); |
---|
[905] | 447 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
---|
[21] | 448 | return sdh; |
---|
[18] | 449 | } |
---|
[805] | 450 | |
---|
[1360] | 451 | void Scantable::setSourceType( int stype ) |
---|
[1068] | 452 | { |
---|
| 453 | if ( stype < 0 || stype > 1 ) |
---|
| 454 | throw(AipsError("Illegal sourcetype.")); |
---|
| 455 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
---|
| 456 | tabvec = Int(stype); |
---|
| 457 | } |
---|
| 458 | |
---|
[2818] | 459 | void Scantable::setSourceName( const std::string& name ) |
---|
| 460 | { |
---|
| 461 | TableVector<String> tabvec(table_, "SRCNAME"); |
---|
| 462 | tabvec = name; |
---|
| 463 | } |
---|
| 464 | |
---|
[845] | 465 | bool Scantable::conformant( const Scantable& other ) |
---|
| 466 | { |
---|
| 467 | return this->getHeader().conformant(other.getHeader()); |
---|
| 468 | } |
---|
| 469 | |
---|
| 470 | |
---|
[50] | 471 | |
---|
[805] | 472 | std::string Scantable::formatSec(Double x) const |
---|
[206] | 473 | { |
---|
[105] | 474 | Double xcop = x; |
---|
| 475 | MVTime mvt(xcop/24./3600.); // make days |
---|
[365] | 476 | |
---|
[105] | 477 | if (x < 59.95) |
---|
[281] | 478 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
[745] | 479 | else if (x < 3599.95) |
---|
[281] | 480 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
| 481 | else { |
---|
| 482 | ostringstream oss; |
---|
| 483 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
| 484 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
| 485 | return String(oss); |
---|
[745] | 486 | } |
---|
[105] | 487 | }; |
---|
| 488 | |
---|
[2969] | 489 | std::string Scantable::formatDirection(const MDirection& md, Int prec) const |
---|
[281] | 490 | { |
---|
| 491 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
[2969] | 492 | if (prec<0) |
---|
| 493 | prec = 7; |
---|
[281] | 494 | |
---|
[2575] | 495 | String ref = md.getRefString(); |
---|
[281] | 496 | MVAngle mvLon(t[0]); |
---|
| 497 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
[987] | 498 | uInt tp = md.getRef().getType(); |
---|
| 499 | if (tp == MDirection::GALACTIC || |
---|
| 500 | tp == MDirection::SUPERGAL ) { |
---|
| 501 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
| 502 | } |
---|
[281] | 503 | MVAngle mvLat(t[1]); |
---|
| 504 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
[2575] | 505 | return ref + String(" ") + sLon + String(" ") + sLat; |
---|
[281] | 506 | } |
---|
| 507 | |
---|
| 508 | |
---|
[805] | 509 | std::string Scantable::getFluxUnit() const |
---|
[206] | 510 | { |
---|
[847] | 511 | return table_.keywordSet().asString("FluxUnit"); |
---|
[206] | 512 | } |
---|
| 513 | |
---|
[805] | 514 | void Scantable::setFluxUnit(const std::string& unit) |
---|
[218] | 515 | { |
---|
| 516 | String tmp(unit); |
---|
| 517 | Unit tU(tmp); |
---|
| 518 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
| 519 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
| 520 | } else { |
---|
| 521 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
| 522 | } |
---|
| 523 | } |
---|
| 524 | |
---|
[805] | 525 | void Scantable::setInstrument(const std::string& name) |
---|
[236] | 526 | { |
---|
[805] | 527 | bool throwIt = true; |
---|
[996] | 528 | // create an Instrument to see if this is valid |
---|
| 529 | STAttr::convertInstrument(name, throwIt); |
---|
[236] | 530 | String nameU(name); |
---|
| 531 | nameU.upcase(); |
---|
| 532 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
| 533 | } |
---|
| 534 | |
---|
[1189] | 535 | void Scantable::setFeedType(const std::string& feedtype) |
---|
| 536 | { |
---|
| 537 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
| 538 | std::string msg = "Illegal feed type "+ feedtype; |
---|
| 539 | throw(casa::AipsError(msg)); |
---|
| 540 | } |
---|
| 541 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
| 542 | } |
---|
| 543 | |
---|
[1743] | 544 | MPosition Scantable::getAntennaPosition() const |
---|
[805] | 545 | { |
---|
| 546 | Vector<Double> antpos; |
---|
| 547 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
| 548 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
| 549 | return MPosition(mvpos); |
---|
| 550 | } |
---|
[281] | 551 | |
---|
[805] | 552 | void Scantable::makePersistent(const std::string& filename) |
---|
| 553 | { |
---|
| 554 | String inname(filename); |
---|
| 555 | Path path(inname); |
---|
[1111] | 556 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
[805] | 557 | inname = path.expandedName(); |
---|
[2030] | 558 | // 2011/03/04 TN |
---|
| 559 | // We can comment out this workaround since the essential bug is |
---|
| 560 | // fixed in casacore (r20889 in google code). |
---|
| 561 | table_.deepCopy(inname, Table::New); |
---|
| 562 | // // WORKAROUND !!! for Table bug |
---|
| 563 | // // Remove when fixed in casacore |
---|
| 564 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
| 565 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
| 566 | // tab.deepCopy(inname, Table::New); |
---|
| 567 | // tab.markForDelete(); |
---|
| 568 | // |
---|
| 569 | // } else { |
---|
| 570 | // table_.deepCopy(inname, Table::New); |
---|
| 571 | // } |
---|
[805] | 572 | } |
---|
| 573 | |
---|
[837] | 574 | int Scantable::nbeam( int scanno ) const |
---|
[805] | 575 | { |
---|
| 576 | if ( scanno < 0 ) { |
---|
| 577 | Int n; |
---|
| 578 | table_.keywordSet().get("nBeam",n); |
---|
| 579 | return int(n); |
---|
[105] | 580 | } else { |
---|
[805] | 581 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 582 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 583 | ROTableRow row(t); |
---|
| 584 | const TableRecord& rec = row.get(0); |
---|
| 585 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 586 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 587 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 588 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
[805] | 589 | return int(v.nelements()); |
---|
[105] | 590 | } |
---|
[805] | 591 | return 0; |
---|
| 592 | } |
---|
[455] | 593 | |
---|
[837] | 594 | int Scantable::nif( int scanno ) const |
---|
[805] | 595 | { |
---|
| 596 | if ( scanno < 0 ) { |
---|
| 597 | Int n; |
---|
| 598 | table_.keywordSet().get("nIF",n); |
---|
| 599 | return int(n); |
---|
| 600 | } else { |
---|
| 601 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 602 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 603 | ROTableRow row(t); |
---|
| 604 | const TableRecord& rec = row.get(0); |
---|
| 605 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 606 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 607 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 608 | if ( subt.nrow() == 0 ) return 0; |
---|
| 609 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
[805] | 610 | return int(v.nelements()); |
---|
[2] | 611 | } |
---|
[805] | 612 | return 0; |
---|
| 613 | } |
---|
[321] | 614 | |
---|
[837] | 615 | int Scantable::npol( int scanno ) const |
---|
[805] | 616 | { |
---|
| 617 | if ( scanno < 0 ) { |
---|
| 618 | Int n; |
---|
| 619 | table_.keywordSet().get("nPol",n); |
---|
| 620 | return n; |
---|
| 621 | } else { |
---|
| 622 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 623 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 624 | ROTableRow row(t); |
---|
| 625 | const TableRecord& rec = row.get(0); |
---|
| 626 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 627 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 628 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 629 | if ( subt.nrow() == 0 ) return 0; |
---|
| 630 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
[805] | 631 | return int(v.nelements()); |
---|
[321] | 632 | } |
---|
[805] | 633 | return 0; |
---|
[2] | 634 | } |
---|
[805] | 635 | |
---|
[845] | 636 | int Scantable::ncycle( int scanno ) const |
---|
[206] | 637 | { |
---|
[805] | 638 | if ( scanno < 0 ) { |
---|
[837] | 639 | Block<String> cols(2); |
---|
| 640 | cols[0] = "SCANNO"; |
---|
| 641 | cols[1] = "CYCLENO"; |
---|
| 642 | TableIterator it(table_, cols); |
---|
| 643 | int n = 0; |
---|
| 644 | while ( !it.pastEnd() ) { |
---|
| 645 | ++n; |
---|
[902] | 646 | ++it; |
---|
[837] | 647 | } |
---|
| 648 | return n; |
---|
[805] | 649 | } else { |
---|
[888] | 650 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 651 | ROTableRow row(t); |
---|
| 652 | const TableRecord& rec = row.get(0); |
---|
| 653 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 654 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 655 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
| 656 | if ( subt.nrow() == 0 ) return 0; |
---|
| 657 | return int(subt.nrow()); |
---|
[805] | 658 | } |
---|
| 659 | return 0; |
---|
[18] | 660 | } |
---|
[455] | 661 | |
---|
| 662 | |
---|
[845] | 663 | int Scantable::nrow( int scanno ) const |
---|
[805] | 664 | { |
---|
[845] | 665 | return int(table_.nrow()); |
---|
| 666 | } |
---|
| 667 | |
---|
| 668 | int Scantable::nchan( int ifno ) const |
---|
| 669 | { |
---|
| 670 | if ( ifno < 0 ) { |
---|
[805] | 671 | Int n; |
---|
| 672 | table_.keywordSet().get("nChan",n); |
---|
| 673 | return int(n); |
---|
| 674 | } else { |
---|
[1360] | 675 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
| 676 | // vary with these |
---|
[2244] | 677 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
[888] | 678 | if ( t.nrow() == 0 ) return 0; |
---|
| 679 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
[923] | 680 | return v.shape(0)(0); |
---|
[805] | 681 | } |
---|
| 682 | return 0; |
---|
[18] | 683 | } |
---|
[455] | 684 | |
---|
[1111] | 685 | int Scantable::nscan() const { |
---|
| 686 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
[1148] | 687 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
[1111] | 688 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 689 | return int(nout); |
---|
| 690 | } |
---|
| 691 | |
---|
[923] | 692 | int Scantable::getChannels(int whichrow) const |
---|
| 693 | { |
---|
| 694 | return specCol_.shape(whichrow)(0); |
---|
| 695 | } |
---|
[847] | 696 | |
---|
| 697 | int Scantable::getBeam(int whichrow) const |
---|
| 698 | { |
---|
| 699 | return beamCol_(whichrow); |
---|
| 700 | } |
---|
| 701 | |
---|
[1694] | 702 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
[1111] | 703 | { |
---|
| 704 | Vector<uInt> nos(col.getColumn()); |
---|
[1148] | 705 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 706 | nos.resize(n, True); |
---|
[1111] | 707 | std::vector<uint> stlout; |
---|
| 708 | nos.tovector(stlout); |
---|
| 709 | return stlout; |
---|
| 710 | } |
---|
| 711 | |
---|
[847] | 712 | int Scantable::getIF(int whichrow) const |
---|
| 713 | { |
---|
| 714 | return ifCol_(whichrow); |
---|
| 715 | } |
---|
| 716 | |
---|
| 717 | int Scantable::getPol(int whichrow) const |
---|
| 718 | { |
---|
| 719 | return polCol_(whichrow); |
---|
| 720 | } |
---|
| 721 | |
---|
[805] | 722 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
| 723 | { |
---|
[1947] | 724 | return formatTime(me, showdate, 0); |
---|
| 725 | } |
---|
| 726 | |
---|
| 727 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
| 728 | { |
---|
[805] | 729 | MVTime mvt(me.getValue()); |
---|
| 730 | if (showdate) |
---|
[1947] | 731 | //mvt.setFormat(MVTime::YMD); |
---|
| 732 | mvt.setFormat(MVTime::YMD, prec); |
---|
[805] | 733 | else |
---|
[1947] | 734 | //mvt.setFormat(MVTime::TIME); |
---|
| 735 | mvt.setFormat(MVTime::TIME, prec); |
---|
[805] | 736 | ostringstream oss; |
---|
| 737 | oss << mvt; |
---|
| 738 | return String(oss); |
---|
| 739 | } |
---|
[488] | 740 | |
---|
[805] | 741 | void Scantable::calculateAZEL() |
---|
[2658] | 742 | { |
---|
| 743 | LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ; |
---|
[805] | 744 | MPosition mp = getAntennaPosition(); |
---|
| 745 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 746 | ostringstream oss; |
---|
[2658] | 747 | oss << mp; |
---|
| 748 | os << "Computed azimuth/elevation using " << endl |
---|
| 749 | << String(oss) << endl; |
---|
[996] | 750 | for (Int i=0; i<nrow(); ++i) { |
---|
[805] | 751 | MEpoch me = timeCol(i); |
---|
[987] | 752 | MDirection md = getDirection(i); |
---|
[2658] | 753 | os << " Time: " << formatTime(me,False) |
---|
| 754 | << " Direction: " << formatDirection(md) |
---|
[805] | 755 | << endl << " => "; |
---|
| 756 | MeasFrame frame(mp, me); |
---|
| 757 | Vector<Double> azel = |
---|
| 758 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
| 759 | frame) |
---|
| 760 | )().getAngle("rad").getValue(); |
---|
[923] | 761 | azCol_.put(i,Float(azel[0])); |
---|
| 762 | elCol_.put(i,Float(azel[1])); |
---|
[2658] | 763 | os << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
| 764 | << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST; |
---|
[16] | 765 | } |
---|
[805] | 766 | } |
---|
[89] | 767 | |
---|
[1819] | 768 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 769 | { |
---|
[2947] | 770 | Vector<uInt> flagrow = flagrowCol_.getColumn(); |
---|
[1819] | 771 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
[2947] | 772 | // apply flag only when specified row is vaild |
---|
| 773 | if (flagrow[i] == 0) { |
---|
| 774 | Vector<uChar> flgs = flagsCol_(i); |
---|
| 775 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
| 776 | flagsCol_.put(i, flgs); |
---|
| 777 | } |
---|
[1819] | 778 | } |
---|
| 779 | } |
---|
| 780 | |
---|
| 781 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 782 | { |
---|
| 783 | Vector<uChar> flags; |
---|
| 784 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 785 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
| 786 | Vector<Bool> bflag(flags.shape()); |
---|
| 787 | convertArray(bflag, flags); |
---|
| 788 | //bflag = !bflag; |
---|
| 789 | |
---|
| 790 | std::vector<bool> mask; |
---|
| 791 | bflag.tovector(mask); |
---|
| 792 | return mask; |
---|
| 793 | } |
---|
| 794 | |
---|
| 795 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
| 796 | Vector<uChar> flgs) |
---|
| 797 | { |
---|
| 798 | Vector<Float> spcs = specCol_(whichrow); |
---|
[2348] | 799 | uInt nchannel = spcs.nelements(); |
---|
[1819] | 800 | if (spcs.nelements() != nchannel) { |
---|
| 801 | throw(AipsError("Data has incorrect number of channels")); |
---|
| 802 | } |
---|
| 803 | uChar userflag = 1 << 7; |
---|
| 804 | if (unflag) { |
---|
| 805 | userflag = 0 << 7; |
---|
| 806 | } |
---|
| 807 | if (clipoutside) { |
---|
| 808 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 809 | Float spc = spcs(j); |
---|
| 810 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
| 811 | flgs(j) = userflag; |
---|
| 812 | } |
---|
| 813 | } |
---|
| 814 | } else { |
---|
| 815 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 816 | Float spc = spcs(j); |
---|
| 817 | if ((spc < uthres) && (spc > dthres)) { |
---|
| 818 | flgs(j) = userflag; |
---|
| 819 | } |
---|
| 820 | } |
---|
| 821 | } |
---|
| 822 | } |
---|
| 823 | |
---|
[1994] | 824 | |
---|
| 825 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
[1333] | 826 | std::vector<bool>::const_iterator it; |
---|
| 827 | uInt ntrue = 0; |
---|
[1994] | 828 | if (whichrow >= int(table_.nrow()) ) { |
---|
| 829 | throw(AipsError("Invalid row number")); |
---|
| 830 | } |
---|
[1333] | 831 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 832 | if ( *it ) { |
---|
| 833 | ntrue++; |
---|
| 834 | } |
---|
| 835 | } |
---|
[1994] | 836 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
| 837 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
[1000] | 838 | throw(AipsError("Trying to flag whole scantable.")); |
---|
[1994] | 839 | uChar userflag = 1 << 7; |
---|
| 840 | if ( unflag ) { |
---|
| 841 | userflag = 0 << 7; |
---|
| 842 | } |
---|
| 843 | if (whichrow > -1 ) { |
---|
[2947] | 844 | // apply flag only when specified row is vaild |
---|
| 845 | if (flagrowCol_(whichrow) == 0) { |
---|
| 846 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
| 847 | } |
---|
[1994] | 848 | } else { |
---|
[2948] | 849 | Vector<uInt> flagrow = flagrowCol_.getColumn(); |
---|
[1000] | 850 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
[2947] | 851 | // apply flag only when specified row is vaild |
---|
[2948] | 852 | if (flagrow[i] == 0) { |
---|
[2947] | 853 | applyChanFlag(i, msk, userflag); |
---|
| 854 | } |
---|
[1000] | 855 | } |
---|
[1994] | 856 | } |
---|
| 857 | } |
---|
| 858 | |
---|
| 859 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
| 860 | { |
---|
| 861 | if (whichrow >= table_.nrow() ) { |
---|
| 862 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
| 863 | } |
---|
| 864 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
| 865 | if ( msk.size() == 0 ) { |
---|
| 866 | flgs = flagval; |
---|
| 867 | flagsCol_.put(whichrow, flgs); |
---|
[1000] | 868 | return; |
---|
| 869 | } |
---|
[2348] | 870 | if ( int(msk.size()) != nchan( getIF(whichrow) ) ) { |
---|
[1000] | 871 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
| 872 | } |
---|
[1994] | 873 | if ( flgs.nelements() != msk.size() ) { |
---|
| 874 | throw(AipsError("Mask has incorrect number of channels." |
---|
| 875 | " Probably varying with IF. Please flag per IF")); |
---|
| 876 | } |
---|
| 877 | std::vector<bool>::const_iterator it; |
---|
| 878 | uInt j = 0; |
---|
| 879 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 880 | if ( *it ) { |
---|
| 881 | flgs(j) = flagval; |
---|
[1000] | 882 | } |
---|
[1994] | 883 | ++j; |
---|
[1000] | 884 | } |
---|
[1994] | 885 | flagsCol_.put(whichrow, flgs); |
---|
[865] | 886 | } |
---|
| 887 | |
---|
[1819] | 888 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
| 889 | { |
---|
[2683] | 890 | if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag) |
---|
[1819] | 891 | throw(AipsError("Trying to flag whole scantable.")); |
---|
| 892 | |
---|
| 893 | uInt rowflag = (unflag ? 0 : 1); |
---|
| 894 | std::vector<uInt>::const_iterator it; |
---|
| 895 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
| 896 | flagrowCol_.put(*it, rowflag); |
---|
| 897 | } |
---|
| 898 | |
---|
[805] | 899 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
| 900 | { |
---|
| 901 | Vector<uChar> flags; |
---|
| 902 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 903 | Vector<Bool> bflag(flags.shape()); |
---|
| 904 | convertArray(bflag, flags); |
---|
| 905 | bflag = !bflag; |
---|
| 906 | std::vector<bool> mask; |
---|
| 907 | bflag.tovector(mask); |
---|
| 908 | return mask; |
---|
| 909 | } |
---|
[89] | 910 | |
---|
[896] | 911 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
[902] | 912 | const std::string& poltype ) const |
---|
[805] | 913 | { |
---|
[2658] | 914 | LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ; |
---|
| 915 | |
---|
[905] | 916 | String ptype = poltype; |
---|
| 917 | if (poltype == "" ) ptype = getPolType(); |
---|
[902] | 918 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
| 919 | throw(AipsError("Illegal row number.")); |
---|
[896] | 920 | std::vector<float> out; |
---|
[805] | 921 | Vector<Float> arr; |
---|
[896] | 922 | uInt requestedpol = polCol_(whichrow); |
---|
| 923 | String basetype = getPolType(); |
---|
[905] | 924 | if ( ptype == basetype ) { |
---|
[896] | 925 | specCol_.get(whichrow, arr); |
---|
| 926 | } else { |
---|
[1598] | 927 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
[1586] | 928 | basetype)); |
---|
[1334] | 929 | uInt row = uInt(whichrow); |
---|
| 930 | stpol->setSpectra(getPolMatrix(row)); |
---|
[2047] | 931 | Float fang,fhand; |
---|
[1586] | 932 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
[1334] | 933 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
[1586] | 934 | stpol->setPhaseCorrections(fang, fhand); |
---|
[1334] | 935 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
[896] | 936 | } |
---|
[902] | 937 | if ( arr.nelements() == 0 ) |
---|
[2658] | 938 | |
---|
| 939 | os << "Not enough polarisations present to do the conversion." |
---|
| 940 | << LogIO::POST; |
---|
[805] | 941 | arr.tovector(out); |
---|
| 942 | return out; |
---|
[89] | 943 | } |
---|
[212] | 944 | |
---|
[1360] | 945 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
[884] | 946 | int whichrow ) |
---|
| 947 | { |
---|
| 948 | Vector<Float> spectrum(spec); |
---|
| 949 | Vector<Float> arr; |
---|
| 950 | specCol_.get(whichrow, arr); |
---|
| 951 | if ( spectrum.nelements() != arr.nelements() ) |
---|
[896] | 952 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
[884] | 953 | specCol_.put(whichrow, spectrum); |
---|
| 954 | } |
---|
| 955 | |
---|
| 956 | |
---|
[805] | 957 | String Scantable::generateName() |
---|
[745] | 958 | { |
---|
[805] | 959 | return (File::newUniqueName("./","temp")).baseName(); |
---|
[212] | 960 | } |
---|
| 961 | |
---|
[805] | 962 | const casa::Table& Scantable::table( ) const |
---|
[212] | 963 | { |
---|
[805] | 964 | return table_; |
---|
[212] | 965 | } |
---|
| 966 | |
---|
[805] | 967 | casa::Table& Scantable::table( ) |
---|
[386] | 968 | { |
---|
[805] | 969 | return table_; |
---|
[386] | 970 | } |
---|
| 971 | |
---|
[896] | 972 | std::string Scantable::getPolType() const |
---|
| 973 | { |
---|
| 974 | return table_.keywordSet().asString("POLTYPE"); |
---|
| 975 | } |
---|
| 976 | |
---|
[805] | 977 | void Scantable::unsetSelection() |
---|
[380] | 978 | { |
---|
[805] | 979 | table_ = originalTable_; |
---|
[847] | 980 | attach(); |
---|
[805] | 981 | selector_.reset(); |
---|
[380] | 982 | } |
---|
[386] | 983 | |
---|
[805] | 984 | void Scantable::setSelection( const STSelector& selection ) |
---|
[430] | 985 | { |
---|
[805] | 986 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
| 987 | if ( tab.nrow() == 0 ) { |
---|
| 988 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
| 989 | } |
---|
| 990 | table_ = tab; |
---|
[847] | 991 | attach(); |
---|
[2084] | 992 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
| 993 | // vector<uint> selectedIFs = getIFNos() ; |
---|
| 994 | // Int newnIF = selectedIFs.size() ; |
---|
| 995 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
| 996 | // if ( newnIF != 0 ) { |
---|
| 997 | // Int newnChan = 0 ; |
---|
| 998 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
| 999 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
| 1000 | // if ( newnChan > nChan ) |
---|
| 1001 | // newnChan = nChan ; |
---|
| 1002 | // } |
---|
| 1003 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
| 1004 | // } |
---|
| 1005 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
[805] | 1006 | selector_ = selection; |
---|
[430] | 1007 | } |
---|
| 1008 | |
---|
[2111] | 1009 | |
---|
[2163] | 1010 | std::string Scantable::headerSummary() |
---|
[447] | 1011 | { |
---|
[805] | 1012 | // Format header info |
---|
[2111] | 1013 | // STHeader sdh; |
---|
| 1014 | // sdh = getHeader(); |
---|
| 1015 | // sdh.print(); |
---|
[805] | 1016 | ostringstream oss; |
---|
| 1017 | oss.flags(std::ios_base::left); |
---|
[2290] | 1018 | String tmp; |
---|
| 1019 | // Project |
---|
| 1020 | table_.keywordSet().get("Project", tmp); |
---|
| 1021 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1022 | // Observation date |
---|
| 1023 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1024 | // Observer |
---|
| 1025 | oss << setw(15) << "Observer:" |
---|
| 1026 | << table_.keywordSet().asString("Observer") << endl; |
---|
| 1027 | // Antenna Name |
---|
| 1028 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1029 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1030 | // Obs type |
---|
| 1031 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1032 | // Records (nrow) |
---|
| 1033 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
| 1034 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1035 | // Beams, IFs, Polarizations, and Channels |
---|
[805] | 1036 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1037 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
[896] | 1038 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1039 | << "(" << getPolType() << ")" << endl |
---|
[1694] | 1040 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[2290] | 1041 | // Flux unit |
---|
| 1042 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1043 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
| 1044 | // Abscissa Unit |
---|
| 1045 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
| 1046 | // Selection |
---|
| 1047 | oss << selector_.print() << endl; |
---|
| 1048 | |
---|
| 1049 | return String(oss); |
---|
| 1050 | } |
---|
| 1051 | |
---|
| 1052 | void Scantable::summary( const std::string& filename ) |
---|
| 1053 | { |
---|
| 1054 | ostringstream oss; |
---|
| 1055 | ofstream ofs; |
---|
| 1056 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1057 | |
---|
| 1058 | if (filename != "") |
---|
| 1059 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1060 | |
---|
| 1061 | oss << endl; |
---|
| 1062 | oss << asap::SEPERATOR << endl; |
---|
| 1063 | oss << " Scan Table Summary" << endl; |
---|
| 1064 | oss << asap::SEPERATOR << endl; |
---|
| 1065 | |
---|
| 1066 | // Format header info |
---|
| 1067 | oss << headerSummary(); |
---|
| 1068 | oss << endl; |
---|
| 1069 | |
---|
| 1070 | if (table_.nrow() <= 0){ |
---|
| 1071 | oss << asap::SEPERATOR << endl; |
---|
| 1072 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
| 1073 | oss << asap::SEPERATOR << endl; |
---|
| 1074 | |
---|
| 1075 | ols << String(oss) << LogIO::POST; |
---|
| 1076 | if (ofs) { |
---|
| 1077 | ofs << String(oss) << flush; |
---|
| 1078 | ofs.close(); |
---|
| 1079 | } |
---|
| 1080 | return; |
---|
| 1081 | } |
---|
| 1082 | |
---|
| 1083 | |
---|
| 1084 | |
---|
| 1085 | // main table |
---|
| 1086 | String dirtype = "Position (" |
---|
| 1087 | + getDirectionRefString() |
---|
| 1088 | + ")"; |
---|
| 1089 | oss.flags(std::ios_base::left); |
---|
| 1090 | oss << setw(5) << "Scan" |
---|
| 1091 | << setw(15) << "Source" |
---|
| 1092 | << setw(35) << "Time range" |
---|
| 1093 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
| 1094 | << setw(7) << "Record" |
---|
| 1095 | << setw(8) << "SrcType" |
---|
| 1096 | << setw(8) << "FreqIDs" |
---|
| 1097 | << setw(7) << "MolIDs" << endl; |
---|
| 1098 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
| 1099 | << setw(23) << dirtype << endl; |
---|
| 1100 | |
---|
| 1101 | oss << asap::SEPERATOR << endl; |
---|
| 1102 | |
---|
| 1103 | // Flush summary and clear up the string |
---|
| 1104 | ols << String(oss) << LogIO::POST; |
---|
| 1105 | if (ofs) ofs << String(oss) << flush; |
---|
| 1106 | oss.str(""); |
---|
| 1107 | oss.clear(); |
---|
| 1108 | |
---|
| 1109 | |
---|
| 1110 | // Get Freq_ID map |
---|
| 1111 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
| 1112 | Int nfid = ftabIds.nrow(); |
---|
| 1113 | if (nfid <= 0){ |
---|
| 1114 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
| 1115 | oss << asap::SEPERATOR << endl; |
---|
| 1116 | |
---|
| 1117 | ols << String(oss) << LogIO::POST; |
---|
| 1118 | if (ofs) { |
---|
| 1119 | ofs << String(oss) << flush; |
---|
| 1120 | ofs.close(); |
---|
| 1121 | } |
---|
| 1122 | return; |
---|
| 1123 | } |
---|
| 1124 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
| 1125 | // the orders are identical to ID in FREQ subtable |
---|
| 1126 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
