[805] | 1 | // |
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| 2 | // C++ Implementation: Scantable |
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| 3 | // |
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| 4 | // Description: |
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| 5 | // |
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| 6 | // |
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| 7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005 |
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| 8 | // |
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| 9 | // Copyright: See COPYING file that comes with this distribution |
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| 10 | // |
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| 11 | // |
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[206] | 12 | #include <map> |
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| 13 | |
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[2186] | 14 | #include <atnf/PKSIO/SrcType.h> |
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| 15 | |
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[125] | 16 | #include <casa/aips.h> |
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[2186] | 17 | #include <casa/iomanip.h> |
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[80] | 18 | #include <casa/iostream.h> |
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[2186] | 19 | #include <casa/OS/File.h> |
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[805] | 20 | #include <casa/OS/Path.h> |
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[80] | 21 | #include <casa/Arrays/Array.h> |
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[2186] | 22 | #include <casa/Arrays/ArrayAccessor.h> |
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| 23 | #include <casa/Arrays/ArrayLogical.h> |
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[80] | 24 | #include <casa/Arrays/ArrayMath.h> |
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| 25 | #include <casa/Arrays/MaskArrMath.h> |
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[2186] | 26 | #include <casa/Arrays/Slice.h> |
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[1325] | 27 | #include <casa/Arrays/Vector.h> |
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[455] | 28 | #include <casa/Arrays/VectorSTLIterator.h> |
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[418] | 29 | #include <casa/BasicMath/Math.h> |
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[504] | 30 | #include <casa/BasicSL/Constants.h> |
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[2186] | 31 | #include <casa/Containers/RecordField.h> |
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| 32 | #include <casa/Logging/LogIO.h> |
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[286] | 33 | #include <casa/Quanta/MVAngle.h> |
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[2186] | 34 | #include <casa/Quanta/MVTime.h> |
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[902] | 35 | #include <casa/Utilities/GenSort.h> |
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[2] | 36 | |
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[2186] | 37 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[2] | 38 | |
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[1325] | 39 | // needed to avoid error in .tcc |
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| 40 | #include <measures/Measures/MCDirection.h> |
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| 41 | // |
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| 42 | #include <measures/Measures/MDirection.h> |
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[2186] | 43 | #include <measures/Measures/MEpoch.h> |
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[80] | 44 | #include <measures/Measures/MFrequency.h> |
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[2186] | 45 | #include <measures/Measures/MeasRef.h> |
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| 46 | #include <measures/Measures/MeasTable.h> |
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| 47 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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| 48 | #include <measures/TableMeasures/TableMeasDesc.h> |
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[805] | 49 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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| 50 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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[2] | 51 | |
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[2186] | 52 | #include <tables/Tables/ArrColDesc.h> |
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| 53 | #include <tables/Tables/ExprNode.h> |
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| 54 | #include <tables/Tables/ScaColDesc.h> |
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| 55 | #include <tables/Tables/SetupNewTab.h> |
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| 56 | #include <tables/Tables/TableCopy.h> |
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| 57 | #include <tables/Tables/TableDesc.h> |
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| 58 | #include <tables/Tables/TableIter.h> |
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| 59 | #include <tables/Tables/TableParse.h> |
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| 60 | #include <tables/Tables/TableRecord.h> |
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| 61 | #include <tables/Tables/TableRow.h> |
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| 62 | #include <tables/Tables/TableVector.h> |
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| 63 | |
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| 64 | #include "MathUtils.h" |
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| 65 | #include "STAttr.h" |
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| 66 | #include "STLineFinder.h" |
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| 67 | #include "STPolCircular.h" |
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[896] | 68 | #include "STPolLinear.h" |
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[913] | 69 | #include "STPolStokes.h" |
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[2186] | 70 | #include "Scantable.h" |
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[2] | 71 | |
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[125] | 72 | using namespace casa; |
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[2] | 73 | |
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[805] | 74 | namespace asap { |
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| 75 | |
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[896] | 76 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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| 77 | |
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| 78 | void Scantable::initFactories() { |
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| 79 | if ( factories_.empty() ) { |
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| 80 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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[1323] | 81 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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[913] | 82 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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[896] | 83 | } |
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| 84 | } |
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| 85 | |
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[805] | 86 | Scantable::Scantable(Table::TableType ttype) : |
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[852] | 87 | type_(ttype) |
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[206] | 88 | { |
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[896] | 89 | initFactories(); |
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[805] | 90 | setupMainTable(); |
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[852] | 91 | freqTable_ = STFrequencies(*this); |
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[805] | 92 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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[852] | 93 | weatherTable_ = STWeather(*this); |
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[805] | 94 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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[852] | 95 | focusTable_ = STFocus(*this); |
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[805] | 96 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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[852] | 97 | tcalTable_ = STTcal(*this); |
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[805] | 98 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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[852] | 99 | moleculeTable_ = STMolecules(*this); |
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[805] | 100 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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[860] | 101 | historyTable_ = STHistory(*this); |
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| 102 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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[959] | 103 | fitTable_ = STFit(*this); |
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| 104 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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[1881] | 105 | table_.tableInfo().setType( "Scantable" ) ; |
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[805] | 106 | originalTable_ = table_; |
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[322] | 107 | attach(); |
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[18] | 108 | } |
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[206] | 109 | |
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[805] | 110 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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[852] | 111 | type_(ttype) |
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[206] | 112 | { |
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[896] | 113 | initFactories(); |
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[1819] | 114 | |
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[865] | 115 | Table tab(name, Table::Update); |
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[1009] | 116 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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[483] | 117 | if (version != version_) { |
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[2162] | 118 | if ( version == 2 && version_ == 3 ) { |
