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