| 1127 | Vector<Int> fIdchans(nfid,-1); |
---|
[2938] | 1128 | Vector<Double> fIdfreq0(nfid,-1); |
---|
| 1129 | Vector<Double> fIdfcent(nfid,-1); |
---|
[2290] | 1130 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
| 1131 | for (Int i=0; i < nfid; i++){ |
---|
| 1132 | // fidMap[freqId] returns row number in FREQ subtable |
---|
| 1133 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
| 1134 | ifNos[i] = Vector<uInt>(); |
---|
| 1135 | polNos[i] = Vector<uInt>(); |
---|
| 1136 | } |
---|
| 1137 | |
---|
| 1138 | TableIterator iter(table_, "SCANNO"); |
---|
| 1139 | |
---|
| 1140 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
[2813] | 1141 | //Vector<uInt> freqids; |
---|
| 1142 | //Vector<uInt> molids; |
---|
[2290] | 1143 | Vector<uInt> beamids(1,0); |
---|
| 1144 | Vector<MDirection> beamDirs; |
---|
| 1145 | Vector<Int> stypeids(1,0); |
---|
| 1146 | Vector<String> stypestrs; |
---|
| 1147 | Int nfreq(1); |
---|
| 1148 | Int nmol(1); |
---|
| 1149 | uInt nbeam(1); |
---|
| 1150 | uInt nstype(1); |
---|
| 1151 | |
---|
| 1152 | Double btime(0.0), etime(0.0); |
---|
| 1153 | Double meanIntTim(0.0); |
---|
| 1154 | |
---|
| 1155 | uInt currFreqId(0), ftabRow(0); |
---|
| 1156 | Int iflen(0), pollen(0); |
---|
| 1157 | |
---|
| 1158 | while (!iter.pastEnd()) { |
---|
| 1159 | Table subt = iter.table(); |
---|
| 1160 | uInt snrow = subt.nrow(); |
---|
| 1161 | ROTableRow row(subt); |
---|
| 1162 | const TableRecord& rec = row.get(0); |
---|
| 1163 | |
---|
| 1164 | // relevant columns |
---|
| 1165 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
| 1166 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
| 1167 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
| 1168 | |
---|
| 1169 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
| 1170 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
| 1171 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
| 1172 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
| 1173 | |
---|
| 1174 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
| 1175 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
| 1176 | |
---|
| 1177 | |
---|
| 1178 | // Times |
---|
| 1179 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
| 1180 | minMax(btime, etime, mjdCol.getColumn()); |
---|
[2969] | 1181 | double shiftInDay(0.5*meanIntTim/C::day); |
---|
| 1182 | btime -= shiftInDay; |
---|
| 1183 | etime += shiftInDay; |
---|
[2290] | 1184 | |
---|
| 1185 | // MOLECULE_ID and FREQ_ID |
---|
[2813] | 1186 | Vector<uInt> molids(getNumbers(molIdCol)); |
---|
[2290] | 1187 | molids.shape(nmol); |
---|
| 1188 | |
---|
[2813] | 1189 | Vector<uInt> freqids(getNumbers(freqIdCol)); |
---|
[2290] | 1190 | freqids.shape(nfreq); |
---|
| 1191 | |
---|
| 1192 | // Add first beamid, and srcNames |
---|
| 1193 | beamids.resize(1,False); |
---|
| 1194 | beamDirs.resize(1,False); |
---|
| 1195 | beamids(0)=beamCol(0); |
---|
| 1196 | beamDirs(0)=dirCol(0); |
---|
| 1197 | nbeam = 1; |
---|
| 1198 | |
---|
| 1199 | stypeids.resize(1,False); |
---|
| 1200 | stypeids(0)=stypeCol(0); |
---|
| 1201 | nstype = 1; |
---|
| 1202 | |
---|
| 1203 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1204 | currFreqId=freqIdCol(0); |
---|
| 1205 | ftabRow = fidMap[currFreqId]; |
---|
| 1206 | // Assumes an identical number of channels per FREQ_ID |
---|
| 1207 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1208 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1209 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
| 1210 | } |
---|
[2938] | 1211 | if (fIdfreq0(ftabRow) < 0 ) { |
---|
| 1212 | SpectralCoordinate spc = frequencies().getSpectralCoordinate(ftabRow); |
---|
| 1213 | Double fs, fe; |
---|
| 1214 | spc.toWorld(fs, 0); |
---|
| 1215 | spc.toWorld(fe, fIdchans(ftabRow)-1); |
---|
| 1216 | fIdfreq0(ftabRow) = fs; |
---|
| 1217 | fIdfcent(ftabRow) = 0.5 * ( fs + fe ); |
---|
| 1218 | } |
---|
[2290] | 1219 | // Should keep ifNos and polNos form the previous SCANNO |
---|
| 1220 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
| 1221 | ifNos[ftabRow].shape(iflen); |
---|
| 1222 | iflen++; |
---|
| 1223 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1224 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
| 1225 | } |
---|
| 1226 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
| 1227 | polNos[ftabRow].shape(pollen); |
---|
| 1228 | pollen++; |
---|
| 1229 | polNos[ftabRow].resize(pollen,True); |
---|
| 1230 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
| 1231 | } |
---|
| 1232 | |
---|
| 1233 | for (uInt i=1; i < snrow; i++){ |
---|
| 1234 | // Need to list BEAMNO and DIRECTION in the same order |
---|
| 1235 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
| 1236 | nbeam++; |
---|
| 1237 | beamids.resize(nbeam,True); |
---|
| 1238 | beamids(nbeam-1)=beamCol(i); |
---|
| 1239 | beamDirs.resize(nbeam,True); |
---|
| 1240 | beamDirs(nbeam-1)=dirCol(i); |
---|
| 1241 | } |
---|
| 1242 | |
---|
| 1243 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
| 1244 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
| 1245 | nstype++; |
---|
| 1246 | stypeids.resize(nstype,True); |
---|
| 1247 | stypeids(nstype-1)=stypeCol(i); |
---|
| 1248 | } |
---|
| 1249 | |
---|
| 1250 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1251 | currFreqId=freqIdCol(i); |
---|
| 1252 | ftabRow = fidMap[currFreqId]; |
---|
| 1253 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1254 | const TableRecord& rec = row.get(i); |
---|
| 1255 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1256 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
| 1257 | } |
---|
[2938] | 1258 | if (fIdfreq0(ftabRow) < 0 ) { |
---|
| 1259 | SpectralCoordinate spc = frequencies().getSpectralCoordinate(ftabRow); |
---|
| 1260 | Double fs, fe; |
---|
| 1261 | spc.toWorld(fs, 0); |
---|
| 1262 | spc.toWorld(fe, fIdchans(ftabRow)-1); |
---|
| 1263 | fIdfreq0(ftabRow) = fs; |
---|
| 1264 | fIdfcent(ftabRow) = 5.e-1 * ( fs + fe ); |
---|
| 1265 | } |
---|
[2290] | 1266 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
| 1267 | ifNos[ftabRow].shape(iflen); |
---|
| 1268 | iflen++; |
---|
| 1269 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1270 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
| 1271 | } |
---|
| 1272 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
| 1273 | polNos[ftabRow].shape(pollen); |
---|
| 1274 | pollen++; |
---|
| 1275 | polNos[ftabRow].resize(pollen,True); |
---|
| 1276 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
| 1277 | } |
---|
| 1278 | } // end of row iteration |
---|
| 1279 | |
---|
| 1280 | stypestrs.resize(nstype,False); |
---|
| 1281 | for (uInt j=0; j < nstype; j++) |
---|
| 1282 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
| 1283 | |
---|
| 1284 | // Format Scan summary |
---|
| 1285 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1286 | << std::left << setw(1) << "" |
---|
| 1287 | << setw(15) << rec.asString("SRCNAME") |
---|
[2969] | 1288 | << setw(21) << MVTime(btime).string(MVTime::YMD,8) |
---|
| 1289 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,8) |
---|
[2290] | 1290 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
| 1291 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
| 1292 | << std::left << stypestrs << setw(1) << "" |
---|
| 1293 | << freqids << setw(1) << "" |
---|
| 1294 | << molids << endl; |
---|
| 1295 | // Format Beam summary |
---|
| 1296 | for (uInt j=0; j < nbeam; j++) { |
---|
| 1297 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
[2969] | 1298 | << formatDirection(beamDirs(j),9) << endl; |
---|
[2290] | 1299 | } |
---|
| 1300 | // Flush summary every scan and clear up the string |
---|
| 1301 | ols << String(oss) << LogIO::POST; |
---|
| 1302 | if (ofs) ofs << String(oss) << flush; |
---|
| 1303 | oss.str(""); |
---|
| 1304 | oss.clear(); |
---|
| 1305 | |
---|
| 1306 | ++iter; |
---|
| 1307 | } // end of scan iteration |
---|
| 1308 | oss << asap::SEPERATOR << endl; |
---|
| 1309 | |
---|
| 1310 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
| 1311 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
[2938] | 1312 | // oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
| 1313 | // << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
| 1314 | // << setw(8) << "Frame" |
---|
| 1315 | // << setw(16) << "RefVal" |
---|
| 1316 | // << setw(7) << "RefPix" |
---|
| 1317 | // << setw(15) << "Increment" |
---|
| 1318 | // << setw(9) << "Channels" |
---|
| 1319 | // << setw(6) << "POLNOs" << endl; |
---|
| 1320 | // Int tmplen; |
---|
| 1321 | // for (Int i=0; i < nfid; i++){ |
---|
| 1322 | // // List row=i of FREQUENCIES subtable |
---|
| 1323 | // ifNos[i].shape(tmplen); |
---|
| 1324 | // if (tmplen >= 1) { |
---|
| 1325 | // oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
| 1326 | // << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
| 1327 | // << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
| 1328 | // << setw(2) << "" |
---|
| 1329 | // << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
| 1330 | // << std::left << polNos[i]; |
---|
| 1331 | // if (tmplen > 1) { |
---|
| 1332 | // oss << " (" << tmplen << " chains)"; |
---|
| 1333 | // } |
---|
| 1334 | // oss << endl; |
---|
| 1335 | // } |
---|
| 1336 | oss << std::right << setw(4) << "ID" << setw(2) << "" |
---|
| 1337 | << std::left << setw(9) << "IFNO(SPW)" << setw(2) << "" |
---|
| 1338 | << setw(8) << "#Chans" |
---|
[2290] | 1339 | << setw(8) << "Frame" |
---|
[2938] | 1340 | << setw(12) << "Ch0[MHz]" |
---|
| 1341 | << setw(14) << "ChanWid[kHz]" |
---|
| 1342 | << setw(14) << "Center[MHz]" |
---|
[2290] | 1343 | << setw(6) << "POLNOs" << endl; |
---|
| 1344 | Int tmplen; |
---|
| 1345 | for (Int i=0; i < nfid; i++){ |
---|
| 1346 | // List row=i of FREQUENCIES subtable |
---|
| 1347 | ifNos[i].shape(tmplen); |
---|
[2938] | 1348 | Double refpix, refval, increment ; |
---|
[2531] | 1349 | if (tmplen >= 1) { |
---|
[2938] | 1350 | freqTable_.getEntry( refpix, refval, increment, ftabIds(i) ) ; |
---|
| 1351 | oss << std::right << setw(4) << ftabIds(i) << setw(2) << "" |
---|
| 1352 | << std::left << setw(9) << ifNos[i](0) << setw(2) << "" |
---|
| 1353 | << std::right << setw(6) << fIdchans[i] << setw(2) << "" |
---|
| 1354 | << setw(6) << frequencies().getFrameString(true) |
---|
| 1355 | << setw(2) << "" |
---|
| 1356 | << setw(10) << std::setprecision(9) << (fIdfreq0[i]*1.e-6) << setw(2) << "" |
---|
| 1357 | << setw(12) << (increment*1.e-3) << setw(2) << "" |
---|
| 1358 | << setw(12) << (fIdfcent[i]*1.e-6) << setw(2) << "" |
---|
[2531] | 1359 | << std::left << polNos[i]; |
---|
| 1360 | if (tmplen > 1) { |
---|
| 1361 | oss << " (" << tmplen << " chains)"; |
---|
| 1362 | } |
---|
| 1363 | oss << endl; |
---|
[2290] | 1364 | } |
---|
[2531] | 1365 | |
---|
[2290] | 1366 | } |
---|
| 1367 | oss << asap::SEPERATOR << endl; |
---|
| 1368 | |
---|
| 1369 | // List MOLECULES Table (currently lists all rows) |
---|
| 1370 | oss << "MOLECULES: " << endl; |
---|
| 1371 | if (molecules().nrow() <= 0) { |
---|
| 1372 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
| 1373 | } else { |
---|
| 1374 | ROTableRow row(molecules().table()); |
---|
| 1375 | oss << std::right << setw(5) << "ID" |
---|
| 1376 | << std::left << setw(3) << "" |
---|
| 1377 | << setw(18) << "RestFreq" |
---|
| 1378 | << setw(15) << "Name" << endl; |
---|
| 1379 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
| 1380 | const TableRecord& rec=row.get(i); |
---|
| 1381 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
| 1382 | << std::left << setw(3) << "" |
---|
| 1383 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
| 1384 | << rec.asArrayString("NAME") << endl; |
---|
| 1385 | } |
---|
| 1386 | } |
---|
| 1387 | oss << asap::SEPERATOR << endl; |
---|
| 1388 | ols << String(oss) << LogIO::POST; |
---|
| 1389 | if (ofs) { |
---|
| 1390 | ofs << String(oss) << flush; |
---|
| 1391 | ofs.close(); |
---|
| 1392 | } |
---|
| 1393 | // return String(oss); |
---|
| 1394 | } |
---|
| 1395 | |
---|
| 1396 | |
---|
| 1397 | std::string Scantable::oldheaderSummary() |
---|
| 1398 | { |
---|
| 1399 | // Format header info |
---|
| 1400 | // STHeader sdh; |
---|
| 1401 | // sdh = getHeader(); |
---|
| 1402 | // sdh.print(); |
---|
| 1403 | ostringstream oss; |
---|
| 1404 | oss.flags(std::ios_base::left); |
---|
| 1405 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1406 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
| 1407 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1408 | << "(" << getPolType() << ")" << endl |
---|
| 1409 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[805] | 1410 | String tmp; |
---|
[860] | 1411 | oss << setw(15) << "Observer:" |
---|
| 1412 | << table_.keywordSet().asString("Observer") << endl; |
---|
[805] | 1413 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1414 | table_.keywordSet().get("Project", tmp); |
---|
| 1415 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1416 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1417 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1418 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1419 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1420 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1421 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
[1819] | 1422 | int nid = moleculeTable_.nrow(); |
---|
| 1423 | Bool firstline = True; |
---|
[805] | 1424 | oss << setw(15) << "Rest Freqs:"; |
---|
[1819] | 1425 | for (int i=0; i<nid; i++) { |
---|
[2244] | 1426 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
[1819] | 1427 | if (t.nrow() > 0) { |
---|
| 1428 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
| 1429 | if (vec.nelements() > 0) { |
---|
| 1430 | if (firstline) { |
---|
| 1431 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1432 | firstline=False; |
---|
| 1433 | } |
---|
| 1434 | else{ |
---|
| 1435 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1436 | } |
---|
| 1437 | } else { |
---|
| 1438 | oss << "none" << endl; |
---|
| 1439 | } |
---|
| 1440 | } |
---|
[805] | 1441 | } |
---|
[941] | 1442 | |
---|
| 1443 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
[805] | 1444 | oss << selector_.print() << endl; |
---|
[2111] | 1445 | return String(oss); |
---|
| 1446 | } |
---|
| 1447 | |
---|
[2286] | 1448 | //std::string Scantable::summary( const std::string& filename ) |
---|
[2290] | 1449 | void Scantable::oldsummary( const std::string& filename ) |
---|
[2111] | 1450 | { |
---|
| 1451 | ostringstream oss; |
---|
[2286] | 1452 | ofstream ofs; |
---|
| 1453 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1454 | |
---|
| 1455 | if (filename != "") |
---|
| 1456 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1457 | |
---|
[805] | 1458 | oss << endl; |
---|
[2111] | 1459 | oss << asap::SEPERATOR << endl; |
---|
| 1460 | oss << " Scan Table Summary" << endl; |
---|
| 1461 | oss << asap::SEPERATOR << endl; |
---|
| 1462 | |
---|
| 1463 | // Format header info |
---|
[2290] | 1464 | oss << oldheaderSummary(); |
---|
[2111] | 1465 | oss << endl; |
---|
| 1466 | |
---|
[805] | 1467 | // main table |
---|
| 1468 | String dirtype = "Position (" |
---|
[987] | 1469 | + getDirectionRefString() |
---|
[805] | 1470 | + ")"; |
---|
[2111] | 1471 | oss.flags(std::ios_base::left); |
---|
[941] | 1472 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
[2005] | 1473 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
| 1474 | << setw(15) << "Source Type" << endl; |
---|
[941] | 1475 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
[1694] | 1476 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
[805] | 1477 | << setw(8) << "Frame" << setw(16) |
---|
[1694] | 1478 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
| 1479 | << setw(7) << "Channels" |
---|
| 1480 | << endl; |
---|
[805] | 1481 | oss << asap::SEPERATOR << endl; |
---|
[2286] | 1482 | |
---|
| 1483 | // Flush summary and clear up the string |
---|
| 1484 | ols << String(oss) << LogIO::POST; |
---|
| 1485 | if (ofs) ofs << String(oss) << flush; |
---|
| 1486 | oss.str(""); |
---|
| 1487 | oss.clear(); |
---|
| 1488 | |
---|
[805] | 1489 | TableIterator iter(table_, "SCANNO"); |
---|
| 1490 | while (!iter.pastEnd()) { |
---|
| 1491 | Table subt = iter.table(); |
---|
| 1492 | ROTableRow row(subt); |
---|
| 1493 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
| 1494 | const TableRecord& rec = row.get(0); |
---|
| 1495 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1496 | << std::left << setw(1) << "" |
---|
| 1497 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1498 | << setw(10) << formatTime(timeCol(0), false); |
---|
| 1499 | // count the cycles in the scan |
---|
| 1500 | TableIterator cyciter(subt, "CYCLENO"); |
---|
| 1501 | int nint = 0; |
---|
| 1502 | while (!cyciter.pastEnd()) { |
---|
| 1503 | ++nint; |
---|
| 1504 | ++cyciter; |
---|
| 1505 | } |
---|
| 1506 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
[2005] | 1507 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
| 1508 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
[447] | 1509 | |
---|
[805] | 1510 | TableIterator biter(subt, "BEAMNO"); |
---|
| 1511 | while (!biter.pastEnd()) { |
---|
| 1512 | Table bsubt = biter.table(); |
---|
| 1513 | ROTableRow brow(bsubt); |
---|
| 1514 | const TableRecord& brec = brow.get(0); |
---|
[1000] | 1515 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
[941] | 1516 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
[987] | 1517 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
[805] | 1518 | TableIterator iiter(bsubt, "IFNO"); |
---|
| 1519 | while (!iiter.pastEnd()) { |
---|
| 1520 | Table isubt = iiter.table(); |
---|
| 1521 | ROTableRow irow(isubt); |
---|
| 1522 | const TableRecord& irec = irow.get(0); |
---|
[1694] | 1523 | oss << setw(9) << ""; |
---|
[941] | 1524 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
[1694] | 1525 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
| 1526 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
[1375] | 1527 | << endl; |
---|
[447] | 1528 | |
---|
[805] | 1529 | ++iiter; |
---|
| 1530 | } |
---|
| 1531 | ++biter; |
---|
| 1532 | } |
---|
[2286] | 1533 | // Flush summary every scan and clear up the string |
---|
| 1534 | ols << String(oss) << LogIO::POST; |
---|
| 1535 | if (ofs) ofs << String(oss) << flush; |
---|
| 1536 | oss.str(""); |
---|
| 1537 | oss.clear(); |
---|
| 1538 | |
---|
[805] | 1539 | ++iter; |
---|
[447] | 1540 | } |
---|
[2286] | 1541 | oss << asap::SEPERATOR << endl; |
---|
| 1542 | ols << String(oss) << LogIO::POST; |
---|
| 1543 | if (ofs) { |
---|
[2290] | 1544 | ofs << String(oss) << flush; |
---|
[2286] | 1545 | ofs.close(); |
---|
| 1546 | } |
---|
| 1547 | // return String(oss); |
---|
[447] | 1548 | } |
---|
| 1549 | |
---|
[1947] | 1550 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
| 1551 | // { |
---|
| 1552 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 1553 | // MEpoch me; |
---|
| 1554 | // if (whichrow > -1) { |
---|
| 1555 | // me = timeCol(uInt(whichrow)); |
---|
| 1556 | // } else { |
---|
| 1557 | // Double tm; |
---|
| 1558 | // table_.keywordSet().get("UTC",tm); |
---|
| 1559 | // me = MEpoch(MVEpoch(tm)); |
---|
| 1560 | // } |
---|
| 1561 | // return formatTime(me, showdate); |
---|
| 1562 | // } |
---|
| 1563 | |
---|
| 1564 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
[777] | 1565 | { |
---|
[805] | 1566 | MEpoch me; |
---|
[1947] | 1567 | me = getEpoch(whichrow); |
---|
| 1568 | return formatTime(me, showdate, prec); |
---|
[777] | 1569 | } |
---|
[805] | 1570 | |
---|
[1411] | 1571 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
| 1572 | { |
---|
| 1573 | if (whichrow > -1) { |
---|
| 1574 | return timeCol_(uInt(whichrow)); |
---|
| 1575 | } else { |
---|
| 1576 | Double tm; |
---|
| 1577 | table_.keywordSet().get("UTC",tm); |
---|
[1598] | 1578 | return MEpoch(MVEpoch(tm)); |
---|
[1411] | 1579 | } |
---|
| 1580 | } |
---|
| 1581 | |
---|
[1068] | 1582 | std::string Scantable::getDirectionString(int whichrow) const |
---|
| 1583 | { |
---|
| 1584 | return formatDirection(getDirection(uInt(whichrow))); |
---|
| 1585 | } |
---|
| 1586 | |
---|
[1598] | 1587 | |
---|
| 1588 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
| 1589 | const MPosition& mp = getAntennaPosition(); |
---|
| 1590 | const MDirection& md = getDirection(whichrow); |
---|
| 1591 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1592 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
| 1593 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[2346] | 1594 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
[1598] | 1595 | mfreqidCol_(whichrow)); |
---|
| 1596 | } |
---|
| 1597 | |
---|
[1360] | 1598 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
[865] | 1599 | { |
---|
[1507] | 1600 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
[865] | 1601 | std::vector<double> stlout; |
---|
| 1602 | int nchan = specCol_(whichrow).nelements(); |
---|
[2346] | 1603 | String us = freqTable_.getUnitString(); |
---|
[865] | 1604 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
| 1605 | for (int i=0; i<nchan; ++i) { |
---|
| 1606 | stlout.push_back(double(i)); |
---|
| 1607 | } |
---|
| 1608 | return stlout; |
---|
| 1609 | } |
---|
[1598] | 1610 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
[865] | 1611 | Vector<Double> pixel(nchan); |
---|
| 1612 | Vector<Double> world; |
---|
| 1613 | indgen(pixel); |
---|
| 1614 | if ( Unit(us) == Unit("Hz") ) { |
---|
| 1615 | for ( int i=0; i < nchan; ++i) { |
---|
| 1616 | Double world; |
---|
| 1617 | spc.toWorld(world, pixel[i]); |
---|
| 1618 | stlout.push_back(double(world)); |
---|
| 1619 | } |
---|
| 1620 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
| 1621 | Vector<Double> world; |
---|
| 1622 | spc.pixelToVelocity(world, pixel); |
---|
| 1623 | world.tovector(stlout); |
---|
| 1624 | } |
---|
| 1625 | return stlout; |
---|
| 1626 | } |
---|
[1360] | 1627 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
[987] | 1628 | { |
---|
| 1629 | MDirection::Types mdt; |
---|
| 1630 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
| 1631 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1632 | } |
---|
| 1633 | if ( refstr == "" ) { |
---|
| 1634 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1635 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
| 1636 | } else { |
---|
| 1637 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
| 1638 | } |
---|
| 1639 | } |
---|
[865] | 1640 | |
---|
[1360] | 1641 | std::string Scantable::getDirectionRefString( ) const |
---|
[987] | 1642 | { |
---|
| 1643 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1644 | } |
---|
| 1645 | |
---|
| 1646 | MDirection Scantable::getDirection(int whichrow ) const |
---|
| 1647 | { |
---|
| 1648 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1649 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1650 | if ( usertype != type ) { |
---|
| 1651 | MDirection::Types mdt; |
---|
| 1652 | if (!MDirection::getType(mdt, usertype)) { |
---|
| 1653 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1654 | } |
---|
| 1655 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
| 1656 | } else { |
---|
| 1657 | return dirCol_(uInt(whichrow)); |
---|
| 1658 | } |
---|
| 1659 | } |
---|
| 1660 | |
---|
[847] | 1661 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
| 1662 | { |
---|
[996] | 1663 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
[847] | 1664 | const MPosition& mp = getAntennaPosition(); |
---|
[987] | 1665 | const MDirection& md = getDirection(whichrow); |
---|
[847] | 1666 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1667 | //const Double& rf = mmolidCol_(whichrow); |
---|
| 1668 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[847] | 1669 | SpectralCoordinate spc = |
---|
[2346] | 1670 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
[847] | 1671 | |
---|
| 1672 | String s = "Channel"; |
---|
[2346] | 1673 | Unit u = Unit(freqTable_.getUnitString()); |
---|
[847] | 1674 | if (u == Unit("km/s")) { |
---|
[1170] | 1675 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
[847] | 1676 | } else if (u == Unit("Hz")) { |
---|
| 1677 | Vector<String> wau(1);wau = u.getName(); |
---|
| 1678 | spc.setWorldAxisUnits(wau); |
---|
[1170] | 1679 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
[847] | 1680 | } |
---|
| 1681 | return s; |
---|
| 1682 | |
---|
| 1683 | } |
---|
| 1684 | |
---|
[1819] | 1685 | /** |
---|
| 1686 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
[1170] | 1687 | const std::string& unit ) |
---|
[1819] | 1688 | **/ |
---|
| 1689 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
| 1690 | const std::string& unit ) |
---|
| 1691 | |
---|
[847] | 1692 | { |
---|
[923] | 1693 | ///@todo lookup in line table to fill in name and formattedname |
---|
[847] | 1694 | Unit u(unit); |
---|
[1819] | 1695 | //Quantum<Double> urf(rf, u); |
---|
| 1696 | Quantum<Vector<Double> >urf(rf, u); |
---|
| 1697 | Vector<String> formattedname(0); |
---|
| 1698 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
| 1699 | |
---|
| 1700 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
| 1701 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
[847] | 1702 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
| 1703 | tabvec = id; |
---|
| 1704 | } |
---|
| 1705 | |
---|
[1819] | 1706 | /** |
---|
| 1707 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
[847] | 1708 | { |
---|
| 1709 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
| 1710 | ///@todo implement |
---|
| 1711 | } |
---|
[1819] | 1712 | **/ |
---|
[2012] | 1713 | |
---|
[1819] | 1714 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
| 1715 | { |
---|
[2163] | 1716 | (void) name; // suppress unused warning |
---|
[1819] | 1717 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
| 1718 | ///@todo implement |
---|
| 1719 | } |
---|
[847] | 1720 | |
---|
[1360] | 1721 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
[852] | 1722 | { |
---|
| 1723 | std::vector<unsigned int> stlout; |
---|
| 1724 | Vector<uInt> vec = table_.rowNumbers(); |
---|
| 1725 | vec.tovector(stlout); |
---|
| 1726 | return stlout; |
---|
| 1727 | } |
---|
| 1728 | |
---|
[865] | 1729 | |
---|
[1360] | 1730 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
[896] | 1731 | { |
---|
| 1732 | ROTableRow row(table_); |
---|
| 1733 | const TableRecord& rec = row.get(whichrow); |
---|
| 1734 | Table t = |
---|
| 1735 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
| 1736 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 1737 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 1738 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 1739 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 1740 | return speccol.getColumn(); |
---|
| 1741 | } |
---|
[865] | 1742 | |
---|
[1360] | 1743 | std::vector< std::string > Scantable::columnNames( ) const |
---|
[902] | 1744 | { |
---|
| 1745 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
| 1746 | return mathutil::tovectorstring(vec); |
---|
| 1747 | } |
---|
[896] | 1748 | |
---|
[1360] | 1749 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
[915] | 1750 | { |
---|
| 1751 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
[972] | 1752 | } |