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| 119 | // run asap2to3 command |
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| 120 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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| 121 | string command="asap2to3" ; |
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| 122 | string exec=command+" in="+name ; |
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| 123 | string outname=name ; |
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| 124 | if ( name.at(name.length()-1) == '/' ) |
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| 125 | outname = outname.substr( 0, name.length()-1 ) ; |
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| 126 | outname += ".asap3" ; |
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| 127 | os << LogIO::WARN |
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| 128 | << name << " is incompatible data format (Scantable v2)." << endl |
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| 129 | << "Running " << command << " to create " << outname << ", " << endl |
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| 130 | << "which is identical to " << name << " but compatible " << endl |
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| 131 | << "data format with current software version (Scantable v3)." |
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| 132 | << LogIO::POST ; |
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| 133 | int ret = system( string("which "+command+" > /dev/null 2>&1").c_str() ) ; |
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| 134 | if ( ret != 0 ) |
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| 135 | throw(AipsError(command+" is not installed")) ; |
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| 136 | os << LogIO::WARN |
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| 137 | << "Data will be loaded from " << outname << " instead of " |
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| 138 | << name << LogIO::POST ; |
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[2163] | 139 | int tmp = system( exec.c_str() ) ; |
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| 140 | (void) tmp; |
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[2162] | 141 | tab = Table(outname, Table::Update ) ; |
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| 142 | //os << "tab.tableName()=" << tab.tableName() << LogIO::POST ; |
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| 143 | } |
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| 144 | else { |
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| 145 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 146 | } |
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[483] | 147 | } |
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[1009] | 148 | if ( type_ == Table::Memory ) { |
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[852] | 149 | table_ = tab.copyToMemoryTable(generateName()); |
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[1009] | 150 | } else { |
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[805] | 151 | table_ = tab; |
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[1009] | 152 | } |
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[1881] | 153 | table_.tableInfo().setType( "Scantable" ) ; |
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[1009] | 154 | |
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[859] | 155 | attachSubtables(); |
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[805] | 156 | originalTable_ = table_; |
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[329] | 157 | attach(); |
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[2] | 158 | } |
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[1819] | 159 | /* |
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| 160 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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| 161 | type_(ttype) |
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| 162 | { |
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| 163 | initFactories(); |
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| 164 | Table tab(name, Table::Update); |
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| 165 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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| 166 | if (version != version_) { |
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| 167 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 168 | } |
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| 169 | if ( type_ == Table::Memory ) { |
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| 170 | table_ = tab.copyToMemoryTable(generateName()); |
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| 171 | } else { |
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| 172 | table_ = tab; |
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| 173 | } |
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[2] | 174 | |
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[1819] | 175 | attachSubtables(); |
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| 176 | originalTable_ = table_; |
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| 177 | attach(); |
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| 178 | } |
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| 179 | */ |
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| 180 | |
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[2163] | 181 | Scantable::Scantable( const Scantable& other, bool clear ): |
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| 182 | Logger() |
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[206] | 183 | { |
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[805] | 184 | // with or without data |
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[859] | 185 | String newname = String(generateName()); |
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[865] | 186 | type_ = other.table_.tableType(); |
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[859] | 187 | if ( other.table_.tableType() == Table::Memory ) { |
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| 188 | if ( clear ) { |
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| 189 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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| 190 | other.table_, True); |
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| 191 | } else |
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| 192 | table_ = other.table_.copyToMemoryTable(newname); |
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[16] | 193 | } else { |
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[915] | 194 | other.table_.deepCopy(newname, Table::New, False, |
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| 195 | other.table_.endianFormat(), |
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[865] | 196 | Bool(clear)); |
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| 197 | table_ = Table(newname, Table::Update); |
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| 198 | table_.markForDelete(); |
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| 199 | } |
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[1881] | 200 | table_.tableInfo().setType( "Scantable" ) ; |
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[1111] | 201 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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[915] | 202 | if ( clear ) copySubtables(other); |
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[859] | 203 | attachSubtables(); |
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[805] | 204 | originalTable_ = table_; |
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[322] | 205 | attach(); |
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[2] | 206 | } |
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| 207 | |
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[865] | 208 | void Scantable::copySubtables(const Scantable& other) { |
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| 209 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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| 210 | TableCopy::copyRows(t, other.freqTable_.table()); |
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| 211 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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| 212 | TableCopy::copyRows(t, other.focusTable_.table()); |
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| 213 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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| 214 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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| 215 | t = table_.rwKeywordSet().asTable("TCAL"); |
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| 216 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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| 217 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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| 218 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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| 219 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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| 220 | TableCopy::copyRows(t, other.historyTable_.table()); |
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[972] | 221 | t = table_.rwKeywordSet().asTable("FIT"); |
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| 222 | TableCopy::copyRows(t, other.fitTable_.table()); |
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[865] | 223 | } |
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| 224 | |
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[859] | 225 | void Scantable::attachSubtables() |
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| 226 | { |
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| 227 | freqTable_ = STFrequencies(table_); |
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| 228 | focusTable_ = STFocus(table_); |
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| 229 | weatherTable_ = STWeather(table_); |
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| 230 | tcalTable_ = STTcal(table_); |
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| 231 | moleculeTable_ = STMolecules(table_); |
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[860] | 232 | historyTable_ = STHistory(table_); |
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[972] | 233 | fitTable_ = STFit(table_); |
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[859] | 234 | } |
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| 235 | |
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[805] | 236 | Scantable::~Scantable() |
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[206] | 237 | { |
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[941] | 238 | //cout << "~Scantable() " << this << endl; |
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[2] | 239 | } |
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| 240 | |
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[805] | 241 | void Scantable::setupMainTable() |
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[206] | 242 | { |
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[805] | 243 | TableDesc td("", "1", TableDesc::Scratch); |
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| 244 | td.comment() = "An ASAP Scantable"; |
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[1009] | 245 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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[2] | 246 | |
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[805] | 247 | // n Cycles |
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| 248 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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| 249 | // new index every nBeam x nIF x nPol |
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| 250 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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[2] | 251 | |
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[805] | 252 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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| 253 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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[972] | 254 | // linear, circular, stokes |
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[805] | 255 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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| 256 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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[138] | 257 | |
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[805] | 258 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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| 259 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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[80] | 260 | |
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[1819] | 261 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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| 262 | refbeamnoColumn.setDefault(Int(-1)); |
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| 263 | td.addColumn(refbeamnoColumn); |
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| 264 | |
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| 265 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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| 266 | flagrowColumn.setDefault(uInt(0)); |
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| 267 | td.addColumn(flagrowColumn); |
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| 268 | |
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[805] | 269 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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| 270 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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| 271 | TableMeasValueDesc measVal(td, "TIME"); |
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| 272 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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| 273 | mepochCol.write(td); |
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[483] | 274 | |
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[805] | 275 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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| 276 | |
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[2] | 277 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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[805] | 278 | // Type of source (on=0, off=1, other=-1) |
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[1503] | 279 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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| 280 | stypeColumn.setDefault(Int(-1)); |
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| 281 | td.addColumn(stypeColumn); |
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[805] | 282 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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| 283 | |
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| 284 | //The actual Data Vectors |
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[2] | 285 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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| 286 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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[89] | 287 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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[805] | 288 | |
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| 289 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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| 290 | IPosition(1,2), |
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| 291 | ColumnDesc::Direct)); |
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| 292 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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| 293 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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| 294 | // the TableMeasDesc gives the column a type |
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| 295 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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[987] | 296 | // a uder set table type e.g. GALCTIC, B1950 ... |
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| 297 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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[805] | 298 | // writing create the measure column |
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| 299 | mdirCol.write(td); |
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[923] | 300 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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| 301 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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[1047] | 302 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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[105] | 303 | |
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[805] | 304 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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[972] | 305 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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[973] | 306 | fitColumn.setDefault(Int(-1)); |
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[972] | 307 | td.addColumn(fitColumn); |
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[805] | 308 | |
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| 309 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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| 310 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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| 311 | |
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[999] | 312 | // columns which just get dragged along, as they aren't used in asap |
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| 313 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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| 314 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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| 315 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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| 316 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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| 317 | |
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[805] | 318 | td.rwKeywordSet().define("OBSMODE", String("")); |
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| 319 | |
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[418] | 320 | // Now create Table SetUp from the description. |
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[859] | 321 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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[852] | 322 | table_ = Table(aNewTab, type_, 0); |
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[805] | 323 | originalTable_ = table_; |
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| 324 | } |
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[418] | 325 | |
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[805] | 326 | void Scantable::attach() |
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[455] | 327 | { |
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[805] | 328 | timeCol_.attach(table_, "TIME"); |
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| 329 | srcnCol_.attach(table_, "SRCNAME"); |
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[1068] | 330 | srctCol_.attach(table_, "SRCTYPE"); |
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[805] | 331 | specCol_.attach(table_, "SPECTRA"); |
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| 332 | flagsCol_.attach(table_, "FLAGTRA"); |
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[865] | 333 | tsysCol_.attach(table_, "TSYS"); |
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[805] | 334 | cycleCol_.attach(table_,"CYCLENO"); |
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| 335 | scanCol_.attach(table_, "SCANNO"); |
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| 336 | beamCol_.attach(table_, "BEAMNO"); |
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[847] | 337 | ifCol_.attach(table_, "IFNO"); |
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| 338 | polCol_.attach(table_, "POLNO"); |
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[805] | 339 | integrCol_.attach(table_, "INTERVAL"); |
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| 340 | azCol_.attach(table_, "AZIMUTH"); |
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| 341 | elCol_.attach(table_, "ELEVATION"); |
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| 342 | dirCol_.attach(table_, "DIRECTION"); |
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| 343 | fldnCol_.attach(table_, "FIELDNAME"); |
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| 344 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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[455] | 345 | |
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[1730] | 346 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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[805] | 347 | mfitidCol_.attach(table_,"FIT_ID"); |