---|
[915] | 1753 | |
---|
[1360] | 1754 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
[972] | 1755 | { |
---|
[1819] | 1756 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
| 1757 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
| 1758 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
[972] | 1759 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
| 1760 | mfitidCol_.put(uInt(row), id); |
---|
| 1761 | } |
---|
[915] | 1762 | |
---|
[1360] | 1763 | void Scantable::shift(int npix) |
---|
| 1764 | { |
---|
| 1765 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
| 1766 | genSort( fids, Sort::Ascending, |
---|
| 1767 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 1768 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
[1567] | 1769 | frequencies().shiftRefPix(npix, fids[i]); |
---|
[1360] | 1770 | } |
---|
| 1771 | } |
---|
[987] | 1772 | |
---|
[1819] | 1773 | String Scantable::getAntennaName() const |
---|
[1391] | 1774 | { |
---|
| 1775 | String out; |
---|
| 1776 | table_.keywordSet().get("AntennaName", out); |
---|
[1987] | 1777 | String::size_type pos1 = out.find("@") ; |
---|
| 1778 | String::size_type pos2 = out.find("//") ; |
---|
| 1779 | if ( pos2 != String::npos ) |
---|
[2036] | 1780 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
[1987] | 1781 | else if ( pos1 != String::npos ) |
---|
| 1782 | out = out.substr(0,pos1) ; |
---|
[1391] | 1783 | return out; |
---|
[987] | 1784 | } |
---|
[1391] | 1785 | |
---|
[1730] | 1786 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
[1391] | 1787 | { |
---|
| 1788 | String tbpath; |
---|
| 1789 | int ret = 0; |
---|
| 1790 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
| 1791 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
| 1792 | Table t(tbpath,Table::Old); |
---|
| 1793 | // check each scan if other scan of the pair exist |
---|
| 1794 | int nscan = scanlist.size(); |
---|
| 1795 | for (int i = 0; i < nscan; i++) { |
---|
[2869] | 1796 | Table subt = t( t.col("SCAN") == scanlist[i] ); |
---|
[1391] | 1797 | if (subt.nrow()==0) { |
---|
[1819] | 1798 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
| 1799 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1800 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1801 | ret = 1; |
---|
| 1802 | break; |
---|
| 1803 | } |
---|
| 1804 | ROTableRow row(subt); |
---|
| 1805 | const TableRecord& rec = row.get(0); |
---|
| 1806 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
| 1807 | int laston1 = rec.asuInt("LASTON"); |
---|
| 1808 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
| 1809 | if ( i < nscan-1 ) { |
---|
[2869] | 1810 | Table subt2 = t( t.col("SCAN") == scanlist[i+1] ); |
---|
[1391] | 1811 | if ( subt2.nrow() == 0) { |
---|
[1819] | 1812 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1813 | |
---|
| 1814 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
| 1815 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1816 | ret = 1; |
---|
| 1817 | break; |
---|
| 1818 | } |
---|
| 1819 | ROTableRow row2(subt2); |
---|
| 1820 | const TableRecord& rec2 = row2.get(0); |
---|
| 1821 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
| 1822 | int laston2 = rec2.asuInt("LASTON"); |
---|
| 1823 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
| 1824 | if (laston1 == laston2) { |
---|
[1819] | 1825 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1826 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1827 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1828 | i +=1; |
---|
| 1829 | } |
---|
| 1830 | else { |
---|
[1819] | 1831 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1832 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1833 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1834 | } |
---|
| 1835 | } |
---|
| 1836 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
| 1837 | if (laston1 == laston2) { |
---|
[1819] | 1838 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1839 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
| 1840 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
[1391] | 1841 | ret = 1; |
---|
| 1842 | break; |
---|
| 1843 | } |
---|
| 1844 | } |
---|
| 1845 | else { |
---|
[1819] | 1846 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1847 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
| 1848 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
[1391] | 1849 | ret = 1; |
---|
| 1850 | break; |
---|
| 1851 | } |
---|
| 1852 | } |
---|
| 1853 | } |
---|
| 1854 | else { |
---|
[1819] | 1855 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1856 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
| 1857 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
[1391] | 1858 | } |
---|
| 1859 | //if ( i >= nscan ) break; |
---|
| 1860 | } |
---|
| 1861 | } |
---|
| 1862 | else { |
---|
[1819] | 1863 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1864 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
| 1865 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
[1391] | 1866 | ret = 1; |
---|
| 1867 | } |
---|
| 1868 | return ret; |
---|
| 1869 | } |
---|
| 1870 | |
---|
[1730] | 1871 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
[1391] | 1872 | { |
---|
| 1873 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
| 1874 | std::vector<double> dir; |
---|
| 1875 | Dir.tovector(dir); |
---|
| 1876 | return dir; |
---|
| 1877 | } |
---|
| 1878 | |
---|
[1819] | 1879 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
| 1880 | throw( casa::AipsError ) |
---|
| 1881 | { |
---|
| 1882 | // assumed that all rows have same nChan |
---|
| 1883 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1884 | int nChan = arr.nelements() ; |
---|
| 1885 | |
---|
| 1886 | // if nmin < 0 or nmax < 0, nothing to do |
---|
| 1887 | if ( nmin < 0 ) { |
---|
| 1888 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1889 | } |
---|
| 1890 | if ( nmax < 0 ) { |
---|
| 1891 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1892 | } |
---|
| 1893 | |
---|
| 1894 | // if nmin > nmax, exchange values |
---|
| 1895 | if ( nmin > nmax ) { |
---|
| 1896 | int tmp = nmax ; |
---|
| 1897 | nmax = nmin ; |
---|
| 1898 | nmin = tmp ; |
---|
| 1899 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1900 | os << "Swap values. Applied range is [" |
---|
| 1901 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
| 1902 | } |
---|
| 1903 | |
---|
| 1904 | // if nmin exceeds nChan, nothing to do |
---|
| 1905 | if ( nmin >= nChan ) { |
---|
| 1906 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
| 1907 | } |
---|
| 1908 | |
---|
| 1909 | // if nmax exceeds nChan, reset nmax to nChan |
---|
[2672] | 1910 | if ( nmax >= nChan-1 ) { |
---|
[1819] | 1911 | if ( nmin == 0 ) { |
---|
| 1912 | // nothing to do |
---|
| 1913 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1914 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
| 1915 | return ; |
---|
| 1916 | } |
---|
| 1917 | else { |
---|
| 1918 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1919 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
| 1920 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
| 1921 | nmax = nChan - 1 ; |
---|
| 1922 | } |
---|
| 1923 | } |
---|
| 1924 | |
---|
| 1925 | // reshape specCol_ and flagCol_ |
---|
| 1926 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1927 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
| 1928 | } |
---|
| 1929 | |
---|
| 1930 | // update FREQUENCIES subtable |
---|
[2908] | 1931 | Vector<uInt> freqIdArray = mfreqidCol_.getColumn(); |
---|
| 1932 | uInt numFreqId = GenSort<uInt>::sort(freqIdArray, Sort::Ascending, |
---|
| 1933 | Sort::HeapSort | Sort::NoDuplicates); |
---|
[1819] | 1934 | Double refpix ; |
---|
| 1935 | Double refval ; |
---|
| 1936 | Double increment ; |
---|
[2908] | 1937 | for (uInt irow = 0; irow < numFreqId; irow++) { |
---|
| 1938 | freqTable_.getEntry( refpix, refval, increment, freqIdArray[irow] ) ; |
---|
[1819] | 1939 | /*** |
---|
| 1940 | * need to shift refpix to nmin |
---|
| 1941 | * note that channel nmin in old index will be channel 0 in new one |
---|
| 1942 | ***/ |
---|
| 1943 | refval = refval - ( refpix - nmin ) * increment ; |
---|
| 1944 | refpix = 0 ; |
---|
[2908] | 1945 | freqTable_.setEntry( refpix, refval, increment, freqIdArray[irow] ) ; |
---|
[1819] | 1946 | } |
---|
| 1947 | |
---|
| 1948 | // update nchan |
---|
| 1949 | int newsize = nmax - nmin + 1 ; |
---|
| 1950 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
| 1951 | |
---|
| 1952 | // update bandwidth |
---|
| 1953 | // assumed all spectra in the scantable have same bandwidth |
---|
| 1954 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
| 1955 | |
---|
| 1956 | return ; |
---|
| 1957 | } |
---|
| 1958 | |
---|
| 1959 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
| 1960 | { |
---|
| 1961 | // reshape specCol_ and flagCol_ |
---|
| 1962 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1963 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
[2475] | 1964 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
[1819] | 1965 | uInt newsize = nmax - nmin + 1 ; |
---|
[2475] | 1966 | Slice slice( nmin, newsize, 1 ) ; |
---|
| 1967 | specCol_.put( irow, oldspec( slice ) ) ; |
---|
| 1968 | flagsCol_.put( irow, oldflag( slice ) ) ; |
---|
| 1969 | if ( oldspec.size() == oldtsys.size() ) |
---|
| 1970 | tsysCol_.put( irow, oldtsys( slice ) ) ; |
---|
[1819] | 1971 | |
---|
| 1972 | return ; |
---|
| 1973 | } |
---|
| 1974 | |
---|
[2435] | 1975 | void asap::Scantable::regridSpecChannel( double dnu, int nChan ) |
---|
| 1976 | { |
---|
| 1977 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1978 | os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ; |
---|
| 1979 | int freqnrow = freqTable_.table().nrow() ; |
---|
| 1980 | Vector<bool> firstTime( freqnrow, true ) ; |
---|
| 1981 | double oldincr, factor; |
---|
| 1982 | uInt currId; |
---|
| 1983 | Double refpix ; |
---|
| 1984 | Double refval ; |
---|
| 1985 | Double increment ; |
---|
| 1986 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1987 | currId = mfreqidCol_(irow); |
---|
| 1988 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1989 | if (nChan < 0) { |
---|
| 1990 | int oldsize = abcissa.size() ; |
---|
| 1991 | double bw = (abcissa[oldsize-1]-abcissa[0]) + \ |
---|
| 1992 | 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ; |
---|
| 1993 | nChan = int( ceil( abs(bw/dnu) ) ) ; |
---|
| 1994 | } |
---|
| 1995 | // actual regridding |
---|
| 1996 | regridChannel( nChan, dnu, irow ) ; |
---|
[2433] | 1997 | |
---|
[2435] | 1998 | // update FREQUENCIES subtable |
---|
| 1999 | if (firstTime[currId]) { |
---|
| 2000 | oldincr = abcissa[1]-abcissa[0] ; |
---|
| 2001 | factor = dnu/oldincr ; |
---|
| 2002 | firstTime[currId] = false ; |
---|
| 2003 | freqTable_.getEntry( refpix, refval, increment, currId ) ; |
---|
[2463] | 2004 | |
---|
[2437] | 2005 | //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ; |
---|
[2463] | 2006 | if (factor > 0 ) { |
---|
[2462] | 2007 | refpix = (refpix + 0.5)/factor - 0.5; |
---|
| 2008 | } else { |
---|
[2463] | 2009 | refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5; |
---|
[2462] | 2010 | } |
---|
[2435] | 2011 | freqTable_.setEntry( refpix, refval, increment*factor, currId ) ; |
---|
[2463] | 2012 | //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ; |
---|
| 2013 | //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ; |
---|
[2435] | 2014 | } |
---|
| 2015 | } |
---|
| 2016 | } |
---|
| 2017 | |
---|
[1819] | 2018 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
| 2019 | { |
---|
| 2020 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 2021 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
| 2022 | // assumed that all rows have same nChan |
---|
| 2023 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 2024 | int oldsize = arr.nelements() ; |
---|
| 2025 | |
---|
| 2026 | // if oldsize == nChan, nothing to do |
---|
| 2027 | if ( oldsize == nChan ) { |
---|
| 2028 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
| 2029 | return ; |
---|
| 2030 | } |
---|
| 2031 | |
---|
| 2032 | // if oldChan < nChan, unphysical operation |
---|
| 2033 | if ( oldsize < nChan ) { |
---|
| 2034 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
| 2035 | return ; |
---|
| 2036 | } |
---|
| 2037 | |
---|
[2433] | 2038 | // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary) |
---|
[1819] | 2039 | vector<string> coordinfo = getCoordInfo() ; |
---|
| 2040 | string oldinfo = coordinfo[0] ; |
---|
| 2041 | coordinfo[0] = "Hz" ; |
---|
| 2042 | setCoordInfo( coordinfo ) ; |
---|
| 2043 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 2044 | regridChannel( nChan, dnu, irow ) ; |
---|
| 2045 | } |
---|
| 2046 | coordinfo[0] = oldinfo ; |
---|
| 2047 | setCoordInfo( coordinfo ) ; |
---|
| 2048 | |
---|
| 2049 | |
---|
| 2050 | // NOTE: this method does not update metadata such as |
---|
| 2051 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
| 2052 | |
---|
| 2053 | return ; |
---|
| 2054 | } |
---|
| 2055 | |
---|
| 2056 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
| 2057 | { |
---|
| 2058 | // logging |
---|
| 2059 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
| 2060 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
| 2061 | |
---|
| 2062 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 2063 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
[2431] | 2064 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
[1819] | 2065 | Vector<Float> newspec( nChan, 0 ) ; |
---|
[2431] | 2066 | Vector<uChar> newflag( nChan, true ) ; |
---|
| 2067 | Vector<Float> newtsys ; |
---|
| 2068 | bool regridTsys = false ; |
---|
| 2069 | if (oldtsys.size() == oldspec.size()) { |
---|
| 2070 | regridTsys = true ; |
---|
| 2071 | newtsys.resize(nChan,false) ; |
---|
| 2072 | newtsys = 0 ; |
---|
| 2073 | } |
---|
[1819] | 2074 | |
---|
| 2075 | // regrid |
---|
| 2076 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 2077 | int oldsize = abcissa.size() ; |
---|
| 2078 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
[2462] | 2079 | //int ichan = 0 ; |
---|
[1819] | 2080 | double wsum = 0.0 ; |
---|
[2433] | 2081 | Vector<double> zi( nChan+1 ) ; |
---|
| 2082 | Vector<double> yi( oldsize + 1 ) ; |
---|
[1819] | 2083 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
[2431] | 2084 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
[2433] | 2085 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
| 2086 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
| 2087 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
[2462] | 2088 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 2089 | zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
| 2090 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
| 2091 | zi[ii] = zi[0] + dnu * ii ; |
---|
| 2092 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
| 2093 | // Access zi and yi in ascending order |
---|
| 2094 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
| 2095 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
| 2096 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
| 2097 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
| 2098 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
| 2099 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
| 2100 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
| 2101 | int ii = izs ; |
---|
| 2102 | while (ii != ize) { |
---|
| 2103 | // always zl < zr |
---|
| 2104 | double zl = zi[ii] ; |
---|
| 2105 | double zr = zi[ii+izincr] ; |
---|
| 2106 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
| 2107 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
| 2108 | int i = min(ii, ii+izincr) ; |
---|
| 2109 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
| 2110 | int jj = ichan ; |
---|
| 2111 | while (jj != iye) { |
---|
| 2112 | // always yl < yr |
---|
| 2113 | double yl = yi[jj] ; |
---|
| 2114 | double yr = yi[jj+iyincr] ; |
---|
| 2115 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
| 2116 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
| 2117 | int j = min(jj, jj+iyincr) ; |
---|
| 2118 | if ( yr <= zl ) { |
---|
| 2119 | jj += iyincr ; |
---|
| 2120 | continue ; |
---|
[1819] | 2121 | } |
---|
[2462] | 2122 | else if ( yl <= zl ) { |
---|
| 2123 | if ( yr < zr ) { |
---|
| 2124 | if (!oldflag[j]) { |
---|
| 2125 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
| 2126 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
| 2127 | wsum += ( yr - zl ) ; |
---|
| 2128 | } |
---|
[2950] | 2129 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
[2462] | 2130 | } |
---|
| 2131 | else { |
---|
| 2132 | if (!oldflag[j]) { |
---|
| 2133 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
| 2134 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
| 2135 | wsum += abs(dnu) ; |
---|
| 2136 | } |
---|
[2950] | 2137 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
[2462] | 2138 | ichan = jj ; |
---|
| 2139 | break ; |
---|
| 2140 | } |
---|
[2431] | 2141 | } |
---|
[2462] | 2142 | else if ( yl < zr ) { |
---|
| 2143 | if ( yr <= zr ) { |
---|
| 2144 | if (!oldflag[j]) { |
---|
| 2145 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
| 2146 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
| 2147 | wsum += ( yr - yl ) ; |
---|
| 2148 | } |
---|
[2950] | 2149 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
[2462] | 2150 | } |
---|
| 2151 | else { |
---|
| 2152 | if (!oldflag[j]) { |
---|
| 2153 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
| 2154 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
| 2155 | wsum += ( zr - yl ) ; |
---|
| 2156 | } |
---|
[2950] | 2157 | newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ; |
---|
[2462] | 2158 | ichan = jj ; |
---|
| 2159 | break ; |
---|
| 2160 | } |
---|
[1819] | 2161 | } |
---|
[2462] | 2162 | else { |
---|
| 2163 | ichan = jj - iyincr ; |
---|
| 2164 | break ; |
---|
[2431] | 2165 | } |
---|
[2462] | 2166 | jj += iyincr ; |
---|
[1819] | 2167 | } |
---|
[2462] | 2168 | if ( wsum != 0.0 ) { |
---|
| 2169 | newspec[i] /= wsum ; |
---|
| 2170 | if (regridTsys) newtsys[i] /= wsum ; |
---|
| 2171 | } |
---|
| 2172 | wsum = 0.0 ; |
---|
| 2173 | ii += izincr ; |
---|
[1819] | 2174 | } |
---|
[2462] | 2175 | // if ( dnu > 0.0 ) { |
---|
| 2176 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 2177 | // double zl = zi[ii] ; |
---|
| 2178 | // double zr = zi[ii+1] ; |
---|
| 2179 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 2180 | // double yl = yi[j] ; |
---|
| 2181 | // double yr = yi[j+1] ; |
---|
| 2182 | // if ( yl <= zl ) { |
---|
| 2183 | // if ( yr <= zl ) { |
---|
| 2184 | // continue ; |
---|
| 2185 | // } |
---|
| 2186 | // else if ( yr <= zr ) { |
---|
| 2187 | // if (!oldflag[j]) { |
---|
| 2188 | // newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
| 2189 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ; |
---|
| 2190 | // wsum += ( yr - zl ) ; |
---|
| 2191 | // } |
---|
| 2192 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2193 | // } |
---|
| 2194 | // else { |
---|
| 2195 | // if (!oldflag[j]) { |
---|
| 2196 | // newspec[ii] += oldspec[j] * dnu ; |
---|
| 2197 | // if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ; |
---|
| 2198 | // wsum += dnu ; |
---|
| 2199 | // } |
---|
| 2200 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2201 | // ichan = j ; |
---|
| 2202 | // break ; |
---|
| 2203 | // } |
---|
| 2204 | // } |
---|
| 2205 | // else if ( yl < zr ) { |
---|
| 2206 | // if ( yr <= zr ) { |
---|
| 2207 | // if (!oldflag[j]) { |
---|
| 2208 | // newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
| 2209 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ; |
---|
| 2210 | // wsum += ( yr - yl ) ; |
---|
| 2211 | // } |
---|
| 2212 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2213 | // } |
---|
| 2214 | // else { |
---|
| 2215 | // if (!oldflag[j]) { |
---|
| 2216 | // newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
| 2217 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ; |
---|
| 2218 | // wsum += ( zr - yl ) ; |
---|
| 2219 | // } |
---|
| 2220 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2221 | // ichan = j ; |
---|
| 2222 | // break ; |
---|
| 2223 | // } |
---|
| 2224 | // } |
---|
| 2225 | // else { |
---|
| 2226 | // ichan = j - 1 ; |
---|
| 2227 | // break ; |
---|
| 2228 | // } |
---|
| 2229 | // } |
---|
| 2230 | // if ( wsum != 0.0 ) { |
---|
| 2231 | // newspec[ii] /= wsum ; |
---|
| 2232 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
| 2233 | // } |
---|
| 2234 | // wsum = 0.0 ; |
---|
| 2235 | // } |
---|
[1819] | 2236 | // } |
---|
[2462] | 2237 | // else if ( dnu < 0.0 ) { |
---|
| 2238 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 2239 | // double zl = zi[ii] ; |
---|
| 2240 | // double zr = zi[ii+1] ; |
---|
| 2241 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 2242 | // double yl = yi[j] ; |
---|
| 2243 | // double yr = yi[j+1] ; |
---|
| 2244 | // if ( yl >= zl ) { |
---|
| 2245 | // if ( yr >= zl ) { |
---|
| 2246 | // continue ; |
---|
| 2247 | // } |
---|
| 2248 | // else if ( yr >= zr ) { |
---|
| 2249 | // if (!oldflag[j]) { |
---|
| 2250 | // newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
| 2251 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ; |
---|
| 2252 | // wsum += abs( yr - zl ) ; |
---|
| 2253 | // } |
---|
| 2254 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2255 | // } |
---|
| 2256 | // else { |
---|
| 2257 | // if (!oldflag[j]) { |
---|
| 2258 | // newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
| 2259 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ; |
---|
| 2260 | // wsum += abs( dnu ) ; |
---|
| 2261 | // } |
---|
| 2262 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2263 | // ichan = j ; |
---|
| 2264 | // break ; |
---|
| 2265 | // } |
---|
| 2266 | // } |
---|
| 2267 | // else if ( yl > zr ) { |
---|
| 2268 | // if ( yr >= zr ) { |
---|
| 2269 | // if (!oldflag[j]) { |
---|
| 2270 | // newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
| 2271 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ; |
---|
| 2272 | // wsum += abs( yr - yl ) ; |
---|
| 2273 | // } |
---|
| 2274 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2275 | // } |
---|
| 2276 | // else { |
---|
| 2277 | // if (!oldflag[j]) { |
---|
| 2278 | // newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
| 2279 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ; |
---|
| 2280 | // wsum += abs( zr - yl ) ; |
---|
| 2281 | // } |
---|
| 2282 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2283 | // ichan = j ; |
---|
| 2284 | // break ; |
---|
| 2285 | // } |
---|
| 2286 | // } |
---|
| 2287 | // else { |
---|
| 2288 | // ichan = j - 1 ; |
---|
| 2289 | // break ; |
---|
| 2290 | // } |
---|
| 2291 | // } |
---|
| 2292 | // if ( wsum != 0.0 ) { |
---|
| 2293 | // newspec[ii] /= wsum ; |
---|
| 2294 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
| 2295 | // } |
---|
| 2296 | // wsum = 0.0 ; |
---|
[1819] | 2297 | // } |
---|
| 2298 | // } |
---|
[2462] | 2299 | // // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
| 2300 | // // pile += dnu ; |
---|
| 2301 | // // wedge = olddnu * ( refChan + 1 ) ; |
---|
| 2302 | // // while ( wedge < pile ) { |
---|
| 2303 | // // newspec[0] += olddnu * oldspec[refChan] ; |
---|
| 2304 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2305 | // // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
| 2306 | // // refChan++ ; |
---|
| 2307 | // // wedge += olddnu ; |
---|
| 2308 | // // wsum += olddnu ; |
---|
| 2309 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2310 | // // } |
---|
| 2311 | // // frac = ( wedge - pile ) / olddnu ; |
---|
| 2312 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2313 | // // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2314 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2315 | // // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2316 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2317 | // // newspec[0] /= wsum ; |
---|
| 2318 | // // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
| 2319 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
[1819] | 2320 | |
---|
[2462] | 2321 | // // /*** |
---|
| 2322 | // // * ichan = 1 - nChan-2 |
---|
| 2323 | // // ***/ |
---|
| 2324 | // // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
| 2325 | // // pile += dnu ; |
---|
| 2326 | // // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
| 2327 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2328 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
| 2329 | // // refChan++ ; |
---|
| 2330 | // // wedge += olddnu ; |
---|
| 2331 | // // wsum = frac * olddnu ; |
---|
| 2332 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2333 | // // while ( wedge < pile ) { |
---|
| 2334 | // // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
| 2335 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2336 | // // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
| 2337 | // // refChan++ ; |
---|
| 2338 | // // wedge += olddnu ; |
---|
| 2339 | // // wsum += olddnu ; |
---|
| 2340 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2341 | // // } |
---|
| 2342 | // // frac = ( wedge - pile ) / olddnu ; |
---|
| 2343 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2344 | // // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2345 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2346 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2347 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2348 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2349 | // // newspec[ichan] /= wsum ; |
---|
| 2350 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
| 2351 | // // } |
---|
[1819] | 2352 | |
---|
[2462] | 2353 | // // /*** |
---|
| 2354 | // // * ichan = nChan-1 |
---|
| 2355 | // // ***/ |
---|
| 2356 | // // // NOTE: Assumed that all spectra have the same bandwidth |
---|
| 2357 | // // pile += dnu ; |
---|
| 2358 | // // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
| 2359 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
| 2360 | // // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2361 | // // refChan++ ; |
---|
| 2362 | // // wedge += olddnu ; |
---|
| 2363 | // // wsum = frac * olddnu ; |
---|
| 2364 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2365 | // // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
| 2366 | // // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
| 2367 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
| 2368 | // // wsum += olddnu ; |
---|
| 2369 | // // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2370 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2371 | // // } |
---|
| 2372 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2373 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2374 | // // newspec[nChan-1] /= wsum ; |
---|
| 2375 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
[1819] | 2376 | |
---|
[2462] | 2377 | // // // ofs.close() ; |
---|
| 2378 | |
---|
[2032] | 2379 | specCol_.put( irow, newspec ) ; |
---|
| 2380 | flagsCol_.put( irow, newflag ) ; |
---|
[2431] | 2381 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
[1819] | 2382 | |
---|
| 2383 | return ; |
---|
| 2384 | } |
---|
| 2385 | |
---|
[2595] | 2386 | void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow ) |
---|
| 2387 | { |
---|
| 2388 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 2389 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 2390 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
| 2391 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 2392 | Vector<uChar> newflag( nChan, true ) ; |
---|
| 2393 | Vector<Float> newtsys ; |
---|
| 2394 | bool regridTsys = false ; |
---|
| 2395 | if (oldtsys.size() == oldspec.size()) { |
---|
| 2396 | regridTsys = true ; |
---|
| 2397 | newtsys.resize(nChan,false) ; |
---|
| 2398 | newtsys = 0 ; |
---|
| 2399 | } |
---|
| 2400 | |
---|
| 2401 | // regrid |
---|
| 2402 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 2403 | int oldsize = abcissa.size() ; |
---|
| 2404 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
| 2405 | //int ichan = 0 ; |
---|
| 2406 | double wsum = 0.0 ; |
---|
| 2407 | Vector<double> zi( nChan+1 ) ; |
---|
| 2408 | Vector<double> yi( oldsize + 1 ) ; |
---|
| 2409 | Block<uInt> count( nChan, 0 ) ; |
---|
| 2410 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 2411 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
| 2412 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
| 2413 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
| 2414 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
| 2415 | // cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ; |
---|
| 2416 | // cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ; |
---|
| 2417 | // cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ; |
---|
| 2418 | |
---|
| 2419 | // do not regrid if input parameters are almost same as current |
---|
| 2420 | // spectral setup |
---|
| 2421 | double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ; |
---|
| 2422 | double oldfmin = min( yi[0], yi[oldsize] ) ; |
---|
| 2423 | double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ; |
---|
| 2424 | double nChanDiff = nChan - oldsize ; |
---|
| 2425 | double eps = 1.0e-8 ; |
---|
| 2426 | if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps ) |
---|
| 2427 | return ; |
---|
| 2428 | |
---|
| 2429 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 2430 | //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
| 2431 | if ( dnu > 0 ) |
---|
| 2432 | zi[0] = fmin - 0.5 * dnu ; |
---|
| 2433 | else |
---|
| 2434 | zi[0] = fmin + nChan * abs(dnu) ; |
---|
| 2435 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
| 2436 | zi[ii] = zi[0] + dnu * ii ; |
---|
| 2437 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
| 2438 | // Access zi and yi in ascending order |
---|
| 2439 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
| 2440 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
| 2441 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
| 2442 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
| 2443 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
| 2444 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
| 2445 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
| 2446 | int ii = izs ; |
---|
| 2447 | while (ii != ize) { |
---|
| 2448 | // always zl < zr |
---|
| 2449 | double zl = zi[ii] ; |
---|
| 2450 | double zr = zi[ii+izincr] ; |
---|
| 2451 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
| 2452 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
| 2453 | int i = min(ii, ii+izincr) ; |
---|
| 2454 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
| 2455 | int jj = ichan ; |
---|
| 2456 | while (jj != iye) { |
---|
| 2457 | // always yl < yr |
---|
| 2458 | double yl = yi[jj] ; |
---|
| 2459 | double yr = yi[jj+iyincr] ; |
---|
| 2460 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
| 2461 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
| 2462 | int j = min(jj, jj+iyincr) ; |
---|
| 2463 | if ( yr <= zl ) { |
---|
| 2464 | jj += iyincr ; |
---|
| 2465 | continue ; |
---|
| 2466 | } |
---|
| 2467 | else if ( yl <= zl ) { |
---|
| 2468 | if ( yr < zr ) { |
---|
| 2469 | if (!oldflag[j]) { |
---|
| 2470 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
| 2471 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
| 2472 | wsum += ( yr - zl ) ; |
---|
| 2473 | count[i]++ ; |
---|
| 2474 | } |
---|
| 2475 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2476 | } |
---|
| 2477 | else { |
---|
| 2478 | if (!oldflag[j]) { |
---|
| 2479 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
| 2480 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
| 2481 | wsum += abs(dnu) ; |
---|
| 2482 | count[i]++ ; |
---|
| 2483 | } |
---|
| 2484 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2485 | ichan = jj ; |
---|
| 2486 | break ; |
---|
| 2487 | } |
---|
| 2488 | } |
---|
| 2489 | else if ( yl < zr ) { |
---|
| 2490 | if ( yr <= zr ) { |
---|
| 2491 | if (!oldflag[j]) { |
---|
| 2492 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
| 2493 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
| 2494 | wsum += ( yr - yl ) ; |
---|
| 2495 | count[i]++ ; |
---|
| 2496 | } |
---|
| 2497 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2498 | } |
---|
| 2499 | else { |
---|
| 2500 | if (!oldflag[j]) { |
---|
| 2501 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
| 2502 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
| 2503 | wsum += ( zr - yl ) ; |
---|
| 2504 | count[i]++ ; |
---|
| 2505 | } |
---|
| 2506 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2507 | ichan = jj ; |
---|
| 2508 | break ; |
---|
| 2509 | } |
---|
| 2510 | } |
---|
| 2511 | else { |
---|
| 2512 | //ichan = jj - iyincr ; |
---|
| 2513 | break ; |
---|
| 2514 | } |
---|
| 2515 | jj += iyincr ; |
---|
| 2516 | } |
---|
| 2517 | if ( wsum != 0.0 ) { |
---|
| 2518 | newspec[i] /= wsum ; |
---|
| 2519 | if (regridTsys) newtsys[i] /= wsum ; |
---|
| 2520 | } |
---|
| 2521 | wsum = 0.0 ; |
---|
| 2522 | ii += izincr ; |
---|
| 2523 | } |
---|
| 2524 | |
---|
| 2525 | // flag out channels without data |
---|
| 2526 | // this is tentative since there is no specific definition |
---|
| 2527 | // on bit flag... |
---|
| 2528 | uChar noData = 1 << 7 ; |
---|
| 2529 | for ( Int i = 0 ; i < nChan ; i++ ) { |
---|
| 2530 | if ( count[i] == 0 ) |
---|
| 2531 | newflag[i] = noData ; |
---|
| 2532 | } |
---|
| 2533 | |
---|
| 2534 | specCol_.put( irow, newspec ) ; |
---|
| 2535 | flagsCol_.put( irow, newflag ) ; |
---|
| 2536 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
| 2537 | |
---|
| 2538 | return ; |
---|
| 2539 | } |
---|
| 2540 | |
---|
[1730] | 2541 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
| 2542 | { |
---|
| 2543 | std::vector<float> out(5); |
---|
| 2544 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
| 2545 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
| 2546 | mweatheridCol_(uInt(whichrow))); |
---|
| 2547 | |
---|
| 2548 | |
---|
| 2549 | return out; |
---|
[1391] | 2550 | } |
---|
[1730] | 2551 | |
---|
[2831] | 2552 | bool Scantable::isAllChannelsFlagged(uInt whichrow) |
---|
[1907] | 2553 | { |
---|
[2831] | 2554 | uInt rflag; |
---|
| 2555 | flagrowCol_.get(whichrow, rflag); |
---|
| 2556 | if (rflag > 0) |
---|
| 2557 | return true; |
---|
[3023] | 2558 | bool flag; |
---|
[1907] | 2559 | Vector<uChar> flags; |
---|
[2047] | 2560 | flagsCol_.get(whichrow, flags); |
---|
[3023] | 2561 | flag = (flags[0]>0); |
---|
[2047] | 2562 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
[3023] | 2563 | flag &= (flags[i]>0); |
---|
[2012] | 2564 | } |
---|
[2837] | 2565 | // return ((flag >> 7) == 1); |
---|
| 2566 | return (flag > 0); |
---|
[2012] | 2567 | } |
---|
| 2568 | |
---|
[3023] | 2569 | std::size_t Scantable::nValidMask(const std::vector<bool>& mask) |
---|
| 2570 | { |
---|
| 2571 | std::size_t nvalid=0; |
---|
[3026] | 2572 | // the assertion lines had better be replaced with static_assert when c++11 is supported |
---|
| 2573 | AlwaysAssert(static_cast<std::size_t>(true)==1, AipsError); |
---|
| 2574 | AlwaysAssert(static_cast<std::size_t>(false)==0, AipsError); |
---|
[3023] | 2575 | for (uInt i = 1; i < mask.size(); ++i) { |
---|
| 2576 | nvalid += static_cast<std::size_t>(mask[i]); |
---|
| 2577 | } |
---|
| 2578 | return nvalid; |
---|
| 2579 | } |
---|
| 2580 | |
---|
| 2581 | |
---|
[2811] | 2582 | std::vector<std::string> Scantable::applyBaselineTable(const std::string& bltable, const bool returnfitresult, const std::string& outbltable, const bool outbltableexists, const bool overwrite) |
---|
[2047] | 2583 | { |
---|
[2773] | 2584 | STBaselineTable btin = STBaselineTable(bltable); |
---|
[2767] | 2585 | |
---|
[2773] | 2586 | Vector<Bool> applyCol = btin.getApply(); |
---|
[2767] | 2587 | int nRowBl = applyCol.size(); |
---|
| 2588 | if (nRowBl != nrow()) { |
---|
| 2589 | throw(AipsError("Scantable and bltable have different number of rows.")); |
---|
| 2590 | } |
---|
| 2591 | |
---|
| 2592 | std::vector<std::string> res; |
---|
| 2593 | res.clear(); |
---|
| 2594 | |
---|
| 2595 | bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite)); |
---|
| 2596 | bool bltableidentical = (bltable == outbltable); |
---|
[2773] | 2597 | STBaselineTable btout = STBaselineTable(*this); |
---|
| 2598 | ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME"); |
---|
| 2599 | Vector<Double> timeSecCol = tcol.getColumn(); |
---|
[2767] | 2600 | |
---|
| 2601 | for (int whichrow = 0; whichrow < nRowBl; ++whichrow) { |
---|
| 2602 | if (applyCol[whichrow]) { |
---|
| 2603 | std::vector<float> spec = getSpectrum(whichrow); |
---|
| 2604 | |
---|
[2773] | 2605 | std::vector<bool> mask = btin.getMask(whichrow); //use mask_bltable only |
---|
[2767] | 2606 | |
---|
[2773] | 2607 | STBaselineFunc::FuncName ftype = btin.getFunctionName(whichrow); |
---|
| 2608 | std::vector<int> fpar = btin.getFuncParam(whichrow); |
---|
[2767] | 2609 | std::vector<float> params; |
---|
| 2610 | float rms; |
---|
[3048] | 2611 | std::vector<float> resfit = doApplyBaselineTable(spec, mask, ftype, fpar, params, rms, whichrow); |
---|
[2767] | 2612 | setSpectrum(resfit, whichrow); |
---|
| 2613 | |
---|
[2811] | 2614 | if (returnfitresult) { |
---|
| 2615 | res.push_back(packFittingResults(whichrow, params, rms)); |
---|
| 2616 | } |
---|
[2767] | 2617 | |
---|
| 2618 | if (outBaselineTable) { |
---|
| 2619 | if (outbltableexists) { |
---|
| 2620 | if (overwrite) { |
---|
| 2621 | if (bltableidentical) { |
---|
[2773] | 2622 | btin.setresult(uInt(whichrow), Vector<Float>(params), Float(rms)); |
---|
[2767] | 2623 | } else { |
---|
[2773] | 2624 | btout.setresult(uInt(whichrow), Vector<Float>(params), Float(rms)); |
---|
[2767] | 2625 | } |
---|
| 2626 | } |
---|
| 2627 | } else { |
---|
[2773] | 2628 | btout.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 2629 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 2630 | true, ftype, fpar, std::vector<float>(), |
---|
| 2631 | getMaskListFromMask(mask), params, rms, spec.size(), |
---|
| 2632 | 3.0, 0, 0.0, 0, std::vector<int>()); |
---|
[2767] | 2633 | } |
---|
| 2634 | } |
---|
| 2635 | } |
---|
| 2636 | } |
---|
| 2637 | |
---|
| 2638 | if (outBaselineTable) { |
---|
| 2639 | if (bltableidentical) { |
---|
[2773] | 2640 | btin.save(outbltable); |
---|
[2767] | 2641 | } else { |
---|
[2773] | 2642 | btout.save(outbltable); |
---|
[2767] | 2643 | } |
---|
| 2644 | } |
---|
| 2645 | |
---|
| 2646 | return res; |
---|
| 2647 | } |
---|
| 2648 | |
---|
[2811] | 2649 | std::vector<std::string> Scantable::subBaseline(const std::vector<std::string>& blInfoList, const bool returnfitresult, const std::string& outbltable, const bool outbltableexists, const bool overwrite) |
---|
[2767] | 2650 | { |
---|
| 2651 | int nRowBl = blInfoList.size(); |
---|
| 2652 | int nRowSt = nrow(); |
---|
| 2653 | |
---|
| 2654 | std::vector<std::string> res; |
---|
| 2655 | res.clear(); |
---|
| 2656 | |
---|
| 2657 | bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite)); |
---|
| 2658 | if ((outbltable != "") && outbltableexists && !overwrite) { |
---|
| 2659 | throw(AipsError("Cannot overwrite bltable. Set overwrite=True.")); |
---|
| 2660 | } |
---|
| 2661 | |
---|
[3042] | 2662 | STBaselineTable* btp = NULL; |
---|
[2773] | 2663 | ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME"); |
---|
| 2664 | Vector<Double> timeSecCol = tcol.getColumn(); |
---|
[2767] | 2665 | |
---|
[2883] | 2666 | if (outBaselineTable) { |
---|
| 2667 | if (outbltableexists) { |
---|
| 2668 | btp = new STBaselineTable((String)outbltable); |
---|
| 2669 | } else { |
---|
| 2670 | btp = new STBaselineTable(*this); |
---|
[3009] | 2671 | // for (int i = 0; i < nRowSt; ++i) { |
---|
| 2672 | // btp->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i), |
---|
| 2673 | // 0, timeSecCol[i]); |
---|
| 2674 | // btp->setApply(i, false); |
---|
| 2675 | // } |
---|
[2767] | 2676 | } |
---|
[3009] | 2677 | int nrow = btp->nrow(); |
---|
| 2678 | for (int i = nrow; i < nRowSt; ++i) { |
---|
| 2679 | btp->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i), |
---|
| 2680 | 0, timeSecCol[i]); |
---|
| 2681 | btp->setApply(i, false); |
---|
| 2682 | } |
---|
[2767] | 2683 | } |
---|
| 2684 | |
---|
| 2685 | for (int i = 0; i < nRowBl; ++i) { |
---|
| 2686 | int irow; |
---|
| 2687 | STBaselineFunc::FuncName ftype; |
---|
| 2688 | std::vector<bool> mask; |
---|
| 2689 | std::vector<int> fpar; |
---|
| 2690 | float clipth; |
---|
| 2691 | int clipn; |
---|
| 2692 | bool uself; |
---|
| 2693 | float lfth; |
---|
| 2694 | std::vector<int> lfedge; |
---|
| 2695 | int lfavg; |
---|
| 2696 | parseBlInfo(blInfoList[i], irow, ftype, fpar, mask, clipth, clipn, uself, lfth, lfedge, lfavg); |
---|
| 2697 | |
---|
| 2698 | if (irow < nRowSt) { |
---|
| 2699 | std::vector<float> spec = getSpectrum(irow); |
---|
| 2700 | std::vector<float> params; |
---|
| 2701 | float rms; |
---|
| 2702 | std::vector<bool> finalmask; |
---|
[3009] | 2703 | Bool doApply = True; |
---|
| 2704 | |
---|
[3018] | 2705 | if (!isAllChannelsFlagged(irow)) { |
---|
[3009] | 2706 | std::vector<float> resfit = doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, clipth, clipn, uself, irow, lfth, lfedge, lfavg); |
---|
| 2707 | setSpectrum(resfit, irow); |
---|
| 2708 | } |
---|
| 2709 | else { |
---|
| 2710 | doApply = False; |
---|
| 2711 | } |
---|
[2767] | 2712 | |
---|
[2811] | 2713 | if (returnfitresult) { |
---|
| 2714 | res.push_back(packFittingResults(irow, params, rms)); |
---|
| 2715 | } |
---|
| 2716 | |
---|
[2767] | 2717 | if (outBaselineTable) { |
---|
| 2718 | Vector<Int> fparam(fpar.size()); |
---|
| 2719 | for (uInt j = 0; j < fparam.size(); ++j) { |
---|
| 2720 | fparam[j] = (Int)fpar[j]; |
---|
| 2721 | } |
---|
| 2722 | |
---|
[2883] | 2723 | btp->setdata(uInt(irow), |
---|
[2767] | 2724 | uInt(getScan(irow)), uInt(getCycle(irow)), |
---|
| 2725 | uInt(getBeam(irow)), uInt(getIF(irow)), uInt(getPol(irow)), |
---|
[3009] | 2726 | uInt(0), timeSecCol[irow], doApply, ftype, fparam, |
---|
[2773] | 2727 | Vector<Float>(), getMaskListFromMask(finalmask), Vector<Float>(params), |
---|
[2767] | 2728 | Float(rms), uInt(spec.size()), Float(clipth), uInt(clipn), |
---|
| 2729 | Float(0.0), uInt(0), Vector<uInt>()); |
---|
| 2730 | } |
---|
| 2731 | |
---|
| 2732 | } |
---|
| 2733 | } |
---|
| 2734 | |
---|
| 2735 | if (outBaselineTable) { |
---|
[2883] | 2736 | btp->save(outbltable); |
---|
[2767] | 2737 | } |
---|
| 2738 | |
---|
[3042] | 2739 | if (btp != NULL) { |
---|
| 2740 | delete btp; |
---|
| 2741 | } |
---|
| 2742 | |
---|
[2767] | 2743 | return res; |
---|
| 2744 | } |
---|
| 2745 | |
---|
[3048] | 2746 | std::vector<float> Scantable::doApplyBaselineTable(std::vector<float>& spec, |
---|
| 2747 | std::vector<bool>& mask, |
---|
| 2748 | const STBaselineFunc::FuncName ftype, |
---|
[2773] | 2749 | std::vector<int>& fpar, |
---|
| 2750 | std::vector<float>& params, |
---|
[3048] | 2751 | float&rms, |
---|
| 2752 | int irow) |
---|
[2767] | 2753 | { |
---|
| 2754 | std::vector<bool> finalmask; |
---|
| 2755 | std::vector<int> lfedge; |
---|
[3048] | 2756 | return doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, 0.0, 0, false, irow, 0.0, lfedge, 0); |
---|
[2767] | 2757 | } |
---|
| 2758 | |
---|
[2774] | 2759 | std::vector<float> Scantable::doSubtractBaseline(std::vector<float>& spec, |
---|
| 2760 | std::vector<bool>& mask, |
---|
| 2761 | const STBaselineFunc::FuncName ftype, |
---|
| 2762 | std::vector<int>& fpar, |
---|
| 2763 | std::vector<float>& params, |
---|
| 2764 | float&rms, |
---|
| 2765 | std::vector<bool>& finalmask, |
---|
| 2766 | float clipth, |
---|
| 2767 | int clipn, |
---|
| 2768 | bool uself, |
---|
| 2769 | int irow, |
---|
| 2770 | float lfth, |
---|
| 2771 | std::vector<int>& lfedge, |
---|
| 2772 | int lfavg) |
---|
[2767] | 2773 | { |
---|
| 2774 | if (uself) { |
---|
| 2775 | STLineFinder lineFinder = STLineFinder(); |
---|
[2774] | 2776 | initLineFinder(lfedge, lfth, lfavg, lineFinder); |
---|
[2767] | 2777 | std::vector<int> currentEdge; |
---|
[2774] | 2778 | mask = getCompositeChanMask(irow, mask, lfedge, currentEdge, lineFinder); |
---|
[2946] | 2779 | } else { |
---|
| 2780 | mask = getCompositeChanMask(irow, mask); |
---|
[2767] | 2781 | } |
---|
| 2782 | |
---|
| 2783 | std::vector<float> res; |
---|
| 2784 | if (ftype == STBaselineFunc::Polynomial) { |
---|
| 2785 | res = doPolynomialFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn); |
---|
| 2786 | } else if (ftype == STBaselineFunc::Chebyshev) { |
---|
| 2787 | res = doChebyshevFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn); |
---|
| 2788 | } else if (ftype == STBaselineFunc::CSpline) { |
---|
[3043] | 2789 | int nclip = 0; |
---|
| 2790 | size_t numChan = spec.size(); |
---|
| 2791 | if (cubicSplineModelPool_.find(numChan) == cubicSplineModelPool_.end()) { |
---|
| 2792 | cubicSplineModelPool_[numChan] = getPolynomialModel(3, numChan, &Scantable::getNormalPolynomial); |
---|
| 2793 | } |
---|
[2767] | 2794 | if (fpar.size() > 1) { // reading from baseline table in which pieceEdges are already calculated and stored. |
---|
[3043] | 2795 | //res = doCubicSplineFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn); |
---|
| 2796 | res = doCubicSplineLeastSquareFitting(spec, mask, |
---|
| 2797 | cubicSplineModelPool_[numChan], |
---|
| 2798 | fpar.size()-1, true, fpar, params, |
---|
| 2799 | rms, finalmask, nclip, clipth, |
---|
| 2800 | clipn); |
---|
[2767] | 2801 | } else { // usual cspline fitting by giving nPiece only. fpar will be replaced with pieceEdges. |
---|
[3043] | 2802 | //res = doCubicSplineFitting(spec, mask, fpar[0], fpar, params, rms, finalmask, clipth, clipn); |
---|
| 2803 | res = doCubicSplineLeastSquareFitting(spec, mask, |
---|
| 2804 | cubicSplineModelPool_[numChan], |
---|
| 2805 | fpar[0], false, fpar, params, |
---|
| 2806 | rms, finalmask, nclip, clipth, |
---|
| 2807 | clipn); |
---|
[2767] | 2808 | } |
---|
| 2809 | } else if (ftype == STBaselineFunc::Sinusoid) { |
---|
| 2810 | res = doSinusoidFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn); |
---|
| 2811 | } |
---|
| 2812 | |
---|
| 2813 | return res; |
---|
| 2814 | } |
---|
| 2815 | |
---|
| 2816 | std::string Scantable::packFittingResults(const int irow, const std::vector<float>& params, const float rms) |
---|
| 2817 | { |
---|
| 2818 | // returned value: "irow:params[0],params[1],..,params[n-1]:rms" |
---|
| 2819 | ostringstream os; |
---|
| 2820 | os << irow << ':'; |
---|
| 2821 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 2822 | if (i > 0) { |
---|
| 2823 | os << ','; |
---|
| 2824 | } |
---|
| 2825 | os << params[i]; |
---|
| 2826 | } |
---|
| 2827 | os << ':' << rms; |
---|
| 2828 | |
---|
| 2829 | return os.str(); |
---|
| 2830 | } |
---|
| 2831 | |
---|
| 2832 | void Scantable::parseBlInfo(const std::string& blInfo, int& irow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF) |
---|
| 2833 | { |
---|
| 2834 | // The baseline info to be parsed must be column-delimited string like |
---|
| 2835 | // "0:chebyshev:5:3,5,169,174,485,487" where the elements are |
---|
| 2836 | // row number, funcType, funcOrder, maskList, clipThreshold, clipNIter, |
---|
| 2837 | // useLineFinder, lfThreshold, lfEdge and lfChanAvgLimit. |
---|
| 2838 | |
---|
| 2839 | std::vector<string> res = splitToStringList(blInfo, ':'); |
---|
| 2840 | if (res.size() < 4) { |
---|
| 2841 | throw(AipsError("baseline info has bad format")) ; |
---|
| 2842 | } |
---|
| 2843 | |
---|
| 2844 | string ftype0, fpar0, masklist0, uself0, edge0; |
---|
| 2845 | std::vector<int> masklist; |
---|
| 2846 | |
---|
| 2847 | stringstream ss; |
---|
| 2848 | ss << res[0]; |
---|
| 2849 | ss >> irow; |
---|
| 2850 | ss.clear(); ss.str(""); |
---|
| 2851 | |
---|
| 2852 | ss << res[1]; |
---|
| 2853 | ss >> ftype0; |
---|
| 2854 | if (ftype0 == "poly") { |
---|
| 2855 | ftype = STBaselineFunc::Polynomial; |
---|
| 2856 | } else if (ftype0 == "cspline") { |
---|
| 2857 | ftype = STBaselineFunc::CSpline; |
---|
| 2858 | } else if (ftype0 == "sinusoid") { |
---|
| 2859 | ftype = STBaselineFunc::Sinusoid; |
---|
| 2860 | } else if (ftype0 == "chebyshev") { |
---|
| 2861 | ftype = STBaselineFunc::Chebyshev; |
---|
| 2862 | } else { |
---|
| 2863 | throw(AipsError("invalid function type.")); |
---|
| 2864 | } |
---|
| 2865 | ss.clear(); ss.str(""); |
---|
| 2866 | |
---|
| 2867 | ss << res[2]; |
---|
| 2868 | ss >> fpar0; |
---|
| 2869 | fpar = splitToIntList(fpar0, ','); |
---|
| 2870 | ss.clear(); ss.str(""); |
---|
| 2871 | |
---|
| 2872 | ss << res[3]; |
---|
| 2873 | ss >> masklist0; |
---|
| 2874 | mask = getMaskFromMaskList(nchan(getIF(irow)), splitToIntList(masklist0, ',')); |
---|
[2883] | 2875 | ss.clear(); ss.str(""); |
---|
[2767] | 2876 | |
---|
| 2877 | ss << res[4]; |
---|
| 2878 | ss >> thresClip; |
---|
| 2879 | ss.clear(); ss.str(""); |
---|
| 2880 | |
---|
| 2881 | ss << res[5]; |
---|
| 2882 | ss >> nIterClip; |
---|
| 2883 | ss.clear(); ss.str(""); |
---|
| 2884 | |
---|
| 2885 | ss << res[6]; |
---|
| 2886 | ss >> uself0; |
---|
| 2887 | if (uself0 == "true") { |
---|
| 2888 | useLineFinder = true; |
---|
| 2889 | } else { |
---|
| 2890 | useLineFinder = false; |
---|
| 2891 | } |
---|
| 2892 | ss.clear(); ss.str(""); |
---|
| 2893 | |
---|
| 2894 | if (useLineFinder) { |
---|
| 2895 | ss << res[7]; |
---|
| 2896 | ss >> thresLF; |
---|
| 2897 | ss.clear(); ss.str(""); |
---|
| 2898 | |
---|
| 2899 | ss << res[8]; |
---|
| 2900 | ss >> edge0; |
---|
| 2901 | edgeLF = splitToIntList(edge0, ','); |
---|
| 2902 | ss.clear(); ss.str(""); |
---|
| 2903 | |
---|
| 2904 | ss << res[9]; |
---|
| 2905 | ss >> avgLF; |
---|
| 2906 | ss.clear(); ss.str(""); |
---|
| 2907 | } |
---|
| 2908 | |
---|
| 2909 | } |
---|
| 2910 | |
---|
| 2911 | std::vector<int> Scantable::splitToIntList(const std::string& s, const char delim) |
---|
| 2912 | { |
---|
| 2913 | istringstream iss(s); |
---|
| 2914 | string tmp; |
---|
| 2915 | int tmpi; |
---|
| 2916 | std::vector<int> res; |
---|
| 2917 | stringstream ss; |
---|
| 2918 | while (getline(iss, tmp, delim)) { |
---|
| 2919 | ss << tmp; |
---|
| 2920 | ss >> tmpi; |
---|
| 2921 | res.push_back(tmpi); |
---|
| 2922 | ss.clear(); ss.str(""); |
---|
| 2923 | } |
---|
| 2924 | |
---|
| 2925 | return res; |
---|
| 2926 | } |
---|
| 2927 | |
---|
| 2928 | std::vector<string> Scantable::splitToStringList(const std::string& s, const char delim) |
---|
| 2929 | { |
---|
| 2930 | istringstream iss(s); |
---|
| 2931 | std::string tmp; |
---|
| 2932 | std::vector<string> res; |
---|
| 2933 | while (getline(iss, tmp, delim)) { |
---|
| 2934 | res.push_back(tmp); |
---|
| 2935 | } |
---|
| 2936 | |
---|
| 2937 | return res; |
---|
| 2938 | } |
---|
| 2939 | |
---|
| 2940 | std::vector<bool> Scantable::getMaskFromMaskList(const int nchan, const std::vector<int>& masklist) |
---|
| 2941 | { |
---|
| 2942 | if (masklist.size() % 2 != 0) { |
---|
| 2943 | throw(AipsError("masklist must have even number of elements.")); |
---|
| 2944 | } |
---|
| 2945 | |
---|
| 2946 | std::vector<bool> res(nchan); |
---|
| 2947 | |
---|
| 2948 | for (int i = 0; i < nchan; ++i) { |
---|
| 2949 | res[i] = false; |
---|
| 2950 | } |
---|
| 2951 | for (uInt j = 0; j < masklist.size(); j += 2) { |
---|
[3009] | 2952 | for (int i = masklist[j]; i <= min(nchan-1, masklist[j+1]); ++i) { |
---|
[2767] | 2953 | res[i] = true; |
---|
| 2954 | } |
---|
| 2955 | } |
---|
| 2956 | |
---|
| 2957 | return res; |
---|
| 2958 | } |
---|
| 2959 | |
---|
[2773] | 2960 | Vector<uInt> Scantable::getMaskListFromMask(const std::vector<bool>& mask) |
---|
[2767] | 2961 | { |
---|
[2773] | 2962 | std::vector<int> masklist; |
---|
| 2963 | masklist.clear(); |
---|
| 2964 | |
---|
| 2965 | for (uInt i = 0; i < mask.size(); ++i) { |
---|
| 2966 | if (mask[i]) { |
---|
| 2967 | if ((i == 0)||(i == mask.size()-1)) { |
---|
| 2968 | masklist.push_back(i); |
---|
| 2969 | } else { |
---|
| 2970 | if ((mask[i])&&(!mask[i-1])) { |
---|
| 2971 | masklist.push_back(i); |
---|
| 2972 | } |
---|
| 2973 | if ((mask[i])&&(!mask[i+1])) { |
---|
| 2974 | masklist.push_back(i); |
---|
| 2975 | } |
---|
| 2976 | } |
---|
| 2977 | } |
---|
| 2978 | } |
---|
| 2979 | |
---|
| 2980 | Vector<uInt> res(masklist.size()); |
---|
| 2981 | for (uInt i = 0; i < masklist.size(); ++i) { |
---|
| 2982 | res[i] = (uInt)masklist[i]; |
---|
| 2983 | } |
---|
| 2984 | |
---|
| 2985 | return res; |
---|
| 2986 | } |
---|
| 2987 | |
---|
| 2988 | void Scantable::initialiseBaselining(const std::string& blfile, |
---|
| 2989 | ofstream& ofs, |
---|
| 2990 | const bool outLogger, |
---|
| 2991 | bool& outTextFile, |
---|
| 2992 | bool& csvFormat, |
---|
| 2993 | String& coordInfo, |
---|
| 2994 | bool& hasSameNchan, |
---|
| 2995 | const std::string& progressInfo, |
---|
| 2996 | bool& showProgress, |
---|
| 2997 | int& minNRow, |
---|
| 2998 | Vector<Double>& timeSecCol) |
---|
| 2999 | { |
---|
| 3000 | csvFormat = false; |
---|
| 3001 | outTextFile = false; |
---|
| 3002 | |
---|
| 3003 | if (blfile != "") { |
---|
| 3004 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3005 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
| 3006 | if (ofs) outTextFile = true; |
---|
| 3007 | } |
---|
| 3008 | |
---|
| 3009 | coordInfo = ""; |
---|
| 3010 | hasSameNchan = true; |
---|
| 3011 | |
---|
| 3012 | if (outLogger || outTextFile) { |
---|
| 3013 | coordInfo = getCoordInfo()[0]; |
---|
| 3014 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3015 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3016 | } |
---|
| 3017 | |
---|
| 3018 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
| 3019 | |
---|
| 3020 | ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME"); |
---|
| 3021 | timeSecCol = tcol.getColumn(); |
---|
| 3022 | } |
---|
| 3023 | |
---|
| 3024 | void Scantable::finaliseBaselining(const bool outBaselineTable, |
---|
| 3025 | STBaselineTable* pbt, |
---|
| 3026 | const string& bltable, |
---|
| 3027 | const bool outTextFile, |
---|
| 3028 | ofstream& ofs) |
---|
| 3029 | { |
---|
| 3030 | if (outBaselineTable) { |
---|
| 3031 | pbt->save(bltable); |
---|
| 3032 | } |
---|
| 3033 | |
---|
| 3034 | if (outTextFile) ofs.close(); |
---|
| 3035 | } |
---|
| 3036 | |
---|
| 3037 | void Scantable::initLineFinder(const std::vector<int>& edge, |
---|
| 3038 | const float threshold, |