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| 348 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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| 349 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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| 350 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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| 351 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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[1819] | 352 | |
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| 353 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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| 354 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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| 355 | |
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[455] | 356 | } |
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| 357 | |
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[1819] | 358 | template<class T, class T2> |
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| 359 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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| 360 | const String& colName, |
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| 361 | const T2& defValue) |
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| 362 | { |
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| 363 | try { |
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| 364 | col.attach(table_, colName); |
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| 365 | } catch (TableError& err) { |
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| 366 | String errMesg = err.getMesg(); |
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| 367 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 368 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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| 369 | col.attach(table_, colName); |
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| 370 | col.fillColumn(static_cast<T>(defValue)); |
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| 371 | } else { |
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| 372 | throw; |
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| 373 | } |
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| 374 | } catch (...) { |
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| 375 | throw; |
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| 376 | } |
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| 377 | } |
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| 378 | |
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| 379 | template<class T, class T2> |
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| 380 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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| 381 | const String& colName, |
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| 382 | const Array<T2>& defValue) |
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| 383 | { |
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| 384 | try { |
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| 385 | col.attach(table_, colName); |
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| 386 | } catch (TableError& err) { |
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| 387 | String errMesg = err.getMesg(); |
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| 388 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 389 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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| 390 | col.attach(table_, colName); |
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| 391 | |
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| 392 | int size = 0; |
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| 393 | ArrayIterator<T2>& it = defValue.begin(); |
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| 394 | while (it != defValue.end()) { |
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| 395 | ++size; |
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| 396 | ++it; |
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| 397 | } |
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| 398 | IPosition ip(1, size); |
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| 399 | Array<T>& arr(ip); |
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| 400 | for (int i = 0; i < size; ++i) |
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| 401 | arr[i] = static_cast<T>(defValue[i]); |
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| 402 | |
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| 403 | col.fillColumn(arr); |
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| 404 | } else { |
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| 405 | throw; |
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| 406 | } |
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| 407 | } catch (...) { |
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| 408 | throw; |
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| 409 | } |
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| 410 | } |
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| 411 | |
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[901] | 412 | void Scantable::setHeader(const STHeader& sdh) |
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[206] | 413 | { |
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[18] | 414 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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| 415 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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| 416 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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| 417 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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| 418 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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| 419 | table_.rwKeywordSet().define("Project", sdh.project); |
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| 420 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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| 421 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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| 422 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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| 423 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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| 424 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
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| 425 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
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| 426 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
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| 427 | table_.rwKeywordSet().define("UTC", sdh.utc); |
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[206] | 428 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
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| 429 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
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[905] | 430 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
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[50] | 431 | } |
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[21] | 432 | |
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[901] | 433 | STHeader Scantable::getHeader() const |
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[206] | 434 | { |
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[901] | 435 | STHeader sdh; |
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[21] | 436 | table_.keywordSet().get("nBeam",sdh.nbeam); |
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| 437 | table_.keywordSet().get("nIF",sdh.nif); |
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| 438 | table_.keywordSet().get("nPol",sdh.npol); |
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| 439 | table_.keywordSet().get("nChan",sdh.nchan); |
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| 440 | table_.keywordSet().get("Observer", sdh.observer); |
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| 441 | table_.keywordSet().get("Project", sdh.project); |
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| 442 | table_.keywordSet().get("Obstype", sdh.obstype); |
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| 443 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
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| 444 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
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| 445 | table_.keywordSet().get("Equinox", sdh.equinox); |
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| 446 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
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| 447 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
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| 448 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
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| 449 | table_.keywordSet().get("UTC", sdh.utc); |
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[206] | 450 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
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| 451 | table_.keywordSet().get("Epoch", sdh.epoch); |
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[905] | 452 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
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[21] | 453 | return sdh; |
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[18] | 454 | } |
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[805] | 455 | |
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[1360] | 456 | void Scantable::setSourceType( int stype ) |
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[1068] | 457 | { |
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| 458 | if ( stype < 0 || stype > 1 ) |
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| 459 | throw(AipsError("Illegal sourcetype.")); |
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| 460 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
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| 461 | tabvec = Int(stype); |
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| 462 | } |
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| 463 | |
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[845] | 464 | bool Scantable::conformant( const Scantable& other ) |
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| 465 | { |
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| 466 | return this->getHeader().conformant(other.getHeader()); |