---|
| 3039 | const int chanAvgLimit, |
---|
| 3040 | STLineFinder& lineFinder) |
---|
| 3041 | { |
---|
[2774] | 3042 | if ((edge.size() > 2) && (edge.size() < getIFNos().size()*2)) { |
---|
[2773] | 3043 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3044 | } |
---|
| 3045 | |
---|
| 3046 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
| 3047 | } |
---|
| 3048 | |
---|
| 3049 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, |
---|
| 3050 | float thresClip, int nIterClip, |
---|
| 3051 | bool getResidual, |
---|
| 3052 | const std::string& progressInfo, |
---|
| 3053 | const bool outLogger, const std::string& blfile, |
---|
| 3054 | const std::string& bltable) |
---|
| 3055 | { |
---|
[2774] | 3056 | /**** |
---|
[2767] | 3057 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
[2774] | 3058 | ****/ |
---|
[2767] | 3059 | |
---|
[2193] | 3060 | try { |
---|
| 3061 | ofstream ofs; |
---|
[2773] | 3062 | String coordInfo; |
---|
| 3063 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
[2193] | 3064 | int minNRow; |
---|
[2767] | 3065 | int nRow = nrow(); |
---|
[2773] | 3066 | std::vector<bool> chanMask, finalChanMask; |
---|
[2767] | 3067 | float rms; |
---|
[2773] | 3068 | bool outBaselineTable = (bltable != ""); |
---|
| 3069 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 3070 | Vector<Double> timeSecCol; |
---|
[3026] | 3071 | size_t flagged=0; |
---|
[2767] | 3072 | |
---|
[2773] | 3073 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 3074 | coordInfo, hasSameNchan, |
---|
| 3075 | progressInfo, showProgress, minNRow, |
---|
| 3076 | timeSecCol); |
---|
[2767] | 3077 | |
---|
[2773] | 3078 | std::vector<int> nChanNos; |
---|
| 3079 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 3080 | modelReservoir = getPolynomialModelReservoir(order, |
---|
| 3081 | &Scantable::getNormalPolynomial, |
---|
| 3082 | nChanNos); |
---|
[2968] | 3083 | int nModel = modelReservoir.size(); |
---|
[2773] | 3084 | |
---|
[2193] | 3085 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2767] | 3086 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2193] | 3087 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[2968] | 3088 | std::vector<float> params; |
---|
[2773] | 3089 | |
---|
[3023] | 3090 | //if (flagrowCol_(whichrow) == 0) { |
---|
| 3091 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 3092 | int nClipped = 0; |
---|
| 3093 | std::vector<float> res; |
---|
| 3094 | res = doLeastSquareFitting(sp, chanMask, |
---|
[2773] | 3095 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
| 3096 | params, rms, finalChanMask, |
---|
| 3097 | nClipped, thresClip, nIterClip, getResidual); |
---|
[2767] | 3098 | |
---|
[2968] | 3099 | if (outBaselineTable) { |
---|
| 3100 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3101 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3102 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
| 3103 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 3104 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 3105 | } else { |
---|
| 3106 | setSpectrum(res, whichrow); |
---|
| 3107 | } |
---|
| 3108 | |
---|
| 3109 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 3110 | coordInfo, hasSameNchan, ofs, "polyBaseline()", |
---|
| 3111 | params, nClipped); |
---|
[2767] | 3112 | } else { |
---|
[3024] | 3113 | // no valid channels to fit (flag the row) |
---|
| 3114 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 3115 | ++flagged; |
---|
[2968] | 3116 | if (outBaselineTable) { |
---|
| 3117 | params.resize(nModel); |
---|
| 3118 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 3119 | params[i] = 0.0; |
---|
| 3120 | } |
---|
| 3121 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3122 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3123 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
| 3124 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 3125 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 3126 | } |
---|
[2767] | 3127 | } |
---|
| 3128 | |
---|
[2193] | 3129 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 3130 | } |
---|
| 3131 | |
---|
[2773] | 3132 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[3026] | 3133 | if (flagged > 0) { |
---|
| 3134 | LogIO os( LogOrigin( "Scantable", "polyBaseline()") ) ; |
---|
| 3135 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 3136 | } |
---|
[2193] | 3137 | } catch (...) { |
---|
| 3138 | throw; |
---|
[2047] | 3139 | } |
---|
[2767] | 3140 | |
---|
[2774] | 3141 | /**** |
---|
[2767] | 3142 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3143 | double elapse1 = TimeEnd - TimeStart; |
---|
| 3144 | std::cout << "poly-new : " << elapse1 << " (sec.)" << endl; |
---|
[2774] | 3145 | ****/ |
---|
[2047] | 3146 | } |
---|
| 3147 | |
---|
[2773] | 3148 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, |
---|
| 3149 | float thresClip, int nIterClip, |
---|
| 3150 | const std::vector<int>& edge, |
---|
| 3151 | float threshold, int chanAvgLimit, |
---|
| 3152 | bool getResidual, |
---|
| 3153 | const std::string& progressInfo, |
---|
| 3154 | const bool outLogger, const std::string& blfile, |
---|
| 3155 | const std::string& bltable) |
---|
[2047] | 3156 | { |
---|
[2193] | 3157 | try { |
---|
| 3158 | ofstream ofs; |
---|
[2773] | 3159 | String coordInfo; |
---|
| 3160 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
[2767] | 3161 | int minNRow; |
---|
| 3162 | int nRow = nrow(); |
---|
[2773] | 3163 | std::vector<bool> chanMask, finalChanMask; |
---|
[2767] | 3164 | float rms; |
---|
[2773] | 3165 | bool outBaselineTable = (bltable != ""); |
---|
| 3166 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 3167 | Vector<Double> timeSecCol; |
---|
| 3168 | STLineFinder lineFinder = STLineFinder(); |
---|
[3026] | 3169 | size_t flagged=0; |
---|
[2189] | 3170 | |
---|
[2773] | 3171 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 3172 | coordInfo, hasSameNchan, |
---|
| 3173 | progressInfo, showProgress, minNRow, |
---|
| 3174 | timeSecCol); |
---|
[2767] | 3175 | |
---|
[2773] | 3176 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
| 3177 | |
---|
| 3178 | std::vector<int> nChanNos; |
---|
| 3179 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 3180 | modelReservoir = getPolynomialModelReservoir(order, |
---|
| 3181 | &Scantable::getNormalPolynomial, |
---|
| 3182 | nChanNos); |
---|
[2968] | 3183 | int nModel = modelReservoir.size(); |
---|
[2773] | 3184 | |
---|
[2193] | 3185 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2767] | 3186 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2193] | 3187 | std::vector<int> currentEdge; |
---|
[2773] | 3188 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
[2968] | 3189 | std::vector<float> params; |
---|
[2193] | 3190 | |
---|
[3023] | 3191 | //if (flagrowCol_(whichrow) == 0) { |
---|
| 3192 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 3193 | int nClipped = 0; |
---|
| 3194 | std::vector<float> res; |
---|
| 3195 | res = doLeastSquareFitting(sp, chanMask, |
---|
[2773] | 3196 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
| 3197 | params, rms, finalChanMask, |
---|
| 3198 | nClipped, thresClip, nIterClip, getResidual); |
---|
[2193] | 3199 | |
---|
[2968] | 3200 | if (outBaselineTable) { |
---|
| 3201 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3202 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3203 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
| 3204 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 3205 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 3206 | } else { |
---|
| 3207 | setSpectrum(res, whichrow); |
---|
| 3208 | } |
---|
| 3209 | |
---|
| 3210 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 3211 | coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", |
---|
| 3212 | params, nClipped); |
---|
[2767] | 3213 | } else { |
---|
[3024] | 3214 | // no valid channels to fit (flag the row) |
---|
| 3215 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 3216 | ++flagged; |
---|
[2968] | 3217 | if (outBaselineTable) { |
---|
| 3218 | params.resize(nModel); |
---|
| 3219 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 3220 | params[i] = 0.0; |
---|
| 3221 | } |
---|
| 3222 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3223 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3224 | true, STBaselineFunc::Polynomial, order, std::vector<float>(), |
---|
| 3225 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 3226 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 3227 | } |
---|
[2767] | 3228 | } |
---|
| 3229 | |
---|
[2193] | 3230 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2047] | 3231 | } |
---|
| 3232 | |
---|
[2773] | 3233 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[3026] | 3234 | if (flagged > 0) { |
---|
| 3235 | LogIO os( LogOrigin( "Scantable", "autoPolyBaseline()") ) ; |
---|
| 3236 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 3237 | } |
---|
[2193] | 3238 | } catch (...) { |
---|
| 3239 | throw; |
---|
[2047] | 3240 | } |
---|
| 3241 | } |
---|
| 3242 | |
---|
[2773] | 3243 | void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order, |
---|
| 3244 | float thresClip, int nIterClip, |
---|
| 3245 | bool getResidual, |
---|
| 3246 | const std::string& progressInfo, |
---|
| 3247 | const bool outLogger, const std::string& blfile, |
---|
| 3248 | const std::string& bltable) |
---|
[2645] | 3249 | { |
---|
[2774] | 3250 | /* |
---|
[2767] | 3251 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
[2774] | 3252 | */ |
---|
[2767] | 3253 | |
---|
[2645] | 3254 | try { |
---|
| 3255 | ofstream ofs; |
---|
[2773] | 3256 | String coordInfo; |
---|
| 3257 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
[2645] | 3258 | int minNRow; |
---|
| 3259 | int nRow = nrow(); |
---|
[2773] | 3260 | std::vector<bool> chanMask, finalChanMask; |
---|
[2737] | 3261 | float rms; |
---|
[2773] | 3262 | bool outBaselineTable = (bltable != ""); |
---|
| 3263 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 3264 | Vector<Double> timeSecCol; |
---|
[3026] | 3265 | size_t flagged=0; |
---|
[2737] | 3266 | |
---|
[2773] | 3267 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 3268 | coordInfo, hasSameNchan, |
---|
| 3269 | progressInfo, showProgress, minNRow, |
---|
| 3270 | timeSecCol); |
---|
[2737] | 3271 | |
---|
[2773] | 3272 | std::vector<int> nChanNos; |
---|
| 3273 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 3274 | modelReservoir = getPolynomialModelReservoir(order, |
---|
| 3275 | &Scantable::getChebyshevPolynomial, |
---|
| 3276 | nChanNos); |
---|
[2968] | 3277 | int nModel = modelReservoir.size(); |
---|
[2773] | 3278 | |
---|
[2645] | 3279 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 3280 | std::vector<float> sp = getSpectrum(whichrow); |
---|
| 3281 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[2968] | 3282 | std::vector<float> params; |
---|
[2773] | 3283 | |
---|
[3023] | 3284 | // if (flagrowCol_(whichrow) == 0) { |
---|
| 3285 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 3286 | int nClipped = 0; |
---|
| 3287 | std::vector<float> res; |
---|
| 3288 | res = doLeastSquareFitting(sp, chanMask, |
---|
[2773] | 3289 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
| 3290 | params, rms, finalChanMask, |
---|
| 3291 | nClipped, thresClip, nIterClip, getResidual); |
---|
[2645] | 3292 | |
---|
[2968] | 3293 | if (outBaselineTable) { |
---|
| 3294 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3295 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3296 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
| 3297 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 3298 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 3299 | } else { |
---|
| 3300 | setSpectrum(res, whichrow); |
---|
| 3301 | } |
---|
| 3302 | |
---|
| 3303 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 3304 | coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", |
---|
| 3305 | params, nClipped); |
---|
[2737] | 3306 | } else { |
---|
[3024] | 3307 | // no valid channels to fit (flag the row) |
---|
| 3308 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 3309 | ++flagged; |
---|
[2968] | 3310 | if (outBaselineTable) { |
---|
| 3311 | params.resize(nModel); |
---|
| 3312 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 3313 | params[i] = 0.0; |
---|
| 3314 | } |
---|
| 3315 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3316 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3317 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
| 3318 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 3319 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 3320 | } |
---|
[2737] | 3321 | } |
---|
| 3322 | |
---|
[2645] | 3323 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 3324 | } |
---|
| 3325 | |
---|
[2773] | 3326 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[2737] | 3327 | |
---|
[3026] | 3328 | if (flagged > 0) { |
---|
| 3329 | LogIO os( LogOrigin( "Scantable", "chebyshevBaseline()") ) ; |
---|
| 3330 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 3331 | } |
---|
[2645] | 3332 | } catch (...) { |
---|
| 3333 | throw; |
---|
| 3334 | } |
---|
[2767] | 3335 | |
---|
[2774] | 3336 | /* |
---|
[2767] | 3337 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3338 | double elapse1 = TimeEnd - TimeStart; |
---|
| 3339 | std::cout << "cheby : " << elapse1 << " (sec.)" << endl; |
---|
[2774] | 3340 | */ |
---|
[2645] | 3341 | } |
---|
| 3342 | |
---|
[2773] | 3343 | void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order, |
---|
| 3344 | float thresClip, int nIterClip, |
---|
| 3345 | const std::vector<int>& edge, |
---|
| 3346 | float threshold, int chanAvgLimit, |
---|
| 3347 | bool getResidual, |
---|
| 3348 | const std::string& progressInfo, |
---|
| 3349 | const bool outLogger, const std::string& blfile, |
---|
| 3350 | const std::string& bltable) |
---|
[2767] | 3351 | { |
---|
| 3352 | try { |
---|
| 3353 | ofstream ofs; |
---|
[2773] | 3354 | String coordInfo; |
---|
| 3355 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
[2767] | 3356 | int minNRow; |
---|
| 3357 | int nRow = nrow(); |
---|
[2773] | 3358 | std::vector<bool> chanMask, finalChanMask; |
---|
[2767] | 3359 | float rms; |
---|
[2773] | 3360 | bool outBaselineTable = (bltable != ""); |
---|
| 3361 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 3362 | Vector<Double> timeSecCol; |
---|
| 3363 | STLineFinder lineFinder = STLineFinder(); |
---|
[3026] | 3364 | size_t flagged=0; |
---|
[2767] | 3365 | |
---|
[2773] | 3366 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 3367 | coordInfo, hasSameNchan, |
---|
| 3368 | progressInfo, showProgress, minNRow, |
---|
| 3369 | timeSecCol); |
---|
[2767] | 3370 | |
---|
[2773] | 3371 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
| 3372 | |
---|
| 3373 | std::vector<int> nChanNos; |
---|
| 3374 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 3375 | modelReservoir = getPolynomialModelReservoir(order, |
---|
| 3376 | &Scantable::getChebyshevPolynomial, |
---|
| 3377 | nChanNos); |
---|
[2968] | 3378 | int nModel = modelReservoir.size(); |
---|
[2773] | 3379 | |
---|
[2767] | 3380 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 3381 | std::vector<float> sp = getSpectrum(whichrow); |
---|
| 3382 | std::vector<int> currentEdge; |
---|
[2773] | 3383 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
[2968] | 3384 | std::vector<float> params; |
---|
[2767] | 3385 | |
---|
[3023] | 3386 | // if (flagrowCol_(whichrow) == 0) { |
---|
| 3387 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 3388 | int nClipped = 0; |
---|
| 3389 | std::vector<float> res; |
---|
| 3390 | res = doLeastSquareFitting(sp, chanMask, |
---|
[2773] | 3391 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
| 3392 | params, rms, finalChanMask, |
---|
| 3393 | nClipped, thresClip, nIterClip, getResidual); |
---|
[2767] | 3394 | |
---|
[2968] | 3395 | if (outBaselineTable) { |
---|
| 3396 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3397 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3398 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
| 3399 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 3400 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 3401 | } else { |
---|
| 3402 | setSpectrum(res, whichrow); |
---|
| 3403 | } |
---|
| 3404 | |
---|
| 3405 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 3406 | coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", |
---|
| 3407 | params, nClipped); |
---|
[2767] | 3408 | } else { |
---|
[3024] | 3409 | // no valid channels to fit (flag the row) |
---|
| 3410 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 3411 | ++flagged; |
---|
[2968] | 3412 | if (outBaselineTable) { |
---|
| 3413 | params.resize(nModel); |
---|
| 3414 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 3415 | params[i] = 0.0; |
---|
| 3416 | } |
---|
| 3417 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3418 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 3419 | true, STBaselineFunc::Chebyshev, order, std::vector<float>(), |
---|
| 3420 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 3421 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 3422 | } |
---|
[2767] | 3423 | } |
---|
| 3424 | |
---|
| 3425 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 3426 | } |
---|
| 3427 | |
---|
[2773] | 3428 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[2767] | 3429 | |
---|
[3026] | 3430 | if (flagged > 0) { |
---|
| 3431 | LogIO os( LogOrigin( "Scantable", "autoChebyshevBaseline()") ) ; |
---|
| 3432 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 3433 | } |
---|
[2767] | 3434 | } catch (...) { |
---|
| 3435 | throw; |
---|
| 3436 | } |
---|
| 3437 | } |
---|
| 3438 | |
---|
[2774] | 3439 | double Scantable::calculateModelSelectionCriteria(const std::string& valname, |
---|
| 3440 | const std::string& blfunc, |
---|
| 3441 | int order, |
---|
| 3442 | const std::vector<bool>& inMask, |
---|
| 3443 | int whichrow, |
---|
| 3444 | bool useLineFinder, |
---|
| 3445 | const std::vector<int>& edge, |
---|
| 3446 | float threshold, |
---|
| 3447 | int chanAvgLimit) |
---|
[2713] | 3448 | { |
---|
[2767] | 3449 | std::vector<float> sp = getSpectrum(whichrow); |
---|
| 3450 | std::vector<bool> chanMask; |
---|
| 3451 | chanMask.clear(); |
---|
| 3452 | |
---|
[2713] | 3453 | if (useLineFinder) { |
---|
[2774] | 3454 | STLineFinder lineFinder = STLineFinder(); |
---|
| 3455 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
[2713] | 3456 | std::vector<int> currentEdge; |
---|
[2774] | 3457 | chanMask = getCompositeChanMask(whichrow, inMask, edge, currentEdge, lineFinder); |
---|
[2713] | 3458 | } else { |
---|
[2767] | 3459 | chanMask = getCompositeChanMask(whichrow, inMask); |
---|
[2713] | 3460 | } |
---|
| 3461 | |
---|
[2767] | 3462 | return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order); |
---|
[2713] | 3463 | } |
---|
| 3464 | |
---|
| 3465 | double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order) |
---|
| 3466 | { |
---|
| 3467 | int nparam; |
---|
| 3468 | std::vector<float> params; |
---|
[2737] | 3469 | std::vector<bool> finalChanMask; |
---|
| 3470 | float rms; |
---|
[2713] | 3471 | int nClipped = 0; |
---|
| 3472 | std::vector<float> res; |
---|
[2767] | 3473 | if (blfunc == "poly") { |
---|
[2713] | 3474 | nparam = order + 1; |
---|
[2767] | 3475 | res = doPolynomialFitting(spec, mask, order, params, rms, finalChanMask, nClipped); |
---|
| 3476 | } else if (blfunc == "chebyshev") { |
---|
| 3477 | nparam = order + 1; |
---|
| 3478 | res = doChebyshevFitting(spec, mask, order, params, rms, finalChanMask, nClipped); |
---|
| 3479 | } else if (blfunc == "cspline") { |
---|
| 3480 | std::vector<int> pieceEdges;//(order+1); //order = npiece |
---|
| 3481 | nparam = order + 3; |
---|
| 3482 | res = doCubicSplineFitting(spec, mask, order, false, pieceEdges, params, rms, finalChanMask, nClipped); |
---|
[2713] | 3483 | } else if (blfunc == "sinusoid") { |
---|
| 3484 | std::vector<int> nWaves; |
---|
| 3485 | nWaves.clear(); |
---|
| 3486 | for (int i = 0; i <= order; ++i) { |
---|
| 3487 | nWaves.push_back(i); |
---|
| 3488 | } |
---|
| 3489 | nparam = 2*order + 1; // order = nwave |
---|
[2767] | 3490 | res = doSinusoidFitting(spec, mask, nWaves, params, rms, finalChanMask, nClipped); |
---|
[2713] | 3491 | } else { |
---|
[2767] | 3492 | throw(AipsError("blfunc must be poly, chebyshev, cspline or sinusoid.")); |
---|
[2713] | 3493 | } |
---|
| 3494 | |
---|
| 3495 | double msq = 0.0; |
---|
| 3496 | int nusedchan = 0; |
---|
| 3497 | int nChan = res.size(); |
---|
| 3498 | for (int i = 0; i < nChan; ++i) { |
---|
| 3499 | if (mask[i]) { |
---|
| 3500 | msq += (double)res[i]*(double)res[i]; |
---|
| 3501 | nusedchan++; |
---|
| 3502 | } |
---|
| 3503 | } |
---|
| 3504 | if (nusedchan == 0) { |
---|
| 3505 | throw(AipsError("all channels masked.")); |
---|
| 3506 | } |
---|
| 3507 | msq /= (double)nusedchan; |
---|
| 3508 | |
---|
| 3509 | nparam++; //add 1 for sigma of Gaussian distribution |
---|
| 3510 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
| 3511 | |
---|
| 3512 | if (valname.find("aic") == 0) { |
---|
| 3513 | // Original Akaike Information Criterion (AIC) |
---|
| 3514 | double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam; |
---|
| 3515 | |
---|
[2767] | 3516 | // Corrected AIC by Sugiura(1978) (AICc) |
---|
[2713] | 3517 | if (valname == "aicc") { |
---|
| 3518 | if (nusedchan - nparam - 1 <= 0) { |
---|
| 3519 | throw(AipsError("channel size is too small to calculate AICc.")); |
---|
| 3520 | } |
---|
| 3521 | aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1); |
---|
| 3522 | } |
---|
| 3523 | |
---|
| 3524 | return aic; |
---|
| 3525 | |
---|
| 3526 | } else if (valname == "bic") { |
---|
| 3527 | // Bayesian Information Criterion (BIC) |
---|
| 3528 | double bic = nusedchan * log(msq) + nparam * log((double)nusedchan); |
---|
| 3529 | return bic; |
---|
| 3530 | |
---|
| 3531 | } else if (valname == "gcv") { |
---|
| 3532 | // Generalised Cross Validation |
---|
| 3533 | double x = 1.0 - (double)nparam / (double)nusedchan; |
---|
| 3534 | double gcv = msq / (x * x); |
---|
| 3535 | return gcv; |
---|
| 3536 | |
---|
| 3537 | } else { |
---|
| 3538 | throw(AipsError("valname must be aic, aicc, bic or gcv.")); |
---|
| 3539 | } |
---|
| 3540 | } |
---|
| 3541 | |
---|
[2767] | 3542 | double Scantable::getNormalPolynomial(int n, double x) { |
---|
| 3543 | if (n == 0) { |
---|
| 3544 | return 1.0; |
---|
| 3545 | } else if (n > 0) { |
---|
| 3546 | double res = 1.0; |
---|
| 3547 | for (int i = 0; i < n; ++i) { |
---|
| 3548 | res *= x; |
---|
[2645] | 3549 | } |
---|
[2767] | 3550 | return res; |
---|
| 3551 | } else { |
---|
| 3552 | if (x == 0.0) { |
---|
| 3553 | throw(AipsError("infinity result: x=0 given for negative power.")); |
---|
| 3554 | } else { |
---|
| 3555 | return pow(x, (double)n); |
---|
[2645] | 3556 | } |
---|
| 3557 | } |
---|
| 3558 | } |
---|
| 3559 | |
---|
| 3560 | double Scantable::getChebyshevPolynomial(int n, double x) { |
---|
| 3561 | if ((x < -1.0)||(x > 1.0)) { |
---|
| 3562 | throw(AipsError("out of definition range (-1 <= x <= 1).")); |
---|
[2713] | 3563 | } else if (x == 1.0) { |
---|
| 3564 | return 1.0; |
---|
| 3565 | } else if (x == 0.0) { |
---|
| 3566 | double res; |
---|
| 3567 | if (n%2 == 0) { |
---|
| 3568 | if (n%4 == 0) { |
---|
| 3569 | res = 1.0; |
---|
| 3570 | } else { |
---|
| 3571 | res = -1.0; |
---|
| 3572 | } |
---|
| 3573 | } else { |
---|
| 3574 | res = 0.0; |
---|
| 3575 | } |
---|
| 3576 | return res; |
---|
| 3577 | } else if (x == -1.0) { |
---|
| 3578 | double res = (n%2 == 0 ? 1.0 : -1.0); |
---|
| 3579 | return res; |
---|
[2645] | 3580 | } else if (n < 0) { |
---|
| 3581 | throw(AipsError("the order must be zero or positive.")); |
---|
| 3582 | } else if (n == 0) { |
---|
| 3583 | return 1.0; |
---|
| 3584 | } else if (n == 1) { |
---|
| 3585 | return x; |
---|
| 3586 | } else { |
---|
[2880] | 3587 | double res[n+1]; |
---|
| 3588 | for (int i = 0; i < n+1; ++i) { |
---|
| 3589 | double res0 = 0.0; |
---|
| 3590 | if (i == 0) { |
---|
| 3591 | res0 = 1.0; |
---|
| 3592 | } else if (i == 1) { |
---|
| 3593 | res0 = x; |
---|
| 3594 | } else { |
---|
| 3595 | res0 = 2.0 * x * res[i-1] - res[i-2]; |
---|
[2645] | 3596 | } |
---|
[2880] | 3597 | res[i] = res0; |
---|
[2645] | 3598 | } |
---|
[2880] | 3599 | return res[n]; |
---|
[2645] | 3600 | } |
---|
| 3601 | } |
---|
| 3602 | |
---|
[2773] | 3603 | std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data, |
---|
| 3604 | const std::vector<bool>& mask, |
---|
| 3605 | int order, |
---|
| 3606 | std::vector<float>& params, |
---|
| 3607 | float& rms, |
---|
| 3608 | std::vector<bool>& finalmask, |
---|
| 3609 | float clipth, |
---|
| 3610 | int clipn) |
---|
[2645] | 3611 | { |
---|
[2767] | 3612 | int nClipped = 0; |
---|
| 3613 | return doPolynomialFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn); |
---|
| 3614 | } |
---|
| 3615 | |
---|
[2773] | 3616 | std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data, |
---|
| 3617 | const std::vector<bool>& mask, |
---|
| 3618 | int order, |
---|
| 3619 | std::vector<float>& params, |
---|
| 3620 | float& rms, |
---|
| 3621 | std::vector<bool>& finalMask, |
---|
| 3622 | int& nClipped, |
---|
| 3623 | float thresClip, |
---|
| 3624 | int nIterClip, |
---|
| 3625 | bool getResidual) |
---|
[2767] | 3626 | { |
---|
[2773] | 3627 | return doLeastSquareFitting(data, mask, |
---|
| 3628 | getPolynomialModel(order, data.size(), &Scantable::getNormalPolynomial), |
---|
| 3629 | params, rms, finalMask, |
---|
| 3630 | nClipped, thresClip, nIterClip, |
---|
| 3631 | getResidual); |
---|
[2767] | 3632 | } |
---|
| 3633 | |
---|
[2773] | 3634 | std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, |
---|
| 3635 | const std::vector<bool>& mask, |
---|
| 3636 | int order, |
---|
| 3637 | std::vector<float>& params, |
---|
| 3638 | float& rms, |
---|
| 3639 | std::vector<bool>& finalmask, |
---|
| 3640 | float clipth, |
---|
| 3641 | int clipn) |
---|
[2767] | 3642 | { |
---|
| 3643 | int nClipped = 0; |
---|
| 3644 | return doChebyshevFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn); |
---|
| 3645 | } |
---|
| 3646 | |
---|
[2773] | 3647 | std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, |
---|
| 3648 | const std::vector<bool>& mask, |
---|
| 3649 | int order, |
---|
| 3650 | std::vector<float>& params, |
---|
| 3651 | float& rms, |
---|
| 3652 | std::vector<bool>& finalMask, |
---|
| 3653 | int& nClipped, |
---|
| 3654 | float thresClip, |
---|
| 3655 | int nIterClip, |
---|
| 3656 | bool getResidual) |
---|
[2767] | 3657 | { |
---|
[2773] | 3658 | return doLeastSquareFitting(data, mask, |
---|
| 3659 | getPolynomialModel(order, data.size(), &Scantable::getChebyshevPolynomial), |
---|
| 3660 | params, rms, finalMask, |
---|
| 3661 | nClipped, thresClip, nIterClip, |
---|
| 3662 | getResidual); |
---|
[2767] | 3663 | } |
---|
| 3664 | |
---|
[2773] | 3665 | std::vector<std::vector<double> > Scantable::getPolynomialModel(int order, int nchan, double (Scantable::*pfunc)(int, double)) |
---|
[2767] | 3666 | { |
---|
[2773] | 3667 | // model : contains model values for computing the least-square matrix. |