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| 467 | } |
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| 468 | |
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| 469 | |
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[50] | 470 | |
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[805] | 471 | std::string Scantable::formatSec(Double x) const |
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[206] | 472 | { |
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[105] | 473 | Double xcop = x; |
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| 474 | MVTime mvt(xcop/24./3600.); // make days |
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[365] | 475 | |
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[105] | 476 | if (x < 59.95) |
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[281] | 477 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
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[745] | 478 | else if (x < 3599.95) |
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[281] | 479 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
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| 480 | else { |
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| 481 | ostringstream oss; |
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| 482 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
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| 483 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
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| 484 | return String(oss); |
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[745] | 485 | } |
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[105] | 486 | }; |
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| 487 | |
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[805] | 488 | std::string Scantable::formatDirection(const MDirection& md) const |
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[281] | 489 | { |
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| 490 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
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| 491 | Int prec = 7; |
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| 492 | |
---|
| 493 | MVAngle mvLon(t[0]); |
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| 494 | String sLon = mvLon.string(MVAngle::TIME,prec); |
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[987] | 495 | uInt tp = md.getRef().getType(); |
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| 496 | if (tp == MDirection::GALACTIC || |
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| 497 | tp == MDirection::SUPERGAL ) { |
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| 498 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
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| 499 | } |
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[281] | 500 | MVAngle mvLat(t[1]); |
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| 501 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
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[380] | 502 | return sLon + String(" ") + sLat; |
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[281] | 503 | } |
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| 504 | |
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| 505 | |
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[805] | 506 | std::string Scantable::getFluxUnit() const |
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[206] | 507 | { |
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[847] | 508 | return table_.keywordSet().asString("FluxUnit"); |
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[206] | 509 | } |
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| 510 | |
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[805] | 511 | void Scantable::setFluxUnit(const std::string& unit) |
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[218] | 512 | { |
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| 513 | String tmp(unit); |
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| 514 | Unit tU(tmp); |
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| 515 | if (tU==Unit("K") || tU==Unit("Jy")) { |
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| 516 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
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| 517 | } else { |
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| 518 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
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| 519 | } |
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| 520 | } |
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| 521 | |
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[805] | 522 | void Scantable::setInstrument(const std::string& name) |
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[236] | 523 | { |
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[805] | 524 | bool throwIt = true; |
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[996] | 525 | // create an Instrument to see if this is valid |
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| 526 | STAttr::convertInstrument(name, throwIt); |
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[236] | 527 | String nameU(name); |
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| 528 | nameU.upcase(); |
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| 529 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
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| 530 | } |
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| 531 | |
---|
[1189] | 532 | void Scantable::setFeedType(const std::string& feedtype) |
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| 533 | { |
---|
| 534 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
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| 535 | std::string msg = "Illegal feed type "+ feedtype; |
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| 536 | throw(casa::AipsError(msg)); |
---|
| 537 | } |
---|
| 538 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
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| 539 | } |
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| 540 | |
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[1743] | 541 | MPosition Scantable::getAntennaPosition() const |
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[805] | 542 | { |
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| 543 | Vector<Double> antpos; |
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| 544 | table_.keywordSet().get("AntennaPosition", antpos); |
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| 545 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
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| 546 | return MPosition(mvpos); |
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| 547 | } |
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[281] | 548 | |
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[805] | 549 | void Scantable::makePersistent(const std::string& filename) |
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| 550 | { |
---|
| 551 | String inname(filename); |
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| 552 | Path path(inname); |
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[1111] | 553 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
[805] | 554 | inname = path.expandedName(); |
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[2030] | 555 | // 2011/03/04 TN |
---|
| 556 | // We can comment out this workaround since the essential bug is |
---|
| 557 | // fixed in casacore (r20889 in google code). |
---|
| 558 | table_.deepCopy(inname, Table::New); |
---|
| 559 | // // WORKAROUND !!! for Table bug |
---|
| 560 | // // Remove when fixed in casacore |
---|
| 561 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
| 562 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
| 563 | // tab.deepCopy(inname, Table::New); |
---|
| 564 | // tab.markForDelete(); |
---|
| 565 | // |
---|
| 566 | // } else { |
---|
| 567 | // table_.deepCopy(inname, Table::New); |
---|
| 568 | // } |
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[805] | 569 | } |
---|
| 570 | |
---|
[837] | 571 | int Scantable::nbeam( int scanno ) const |
---|
[805] | 572 | { |
---|
| 573 | if ( scanno < 0 ) { |
---|
| 574 | Int n; |
---|
| 575 | table_.keywordSet().get("nBeam",n); |
---|
| 576 | return int(n); |
---|
[105] | 577 | } else { |
---|
[805] | 578 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 579 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 580 | ROTableRow row(t); |
---|
| 581 | const TableRecord& rec = row.get(0); |
---|
| 582 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 583 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 584 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 585 | ROTableVector<uInt> v(subt, "BEAMNO"); |
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[805] | 586 | return int(v.nelements()); |
---|
[105] | 587 | } |
---|
[805] | 588 | return 0; |
---|
| 589 | } |
---|
[455] | 590 | |
---|
[837] | 591 | int Scantable::nif( int scanno ) const |
---|
[805] | 592 | { |
---|
| 593 | if ( scanno < 0 ) { |
---|
| 594 | Int n; |
---|
| 595 | table_.keywordSet().get("nIF",n); |
---|
| 596 | return int(n); |
---|
| 597 | } else { |
---|
| 598 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 599 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 600 | ROTableRow row(t); |
---|
| 601 | const TableRecord& rec = row.get(0); |
---|
| 602 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 603 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 604 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 605 | if ( subt.nrow() == 0 ) return 0; |
---|
| 606 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
[805] | 607 | return int(v.nelements()); |
---|
[2] | 608 | } |
---|
[805] | 609 | return 0; |
---|
| 610 | } |
---|
[321] | 611 | |
---|
[837] | 612 | int Scantable::npol( int scanno ) const |
---|
[805] | 613 | { |
---|
| 614 | if ( scanno < 0 ) { |
---|
| 615 | Int n; |
---|
| 616 | table_.keywordSet().get("nPol",n); |
---|
| 617 | return n; |
---|
| 618 | } else { |
---|
| 619 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 620 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 621 | ROTableRow row(t); |
---|
| 622 | const TableRecord& rec = row.get(0); |
---|
| 623 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 624 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 625 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 626 | if ( subt.nrow() == 0 ) return 0; |
---|
| 627 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
[805] | 628 | return int(v.nelements()); |
---|
[321] | 629 | } |
---|
[805] | 630 | return 0; |
---|
[2] | 631 | } |
---|
[805] | 632 | |
---|
[845] | 633 | int Scantable::ncycle( int scanno ) const |
---|
[206] | 634 | { |
---|
[805] | 635 | if ( scanno < 0 ) { |
---|
[837] | 636 | Block<String> cols(2); |
---|
| 637 | cols[0] = "SCANNO"; |
---|
| 638 | cols[1] = "CYCLENO"; |
---|
| 639 | TableIterator it(table_, cols); |
---|
| 640 | int n = 0; |
---|
| 641 | while ( !it.pastEnd() ) { |
---|
| 642 | ++n; |
---|
[902] | 643 | ++it; |
---|
[837] | 644 | } |
---|
| 645 | return n; |
---|
[805] | 646 | } else { |
---|
[888] | 647 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 648 | ROTableRow row(t); |
---|
| 649 | const TableRecord& rec = row.get(0); |
---|
| 650 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 651 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 652 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
| 653 | if ( subt.nrow() == 0 ) return 0; |
---|
| 654 | return int(subt.nrow()); |
---|
[805] | 655 | } |
---|
| 656 | return 0; |
---|
[18] | 657 | } |
---|
[455] | 658 | |
---|
| 659 | |
---|
[845] | 660 | int Scantable::nrow( int scanno ) const |
---|
[805] | 661 | { |
---|
[845] | 662 | return int(table_.nrow()); |
---|
| 663 | } |
---|
| 664 | |
---|
| 665 | int Scantable::nchan( int ifno ) const |
---|
| 666 | { |
---|
| 667 | if ( ifno < 0 ) { |
---|
[805] | 668 | Int n; |
---|
| 669 | table_.keywordSet().get("nChan",n); |
---|
| 670 | return int(n); |
---|
| 671 | } else { |
---|
[1360] | 672 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
| 673 | // vary with these |
---|
[2244] | 674 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
[888] | 675 | if ( t.nrow() == 0 ) return 0; |
---|
| 676 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
[923] | 677 | return v.shape(0)(0); |
---|
[805] | 678 | } |
---|
| 679 | return 0; |
---|
[18] | 680 | } |
---|
[455] | 681 | |
---|
[1111] | 682 | int Scantable::nscan() const { |
---|
| 683 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
[1148] | 684 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
[1111] | 685 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 686 | return int(nout); |
---|
| 687 | } |
---|
| 688 | |
---|
[923] | 689 | int Scantable::getChannels(int whichrow) const |
---|
| 690 | { |
---|
| 691 | return specCol_.shape(whichrow)(0); |
---|
| 692 | } |
---|
[847] | 693 | |
---|
| 694 | int Scantable::getBeam(int whichrow) const |
---|
| 695 | { |
---|
| 696 | return beamCol_(whichrow); |
---|
| 697 | } |
---|
| 698 | |
---|
[1694] | 699 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
[1111] | 700 | { |
---|
| 701 | Vector<uInt> nos(col.getColumn()); |
---|
[1148] | 702 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 703 | nos.resize(n, True); |
---|
[1111] | 704 | std::vector<uint> stlout; |
---|
| 705 | nos.tovector(stlout); |
---|
| 706 | return stlout; |
---|
| 707 | } |
---|
| 708 | |
---|
[847] | 709 | int Scantable::getIF(int whichrow) const |
---|
| 710 | { |
---|
| 711 | return ifCol_(whichrow); |
---|
| 712 | } |
---|
| 713 | |
---|
| 714 | int Scantable::getPol(int whichrow) const |
---|
| 715 | { |
---|
| 716 | return polCol_(whichrow); |
---|
| 717 | } |
---|
| 718 | |
---|
[805] | 719 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
| 720 | { |
---|
[1947] | 721 | return formatTime(me, showdate, 0); |
---|
| 722 | } |
---|
| 723 | |
---|
| 724 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
| 725 | { |
---|
[805] | 726 | MVTime mvt(me.getValue()); |
---|
| 727 | if (showdate) |
---|
[1947] | 728 | //mvt.setFormat(MVTime::YMD); |
---|
| 729 | mvt.setFormat(MVTime::YMD, prec); |
---|
[805] | 730 | else |
---|
[1947] | 731 | //mvt.setFormat(MVTime::TIME); |
---|
| 732 | mvt.setFormat(MVTime::TIME, prec); |
---|
[805] | 733 | ostringstream oss; |
---|
| 734 | oss << mvt; |
---|
| 735 | return String(oss); |
---|
| 736 | } |
---|
[488] | 737 | |
---|
[805] | 738 | void Scantable::calculateAZEL() |
---|
| 739 | { |
---|
| 740 | MPosition mp = getAntennaPosition(); |
---|
| 741 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 742 | ostringstream oss; |
---|
| 743 | oss << "Computed azimuth/elevation using " << endl |
---|
| 744 | << mp << endl; |
---|
[996] | 745 | for (Int i=0; i<nrow(); ++i) { |
---|
[805] | 746 | MEpoch me = timeCol(i); |
---|
[987] | 747 | MDirection md = getDirection(i); |
---|
[805] | 748 | oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md) |
---|
| 749 | << endl << " => "; |
---|
| 750 | MeasFrame frame(mp, me); |
---|
| 751 | Vector<Double> azel = |
---|
| 752 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
| 753 | frame) |
---|
| 754 | )().getAngle("rad").getValue(); |
---|
[923] | 755 | azCol_.put(i,Float(azel[0])); |
---|
| 756 | elCol_.put(i,Float(azel[1])); |
---|
[805] | 757 | oss << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
| 758 | << azel[1]/C::pi*180.0 << " (deg)" << endl; |
---|
[16] | 759 | } |
---|
[805] | 760 | pushLog(String(oss)); |
---|
| 761 | } |
---|
[89] | 762 | |
---|
[1819] | 763 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 764 | { |
---|
| 765 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
| 766 | Vector<uChar> flgs = flagsCol_(i); |
---|
| 767 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
| 768 | flagsCol_.put(i, flgs); |
---|
| 769 | } |
---|
| 770 | } |
---|
| 771 | |
---|
| 772 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 773 | { |
---|
| 774 | Vector<uChar> flags; |
---|
| 775 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 776 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
| 777 | Vector<Bool> bflag(flags.shape()); |
---|
| 778 | convertArray(bflag, flags); |
---|
| 779 | //bflag = !bflag; |
---|
| 780 | |
---|
| 781 | std::vector<bool> mask; |
---|
| 782 | bflag.tovector(mask); |
---|
| 783 | return mask; |
---|
| 784 | } |
---|
| 785 | |
---|
| 786 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
| 787 | Vector<uChar> flgs) |
---|
| 788 | { |
---|
| 789 | Vector<Float> spcs = specCol_(whichrow); |
---|
| 790 | uInt nchannel = nchan(); |
---|
| 791 | if (spcs.nelements() != nchannel) { |
---|
| 792 | throw(AipsError("Data has incorrect number of channels")); |
---|
| 793 | } |
---|
| 794 | uChar userflag = 1 << 7; |
---|
| 795 | if (unflag) { |
---|
| 796 | userflag = 0 << 7; |
---|
| 797 | } |
---|
| 798 | if (clipoutside) { |
---|
| 799 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 800 | Float spc = spcs(j); |
---|
| 801 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
| 802 | flgs(j) = userflag; |
---|
| 803 | } |
---|
| 804 | } |
---|
| 805 | } else { |
---|
| 806 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 807 | Float spc = spcs(j); |
---|
| 808 | if ((spc < uthres) && (spc > dthres)) { |
---|
| 809 | flgs(j) = userflag; |
---|
| 810 | } |
---|
| 811 | } |
---|
| 812 | } |
---|
| 813 | } |
---|
| 814 | |
---|
[1994] | 815 | |
---|
| 816 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
[1333] | 817 | std::vector<bool>::const_iterator it; |
---|
| 818 | uInt ntrue = 0; |
---|
[1994] | 819 | if (whichrow >= int(table_.nrow()) ) { |
---|
| 820 | throw(AipsError("Invalid row number")); |
---|
| 821 | } |
---|
[1333] | 822 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 823 | if ( *it ) { |
---|
| 824 | ntrue++; |
---|
| 825 | } |
---|
| 826 | } |
---|
[1994] | 827 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
| 828 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
[1000] | 829 | throw(AipsError("Trying to flag whole scantable.")); |
---|
[1994] | 830 | uChar userflag = 1 << 7; |
---|
| 831 | if ( unflag ) { |
---|
| 832 | userflag = 0 << 7; |
---|
| 833 | } |
---|
| 834 | if (whichrow > -1 ) { |
---|
| 835 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
| 836 | } else { |
---|
[1000] | 837 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
[1994] | 838 | applyChanFlag(i, msk, userflag); |
---|
[1000] | 839 | } |
---|
[1994] | 840 | } |
---|
| 841 | } |
---|
| 842 | |
---|
| 843 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
| 844 | { |
---|
| 845 | if (whichrow >= table_.nrow() ) { |
---|
| 846 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
| 847 | } |
---|
| 848 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
| 849 | if ( msk.size() == 0 ) { |
---|
| 850 | flgs = flagval; |
---|
| 851 | flagsCol_.put(whichrow, flgs); |
---|
[1000] | 852 | return; |
---|
| 853 | } |
---|
| 854 | if ( int(msk.size()) != nchan() ) { |
---|
| 855 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
| 856 | } |
---|
[1994] | 857 | if ( flgs.nelements() != msk.size() ) { |
---|
| 858 | throw(AipsError("Mask has incorrect number of channels." |
---|
| 859 | " Probably varying with IF. Please flag per IF")); |
---|
| 860 | } |
---|
| 861 | std::vector<bool>::const_iterator it; |
---|
| 862 | uInt j = 0; |
---|
| 863 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 864 | if ( *it ) { |
---|
| 865 | flgs(j) = flagval; |
---|
[1000] | 866 | } |
---|
[1994] | 867 | ++j; |
---|
[1000] | 868 | } |
---|
[1994] | 869 | flagsCol_.put(whichrow, flgs); |
---|
[865] | 870 | } |
---|
| 871 | |
---|
[1819] | 872 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
| 873 | { |
---|
| 874 | if ( selector_.empty() && (rows.size() == table_.nrow()) ) |
---|
| 875 | throw(AipsError("Trying to flag whole scantable.")); |
---|
| 876 | |
---|
| 877 | uInt rowflag = (unflag ? 0 : 1); |
---|
| 878 | std::vector<uInt>::const_iterator it; |
---|
| 879 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
| 880 | flagrowCol_.put(*it, rowflag); |
---|
| 881 | } |
---|
| 882 | |
---|
[805] | 883 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
| 884 | { |
---|
| 885 | Vector<uChar> flags; |
---|
| 886 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 887 | Vector<Bool> bflag(flags.shape()); |
---|
| 888 | convertArray(bflag, flags); |
---|
| 889 | bflag = !bflag; |
---|
| 890 | std::vector<bool> mask; |
---|
| 891 | bflag.tovector(mask); |
---|
| 892 | return mask; |
---|
| 893 | } |
---|
[89] | 894 | |
---|
[896] | 895 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
[902] | 896 | const std::string& poltype ) const |
---|
[805] | 897 | { |
---|
[905] | 898 | String ptype = poltype; |
---|
| 899 | if (poltype == "" ) ptype = getPolType(); |
---|
[902] | 900 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
| 901 | throw(AipsError("Illegal row number.")); |
---|
[896] | 902 | std::vector<float> out; |
---|
[805] | 903 | Vector<Float> arr; |
---|
[896] | 904 | uInt requestedpol = polCol_(whichrow); |
---|
| 905 | String basetype = getPolType(); |
---|
[905] | 906 | if ( ptype == basetype ) { |
---|
[896] | 907 | specCol_.get(whichrow, arr); |
---|
| 908 | } else { |
---|
[1598] | 909 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
[1586] | 910 | basetype)); |
---|
[1334] | 911 | uInt row = uInt(whichrow); |
---|
| 912 | stpol->setSpectra(getPolMatrix(row)); |
---|
[2047] | 913 | Float fang,fhand; |
---|