---|
| 3668 | // model.size() is nmodel and model[*].size() is nchan. |
---|
| 3669 | // Each model element are as follows: |
---|
| 3670 | // |
---|
| 3671 | // (for normal polynomials) |
---|
| 3672 | // model[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
| 3673 | // model[1] = {0.0, 1.0, 2.0, ..., (nchan-1)} |
---|
| 3674 | // model[n-1] = ..., |
---|
| 3675 | // model[n] = {0.0^n, 1.0^n, 2.0^n, ..., (nchan-1)^n} |
---|
| 3676 | // where (0 <= n <= order) |
---|
| 3677 | // |
---|
| 3678 | // (for Chebyshev polynomials) |
---|
| 3679 | // model[0] = {T0(-1), T0(2/(nchan-1)-1), T0(4/(nchan-1)-1), ..., T0(1)}, |
---|
| 3680 | // model[n-1] = ..., |
---|
| 3681 | // model[n] = {Tn(-1), Tn(2/(nchan-1)-1), Tn(4/(nchan-1)-1), ..., Tn(1)} |
---|
| 3682 | // where (0 <= n <= order), |
---|
| 3683 | |
---|
| 3684 | int nmodel = order + 1; |
---|
| 3685 | std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan)); |
---|
| 3686 | |
---|
| 3687 | double stretch, shift; |
---|
| 3688 | if (pfunc == &Scantable::getChebyshevPolynomial) { |
---|
| 3689 | stretch = 2.0/(double)(nchan - 1); |
---|
| 3690 | shift = -1.0; |
---|
| 3691 | } else { |
---|
| 3692 | stretch = 1.0; |
---|
| 3693 | shift = 0.0; |
---|
[2645] | 3694 | } |
---|
[2773] | 3695 | |
---|
| 3696 | for (int i = 0; i < nmodel; ++i) { |
---|
| 3697 | for (int j = 0; j < nchan; ++j) { |
---|
| 3698 | model[i][j] = (this->*pfunc)(i, stretch*(double)j + shift); |
---|
| 3699 | } |
---|
[2645] | 3700 | } |
---|
| 3701 | |
---|
[2773] | 3702 | return model; |
---|
| 3703 | } |
---|
| 3704 | |
---|
| 3705 | std::vector<std::vector<std::vector<double> > > Scantable::getPolynomialModelReservoir(int order, |
---|
| 3706 | double (Scantable::*pfunc)(int, double), |
---|
| 3707 | std::vector<int>& nChanNos) |
---|
| 3708 | { |
---|
| 3709 | std::vector<std::vector<std::vector<double> > > res; |
---|
| 3710 | res.clear(); |
---|
| 3711 | nChanNos.clear(); |
---|
| 3712 | |
---|
| 3713 | std::vector<uint> ifNos = getIFNos(); |
---|
| 3714 | for (uint i = 0; i < ifNos.size(); ++i) { |
---|
| 3715 | int currNchan = nchan(ifNos[i]); |
---|
| 3716 | bool hasDifferentNchan = (i == 0); |
---|
| 3717 | for (uint j = 0; j < i; ++j) { |
---|
| 3718 | if (currNchan != nchan(ifNos[j])) { |
---|
| 3719 | hasDifferentNchan = true; |
---|
| 3720 | break; |
---|
| 3721 | } |
---|
| 3722 | } |
---|
| 3723 | if (hasDifferentNchan) { |
---|
| 3724 | res.push_back(getPolynomialModel(order, currNchan, pfunc)); |
---|
| 3725 | nChanNos.push_back(currNchan); |
---|
| 3726 | } |
---|
| 3727 | } |
---|
| 3728 | |
---|
| 3729 | return res; |
---|
| 3730 | } |
---|
| 3731 | |
---|
| 3732 | std::vector<float> Scantable::doLeastSquareFitting(const std::vector<float>& data, |
---|
| 3733 | const std::vector<bool>& mask, |
---|
| 3734 | const std::vector<std::vector<double> >& model, |
---|
| 3735 | std::vector<float>& params, |
---|
| 3736 | float& rms, |
---|
| 3737 | std::vector<bool>& finalMask, |
---|
| 3738 | int& nClipped, |
---|
| 3739 | float thresClip, |
---|
| 3740 | int nIterClip, |
---|
| 3741 | bool getResidual) |
---|
| 3742 | { |
---|
| 3743 | int nDOF = model.size(); |
---|
[2645] | 3744 | int nChan = data.size(); |
---|
[2737] | 3745 | |
---|
[2773] | 3746 | if (nDOF == 0) { |
---|
| 3747 | throw(AipsError("no model data given")); |
---|
| 3748 | } |
---|
| 3749 | if (nChan < 2) { |
---|
| 3750 | throw(AipsError("data size is too few")); |
---|
| 3751 | } |
---|
| 3752 | if (nChan != (int)mask.size()) { |
---|
| 3753 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 3754 | } |
---|
| 3755 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3756 | if (nChan != (int)model[i].size()) { |
---|
| 3757 | throw(AipsError("data and model sizes are not identical")); |
---|
| 3758 | } |
---|
| 3759 | } |
---|
| 3760 | |
---|
| 3761 | params.clear(); |
---|
| 3762 | params.resize(nDOF); |
---|
| 3763 | |
---|
[2737] | 3764 | finalMask.clear(); |
---|
| 3765 | finalMask.resize(nChan); |
---|
| 3766 | |
---|
[2773] | 3767 | std::vector<int> maskArray(nChan); |
---|
| 3768 | int j = 0; |
---|
[2645] | 3769 | for (int i = 0; i < nChan; ++i) { |
---|
[2773] | 3770 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2890] | 3771 | if (isnan(data[i])) maskArray[i] = 0; |
---|
| 3772 | if (isinf(data[i])) maskArray[i] = 0; |
---|
| 3773 | |
---|
| 3774 | finalMask[i] = (maskArray[i] == 1); |
---|
| 3775 | if (finalMask[i]) { |
---|
| 3776 | j++; |
---|
| 3777 | } |
---|
| 3778 | |
---|
| 3779 | /* |
---|
| 3780 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2645] | 3781 | if (mask[i]) { |
---|
[2773] | 3782 | j++; |
---|
[2645] | 3783 | } |
---|
[2737] | 3784 | finalMask[i] = mask[i]; |
---|
[2890] | 3785 | */ |
---|
[2645] | 3786 | } |
---|
| 3787 | |
---|
[2773] | 3788 | int initNData = j; |
---|
[2645] | 3789 | int nData = initNData; |
---|
| 3790 | |
---|
[2773] | 3791 | std::vector<double> z1(nChan), r1(nChan), residual(nChan); |
---|
[2645] | 3792 | for (int i = 0; i < nChan; ++i) { |
---|
[2773] | 3793 | z1[i] = (double)data[i]; |
---|
| 3794 | r1[i] = 0.0; |
---|
| 3795 | residual[i] = 0.0; |
---|
[2645] | 3796 | } |
---|
| 3797 | |
---|
| 3798 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
| 3799 | // xMatrix : horizontal concatenation of |
---|
| 3800 | // the least-sq. matrix (left) and an |
---|
| 3801 | // identity matrix (right). |
---|
| 3802 | // the right part is used to calculate the inverse matrix of the left part. |
---|
| 3803 | double xMatrix[nDOF][2*nDOF]; |
---|
| 3804 | double zMatrix[nDOF]; |
---|
| 3805 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3806 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 3807 | xMatrix[i][j] = 0.0; |
---|
| 3808 | } |
---|
| 3809 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 3810 | zMatrix[i] = 0.0; |
---|
| 3811 | } |
---|
| 3812 | |
---|
| 3813 | int nUseData = 0; |
---|
| 3814 | for (int k = 0; k < nChan; ++k) { |
---|
| 3815 | if (maskArray[k] == 0) continue; |
---|
| 3816 | |
---|
| 3817 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3818 | for (int j = i; j < nDOF; ++j) { |
---|
[2773] | 3819 | xMatrix[i][j] += model[i][k] * model[j][k]; |
---|
[2645] | 3820 | } |
---|
[2773] | 3821 | zMatrix[i] += z1[k] * model[i][k]; |
---|
[2645] | 3822 | } |
---|
| 3823 | |
---|
| 3824 | nUseData++; |
---|
| 3825 | } |
---|
| 3826 | |
---|
| 3827 | if (nUseData < 1) { |
---|
| 3828 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
| 3829 | } |
---|
| 3830 | |
---|
| 3831 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3832 | for (int j = 0; j < i; ++j) { |
---|
| 3833 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 3834 | } |
---|
| 3835 | } |
---|
| 3836 | |
---|
[2890] | 3837 | //compute inverse matrix of the left half of xMatrix |
---|
[2773] | 3838 | std::vector<double> invDiag(nDOF); |
---|
[2645] | 3839 | for (int i = 0; i < nDOF; ++i) { |
---|
[2773] | 3840 | invDiag[i] = 1.0 / xMatrix[i][i]; |
---|
[2645] | 3841 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3842 | xMatrix[i][j] *= invDiag[i]; |
---|
| 3843 | } |
---|
| 3844 | } |
---|
| 3845 | |
---|
| 3846 | for (int k = 0; k < nDOF; ++k) { |
---|
| 3847 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3848 | if (i != k) { |
---|
| 3849 | double factor1 = xMatrix[k][k]; |
---|
[2773] | 3850 | double invfactor1 = 1.0 / factor1; |
---|
[2645] | 3851 | double factor2 = xMatrix[i][k]; |
---|
| 3852 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3853 | xMatrix[i][j] *= factor1; |
---|
| 3854 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
[2773] | 3855 | xMatrix[i][j] *= invfactor1; |
---|
[2645] | 3856 | } |
---|
| 3857 | } |
---|
| 3858 | } |
---|
[2773] | 3859 | double invXDiag = 1.0 / xMatrix[k][k]; |
---|
[2645] | 3860 | for (int j = k; j < 2*nDOF; ++j) { |
---|
[2773] | 3861 | xMatrix[k][j] *= invXDiag; |
---|
[2645] | 3862 | } |
---|
| 3863 | } |
---|
| 3864 | |
---|
| 3865 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3866 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3867 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 3868 | } |
---|
| 3869 | } |
---|
[2773] | 3870 | //compute a vector y in which coefficients of the best-fit |
---|
| 3871 | //model functions are stored. |
---|
| 3872 | //in case of polynomials, y consists of (a0,a1,a2,...) |
---|
| 3873 | //where ai is the coefficient of the term x^i. |
---|
| 3874 | //in case of sinusoids, y consists of (a0,s1,c1,s2,c2,...) |
---|
| 3875 | //where a0 is constant term and s* and c* are of sine |
---|
| 3876 | //and cosine functions, respectively. |
---|
| 3877 | std::vector<double> y(nDOF); |
---|
[2645] | 3878 | for (int i = 0; i < nDOF; ++i) { |
---|
[2773] | 3879 | y[i] = 0.0; |
---|
[2645] | 3880 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3881 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 3882 | } |
---|
[2773] | 3883 | params[i] = (float)y[i]; |
---|
[2645] | 3884 | } |
---|
| 3885 | |
---|
| 3886 | for (int i = 0; i < nChan; ++i) { |
---|
| 3887 | r1[i] = y[0]; |
---|
| 3888 | for (int j = 1; j < nDOF; ++j) { |
---|
[2773] | 3889 | r1[i] += y[j]*model[j][i]; |
---|
[2645] | 3890 | } |
---|
| 3891 | residual[i] = z1[i] - r1[i]; |
---|
| 3892 | } |
---|
| 3893 | |
---|
[3032] | 3894 | double mean = 0.0; |
---|
| 3895 | double mean2 = 0.0; |
---|
[2737] | 3896 | for (int i = 0; i < nChan; ++i) { |
---|
[2890] | 3897 | if (maskArray[i] == 0) continue; |
---|
[3032] | 3898 | mean += residual[i]; |
---|
| 3899 | mean2 += residual[i]*residual[i]; |
---|
[2737] | 3900 | } |
---|
[3032] | 3901 | mean /= (double)nData; |
---|
| 3902 | mean2 /= (double)nData; |
---|
| 3903 | double rmsd = sqrt(mean2 - mean*mean); |
---|
| 3904 | rms = (float)rmsd; |
---|
[2737] | 3905 | |
---|
[2645] | 3906 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 3907 | break; |
---|
| 3908 | } else { |
---|
[2737] | 3909 | |
---|
[3032] | 3910 | double thres = rmsd * thresClip; |
---|
[2645] | 3911 | int newNData = 0; |
---|
| 3912 | for (int i = 0; i < nChan; ++i) { |
---|
| 3913 | if (abs(residual[i]) >= thres) { |
---|
| 3914 | maskArray[i] = 0; |
---|
[2737] | 3915 | finalMask[i] = false; |
---|
[2645] | 3916 | } |
---|
| 3917 | if (maskArray[i] > 0) { |
---|
| 3918 | newNData++; |
---|
| 3919 | } |
---|
| 3920 | } |
---|
| 3921 | if (newNData == nData) { |
---|
[2890] | 3922 | break; //no more flag to add. stop iteration. |
---|
[2645] | 3923 | } else { |
---|
| 3924 | nData = newNData; |
---|
| 3925 | } |
---|
[2737] | 3926 | |
---|
[2645] | 3927 | } |
---|
| 3928 | } |
---|
| 3929 | |
---|
| 3930 | nClipped = initNData - nData; |
---|
| 3931 | |
---|
[2773] | 3932 | std::vector<float> result(nChan); |
---|
[2645] | 3933 | if (getResidual) { |
---|
| 3934 | for (int i = 0; i < nChan; ++i) { |
---|
[2773] | 3935 | result[i] = (float)residual[i]; |
---|
[2645] | 3936 | } |
---|
| 3937 | } else { |
---|
| 3938 | for (int i = 0; i < nChan; ++i) { |
---|
[2773] | 3939 | result[i] = (float)r1[i]; |
---|
[2645] | 3940 | } |
---|
| 3941 | } |
---|
| 3942 | |
---|
| 3943 | return result; |
---|
[2890] | 3944 | } //xMatrix |
---|
[2645] | 3945 | |
---|
[2773] | 3946 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, |
---|
| 3947 | float thresClip, int nIterClip, |
---|
| 3948 | bool getResidual, |
---|
| 3949 | const std::string& progressInfo, |
---|
| 3950 | const bool outLogger, const std::string& blfile, |
---|
| 3951 | const std::string& bltable) |
---|
[2081] | 3952 | { |
---|
[2774] | 3953 | /**** |
---|
[2773] | 3954 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
[2774] | 3955 | ****/ |
---|
[2773] | 3956 | |
---|
[2193] | 3957 | try { |
---|
| 3958 | ofstream ofs; |
---|
[2773] | 3959 | String coordInfo; |
---|
| 3960 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
[2193] | 3961 | int minNRow; |
---|
[2344] | 3962 | int nRow = nrow(); |
---|
[2773] | 3963 | std::vector<bool> chanMask, finalChanMask; |
---|
[2767] | 3964 | float rms; |
---|
[2773] | 3965 | bool outBaselineTable = (bltable != ""); |
---|
| 3966 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 3967 | Vector<Double> timeSecCol; |
---|
[3026] | 3968 | size_t flagged=0; |
---|
[2344] | 3969 | |
---|
[2773] | 3970 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 3971 | coordInfo, hasSameNchan, |
---|
| 3972 | progressInfo, showProgress, minNRow, |
---|
| 3973 | timeSecCol); |
---|
[2767] | 3974 | |
---|
[2773] | 3975 | std::vector<int> nChanNos; |
---|
| 3976 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 3977 | modelReservoir = getPolynomialModelReservoir(3, |
---|
| 3978 | &Scantable::getNormalPolynomial, |
---|
| 3979 | nChanNos); |
---|
[2968] | 3980 | int nDOF = nPiece + 3; |
---|
[2767] | 3981 | |
---|
[2193] | 3982 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2591] | 3983 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2193] | 3984 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[2773] | 3985 | std::vector<int> pieceEdges; |
---|
| 3986 | std::vector<float> params; |
---|
[2591] | 3987 | |
---|
[3023] | 3988 | //if (flagrowCol_(whichrow) == 0) { |
---|
| 3989 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 3990 | int nClipped = 0; |
---|
| 3991 | std::vector<float> res; |
---|
| 3992 | res = doCubicSplineLeastSquareFitting(sp, chanMask, |
---|
| 3993 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
| 3994 | nPiece, false, pieceEdges, params, rms, finalChanMask, |
---|
| 3995 | nClipped, thresClip, nIterClip, getResidual); |
---|
| 3996 | |
---|
| 3997 | if (outBaselineTable) { |
---|
| 3998 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 3999 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4000 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
| 4001 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 4002 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 4003 | } else { |
---|
| 4004 | setSpectrum(res, whichrow); |
---|
| 4005 | } |
---|
| 4006 | |
---|
| 4007 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 4008 | coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", |
---|
| 4009 | pieceEdges, params, nClipped); |
---|
[2767] | 4010 | } else { |
---|
[3024] | 4011 | // no valid channels to fit (flag the row) |
---|
| 4012 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 4013 | ++flagged; |
---|
[2968] | 4014 | if (outBaselineTable) { |
---|
| 4015 | pieceEdges.resize(nPiece+1); |
---|
| 4016 | for (uInt i = 0; i < pieceEdges.size(); ++i) { |
---|
| 4017 | pieceEdges[i] = 0; |
---|
| 4018 | } |
---|
| 4019 | params.resize(nDOF); |
---|
| 4020 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 4021 | params[i] = 0.0; |
---|
| 4022 | } |
---|
| 4023 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4024 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4025 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
| 4026 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 4027 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 4028 | } |
---|
[2767] | 4029 | } |
---|
[2591] | 4030 | |
---|
[2193] | 4031 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 4032 | } |
---|
[2344] | 4033 | |
---|
[2773] | 4034 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[2767] | 4035 | |
---|
[3026] | 4036 | if (flagged > 0) { |
---|
| 4037 | LogIO os( LogOrigin( "Scantable", "cubicSplineBaseline()") ) ; |
---|
| 4038 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 4039 | } |
---|
[2193] | 4040 | } catch (...) { |
---|
| 4041 | throw; |
---|
[2012] | 4042 | } |
---|
[2773] | 4043 | |
---|
[2774] | 4044 | /**** |
---|
[2773] | 4045 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4046 | double elapse1 = TimeEnd - TimeStart; |
---|
| 4047 | std::cout << "cspline-new : " << elapse1 << " (sec.)" << endl; |
---|
[2774] | 4048 | ****/ |
---|
[2012] | 4049 | } |
---|
| 4050 | |
---|
[2773] | 4051 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, |
---|
| 4052 | float thresClip, int nIterClip, |
---|
| 4053 | const std::vector<int>& edge, |
---|
| 4054 | float threshold, int chanAvgLimit, |
---|
| 4055 | bool getResidual, |
---|
| 4056 | const std::string& progressInfo, |
---|
| 4057 | const bool outLogger, const std::string& blfile, |
---|
| 4058 | const std::string& bltable) |
---|
[2012] | 4059 | { |
---|
[2193] | 4060 | try { |
---|
| 4061 | ofstream ofs; |
---|
[2773] | 4062 | String coordInfo; |
---|
| 4063 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
[2767] | 4064 | int minNRow; |
---|
| 4065 | int nRow = nrow(); |
---|
[2773] | 4066 | std::vector<bool> chanMask, finalChanMask; |
---|
[2767] | 4067 | float rms; |
---|
[2773] | 4068 | bool outBaselineTable = (bltable != ""); |
---|
| 4069 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 4070 | Vector<Double> timeSecCol; |
---|
| 4071 | STLineFinder lineFinder = STLineFinder(); |
---|
[3026] | 4072 | size_t flagged=0; |
---|
[2189] | 4073 | |
---|
[2773] | 4074 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 4075 | coordInfo, hasSameNchan, |
---|
| 4076 | progressInfo, showProgress, minNRow, |
---|
| 4077 | timeSecCol); |
---|
[2767] | 4078 | |
---|
[2773] | 4079 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
| 4080 | |
---|
| 4081 | std::vector<int> nChanNos; |
---|
| 4082 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 4083 | modelReservoir = getPolynomialModelReservoir(3, |
---|
| 4084 | &Scantable::getNormalPolynomial, |
---|
| 4085 | nChanNos); |
---|
[2968] | 4086 | int nDOF = nPiece + 3; |
---|
[2773] | 4087 | |
---|
[2193] | 4088 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2591] | 4089 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2193] | 4090 | std::vector<int> currentEdge; |
---|
[2773] | 4091 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
| 4092 | std::vector<int> pieceEdges; |
---|
| 4093 | std::vector<float> params; |
---|
[2193] | 4094 | |
---|
[3023] | 4095 | //if (flagrowCol_(whichrow) == 0) { |
---|
| 4096 | if (flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 4097 | int nClipped = 0; |
---|
| 4098 | std::vector<float> res; |
---|
| 4099 | res = doCubicSplineLeastSquareFitting(sp, chanMask, |
---|
| 4100 | modelReservoir[getIdxOfNchan(sp.size(), nChanNos)], |
---|
| 4101 | nPiece, false, pieceEdges, params, rms, finalChanMask, |
---|
| 4102 | nClipped, thresClip, nIterClip, getResidual); |
---|
| 4103 | |
---|
| 4104 | if (outBaselineTable) { |
---|
| 4105 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4106 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4107 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
| 4108 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 4109 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 4110 | } else { |
---|
| 4111 | setSpectrum(res, whichrow); |
---|
| 4112 | } |
---|
| 4113 | |
---|
| 4114 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 4115 | coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", |
---|
| 4116 | pieceEdges, params, nClipped); |
---|
[2767] | 4117 | } else { |
---|
[3024] | 4118 | // no valid channels to fit (flag the row) |
---|
| 4119 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 4120 | ++flagged; |
---|
[2968] | 4121 | if (outBaselineTable) { |
---|
| 4122 | pieceEdges.resize(nPiece+1); |
---|
| 4123 | for (uInt i = 0; i < pieceEdges.size(); ++i) { |
---|
| 4124 | pieceEdges[i] = 0; |
---|
| 4125 | } |
---|
| 4126 | params.resize(nDOF); |
---|
| 4127 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 4128 | params[i] = 0.0; |
---|
| 4129 | } |
---|
| 4130 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4131 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4132 | true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(), |
---|
| 4133 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 4134 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 4135 | } |
---|
[2767] | 4136 | } |
---|
| 4137 | |
---|
[2193] | 4138 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[1907] | 4139 | } |
---|
[2012] | 4140 | |
---|
[2773] | 4141 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[2767] | 4142 | |
---|
[3026] | 4143 | if (flagged > 0) { |
---|
| 4144 | LogIO os( LogOrigin( "Scantable", "autoCubicSplineBaseline()") ) ; |
---|
| 4145 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 4146 | } |
---|
[2193] | 4147 | } catch (...) { |
---|
| 4148 | throw; |
---|
[2012] | 4149 | } |
---|
[1730] | 4150 | } |
---|
[1907] | 4151 | |
---|
[2773] | 4152 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, |
---|
| 4153 | const std::vector<bool>& mask, |
---|
| 4154 | std::vector<int>& idxEdge, |
---|
| 4155 | std::vector<float>& params, |
---|
| 4156 | float& rms, |
---|
| 4157 | std::vector<bool>& finalmask, |
---|
| 4158 | float clipth, |
---|
| 4159 | int clipn) |
---|
[2081] | 4160 | { |
---|
[2767] | 4161 | int nClipped = 0; |
---|
| 4162 | return doCubicSplineFitting(data, mask, idxEdge.size()-1, true, idxEdge, params, rms, finalmask, nClipped, clipth, clipn); |
---|
| 4163 | } |
---|
| 4164 | |
---|
[2773] | 4165 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, |
---|
| 4166 | const std::vector<bool>& mask, |
---|
| 4167 | int nPiece, |
---|
| 4168 | std::vector<int>& idxEdge, |
---|
| 4169 | std::vector<float>& params, |
---|
| 4170 | float& rms, |
---|
| 4171 | std::vector<bool>& finalmask, |
---|
| 4172 | float clipth, |
---|
| 4173 | int clipn) |
---|
[2767] | 4174 | { |
---|
| 4175 | int nClipped = 0; |
---|
| 4176 | return doCubicSplineFitting(data, mask, nPiece, false, idxEdge, params, rms, finalmask, nClipped, clipth, clipn); |
---|
| 4177 | } |
---|
| 4178 | |
---|
[2773] | 4179 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, |
---|
| 4180 | const std::vector<bool>& mask, |
---|
| 4181 | int nPiece, |
---|
| 4182 | bool useGivenPieceBoundary, |
---|
| 4183 | std::vector<int>& idxEdge, |
---|
| 4184 | std::vector<float>& params, |
---|
| 4185 | float& rms, |
---|
| 4186 | std::vector<bool>& finalMask, |
---|
| 4187 | int& nClipped, |
---|
| 4188 | float thresClip, |
---|
| 4189 | int nIterClip, |
---|
| 4190 | bool getResidual) |
---|
[2767] | 4191 | { |
---|
[2773] | 4192 | return doCubicSplineLeastSquareFitting(data, mask, |
---|
| 4193 | getPolynomialModel(3, data.size(), &Scantable::getNormalPolynomial), |
---|
| 4194 | nPiece, useGivenPieceBoundary, idxEdge, |
---|
| 4195 | params, rms, finalMask, |
---|
| 4196 | nClipped, thresClip, nIterClip, |
---|
| 4197 | getResidual); |
---|
| 4198 | } |
---|
| 4199 | |
---|
| 4200 | std::vector<float> Scantable::doCubicSplineLeastSquareFitting(const std::vector<float>& data, |
---|
| 4201 | const std::vector<bool>& mask, |
---|
| 4202 | const std::vector<std::vector<double> >& model, |
---|
| 4203 | int nPiece, |
---|
| 4204 | bool useGivenPieceBoundary, |
---|
| 4205 | std::vector<int>& idxEdge, |
---|
| 4206 | std::vector<float>& params, |
---|
| 4207 | float& rms, |
---|
| 4208 | std::vector<bool>& finalMask, |
---|
| 4209 | int& nClipped, |
---|
| 4210 | float thresClip, |
---|
| 4211 | int nIterClip, |
---|
| 4212 | bool getResidual) |
---|
| 4213 | { |
---|
| 4214 | int nDOF = nPiece + 3; //number of independent parameters to solve, namely, 4+(nPiece-1). |
---|
| 4215 | int nModel = model.size(); |
---|
| 4216 | int nChan = data.size(); |
---|
| 4217 | |
---|
| 4218 | if (nModel != 4) { |
---|
| 4219 | throw(AipsError("model size must be 4.")); |
---|
[2081] | 4220 | } |
---|
[2012] | 4221 | if (nPiece < 1) { |
---|
[2094] | 4222 | throw(AipsError("number of the sections must be one or more")); |
---|
[2012] | 4223 | } |
---|
[2773] | 4224 | if (nChan < 2*nPiece) { |
---|
| 4225 | throw(AipsError("data size is too few")); |
---|
| 4226 | } |
---|
| 4227 | if (nChan != (int)mask.size()) { |
---|
| 4228 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 4229 | } |
---|
| 4230 | for (int i = 0; i < nModel; ++i) { |
---|
| 4231 | if (nChan != (int)model[i].size()) { |
---|
| 4232 | throw(AipsError("data and model sizes are not identical")); |
---|
| 4233 | } |
---|
| 4234 | } |
---|
[2012] | 4235 | |
---|
[2773] | 4236 | params.clear(); |
---|
| 4237 | params.resize(nPiece*nModel); |
---|
[2767] | 4238 | |
---|
| 4239 | finalMask.clear(); |
---|
| 4240 | finalMask.resize(nChan); |
---|
| 4241 | |
---|
[2344] | 4242 | std::vector<int> maskArray(nChan); |
---|
| 4243 | std::vector<int> x(nChan); |
---|
| 4244 | int j = 0; |
---|
[2012] | 4245 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 4246 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2890] | 4247 | if (isnan(data[i])) maskArray[i] = 0; |
---|
| 4248 | if (isinf(data[i])) maskArray[i] = 0; |
---|
| 4249 | |
---|
| 4250 | finalMask[i] = (maskArray[i] == 1); |
---|
| 4251 | if (finalMask[i]) { |
---|
| 4252 | x[j] = i; |
---|
| 4253 | j++; |
---|
| 4254 | } |
---|
| 4255 | |
---|
| 4256 | /* |
---|
| 4257 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2012] | 4258 | if (mask[i]) { |
---|
[2344] | 4259 | x[j] = i; |
---|
| 4260 | j++; |
---|
[2012] | 4261 | } |
---|
[2767] | 4262 | finalMask[i] = mask[i]; |
---|
[2890] | 4263 | */ |
---|
[2012] | 4264 | } |
---|
[2773] | 4265 | |
---|
[2344] | 4266 | int initNData = j; |
---|
[2773] | 4267 | int nData = initNData; |
---|
[2012] | 4268 | |
---|
[2193] | 4269 | if (initNData < nPiece) { |
---|
| 4270 | throw(AipsError("too few non-flagged channels")); |
---|
| 4271 | } |
---|
[2081] | 4272 | |
---|
| 4273 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
[2344] | 4274 | std::vector<double> invEdge(nPiece-1); |
---|
[2767] | 4275 | |
---|
| 4276 | if (useGivenPieceBoundary) { |
---|
| 4277 | if ((int)idxEdge.size() != nPiece+1) { |
---|
| 4278 | throw(AipsError("pieceEdge.size() must be equal to nPiece+1.")); |
---|
| 4279 | } |
---|
| 4280 | } else { |
---|
| 4281 | idxEdge.clear(); |
---|
| 4282 | idxEdge.resize(nPiece+1); |
---|
| 4283 | idxEdge[0] = x[0]; |
---|
| 4284 | } |
---|
[2012] | 4285 | for (int i = 1; i < nPiece; ++i) { |
---|
[2047] | 4286 | int valX = x[nElement*i]; |
---|
[2767] | 4287 | if (!useGivenPieceBoundary) { |
---|
| 4288 | idxEdge[i] = valX; |
---|
| 4289 | } |
---|
[2344] | 4290 | invEdge[i-1] = 1.0/(double)valX; |
---|
[2012] | 4291 | } |
---|
[2767] | 4292 | if (!useGivenPieceBoundary) { |
---|
| 4293 | idxEdge[nPiece] = x[initNData-1]+1; |
---|
| 4294 | } |
---|
[2064] | 4295 | |
---|
[2773] | 4296 | std::vector<double> z1(nChan), r1(nChan), residual(nChan); |
---|
[2012] | 4297 | for (int i = 0; i < nChan; ++i) { |
---|
[2773] | 4298 | z1[i] = (double)data[i]; |
---|
| 4299 | r1[i] = 0.0; |
---|
[2344] | 4300 | residual[i] = 0.0; |
---|
[2012] | 4301 | } |
---|
| 4302 | |
---|
| 4303 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2064] | 4304 | // xMatrix : horizontal concatenation of |
---|
| 4305 | // the least-sq. matrix (left) and an |
---|
| 4306 | // identity matrix (right). |
---|
| 4307 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2767] | 4308 | |
---|
[2012] | 4309 | double xMatrix[nDOF][2*nDOF]; |
---|
| 4310 | double zMatrix[nDOF]; |
---|
| 4311 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4312 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 4313 | xMatrix[i][j] = 0.0; |
---|
| 4314 | } |
---|
| 4315 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 4316 | zMatrix[i] = 0.0; |
---|
| 4317 | } |
---|
| 4318 | |
---|
| 4319 | for (int n = 0; n < nPiece; ++n) { |
---|