[1586] | 914 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
[1334] | 915 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
[1586] | 916 | stpol->setPhaseCorrections(fang, fhand); |
---|
[1334] | 917 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
[896] | 918 | } |
---|
[902] | 919 | if ( arr.nelements() == 0 ) |
---|
| 920 | pushLog("Not enough polarisations present to do the conversion."); |
---|
[805] | 921 | arr.tovector(out); |
---|
| 922 | return out; |
---|
[89] | 923 | } |
---|
[212] | 924 | |
---|
[1360] | 925 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
[884] | 926 | int whichrow ) |
---|
| 927 | { |
---|
| 928 | Vector<Float> spectrum(spec); |
---|
| 929 | Vector<Float> arr; |
---|
| 930 | specCol_.get(whichrow, arr); |
---|
| 931 | if ( spectrum.nelements() != arr.nelements() ) |
---|
[896] | 932 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
[884] | 933 | specCol_.put(whichrow, spectrum); |
---|
| 934 | } |
---|
| 935 | |
---|
| 936 | |
---|
[805] | 937 | String Scantable::generateName() |
---|
[745] | 938 | { |
---|
[805] | 939 | return (File::newUniqueName("./","temp")).baseName(); |
---|
[212] | 940 | } |
---|
| 941 | |
---|
[805] | 942 | const casa::Table& Scantable::table( ) const |
---|
[212] | 943 | { |
---|
[805] | 944 | return table_; |
---|
[212] | 945 | } |
---|
| 946 | |
---|
[805] | 947 | casa::Table& Scantable::table( ) |
---|
[386] | 948 | { |
---|
[805] | 949 | return table_; |
---|
[386] | 950 | } |
---|
| 951 | |
---|
[896] | 952 | std::string Scantable::getPolType() const |
---|
| 953 | { |
---|
| 954 | return table_.keywordSet().asString("POLTYPE"); |
---|
| 955 | } |
---|
| 956 | |
---|
[805] | 957 | void Scantable::unsetSelection() |
---|
[380] | 958 | { |
---|
[805] | 959 | table_ = originalTable_; |
---|
[847] | 960 | attach(); |
---|
[805] | 961 | selector_.reset(); |
---|
[380] | 962 | } |
---|
[386] | 963 | |
---|
[805] | 964 | void Scantable::setSelection( const STSelector& selection ) |
---|
[430] | 965 | { |
---|
[805] | 966 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
| 967 | if ( tab.nrow() == 0 ) { |
---|
| 968 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
| 969 | } |
---|
| 970 | table_ = tab; |
---|
[847] | 971 | attach(); |
---|
[2084] | 972 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
| 973 | // vector<uint> selectedIFs = getIFNos() ; |
---|
| 974 | // Int newnIF = selectedIFs.size() ; |
---|
| 975 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
| 976 | // if ( newnIF != 0 ) { |
---|
| 977 | // Int newnChan = 0 ; |
---|
| 978 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
| 979 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
| 980 | // if ( newnChan > nChan ) |
---|
| 981 | // newnChan = nChan ; |
---|
| 982 | // } |
---|
| 983 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
| 984 | // } |
---|
| 985 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
[805] | 986 | selector_ = selection; |
---|
[430] | 987 | } |
---|
| 988 | |
---|
[2111] | 989 | |
---|
[2163] | 990 | std::string Scantable::headerSummary() |
---|
[447] | 991 | { |
---|
[805] | 992 | // Format header info |
---|
[2111] | 993 | // STHeader sdh; |
---|
| 994 | // sdh = getHeader(); |
---|
| 995 | // sdh.print(); |
---|
[805] | 996 | ostringstream oss; |
---|
| 997 | oss.flags(std::ios_base::left); |
---|
[2290] | 998 | String tmp; |
---|
| 999 | // Project |
---|
| 1000 | table_.keywordSet().get("Project", tmp); |
---|
| 1001 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1002 | // Observation date |
---|
| 1003 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1004 | // Observer |
---|
| 1005 | oss << setw(15) << "Observer:" |
---|
| 1006 | << table_.keywordSet().asString("Observer") << endl; |
---|
| 1007 | // Antenna Name |
---|
| 1008 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1009 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1010 | // Obs type |
---|
| 1011 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1012 | // Records (nrow) |
---|
| 1013 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
| 1014 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1015 | // Beams, IFs, Polarizations, and Channels |
---|
[805] | 1016 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1017 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
[896] | 1018 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1019 | << "(" << getPolType() << ")" << endl |
---|
[1694] | 1020 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[2290] | 1021 | // Flux unit |
---|
| 1022 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1023 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
| 1024 | // Abscissa Unit |
---|
| 1025 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
| 1026 | // Selection |
---|
| 1027 | oss << selector_.print() << endl; |
---|
| 1028 | |
---|
| 1029 | return String(oss); |
---|
| 1030 | } |
---|
| 1031 | |
---|
| 1032 | void Scantable::summary( const std::string& filename ) |
---|
| 1033 | { |
---|
| 1034 | ostringstream oss; |
---|
| 1035 | ofstream ofs; |
---|
| 1036 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1037 | |
---|
| 1038 | if (filename != "") |
---|
| 1039 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1040 | |
---|
| 1041 | oss << endl; |
---|
| 1042 | oss << asap::SEPERATOR << endl; |
---|
| 1043 | oss << " Scan Table Summary" << endl; |
---|
| 1044 | oss << asap::SEPERATOR << endl; |
---|
| 1045 | |
---|
| 1046 | // Format header info |
---|
| 1047 | oss << headerSummary(); |
---|
| 1048 | oss << endl; |
---|
| 1049 | |
---|
| 1050 | if (table_.nrow() <= 0){ |
---|
| 1051 | oss << asap::SEPERATOR << endl; |
---|
| 1052 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
| 1053 | oss << asap::SEPERATOR << endl; |
---|
| 1054 | |
---|
| 1055 | ols << String(oss) << LogIO::POST; |
---|
| 1056 | if (ofs) { |
---|
| 1057 | ofs << String(oss) << flush; |
---|
| 1058 | ofs.close(); |
---|
| 1059 | } |
---|
| 1060 | return; |
---|
| 1061 | } |
---|
| 1062 | |
---|
| 1063 | |
---|
| 1064 | |
---|
| 1065 | // main table |
---|
| 1066 | String dirtype = "Position (" |
---|
| 1067 | + getDirectionRefString() |
---|
| 1068 | + ")"; |
---|
| 1069 | oss.flags(std::ios_base::left); |
---|
| 1070 | oss << setw(5) << "Scan" |
---|
| 1071 | << setw(15) << "Source" |
---|
| 1072 | << setw(35) << "Time range" |
---|
| 1073 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
| 1074 | << setw(7) << "Record" |
---|
| 1075 | << setw(8) << "SrcType" |
---|
| 1076 | << setw(8) << "FreqIDs" |
---|
| 1077 | << setw(7) << "MolIDs" << endl; |
---|
| 1078 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
| 1079 | << setw(23) << dirtype << endl; |
---|
| 1080 | |
---|
| 1081 | oss << asap::SEPERATOR << endl; |
---|
| 1082 | |
---|
| 1083 | // Flush summary and clear up the string |
---|
| 1084 | ols << String(oss) << LogIO::POST; |
---|
| 1085 | if (ofs) ofs << String(oss) << flush; |
---|
| 1086 | oss.str(""); |
---|
| 1087 | oss.clear(); |
---|
| 1088 | |
---|
| 1089 | |
---|
| 1090 | // Get Freq_ID map |
---|
| 1091 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
| 1092 | Int nfid = ftabIds.nrow(); |
---|
| 1093 | if (nfid <= 0){ |
---|
| 1094 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
| 1095 | oss << asap::SEPERATOR << endl; |
---|
| 1096 | |
---|
| 1097 | ols << String(oss) << LogIO::POST; |
---|
| 1098 | if (ofs) { |
---|
| 1099 | ofs << String(oss) << flush; |
---|
| 1100 | ofs.close(); |
---|
| 1101 | } |
---|
| 1102 | return; |
---|
| 1103 | } |
---|
| 1104 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
| 1105 | // the orders are identical to ID in FREQ subtable |
---|
| 1106 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
| 1107 | Vector<Int> fIdchans(nfid,-1); |
---|
| 1108 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
| 1109 | for (Int i=0; i < nfid; i++){ |
---|
| 1110 | // fidMap[freqId] returns row number in FREQ subtable |
---|
| 1111 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
| 1112 | ifNos[i] = Vector<uInt>(); |
---|
| 1113 | polNos[i] = Vector<uInt>(); |
---|
| 1114 | } |
---|
| 1115 | |
---|
| 1116 | TableIterator iter(table_, "SCANNO"); |
---|
| 1117 | |
---|
| 1118 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
| 1119 | Vector<uInt> freqids; |
---|
| 1120 | Vector<uInt> molids; |
---|
| 1121 | Vector<uInt> beamids(1,0); |
---|
| 1122 | Vector<MDirection> beamDirs; |
---|
| 1123 | Vector<Int> stypeids(1,0); |
---|
| 1124 | Vector<String> stypestrs; |
---|
| 1125 | Int nfreq(1); |
---|
| 1126 | Int nmol(1); |
---|
| 1127 | uInt nbeam(1); |
---|
| 1128 | uInt nstype(1); |
---|
| 1129 | |
---|
| 1130 | Double btime(0.0), etime(0.0); |
---|
| 1131 | Double meanIntTim(0.0); |
---|
| 1132 | |
---|
| 1133 | uInt currFreqId(0), ftabRow(0); |
---|
| 1134 | Int iflen(0), pollen(0); |
---|
| 1135 | |
---|
| 1136 | while (!iter.pastEnd()) { |
---|
| 1137 | Table subt = iter.table(); |
---|
| 1138 | uInt snrow = subt.nrow(); |
---|
| 1139 | ROTableRow row(subt); |
---|
| 1140 | const TableRecord& rec = row.get(0); |
---|
| 1141 | |
---|
| 1142 | // relevant columns |
---|
| 1143 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
| 1144 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
| 1145 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
| 1146 | |
---|
| 1147 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
| 1148 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
| 1149 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
| 1150 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
| 1151 | |
---|
| 1152 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
| 1153 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
| 1154 | |
---|
| 1155 | |
---|
| 1156 | // Times |
---|
| 1157 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
| 1158 | minMax(btime, etime, mjdCol.getColumn()); |
---|
| 1159 | etime += meanIntTim/C::day; |
---|
| 1160 | |
---|
| 1161 | // MOLECULE_ID and FREQ_ID |
---|
| 1162 | molids = getNumbers(molIdCol); |
---|
| 1163 | molids.shape(nmol); |
---|
| 1164 | |
---|
| 1165 | freqids = getNumbers(freqIdCol); |
---|
| 1166 | freqids.shape(nfreq); |
---|
| 1167 | |
---|
| 1168 | // Add first beamid, and srcNames |
---|
| 1169 | beamids.resize(1,False); |
---|
| 1170 | beamDirs.resize(1,False); |
---|
| 1171 | beamids(0)=beamCol(0); |
---|
| 1172 | beamDirs(0)=dirCol(0); |
---|
| 1173 | nbeam = 1; |
---|
| 1174 | |
---|
| 1175 | stypeids.resize(1,False); |
---|
| 1176 | stypeids(0)=stypeCol(0); |
---|
| 1177 | nstype = 1; |
---|
| 1178 | |
---|
| 1179 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1180 | currFreqId=freqIdCol(0); |
---|
| 1181 | ftabRow = fidMap[currFreqId]; |
---|
| 1182 | // Assumes an identical number of channels per FREQ_ID |
---|
| 1183 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1184 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1185 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