[2193] | 4320 | int nUseDataInPiece = 0; |
---|
[2773] | 4321 | for (int k = idxEdge[n]; k < idxEdge[n+1]; ++k) { |
---|
[2064] | 4322 | |
---|
[2773] | 4323 | if (maskArray[k] == 0) continue; |
---|
[2064] | 4324 | |
---|
[2773] | 4325 | for (int i = 0; i < nModel; ++i) { |
---|
| 4326 | for (int j = i; j < nModel; ++j) { |
---|
| 4327 | xMatrix[i][j] += model[i][k] * model[j][k]; |
---|
| 4328 | } |
---|
| 4329 | zMatrix[i] += z1[k] * model[i][k]; |
---|
| 4330 | } |
---|
[2064] | 4331 | |
---|
[2773] | 4332 | for (int i = 0; i < n; ++i) { |
---|
| 4333 | double q = 1.0 - model[1][k]*invEdge[i]; |
---|
[2012] | 4334 | q = q*q*q; |
---|
[2773] | 4335 | for (int j = 0; j < nModel; ++j) { |
---|
| 4336 | xMatrix[j][i+nModel] += q * model[j][k]; |
---|
| 4337 | } |
---|
| 4338 | for (int j = 0; j < i; ++j) { |
---|
| 4339 | double r = 1.0 - model[1][k]*invEdge[j]; |
---|
[2012] | 4340 | r = r*r*r; |
---|
[2773] | 4341 | xMatrix[j+nModel][i+nModel] += r*q; |
---|
[2012] | 4342 | } |
---|
[2773] | 4343 | xMatrix[i+nModel][i+nModel] += q*q; |
---|
| 4344 | zMatrix[i+nModel] += q*z1[k]; |
---|
[2012] | 4345 | } |
---|
[2064] | 4346 | |
---|
[2193] | 4347 | nUseDataInPiece++; |
---|
[2012] | 4348 | } |
---|
[2193] | 4349 | |
---|
| 4350 | if (nUseDataInPiece < 1) { |
---|
| 4351 | std::vector<string> suffixOfPieceNumber(4); |
---|
| 4352 | suffixOfPieceNumber[0] = "th"; |
---|
| 4353 | suffixOfPieceNumber[1] = "st"; |
---|
| 4354 | suffixOfPieceNumber[2] = "nd"; |
---|
| 4355 | suffixOfPieceNumber[3] = "rd"; |
---|
| 4356 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
| 4357 | ostringstream oss; |
---|
| 4358 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
| 4359 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
| 4360 | throw(AipsError(String(oss))); |
---|
| 4361 | } |
---|
[2012] | 4362 | } |
---|
| 4363 | |
---|
| 4364 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4365 | for (int j = 0; j < i; ++j) { |
---|
| 4366 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 4367 | } |
---|
| 4368 | } |
---|
| 4369 | |
---|
[2344] | 4370 | std::vector<double> invDiag(nDOF); |
---|
[2012] | 4371 | for (int i = 0; i < nDOF; ++i) { |
---|
[2773] | 4372 | invDiag[i] = 1.0 / xMatrix[i][i]; |
---|
[2012] | 4373 | for (int j = 0; j < nDOF; ++j) { |
---|
| 4374 | xMatrix[i][j] *= invDiag[i]; |
---|
| 4375 | } |
---|
| 4376 | } |
---|
| 4377 | |
---|
| 4378 | for (int k = 0; k < nDOF; ++k) { |
---|
| 4379 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4380 | if (i != k) { |
---|
| 4381 | double factor1 = xMatrix[k][k]; |
---|
[2773] | 4382 | double invfactor1 = 1.0 / factor1; |
---|
[2012] | 4383 | double factor2 = xMatrix[i][k]; |
---|
| 4384 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 4385 | xMatrix[i][j] *= factor1; |
---|
| 4386 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
[2773] | 4387 | xMatrix[i][j] *= invfactor1; |
---|
[2012] | 4388 | } |
---|
| 4389 | } |
---|
| 4390 | } |
---|
[2773] | 4391 | double invXDiag = 1.0 / xMatrix[k][k]; |
---|
[2012] | 4392 | for (int j = k; j < 2*nDOF; ++j) { |
---|
[2773] | 4393 | xMatrix[k][j] *= invXDiag; |
---|
[2012] | 4394 | } |
---|
| 4395 | } |
---|
| 4396 | |
---|
| 4397 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4398 | for (int j = 0; j < nDOF; ++j) { |
---|
| 4399 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 4400 | } |
---|
| 4401 | } |
---|
[2767] | 4402 | |
---|
[2012] | 4403 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
| 4404 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
| 4405 | //cubic terms for the other pieces (in case nPiece>1). |
---|
[2344] | 4406 | std::vector<double> y(nDOF); |
---|
[2012] | 4407 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 4408 | y[i] = 0.0; |
---|
[2012] | 4409 | for (int j = 0; j < nDOF; ++j) { |
---|
| 4410 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 4411 | } |
---|
| 4412 | } |
---|
| 4413 | |
---|
[2773] | 4414 | std::vector<double> a(nModel); |
---|
| 4415 | for (int i = 0; i < nModel; ++i) { |
---|
| 4416 | a[i] = y[i]; |
---|
| 4417 | } |
---|
[2012] | 4418 | |
---|
[2344] | 4419 | int j = 0; |
---|
[2012] | 4420 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 4421 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
[2773] | 4422 | r1[i] = 0.0; |
---|
| 4423 | for (int j = 0; j < nModel; ++j) { |
---|
| 4424 | r1[i] += a[j] * model[j][i]; |
---|
| 4425 | } |
---|
[2012] | 4426 | } |
---|
[2773] | 4427 | for (int i = 0; i < nModel; ++i) { |
---|
| 4428 | params[j+i] = a[i]; |
---|
| 4429 | } |
---|
| 4430 | j += nModel; |
---|
[2012] | 4431 | |
---|
| 4432 | if (n == nPiece-1) break; |
---|
| 4433 | |
---|
[2773] | 4434 | double d = y[n+nModel]; |
---|
[2064] | 4435 | double iE = invEdge[n]; |
---|
[2773] | 4436 | a[0] += d; |
---|
| 4437 | a[1] -= 3.0 * d * iE; |
---|
| 4438 | a[2] += 3.0 * d * iE * iE; |
---|
| 4439 | a[3] -= d * iE * iE * iE; |
---|
[2012] | 4440 | } |
---|
| 4441 | |
---|
[2344] | 4442 | //subtract constant value for masked regions at the edge of spectrum |
---|
| 4443 | if (idxEdge[0] > 0) { |
---|
| 4444 | int n = idxEdge[0]; |
---|
| 4445 | for (int i = 0; i < idxEdge[0]; ++i) { |
---|
| 4446 | //--cubic extrapolate-- |
---|
| 4447 | //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i]; |
---|
| 4448 | //--linear extrapolate-- |
---|
| 4449 | //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 4450 | //--constant-- |
---|
| 4451 | r1[i] = r1[n]; |
---|
| 4452 | } |
---|
| 4453 | } |
---|
[2767] | 4454 | |
---|
[2344] | 4455 | if (idxEdge[nPiece] < nChan) { |
---|
| 4456 | int n = idxEdge[nPiece]-1; |
---|
| 4457 | for (int i = idxEdge[nPiece]; i < nChan; ++i) { |
---|
| 4458 | //--cubic extrapolate-- |
---|
| 4459 | //int m = 4*(nPiece-1); |
---|
| 4460 | //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i]; |
---|
| 4461 | //--linear extrapolate-- |
---|
| 4462 | //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 4463 | //--constant-- |
---|
| 4464 | r1[i] = r1[n]; |
---|
| 4465 | } |
---|
| 4466 | } |
---|
| 4467 | |
---|
| 4468 | for (int i = 0; i < nChan; ++i) { |
---|
| 4469 | residual[i] = z1[i] - r1[i]; |
---|
| 4470 | } |
---|
| 4471 | |
---|
[3032] | 4472 | double mean = 0.0; |
---|
| 4473 | double mean2 = 0.0; |
---|
[2767] | 4474 | for (int i = 0; i < nChan; ++i) { |
---|
[2890] | 4475 | if (maskArray[i] == 0) continue; |
---|
[3032] | 4476 | mean += residual[i]; |
---|
| 4477 | mean2 += residual[i]*residual[i]; |
---|
[2767] | 4478 | } |
---|
[3032] | 4479 | mean /= (double)nData; |
---|
| 4480 | mean2 /= (double)nData; |
---|
| 4481 | double rmsd = sqrt(mean2 - mean*mean); |
---|
| 4482 | rms = (float)rmsd; |
---|
[2767] | 4483 | |
---|
[2012] | 4484 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 4485 | break; |
---|
| 4486 | } else { |
---|
| 4487 | |
---|
[3032] | 4488 | double thres = rmsd * thresClip; |
---|
[2012] | 4489 | int newNData = 0; |
---|
| 4490 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 4491 | if (abs(residual[i]) >= thres) { |
---|
[2012] | 4492 | maskArray[i] = 0; |
---|
[2767] | 4493 | finalMask[i] = false; |
---|
[2012] | 4494 | } |
---|
| 4495 | if (maskArray[i] > 0) { |
---|
| 4496 | newNData++; |
---|
| 4497 | } |
---|
| 4498 | } |
---|
[2081] | 4499 | if (newNData == nData) { |
---|
[2064] | 4500 | break; //no more flag to add. iteration stops. |
---|
[2012] | 4501 | } else { |
---|
[2081] | 4502 | nData = newNData; |
---|
[2012] | 4503 | } |
---|
[2767] | 4504 | |
---|
[2012] | 4505 | } |
---|
| 4506 | } |
---|
| 4507 | |
---|
[2193] | 4508 | nClipped = initNData - nData; |
---|
| 4509 | |
---|
[2344] | 4510 | std::vector<float> result(nChan); |
---|
[2058] | 4511 | if (getResidual) { |
---|
| 4512 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 4513 | result[i] = (float)residual[i]; |
---|
[2058] | 4514 | } |
---|
| 4515 | } else { |
---|
| 4516 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 4517 | result[i] = (float)r1[i]; |
---|
[2058] | 4518 | } |
---|
[2012] | 4519 | } |
---|
| 4520 | |
---|
[2058] | 4521 | return result; |
---|
[2012] | 4522 | } |
---|
| 4523 | |
---|
[2773] | 4524 | std::vector<int> Scantable::selectWaveNumbers(const std::vector<int>& addNWaves, |
---|
| 4525 | const std::vector<int>& rejectNWaves) |
---|
[2081] | 4526 | { |
---|
[2773] | 4527 | std::vector<bool> chanMask; |
---|
[2767] | 4528 | std::string fftMethod; |
---|
| 4529 | std::string fftThresh; |
---|
| 4530 | |
---|
[2773] | 4531 | return selectWaveNumbers(0, chanMask, false, fftMethod, fftThresh, addNWaves, rejectNWaves); |
---|
| 4532 | } |
---|
| 4533 | |
---|
| 4534 | std::vector<int> Scantable::selectWaveNumbers(const int whichrow, |
---|
| 4535 | const std::vector<bool>& chanMask, |
---|
| 4536 | const bool applyFFT, |
---|
| 4537 | const std::string& fftMethod, |
---|
| 4538 | const std::string& fftThresh, |
---|
| 4539 | const std::vector<int>& addNWaves, |
---|
| 4540 | const std::vector<int>& rejectNWaves) |
---|
| 4541 | { |
---|
| 4542 | std::vector<int> nWaves; |
---|
[2186] | 4543 | nWaves.clear(); |
---|
| 4544 | |
---|
| 4545 | if (applyFFT) { |
---|
| 4546 | string fftThAttr; |
---|
| 4547 | float fftThSigma; |
---|
| 4548 | int fftThTop; |
---|
[2773] | 4549 | parseFFTThresholdInfo(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
[2186] | 4550 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
| 4551 | } |
---|
| 4552 | |
---|
[2411] | 4553 | addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves); |
---|
[2773] | 4554 | |
---|
| 4555 | return nWaves; |
---|
[2186] | 4556 | } |
---|
| 4557 | |
---|
[2773] | 4558 | int Scantable::getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos) |
---|
| 4559 | { |
---|
| 4560 | int idx = -1; |
---|
| 4561 | for (uint i = 0; i < nChanNos.size(); ++i) { |
---|
| 4562 | if (nChan == nChanNos[i]) { |
---|
| 4563 | idx = i; |
---|
| 4564 | break; |
---|
| 4565 | } |
---|
| 4566 | } |
---|
| 4567 | |
---|
| 4568 | if (idx < 0) { |
---|
| 4569 | throw(AipsError("nChan not found in nChhanNos.")); |
---|
| 4570 | } |
---|
| 4571 | |
---|
| 4572 | return idx; |
---|
| 4573 | } |
---|
| 4574 | |
---|
[2767] | 4575 | void Scantable::parseFFTInfo(const std::string& fftInfo, bool& applyFFT, std::string& fftMethod, std::string& fftThresh) |
---|
| 4576 | { |
---|
| 4577 | istringstream iss(fftInfo); |
---|
| 4578 | std::string tmp; |
---|
| 4579 | std::vector<string> res; |
---|
| 4580 | while (getline(iss, tmp, ',')) { |
---|
| 4581 | res.push_back(tmp); |
---|
| 4582 | } |
---|
| 4583 | if (res.size() < 3) { |
---|
| 4584 | throw(AipsError("wrong value in 'fftinfo' parameter")) ; |
---|
| 4585 | } |
---|
| 4586 | applyFFT = (res[0] == "true"); |
---|
| 4587 | fftMethod = res[1]; |
---|
| 4588 | fftThresh = res[2]; |
---|
| 4589 | } |
---|
| 4590 | |
---|
[2773] | 4591 | void Scantable::parseFFTThresholdInfo(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
[2186] | 4592 | { |
---|
| 4593 | uInt idxSigma = fftThresh.find("sigma"); |
---|
| 4594 | uInt idxTop = fftThresh.find("top"); |
---|
| 4595 | |
---|
| 4596 | if (idxSigma == fftThresh.size() - 5) { |
---|
| 4597 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
| 4598 | is >> fftThSigma; |
---|
| 4599 | fftThAttr = "sigma"; |
---|
| 4600 | } else if (idxTop == 0) { |
---|
| 4601 | std::istringstream is(fftThresh.substr(3)); |
---|
| 4602 | is >> fftThTop; |
---|
| 4603 | fftThAttr = "top"; |
---|
| 4604 | } else { |
---|
| 4605 | bool isNumber = true; |
---|
| 4606 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
| 4607 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
| 4608 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
| 4609 | isNumber = false; |
---|
| 4610 | break; |
---|
| 4611 | } |
---|
| 4612 | } |
---|
| 4613 | if (isNumber) { |
---|
| 4614 | std::istringstream is(fftThresh); |
---|
| 4615 | is >> fftThSigma; |
---|
| 4616 | fftThAttr = "sigma"; |
---|
| 4617 | } else { |
---|
| 4618 | throw(AipsError("fftthresh has a wrong value")); |
---|
| 4619 | } |
---|
| 4620 | } |
---|
| 4621 | } |
---|
| 4622 | |
---|
| 4623 | 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) |
---|
| 4624 | { |
---|
| 4625 | std::vector<float> fspec; |
---|
| 4626 | if (fftMethod == "fft") { |
---|
| 4627 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
| 4628 | //} else if (fftMethod == "lsp") { |
---|
| 4629 | // fspec = lombScarglePeriodogram(whichrow); |
---|
| 4630 | } |
---|
| 4631 | |
---|
| 4632 | if (fftThAttr == "sigma") { |
---|
| 4633 | float mean = 0.0; |
---|
| 4634 | float mean2 = 0.0; |
---|
| 4635 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 4636 | mean += fspec[i]; |
---|
| 4637 | mean2 += fspec[i]*fspec[i]; |
---|
| 4638 | } |
---|
| 4639 | mean /= float(fspec.size()); |
---|
| 4640 | mean2 /= float(fspec.size()); |
---|
| 4641 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
| 4642 | |
---|
| 4643 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 4644 | if (fspec[i] >= thres) { |
---|
| 4645 | nWaves.push_back(i); |
---|
| 4646 | } |
---|
| 4647 | } |
---|
| 4648 | |
---|
| 4649 | } else if (fftThAttr == "top") { |
---|
| 4650 | for (int i = 0; i < fftThTop; ++i) { |
---|
| 4651 | float max = 0.0; |
---|
| 4652 | int maxIdx = 0; |
---|
| 4653 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
| 4654 | if (fspec[j] > max) { |
---|
| 4655 | max = fspec[j]; |
---|
| 4656 | maxIdx = j; |
---|
| 4657 | } |
---|
| 4658 | } |
---|
| 4659 | nWaves.push_back(maxIdx); |
---|
| 4660 | fspec[maxIdx] = 0.0; |
---|
| 4661 | } |
---|
| 4662 | |
---|
| 4663 | } |
---|
| 4664 | |
---|
| 4665 | if (nWaves.size() > 1) { |
---|
| 4666 | sort(nWaves.begin(), nWaves.end()); |
---|
| 4667 | } |
---|
| 4668 | } |
---|
| 4669 | |
---|
[2411] | 4670 | void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2186] | 4671 | { |
---|
[2411] | 4672 | std::vector<int> tempAddNWaves, tempRejectNWaves; |
---|
[2767] | 4673 | tempAddNWaves.clear(); |
---|
| 4674 | tempRejectNWaves.clear(); |
---|
| 4675 | |
---|
[2186] | 4676 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
[2411] | 4677 | tempAddNWaves.push_back(addNWaves[i]); |
---|
| 4678 | } |
---|
| 4679 | if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) { |
---|
| 4680 | setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves); |
---|
| 4681 | } |
---|
| 4682 | |
---|
| 4683 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
| 4684 | tempRejectNWaves.push_back(rejectNWaves[i]); |
---|
| 4685 | } |
---|
| 4686 | if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) { |
---|
| 4687 | setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves); |
---|
| 4688 | } |
---|
| 4689 | |
---|
| 4690 | for (uInt i = 0; i < tempAddNWaves.size(); ++i) { |
---|
[2186] | 4691 | bool found = false; |
---|
| 4692 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
[2411] | 4693 | if (nWaves[j] == tempAddNWaves[i]) { |
---|
[2186] | 4694 | found = true; |
---|
| 4695 | break; |
---|
| 4696 | } |
---|
| 4697 | } |
---|
[2411] | 4698 | if (!found) nWaves.push_back(tempAddNWaves[i]); |
---|
[2186] | 4699 | } |
---|
| 4700 | |
---|
[2411] | 4701 | for (uInt i = 0; i < tempRejectNWaves.size(); ++i) { |
---|
[2186] | 4702 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
[2411] | 4703 | if (*j == tempRejectNWaves[i]) { |
---|
[2186] | 4704 | j = nWaves.erase(j); |
---|
| 4705 | } else { |
---|
| 4706 | ++j; |
---|
| 4707 | } |
---|
| 4708 | } |
---|
| 4709 | } |
---|
| 4710 | |
---|
| 4711 | if (nWaves.size() > 1) { |
---|
| 4712 | sort(nWaves.begin(), nWaves.end()); |
---|
| 4713 | unique(nWaves.begin(), nWaves.end()); |
---|
| 4714 | } |
---|
| 4715 | } |
---|
| 4716 | |
---|
[2411] | 4717 | void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves) |
---|
| 4718 | { |
---|
[2767] | 4719 | int val = nWaves[0]; |
---|
| 4720 | int nyquistFreq = nchan(getIF(whichrow))/2+1; |
---|
| 4721 | nWaves.clear(); |
---|
| 4722 | if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759 |
---|
| 4723 | nWaves.push_back(0); |
---|
[2411] | 4724 | } |
---|
[2767] | 4725 | while (val <= nyquistFreq) { |
---|
| 4726 | nWaves.push_back(val); |
---|
| 4727 | val++; |
---|
| 4728 | } |
---|
[2411] | 4729 | } |
---|
| 4730 | |
---|
[2773] | 4731 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo, |
---|
| 4732 | const std::vector<int>& addNWaves, |
---|
| 4733 | const std::vector<int>& rejectNWaves, |
---|
| 4734 | float thresClip, int nIterClip, |
---|
| 4735 | bool getResidual, |
---|
| 4736 | const std::string& progressInfo, |
---|
| 4737 | const bool outLogger, const std::string& blfile, |
---|
| 4738 | const std::string& bltable) |
---|
[2186] | 4739 | { |
---|
[2774] | 4740 | /**** |
---|
[2773] | 4741 | double TimeStart = mathutil::gettimeofday_sec(); |
---|
[2774] | 4742 | ****/ |
---|
[2773] | 4743 | |
---|
[2193] | 4744 | try { |
---|
| 4745 | ofstream ofs; |
---|
[2773] | 4746 | String coordInfo; |
---|
| 4747 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
| 4748 | int minNRow; |
---|
| 4749 | int nRow = nrow(); |
---|
| 4750 | std::vector<bool> chanMask, finalChanMask; |
---|
| 4751 | float rms; |
---|
| 4752 | bool outBaselineTable = (bltable != ""); |
---|
| 4753 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 4754 | Vector<Double> timeSecCol; |
---|
[3026] | 4755 | size_t flagged=0; |
---|
[2012] | 4756 | |
---|
[2773] | 4757 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 4758 | coordInfo, hasSameNchan, |
---|
| 4759 | progressInfo, showProgress, minNRow, |
---|
| 4760 | timeSecCol); |
---|
[2012] | 4761 | |
---|
[2773] | 4762 | bool applyFFT; |
---|
| 4763 | std::string fftMethod, fftThresh; |
---|
| 4764 | parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh); |
---|
[2012] | 4765 | |
---|
[2193] | 4766 | std::vector<int> nWaves; |
---|
[2773] | 4767 | std::vector<int> nChanNos; |
---|
| 4768 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 4769 | if (!applyFFT) { |
---|
| 4770 | nWaves = selectWaveNumbers(addNWaves, rejectNWaves); |
---|
[3044] | 4771 | if (nWaves.size()==0) //no wave numbers to fit |
---|
| 4772 | throw(AipsError("No valid wave numbers to fit")); |
---|
[2773] | 4773 | modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos); |
---|
| 4774 | } |
---|
[2012] | 4775 | |
---|
[2193] | 4776 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2767] | 4777 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2193] | 4778 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[3044] | 4779 | std::vector<std::vector<double> > model; |
---|
| 4780 | bool canfit = true; |
---|
[2773] | 4781 | if (applyFFT) { |
---|
| 4782 | nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh, |
---|
| 4783 | addNWaves, rejectNWaves); |
---|
[3044] | 4784 | if (nWaves.size()==0) {// no wave numbers to fit. |
---|
| 4785 | canfit = false; |
---|
| 4786 | break; |
---|
| 4787 | } |
---|
[2773] | 4788 | model = getSinusoidModel(nWaves, sp.size()); |
---|
| 4789 | } else { |
---|
| 4790 | model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)]; |
---|
| 4791 | } |
---|
[2968] | 4792 | int nModel = modelReservoir.size(); |
---|
[2186] | 4793 | |
---|
[2767] | 4794 | std::vector<float> params; |
---|
[2968] | 4795 | |
---|
[3023] | 4796 | //if (flagrowCol_(whichrow) == 0) { |
---|
[3044] | 4797 | if (canfit && flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 4798 | int nClipped = 0; |
---|
| 4799 | std::vector<float> res; |
---|
| 4800 | res = doLeastSquareFitting(sp, chanMask, model, |
---|
[2773] | 4801 | params, rms, finalChanMask, |
---|
| 4802 | nClipped, thresClip, nIterClip, getResidual); |
---|
[2767] | 4803 | |
---|
[2968] | 4804 | if (outBaselineTable) { |
---|
| 4805 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4806 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4807 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
| 4808 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 4809 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 4810 | } else { |
---|
| 4811 | setSpectrum(res, whichrow); |
---|
| 4812 | } |
---|
| 4813 | |
---|
| 4814 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 4815 | coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", |
---|
| 4816 | params, nClipped); |
---|
[2767] | 4817 | } else { |
---|
[3024] | 4818 | // no valid channels to fit (flag the row) |
---|
| 4819 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 4820 | ++flagged; |
---|
[2968] | 4821 | if (outBaselineTable) { |
---|
| 4822 | params.resize(nModel); |
---|
| 4823 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 4824 | params[i] = 0.0; |
---|
| 4825 | } |
---|
| 4826 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4827 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4828 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
| 4829 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 4830 | thresClip, nIterClip, 0.0, 0, std::vector<int>()); |
---|
| 4831 | } |
---|
[2186] | 4832 | } |
---|
[2193] | 4833 | |
---|
| 4834 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2186] | 4835 | } |
---|
| 4836 | |
---|
[2773] | 4837 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[2767] | 4838 | |
---|
[3026] | 4839 | if (flagged > 0) { |
---|
| 4840 | LogIO os( LogOrigin( "Scantable", "sinusoidBaseline()") ) ; |
---|
| 4841 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 4842 | } |
---|
[2193] | 4843 | } catch (...) { |
---|
| 4844 | throw; |
---|
[1931] | 4845 | } |
---|
[2773] | 4846 | |
---|
[2774] | 4847 | /**** |
---|
[2773] | 4848 | double TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4849 | double elapse1 = TimeEnd - TimeStart; |
---|
| 4850 | std::cout << "sinusoid-old : " << elapse1 << " (sec.)" << endl; |
---|
[2774] | 4851 | ****/ |
---|
[1907] | 4852 | } |
---|
| 4853 | |
---|
[2773] | 4854 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo, |
---|
| 4855 | const std::vector<int>& addNWaves, |
---|
| 4856 | const std::vector<int>& rejectNWaves, |
---|
| 4857 | float thresClip, int nIterClip, |
---|
| 4858 | const std::vector<int>& edge, |
---|
| 4859 | float threshold, int chanAvgLimit, |
---|
| 4860 | bool getResidual, |
---|
| 4861 | const std::string& progressInfo, |
---|
| 4862 | const bool outLogger, const std::string& blfile, |
---|
| 4863 | const std::string& bltable) |
---|
[2012] | 4864 | { |
---|
[2193] | 4865 | try { |
---|
| 4866 | ofstream ofs; |
---|
[2773] | 4867 | String coordInfo; |
---|
| 4868 | bool hasSameNchan, outTextFile, csvFormat, showProgress; |
---|
| 4869 | int minNRow; |
---|
| 4870 | int nRow = nrow(); |
---|
| 4871 | std::vector<bool> chanMask, finalChanMask; |
---|
| 4872 | float rms; |
---|
| 4873 | bool outBaselineTable = (bltable != ""); |
---|
| 4874 | STBaselineTable bt = STBaselineTable(*this); |
---|
| 4875 | Vector<Double> timeSecCol; |
---|
| 4876 | STLineFinder lineFinder = STLineFinder(); |
---|
[3026] | 4877 | size_t flagged=0; |
---|
[2012] | 4878 | |
---|
[2773] | 4879 | initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat, |
---|
| 4880 | coordInfo, hasSameNchan, |
---|
| 4881 | progressInfo, showProgress, minNRow, |
---|
| 4882 | timeSecCol); |
---|
[2012] | 4883 | |
---|
[2773] | 4884 | initLineFinder(edge, threshold, chanAvgLimit, lineFinder); |
---|
[2012] | 4885 | |
---|
[2773] | 4886 | bool applyFFT; |
---|
| 4887 | string fftMethod, fftThresh; |
---|
| 4888 | parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh); |
---|
[2012] | 4889 | |
---|
[2193] | 4890 | std::vector<int> nWaves; |
---|
[2773] | 4891 | std::vector<int> nChanNos; |
---|
| 4892 | std::vector<std::vector<std::vector<double> > > modelReservoir; |
---|
| 4893 | if (!applyFFT) { |
---|
| 4894 | nWaves = selectWaveNumbers(addNWaves, rejectNWaves); |
---|
[3044] | 4895 | if (nWaves.size()==0) //no wave numbers to fit |
---|
| 4896 | throw(AipsError("No valid wave numbers to fit")); |
---|
[2773] | 4897 | modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos); |
---|
| 4898 | } |
---|
[2186] | 4899 | |
---|
[2193] | 4900 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2767] | 4901 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2193] | 4902 | std::vector<int> currentEdge; |
---|
[2773] | 4903 | chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder); |
---|
| 4904 | std::vector<std::vector<double> > model; |
---|
[3044] | 4905 | bool canfit=true; |
---|
[2773] | 4906 | if (applyFFT) { |
---|
| 4907 | nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh, |
---|
| 4908 | addNWaves, rejectNWaves); |
---|
[3044] | 4909 | if (nWaves.size()==0) { // no wave numbers to fit. |
---|
| 4910 | canfit = false; |
---|
| 4911 | break; |
---|
| 4912 | } |
---|
[2773] | 4913 | model = getSinusoidModel(nWaves, sp.size()); |
---|
[2193] | 4914 | } else { |
---|
[2773] | 4915 | model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)]; |
---|
[2012] | 4916 | } |
---|
[2968] | 4917 | int nModel = modelReservoir.size(); |
---|
[2193] | 4918 | |
---|
| 4919 | std::vector<float> params; |
---|
[2968] | 4920 | |
---|
[3023] | 4921 | //if (flagrowCol_(whichrow) == 0) { |
---|
[3044] | 4922 | if (canfit && flagrowCol_(whichrow)==0 && nValidMask(chanMask)>0) { |
---|
[2968] | 4923 | int nClipped = 0; |
---|
| 4924 | std::vector<float> res; |
---|
| 4925 | res = doLeastSquareFitting(sp, chanMask, model, |
---|
[2773] | 4926 | params, rms, finalChanMask, |
---|
| 4927 | nClipped, thresClip, nIterClip, getResidual); |
---|
[2193] | 4928 | |
---|
[2968] | 4929 | if (outBaselineTable) { |
---|
| 4930 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4931 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4932 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
| 4933 | getMaskListFromMask(finalChanMask), params, rms, sp.size(), |
---|
| 4934 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 4935 | } else { |
---|
| 4936 | setSpectrum(res, whichrow); |
---|
| 4937 | } |
---|
| 4938 | |
---|
| 4939 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, |
---|
| 4940 | coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", |
---|
| 4941 | params, nClipped); |
---|
[2767] | 4942 | } else { |
---|
[3024] | 4943 | // no valid channels to fit (flag the row) |
---|
| 4944 | flagrowCol_.put(whichrow, 1); |
---|
[3026] | 4945 | ++flagged; |
---|
[2968] | 4946 | if (outBaselineTable) { |
---|
| 4947 | params.resize(nModel); |
---|
| 4948 | for (uInt i = 0; i < params.size(); ++i) { |
---|
| 4949 | params[i] = 0.0; |
---|
| 4950 | } |
---|
| 4951 | bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow), |
---|
| 4952 | getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow], |
---|
| 4953 | true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(), |
---|
| 4954 | getMaskListFromMask(chanMask), params, 0.0, sp.size(), |
---|
| 4955 | thresClip, nIterClip, threshold, chanAvgLimit, currentEdge); |
---|
| 4956 | } |
---|
[2767] | 4957 | } |
---|
| 4958 | |
---|
[2193] | 4959 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2012] | 4960 | } |
---|
| 4961 | |
---|
[2773] | 4962 | finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs); |
---|
[2767] | 4963 | |
---|
[3026] | 4964 | if (flagged > 0) { |
---|
| 4965 | LogIO os( LogOrigin( "Scantable", "autoSinusoidBaseline()") ) ; |
---|
| 4966 | os << LogIO::WARN << "Baseline subtraction is skipped for " << flagged << " spectra due to too few valid channels to operate fit. The spectra will be flagged in output data." << LogIO::POST; |
---|
| 4967 | } |
---|
[2193] | 4968 | } catch (...) { |
---|
| 4969 | throw; |
---|
[2047] | 4970 | } |
---|
| 4971 | } |
---|
| 4972 | |
---|
[2773] | 4973 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, |
---|
| 4974 | const std::vector<bool>& mask, |
---|
| 4975 | const std::vector<int>& waveNumbers, |
---|
| 4976 | std::vector<float>& params, |
---|
| 4977 | float& rms, |
---|
| 4978 | std::vector<bool>& finalmask, |
---|
| 4979 | float clipth, |
---|
| 4980 | int clipn) |
---|
[2081] | 4981 | { |
---|
[2767] | 4982 | int nClipped = 0; |
---|
| 4983 | return doSinusoidFitting(data, mask, waveNumbers, params, rms, finalmask, nClipped, clipth, clipn); |
---|
| 4984 | } |
---|
| 4985 | |
---|
[2773] | 4986 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, |
---|
| 4987 | const std::vector<bool>& mask, |
---|
| 4988 | const std::vector<int>& waveNumbers, |
---|
| 4989 | std::vector<float>& params, |
---|
| 4990 | float& rms, |
---|
| 4991 | std::vector<bool>& finalMask, |
---|
| 4992 | int& nClipped, |
---|
| 4993 | float thresClip, |
---|
| 4994 | int nIterClip, |
---|
| 4995 | bool getResidual) |
---|
[2767] | 4996 | { |
---|
[2773] | 4997 | return doLeastSquareFitting(data, mask, |
---|
| 4998 | getSinusoidModel(waveNumbers, data.size()), |
---|
| 4999 | params, rms, finalMask, |
---|
| 5000 | nClipped, thresClip, nIterClip, |
---|
| 5001 | getResidual); |
---|
| 5002 | } |
---|
| 5003 | |
---|
| 5004 | std::vector<std::vector<std::vector<double> > > Scantable::getSinusoidModelReservoir(const std::vector<int>& waveNumbers, |
---|
| 5005 | std::vector<int>& nChanNos) |
---|
| 5006 | { |
---|
| 5007 | std::vector<std::vector<std::vector<double> > > res; |
---|
| 5008 | res.clear(); |
---|
| 5009 | nChanNos.clear(); |
---|
| 5010 | |
---|
| 5011 | std::vector<uint> ifNos = getIFNos(); |
---|
| 5012 | for (uint i = 0; i < ifNos.size(); ++i) { |
---|
| 5013 | int currNchan = nchan(ifNos[i]); |
---|
| 5014 | bool hasDifferentNchan = (i == 0); |
---|
| 5015 | for (uint j = 0; j < i; ++j) { |
---|
| 5016 | if (currNchan != nchan(ifNos[j])) { |
---|
| 5017 | hasDifferentNchan = true; |
---|
| 5018 | break; |
---|
| 5019 | } |
---|
| 5020 | } |
---|
| 5021 | if (hasDifferentNchan) { |
---|
| 5022 | res.push_back(getSinusoidModel(waveNumbers, currNchan)); |
---|
| 5023 | nChanNos.push_back(currNchan); |
---|
| 5024 | } |
---|
[2047] | 5025 | } |
---|
[2773] | 5026 | |
---|
| 5027 | return res; |
---|
| 5028 | } |
---|
| 5029 | |
---|
| 5030 | std::vector<std::vector<double> > Scantable::getSinusoidModel(const std::vector<int>& waveNumbers, int nchan) |
---|
| 5031 | { |
---|
| 5032 | // model : contains elemental values for computing the least-square matrix. |
---|
| 5033 | // model.size() is nmodel and model[*].size() is nchan. |
---|
| 5034 | // Each model element are as follows: |
---|
| 5035 | // model[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
| 5036 | // model[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nchan])}, |
---|
| 5037 | // model[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nchan])}, |
---|
| 5038 | // where (1 <= n <= nMaxWavesInSW), |
---|
| 5039 | // or, |
---|
| 5040 | // model[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nchan])}, |
---|
| 5041 | // model[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nchan])}, |
---|
| 5042 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
| 5043 | |
---|
[2081] | 5044 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
| 5045 | nWaves.reserve(waveNumbers.size()); |
---|
| 5046 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
| 5047 | sort(nWaves.begin(), nWaves.end()); |
---|
| 5048 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
| 5049 | nWaves.erase(end_it, nWaves.end()); |
---|
| 5050 | |
---|
[3047] | 5051 | if (nWaves.size()==0) |
---|
| 5052 | throw(AipsError("No valid wavenumbers to fit.")); |
---|
| 5053 | |
---|
[2081] | 5054 | int minNWaves = nWaves[0]; |
---|
| 5055 | if (minNWaves < 0) { |
---|
[2058] | 5056 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
| 5057 | } |
---|
[2081] | 5058 | bool hasConstantTerm = (minNWaves == 0); |
---|
[2773] | 5059 | int nmodel = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
[2047] | 5060 | |
---|
[2773] | 5061 | std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan)); |
---|
[2767] | 5062 | |
---|
[2773] | 5063 | if (hasConstantTerm) { |
---|
| 5064 | for (int j = 0; j < nchan; ++j) { |
---|
| 5065 | model[0][j] = 1.0; |
---|
[2047] | 5066 | } |
---|
| 5067 | } |
---|
| 5068 | |
---|
[2081] | 5069 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
[2773] | 5070 | double stretch0 = 2.0*PI/(double)(nchan-1); |
---|
[2081] | 5071 | |
---|
| 5072 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
[2773] | 5073 | int sidx = hasConstantTerm ? 2*i-1 : 2*i; |
---|
| 5074 | int cidx = sidx + 1; |
---|
| 5075 | double stretch = stretch0*(double)nWaves[i]; |
---|
[2081] | 5076 | |
---|
[2773] | 5077 | for (int j = 0; j < nchan; ++j) { |
---|
| 5078 | model[sidx][j] = sin(stretch*(double)j); |
---|
| 5079 | model[cidx][j] = cos(stretch*(double)j); |
---|
[2047] | 5080 | } |
---|
[2012] | 5081 | } |
---|
| 5082 | |
---|
[2773] | 5083 | return model; |
---|
[2012] | 5084 | } |
---|
| 5085 | |
---|
[2773] | 5086 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, |
---|
| 5087 | const std::vector<bool>& inMask) |
---|
[2047] | 5088 | { |
---|
[2186] | 5089 | std::vector<bool> mask = getMask(whichrow); |
---|
| 5090 | uInt maskSize = mask.size(); |
---|
[2410] | 5091 | if (inMask.size() != 0) { |
---|
| 5092 | if (maskSize != inMask.size()) { |
---|
| 5093 | throw(AipsError("mask sizes are not the same.")); |
---|
| 5094 | } |
---|
| 5095 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 5096 | mask[i] = mask[i] && inMask[i]; |
---|
| 5097 | } |
---|
[2047] | 5098 | } |
---|
| 5099 | |
---|
[2186] | 5100 | return mask; |
---|
[2047] | 5101 | } |
---|
| 5102 | |
---|
[2773] | 5103 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, |
---|
| 5104 | const std::vector<bool>& inMask, |
---|
| 5105 | const std::vector<int>& edge, |
---|
| 5106 | std::vector<int>& currEdge, |
---|
| 5107 | STLineFinder& lineFinder) |
---|
[2047] | 5108 | { |
---|
[3023] | 5109 | if (isAllChannelsFlagged(whichrow)) {//all channels flagged |
---|
[3039] | 5110 | std::vector<bool> res_mask(nchan(getIF(whichrow)),false); |
---|
[3023] | 5111 | return res_mask; |
---|
[3039] | 5112 | } else if (inMask.size() != 0 && nValidMask(inMask)==0){ //no valid mask channels |
---|
[3023] | 5113 | std::vector<bool> res_mask(inMask); |
---|
| 5114 | return res_mask; |
---|
| 5115 | } |
---|
| 5116 | |
---|
[2773] | 5117 | std::vector<uint> ifNos = getIFNos(); |
---|
[2774] | 5118 | if ((edge.size() > 2) && (edge.size() < ifNos.size()*2)) { |
---|
[2773] | 5119 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
[2047] | 5120 | } |
---|
| 5121 | |
---|
[2774] | 5122 | uint idx = 0; |
---|
| 5123 | if (edge.size() > 2) { |
---|
| 5124 | int ifVal = getIF(whichrow); |
---|
| 5125 | bool foundIF = false; |
---|
| 5126 | for (uint i = 0; i < ifNos.size(); ++i) { |
---|
| 5127 | if (ifVal == (int)ifNos[i]) { |
---|
| 5128 | idx = 2*i; |
---|
| 5129 | foundIF = true; |
---|
| 5130 | break; |
---|
| 5131 | } |
---|
[2773] | 5132 | } |
---|
[2774] | 5133 | if (!foundIF) { |
---|
| 5134 | throw(AipsError("bad IF number")); |
---|
| 5135 | } |
---|
[2773] | 5136 | } |
---|
| 5137 | |
---|
| 5138 | currEdge.clear(); |
---|
| 5139 | currEdge.resize(2); |
---|
| 5140 | currEdge[0] = edge[idx]; |
---|
| 5141 | currEdge[1] = edge[idx+1]; |
---|
| 5142 | |
---|
[2047] | 5143 | lineFinder.setData(getSpectrum(whichrow)); |
---|
[2773] | 5144 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currEdge, whichrow); |
---|
[2047] | 5145 | return lineFinder.getMask(); |
---|
| 5146 | } |
---|
| 5147 | |
---|
| 5148 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
[2773] | 5149 | void Scantable::outputFittingResult(bool outLogger, |
---|
| 5150 | bool outTextFile, |
---|
| 5151 | bool csvFormat, |
---|
| 5152 | const std::vector<bool>& chanMask, |
---|
| 5153 | int whichrow, |
---|
| 5154 | const casa::String& coordInfo, |
---|
| 5155 | bool hasSameNchan, |
---|
| 5156 | ofstream& ofs, |
---|
| 5157 | const casa::String& funcName, |
---|
| 5158 | const std::vector<int>& edge, |
---|
| 5159 | const std::vector<float>& params, |
---|
| 5160 | const int nClipped) |
---|
[2186] | 5161 | { |
---|
[2047] | 5162 | if (outLogger || outTextFile) { |
---|
| 5163 | float rms = getRms(chanMask, whichrow); |
---|
| 5164 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 5165 | std::vector<bool> fixed; |
---|
| 5166 | fixed.clear(); |
---|
[2047] | 5167 | |
---|
| 5168 | if (outLogger) { |
---|
| 5169 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2773] | 5170 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, |
---|
| 5171 | masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 5172 | } |
---|
| 5173 | if (outTextFile) { |
---|
[2773] | 5174 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, |
---|
| 5175 | masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 5176 | } |
---|
| 5177 | } |
---|
| 5178 | } |
---|
| 5179 | |
---|
[2773] | 5180 | /* for poly/chebyshev/sinusoid. */ |
---|
| 5181 | void Scantable::outputFittingResult(bool outLogger, |
---|
| 5182 | bool outTextFile, |
---|
| 5183 | bool csvFormat, |
---|
| 5184 | const std::vector<bool>& chanMask, |
---|
| 5185 | int whichrow, |
---|
| 5186 | const casa::String& coordInfo, |
---|
| 5187 | bool hasSameNchan, |
---|
| 5188 | ofstream& ofs, |
---|
| 5189 | const casa::String& funcName, |
---|
| 5190 | const std::vector<float>& params, |
---|
| 5191 | const int nClipped) |
---|
[2186] | 5192 | { |
---|
[2047] | 5193 | if (outLogger || outTextFile) { |
---|
| 5194 | float rms = getRms(chanMask, whichrow); |
---|
| 5195 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 5196 | std::vector<bool> fixed; |
---|
| 5197 | fixed.clear(); |
---|
[2047] | 5198 | |
---|
| 5199 | if (outLogger) { |
---|
| 5200 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2773] | 5201 | ols << formatBaselineParams(params, fixed, rms, nClipped, |
---|
| 5202 | masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 5203 | } |
---|
| 5204 | if (outTextFile) { |
---|
[2773] | 5205 | ofs << formatBaselineParams(params, fixed, rms, nClipped, |
---|
| 5206 | masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 5207 | } |
---|
| 5208 | } |
---|
| 5209 | } |
---|
| 5210 | |
---|
[2189] | 5211 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
[2186] | 5212 | { |
---|
[2189] | 5213 | int idxDelimiter = progressInfo.find(","); |
---|
| 5214 | if (idxDelimiter < 0) { |
---|
| 5215 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
| 5216 | } |
---|
| 5217 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
| 5218 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
| 5219 | is >> minNRow; |
---|
| 5220 | } |
---|
| 5221 | |
---|
| 5222 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
| 5223 | { |
---|
| 5224 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
[2186] | 5225 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
| 5226 | if (nInterval == 0) nInterval++; |
---|
| 5227 | |
---|
[2193] | 5228 | if (nProcessed % nInterval == 0) { |
---|
[2189] | 5229 | printf("\r"); //go to the head of line |
---|
[2186] | 5230 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
[2189] | 5231 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
| 5232 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
[2186] | 5233 | fflush(NULL); |
---|
| 5234 | } |
---|
[2193] | 5235 | |
---|
[2186] | 5236 | if (nProcessed == nTotal - 1) { |
---|
| 5237 | printf("\r\x1b[K"); //clear |
---|
| 5238 | fflush(NULL); |
---|
| 5239 | } |
---|
[2193] | 5240 | |
---|
[2186] | 5241 | } |
---|
| 5242 | } |
---|
| 5243 | |
---|
| 5244 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
| 5245 | { |
---|
| 5246 | std::vector<bool> mask = getMask(whichrow); |
---|
| 5247 | |
---|
| 5248 | if (inMask.size() > 0) { |
---|
| 5249 | uInt maskSize = mask.size(); |
---|
| 5250 | if (maskSize != inMask.size()) { |
---|
| 5251 | throw(AipsError("mask sizes are not the same.")); |
---|
| 5252 | } |
---|
| 5253 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 5254 | mask[i] = mask[i] && inMask[i]; |
---|
| 5255 | } |
---|
| 5256 | } |
---|
| 5257 | |
---|
| 5258 | Vector<Float> spec = getSpectrum(whichrow); |
---|
| 5259 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
| 5260 | |
---|
| 5261 | FFTServer<Float,Complex> ffts; |
---|
| 5262 | Vector<Complex> fftres; |
---|
| 5263 | ffts.fft0(fftres, spec); |
---|
| 5264 | |
---|
| 5265 | std::vector<float> res; |
---|
| 5266 | float norm = float(2.0/double(spec.size())); |
---|
| 5267 | |
---|
| 5268 | if (getRealImag) { |
---|
| 5269 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 5270 | res.push_back(real(fftres[i])*norm); |
---|
| 5271 | res.push_back(imag(fftres[i])*norm); |
---|
| 5272 | } |
---|
| 5273 | } else { |
---|
| 5274 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 5275 | res.push_back(abs(fftres[i])*norm); |
---|
| 5276 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
| 5277 | } |
---|
| 5278 | } |
---|
| 5279 | |
---|
| 5280 | return res; |
---|
| 5281 | } |
---|
| 5282 | |
---|
| 5283 | |
---|
| 5284 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
| 5285 | { |
---|
[2591] | 5286 | /**** |
---|
[2737] | 5287 | double ms1TimeStart, ms1TimeEnd; |
---|
[2591] | 5288 | double elapse1 = 0.0; |
---|
| 5289 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
| 5290 | ****/ |
---|
| 5291 | |
---|
[2012] | 5292 | Vector<Float> spec; |
---|
| 5293 | specCol_.get(whichrow, spec); |
---|
| 5294 | |
---|
[2591] | 5295 | /**** |
---|
| 5296 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 5297 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
| 5298 | std::cout << "rm1 : " << elapse1 << " (sec.)" << endl; |
---|
| 5299 | ****/ |
---|
| 5300 | |
---|
[2737] | 5301 | return (float)doGetRms(mask, spec); |
---|
| 5302 | } |
---|
| 5303 | |
---|
| 5304 | double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec) |
---|
| 5305 | { |
---|
| 5306 | double mean = 0.0; |
---|
| 5307 | double smean = 0.0; |
---|
[2012] | 5308 | int n = 0; |
---|
[2047] | 5309 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
[2012] | 5310 | if (mask[i]) { |
---|
[2737] | 5311 | double val = (double)spec[i]; |
---|
| 5312 | mean += val; |
---|
| 5313 | smean += val*val; |
---|
[2012] | 5314 | n++; |
---|
| 5315 | } |
---|
| 5316 | } |
---|
| 5317 | |
---|
[2737] | 5318 | mean /= (double)n; |
---|
| 5319 | smean /= (double)n; |
---|
[2012] | 5320 | |
---|
| 5321 | return sqrt(smean - mean*mean); |
---|
| 5322 | } |
---|
| 5323 | |
---|
[2641] | 5324 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const |
---|
[2012] | 5325 | { |
---|
[2641] | 5326 | if (verbose) { |
---|
| 5327 | ostringstream oss; |
---|
[2012] | 5328 | |
---|
[2641] | 5329 | if (csvformat) { |
---|
| 5330 | oss << getScan(whichrow) << ","; |
---|
| 5331 | oss << getBeam(whichrow) << ","; |
---|
| 5332 | oss << getIF(whichrow) << ","; |
---|
| 5333 | oss << getPol(whichrow) << ","; |
---|
| 5334 | oss << getCycle(whichrow) << ","; |
---|
| 5335 | String commaReplacedMasklist = masklist; |
---|
| 5336 | string::size_type pos = 0; |
---|
| 5337 | while (pos = commaReplacedMasklist.find(","), pos != string::npos) { |
---|
| 5338 | commaReplacedMasklist.replace(pos, 1, ";"); |
---|
| 5339 | pos++; |
---|
| 5340 | } |
---|
| 5341 | oss << commaReplacedMasklist << ","; |
---|
| 5342 | } else { |
---|
| 5343 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
| 5344 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
| 5345 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
| 5346 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
| 5347 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
| 5348 | oss << "Fitter range = " << masklist << endl; |
---|
| 5349 | oss << "Baseline parameters" << endl; |
---|
| 5350 | } |
---|
[2012] | 5351 | oss << flush; |
---|
[2641] | 5352 | |
---|
| 5353 | return String(oss); |
---|
[2012] | 5354 | } |
---|
| 5355 | |
---|
[2641] | 5356 | return ""; |
---|
[2012] | 5357 | } |
---|
| 5358 | |
---|
[2641] | 5359 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const |
---|
[2012] | 5360 | { |
---|
[2641] | 5361 | if (verbose) { |
---|
| 5362 | ostringstream oss; |
---|
[2012] | 5363 | |
---|
[2641] | 5364 | if (csvformat) { |
---|
| 5365 | oss << rms << ","; |
---|
| 5366 | if (nClipped >= 0) { |
---|
| 5367 | oss << nClipped; |
---|
| 5368 | } |
---|
| 5369 | } else { |
---|
| 5370 | oss << "Results of baseline fit" << endl; |
---|
| 5371 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
| 5372 | if (nClipped >= 0) { |
---|
| 5373 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
| 5374 | } |
---|
| 5375 | for (int i = 0; i < 60; ++i) { |
---|
| 5376 | oss << "-"; |
---|
| 5377 | } |
---|
[2193] | 5378 | } |
---|
[2131] | 5379 | oss << endl; |
---|
[2094] | 5380 | oss << flush; |
---|
[2641] | 5381 | |
---|
| 5382 | return String(oss); |
---|
[2012] | 5383 | } |
---|
| 5384 | |
---|
[2641] | 5385 | return ""; |
---|
[2012] | 5386 | } |
---|
| 5387 | |
---|
[2186] | 5388 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
| 5389 | const std::vector<bool>& fixed, |
---|
| 5390 | float rms, |
---|
[2193] | 5391 | int nClipped, |
---|
[2186] | 5392 | const std::string& masklist, |
---|
| 5393 | int whichrow, |
---|
| 5394 | bool verbose, |
---|
[2641] | 5395 | bool csvformat, |
---|
[2186] | 5396 | int start, int count, |
---|
| 5397 | bool resetparamid) const |
---|
[2047] | 5398 | { |
---|
[2064] | 5399 | int nParam = (int)(params.size()); |
---|
[2047] | 5400 | |
---|
[2064] | 5401 | if (nParam < 1) { |
---|
| 5402 | return(" Not fitted"); |
---|
| 5403 | } else { |
---|
| 5404 | |
---|
| 5405 | ostringstream oss; |
---|
[2641] | 5406 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
[2064] | 5407 | |
---|
| 5408 | if (start < 0) start = 0; |
---|
| 5409 | if (count < 0) count = nParam; |
---|
| 5410 | int end = start + count; |
---|
| 5411 | if (end > nParam) end = nParam; |
---|
| 5412 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
| 5413 | |
---|
| 5414 | for (int i = start; i < end; ++i) { |
---|
| 5415 | if (i > start) { |
---|
[2047] | 5416 | oss << ","; |
---|
| 5417 | } |
---|
[2064] | 5418 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
[2641] | 5419 | if (csvformat) { |
---|
| 5420 | oss << params[i] << sFix; |
---|
| 5421 | } else { |
---|
| 5422 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
| 5423 | } |
---|
[2047] | 5424 | } |
---|
[2064] | 5425 | |
---|
[2641] | 5426 | if (csvformat) { |
---|
| 5427 | oss << ","; |
---|
[2644] | 5428 | } else { |
---|
| 5429 | oss << endl; |
---|
[2641] | 5430 | } |
---|
| 5431 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
[2064] | 5432 | |
---|
| 5433 | return String(oss); |
---|
[2047] | 5434 | } |
---|
| 5435 | |
---|
| 5436 | } |
---|
| 5437 | |
---|
[2641] | 5438 | 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, bool csvformat) const |
---|
[2012] | 5439 | { |
---|
[2064] | 5440 | int nOutParam = (int)(params.size()); |
---|
| 5441 | int nPiece = (int)(ranges.size()) - 1; |
---|
[2012] | 5442 | |
---|
[2064] | 5443 | if (nOutParam < 1) { |
---|
| 5444 | return(" Not fitted"); |
---|
| 5445 | } else if (nPiece < 0) { |
---|
[2641] | 5446 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat); |
---|
[2064] | 5447 | } else if (nPiece < 1) { |
---|
| 5448 | return(" Bad count of the piece edge info"); |
---|
| 5449 | } else if (nOutParam % nPiece != 0) { |
---|
| 5450 | return(" Bad count of the output baseline parameters"); |
---|
| 5451 | } else { |
---|
| 5452 | |
---|
| 5453 | int nParam = nOutParam / nPiece; |
---|
| 5454 | |
---|
| 5455 | ostringstream oss; |
---|
[2641] | 5456 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
[2064] | 5457 | |
---|
[2641] | 5458 | if (csvformat) { |
---|
| 5459 | for (int i = 0; i < nPiece; ++i) { |
---|
| 5460 | oss << ranges[i] << "," << (ranges[i+1]-1) << ","; |
---|
| 5461 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
| 5462 | } |
---|
| 5463 | } else { |
---|
| 5464 | stringstream ss; |
---|
| 5465 | ss << ranges[nPiece] << flush; |
---|
| 5466 | int wRange = ss.str().size() * 2 + 5; |
---|
[2064] | 5467 | |
---|
[2641] | 5468 | for (int i = 0; i < nPiece; ++i) { |
---|
| 5469 | ss.str(""); |
---|
| 5470 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
| 5471 | oss << left << setw(wRange) << ss.str(); |
---|
| 5472 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
[2644] | 5473 | //oss << endl; |
---|
[2641] | 5474 | } |
---|
[2012] | 5475 | } |
---|
[2064] | 5476 | |
---|
[2641] | 5477 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
[2064] | 5478 | |
---|
| 5479 | return String(oss); |
---|
[2012] | 5480 | } |
---|
| 5481 | |
---|
| 5482 | } |
---|
| 5483 | |
---|
[2047] | 5484 | bool Scantable::hasSameNchanOverIFs() |
---|
[2012] | 5485 | { |
---|
[2047] | 5486 | int nIF = nif(-1); |
---|
| 5487 | int nCh; |
---|
| 5488 | int totalPositiveNChan = 0; |
---|
| 5489 | int nPositiveNChan = 0; |
---|
[2012] | 5490 | |
---|
[2047] | 5491 | for (int i = 0; i < nIF; ++i) { |
---|
| 5492 | nCh = nchan(i); |
---|
| 5493 | if (nCh > 0) { |
---|
| 5494 | totalPositiveNChan += nCh; |
---|
| 5495 | nPositiveNChan++; |
---|
[2012] | 5496 | } |
---|
| 5497 | } |
---|
| 5498 | |
---|
[2047] | 5499 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
[2012] | 5500 | } |
---|
| 5501 | |
---|
[2047] | 5502 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
[2012] | 5503 | { |
---|
[2427] | 5504 | if (mask.size() <= 0) { |
---|
| 5505 | throw(AipsError("The mask elements should be > 0")); |
---|
[2012] | 5506 | } |
---|
[2047] | 5507 | int IF = getIF(whichrow); |
---|
| 5508 | if (mask.size() != (uInt)nchan(IF)) { |
---|
[2012] | 5509 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
| 5510 | } |
---|
| 5511 | |
---|
[2047] | 5512 | if (verbose) { |
---|
[2012] | 5513 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
| 5514 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
| 5515 | if (!hasSameNchan) { |
---|
[2047] | 5516 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
[2012] | 5517 | } |
---|
| 5518 | logOs << LogIO::POST; |
---|
| 5519 | } |
---|
| 5520 | |
---|
| 5521 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
[2047] | 5522 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
| 5523 | |
---|
[2012] | 5524 | ostringstream oss; |
---|
| 5525 | oss.setf(ios::fixed); |
---|
| 5526 | oss << setprecision(1) << "["; |
---|
[2047] | 5527 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
[2012] | 5528 | if (i > 0) oss << ","; |
---|
[2047] | 5529 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
[2012] | 5530 | } |
---|
| 5531 | oss << "]" << flush; |
---|
| 5532 | |
---|
| 5533 | return String(oss); |
---|
| 5534 | } |
---|
| 5535 | |
---|
[2047] | 5536 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
[2012] | 5537 | { |
---|
[2427] | 5538 | if (mask.size() <= 0) { |
---|
| 5539 | throw(AipsError("The mask elements should be > 0")); |
---|
[2012] | 5540 | } |
---|
| 5541 | |
---|
[2047] | 5542 | std::vector<int> out, startIndices, endIndices; |
---|
| 5543 | int maskSize = mask.size(); |
---|
[2012] | 5544 | |
---|
[2047] | 5545 | startIndices.clear(); |
---|
| 5546 | endIndices.clear(); |
---|
| 5547 | |
---|
| 5548 | if (mask[0]) { |
---|
| 5549 | startIndices.push_back(0); |
---|
[2012] | 5550 | } |
---|
[2047] | 5551 | for (int i = 1; i < maskSize; ++i) { |
---|
| 5552 | if ((!mask[i-1]) && mask[i]) { |
---|
| 5553 | startIndices.push_back(i); |
---|
| 5554 | } else if (mask[i-1] && (!mask[i])) { |
---|
| 5555 | endIndices.push_back(i-1); |
---|
| 5556 | } |
---|
[2012] | 5557 | } |
---|
[2047] | 5558 | if (mask[maskSize-1]) { |
---|
| 5559 | endIndices.push_back(maskSize-1); |
---|
| 5560 | } |
---|
[2012] | 5561 | |
---|
[2047] | 5562 | if (startIndices.size() != endIndices.size()) { |
---|
| 5563 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
| 5564 | } |
---|
| 5565 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 5566 | if (startIndices[i] > endIndices[i]) { |
---|
| 5567 | throw(AipsError("Mask start index > mask end index")); |
---|
[2012] | 5568 | } |
---|
| 5569 | } |
---|
| 5570 | |
---|
[2047] | 5571 | out.clear(); |
---|
| 5572 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 5573 | out.push_back(startIndices[i]); |
---|
| 5574 | out.push_back(endIndices[i]); |
---|
| 5575 | } |
---|
| 5576 | |
---|
[2012] | 5577 | return out; |
---|
| 5578 | } |
---|
| 5579 | |
---|
[2791] | 5580 | void Scantable::setTsys(const std::vector<float>& newvals, int whichrow) { |
---|
| 5581 | Vector<Float> tsys(newvals); |
---|
| 5582 | if (whichrow > -1) { |
---|
| 5583 | if (tsysCol_.shape(whichrow) != tsys.shape()) |
---|
| 5584 | throw(AipsError("Given Tsys values are not of the same shape")); |
---|
| 5585 | tsysCol_.put(whichrow, tsys); |
---|
| 5586 | } else { |
---|
| 5587 | tsysCol_.fillColumn(tsys); |
---|
| 5588 | } |
---|
| 5589 | } |
---|
| 5590 | |
---|
[2161] | 5591 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
| 5592 | { |
---|
| 5593 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
| 5594 | vector<float> stlTsys ; |
---|
| 5595 | tsys.tovector( stlTsys ) ; |
---|
| 5596 | return stlTsys ; |
---|
| 5597 | } |
---|
[2012] | 5598 | |
---|
[2591] | 5599 | vector<uint> Scantable::getMoleculeIdColumnData() const |
---|
| 5600 | { |
---|
| 5601 | Vector<uInt> molIds(mmolidCol_.getColumn()); |
---|
| 5602 | vector<uint> res; |
---|
| 5603 | molIds.tovector(res); |
---|
| 5604 | return res; |
---|
| 5605 | } |
---|
[2012] | 5606 | |
---|
[2591] | 5607 | void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids) |
---|
| 5608 | { |
---|
| 5609 | Vector<uInt> molIds(molids); |
---|
| 5610 | Vector<uInt> arr(mmolidCol_.getColumn()); |
---|
| 5611 | if ( molIds.nelements() != arr.nelements() ) |
---|
| 5612 | throw AipsError("The input data size must be the number of rows."); |
---|
| 5613 | mmolidCol_.putColumn(molIds); |
---|
[1907] | 5614 | } |
---|
[2591] | 5615 | |
---|
| 5616 | |
---|
[2888] | 5617 | std::vector<uint> Scantable::getRootTableRowNumbers() const |
---|
| 5618 | { |
---|
| 5619 | Vector<uInt> rowIds(table_.rowNumbers()); |
---|
| 5620 | vector<uint> res; |
---|
| 5621 | rowIds.tovector(res); |
---|
| 5622 | return res; |
---|
| 5623 | } |
---|
| 5624 | |
---|
| 5625 | |
---|
[2789] | 5626 | void Scantable::dropXPol() |
---|
| 5627 | { |
---|
| 5628 | if (npol() <= 2) { |
---|
| 5629 | return; |
---|
| 5630 | } |
---|
| 5631 | if (!selector_.empty()) { |
---|
| 5632 | throw AipsError("Can only operate with empty selection"); |
---|
| 5633 | } |
---|
| 5634 | std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]"; |
---|
| 5635 | Table tab = tableCommand(taql, table_); |
---|
| 5636 | table_ = tab; |
---|
| 5637 | table_.rwKeywordSet().define("nPol", Int(2)); |
---|
| 5638 | originalTable_ = table_; |
---|
| 5639 | attach(); |
---|
[2591] | 5640 | } |
---|
[2789] | 5641 | |
---|
| 5642 | } |
---|
[1819] | 5643 | //namespace asap |
---|