| 1186 | } |
---|
| 1187 | // Should keep ifNos and polNos form the previous SCANNO |
---|
| 1188 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
| 1189 | ifNos[ftabRow].shape(iflen); |
---|
| 1190 | iflen++; |
---|
| 1191 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1192 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
| 1193 | } |
---|
| 1194 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
| 1195 | polNos[ftabRow].shape(pollen); |
---|
| 1196 | pollen++; |
---|
| 1197 | polNos[ftabRow].resize(pollen,True); |
---|
| 1198 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
| 1199 | } |
---|
| 1200 | |
---|
| 1201 | for (uInt i=1; i < snrow; i++){ |
---|
| 1202 | // Need to list BEAMNO and DIRECTION in the same order |
---|
| 1203 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
| 1204 | nbeam++; |
---|
| 1205 | beamids.resize(nbeam,True); |
---|
| 1206 | beamids(nbeam-1)=beamCol(i); |
---|
| 1207 | beamDirs.resize(nbeam,True); |
---|
| 1208 | beamDirs(nbeam-1)=dirCol(i); |
---|
| 1209 | } |
---|
| 1210 | |
---|
| 1211 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
| 1212 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
| 1213 | nstype++; |
---|
| 1214 | stypeids.resize(nstype,True); |
---|
| 1215 | stypeids(nstype-1)=stypeCol(i); |
---|
| 1216 | } |
---|
| 1217 | |
---|
| 1218 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1219 | currFreqId=freqIdCol(i); |
---|
| 1220 | ftabRow = fidMap[currFreqId]; |
---|
| 1221 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1222 | const TableRecord& rec = row.get(i); |
---|
| 1223 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1224 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
| 1225 | } |
---|
| 1226 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
| 1227 | ifNos[ftabRow].shape(iflen); |
---|
| 1228 | iflen++; |
---|
| 1229 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1230 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
| 1231 | } |
---|
| 1232 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
| 1233 | polNos[ftabRow].shape(pollen); |
---|
| 1234 | pollen++; |
---|
| 1235 | polNos[ftabRow].resize(pollen,True); |
---|
| 1236 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
| 1237 | } |
---|
| 1238 | } // end of row iteration |
---|
| 1239 | |
---|
| 1240 | stypestrs.resize(nstype,False); |
---|
| 1241 | for (uInt j=0; j < nstype; j++) |
---|
| 1242 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
| 1243 | |
---|
| 1244 | // Format Scan summary |
---|
| 1245 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1246 | << std::left << setw(1) << "" |
---|
| 1247 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1248 | << setw(21) << MVTime(btime).string(MVTime::YMD,7) |
---|
| 1249 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7) |
---|
| 1250 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
| 1251 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
| 1252 | << std::left << stypestrs << setw(1) << "" |
---|
| 1253 | << freqids << setw(1) << "" |
---|
| 1254 | << molids << endl; |
---|
| 1255 | // Format Beam summary |
---|
| 1256 | for (uInt j=0; j < nbeam; j++) { |
---|
| 1257 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
| 1258 | << formatDirection(beamDirs(j)) << endl; |
---|
| 1259 | } |
---|
| 1260 | // Flush summary every scan and clear up the string |
---|
| 1261 | ols << String(oss) << LogIO::POST; |
---|
| 1262 | if (ofs) ofs << String(oss) << flush; |
---|
| 1263 | oss.str(""); |
---|
| 1264 | oss.clear(); |
---|
| 1265 | |
---|
| 1266 | ++iter; |
---|
| 1267 | } // end of scan iteration |
---|
| 1268 | oss << asap::SEPERATOR << endl; |
---|
| 1269 | |
---|
| 1270 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
| 1271 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
| 1272 | oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
| 1273 | << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
| 1274 | << setw(8) << "Frame" |
---|
| 1275 | << setw(16) << "RefVal" |
---|
| 1276 | << setw(7) << "RefPix" |
---|
| 1277 | << setw(15) << "Increment" |
---|
| 1278 | << setw(9) << "Channels" |
---|
| 1279 | << setw(6) << "POLNOs" << endl; |
---|
| 1280 | Int tmplen; |
---|
| 1281 | for (Int i=0; i < nfid; i++){ |
---|
| 1282 | // List row=i of FREQUENCIES subtable |
---|
| 1283 | ifNos[i].shape(tmplen); |
---|
| 1284 | if (tmplen == 1) { |
---|
| 1285 | oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
| 1286 | << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
| 1287 | << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
| 1288 | << setw(2) << "" |
---|
| 1289 | << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
| 1290 | << std::left << polNos[i] << endl; |
---|
| 1291 | } else if (tmplen > 0 ) { |
---|
| 1292 | // You shouldn't come here |
---|
| 1293 | oss << std::left |
---|
| 1294 | << "Multiple IFNOs in FREQ_ID = " << ftabIds(i) |
---|
| 1295 | << " !!!" << endl; |
---|
| 1296 | } |
---|
| 1297 | } |
---|
| 1298 | oss << asap::SEPERATOR << endl; |
---|
| 1299 | |
---|
| 1300 | // List MOLECULES Table (currently lists all rows) |
---|
| 1301 | oss << "MOLECULES: " << endl; |
---|
| 1302 | if (molecules().nrow() <= 0) { |
---|
| 1303 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
| 1304 | } else { |
---|
| 1305 | ROTableRow row(molecules().table()); |
---|
| 1306 | oss << std::right << setw(5) << "ID" |
---|
| 1307 | << std::left << setw(3) << "" |
---|
| 1308 | << setw(18) << "RestFreq" |
---|
| 1309 | << setw(15) << "Name" << endl; |
---|
| 1310 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
| 1311 | const TableRecord& rec=row.get(i); |
---|
| 1312 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
| 1313 | << std::left << setw(3) << "" |
---|
| 1314 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
| 1315 | << rec.asArrayString("NAME") << endl; |
---|
| 1316 | } |
---|
| 1317 | } |
---|
| 1318 | oss << asap::SEPERATOR << endl; |
---|
| 1319 | ols << String(oss) << LogIO::POST; |
---|
| 1320 | if (ofs) { |
---|
| 1321 | ofs << String(oss) << flush; |
---|
| 1322 | ofs.close(); |
---|
| 1323 | } |
---|
| 1324 | // return String(oss); |
---|
| 1325 | } |
---|
| 1326 | |
---|
| 1327 | |
---|
| 1328 | std::string Scantable::oldheaderSummary() |
---|
| 1329 | { |
---|
| 1330 | // Format header info |
---|
| 1331 | // STHeader sdh; |
---|
| 1332 | // sdh = getHeader(); |
---|
| 1333 | // sdh.print(); |
---|
| 1334 | ostringstream oss; |
---|
| 1335 | oss.flags(std::ios_base::left); |
---|
| 1336 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1337 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
| 1338 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1339 | << "(" << getPolType() << ")" << endl |
---|
| 1340 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[805] | 1341 | String tmp; |
---|
[860] | 1342 | oss << setw(15) << "Observer:" |
---|
| 1343 | << table_.keywordSet().asString("Observer") << endl; |
---|
[805] | 1344 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1345 | table_.keywordSet().get("Project", tmp); |
---|
| 1346 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1347 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1348 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1349 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1350 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1351 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1352 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
[1819] | 1353 | int nid = moleculeTable_.nrow(); |
---|
| 1354 | Bool firstline = True; |
---|
[805] | 1355 | oss << setw(15) << "Rest Freqs:"; |
---|
[1819] | 1356 | for (int i=0; i<nid; i++) { |
---|
[2244] | 1357 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
[1819] | 1358 | if (t.nrow() > 0) { |
---|
| 1359 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
| 1360 | if (vec.nelements() > 0) { |
---|
| 1361 | if (firstline) { |
---|
| 1362 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1363 | firstline=False; |
---|
| 1364 | } |
---|
| 1365 | else{ |
---|
| 1366 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1367 | } |
---|
| 1368 | } else { |
---|
| 1369 | oss << "none" << endl; |
---|
| 1370 | } |
---|
| 1371 | } |
---|
[805] | 1372 | } |
---|
[941] | 1373 | |
---|
| 1374 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
[805] | 1375 | oss << selector_.print() << endl; |
---|
[2111] | 1376 | return String(oss); |
---|
| 1377 | } |
---|
| 1378 | |
---|
[2286] | 1379 | //std::string Scantable::summary( const std::string& filename ) |
---|
[2290] | 1380 | void Scantable::oldsummary( const std::string& filename ) |
---|
[2111] | 1381 | { |
---|
| 1382 | ostringstream oss; |
---|
[2286] | 1383 | ofstream ofs; |
---|
| 1384 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1385 | |
---|
| 1386 | if (filename != "") |
---|
| 1387 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1388 | |
---|
[805] | 1389 | oss << endl; |
---|
[2111] | 1390 | oss << asap::SEPERATOR << endl; |
---|
| 1391 | oss << " Scan Table Summary" << endl; |
---|
| 1392 | oss << asap::SEPERATOR << endl; |
---|
| 1393 | |
---|
| 1394 | // Format header info |
---|
[2290] | 1395 | oss << oldheaderSummary(); |
---|
[2111] | 1396 | oss << endl; |
---|
| 1397 | |
---|
[805] | 1398 | // main table |
---|
| 1399 | String dirtype = "Position (" |
---|
[987] | 1400 | + getDirectionRefString() |
---|
[805] | 1401 | + ")"; |
---|
[2111] | 1402 | oss.flags(std::ios_base::left); |
---|
[941] | 1403 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
[2005] | 1404 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
| 1405 | << setw(15) << "Source Type" << endl; |
---|
[941] | 1406 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
[1694] | 1407 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
[805] | 1408 | << setw(8) << "Frame" << setw(16) |
---|
[1694] | 1409 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
| 1410 | << setw(7) << "Channels" |
---|
| 1411 | << endl; |
---|
[805] | 1412 | oss << asap::SEPERATOR << endl; |
---|
[2286] | 1413 | |
---|
| 1414 | // Flush summary and clear up the string |
---|
| 1415 | ols << String(oss) << LogIO::POST; |
---|
| 1416 | if (ofs) ofs << String(oss) << flush; |
---|
| 1417 | oss.str(""); |
---|
| 1418 | oss.clear(); |
---|
| 1419 | |
---|
[805] | 1420 | TableIterator iter(table_, "SCANNO"); |
---|
| 1421 | while (!iter.pastEnd()) { |
---|
| 1422 | Table subt = iter.table(); |
---|
| 1423 | ROTableRow row(subt); |
---|
| 1424 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
| 1425 | const TableRecord& rec = row.get(0); |
---|
| 1426 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1427 | << std::left << setw(1) << "" |
---|
| 1428 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1429 | << setw(10) << formatTime(timeCol(0), false); |
---|
| 1430 | // count the cycles in the scan |
---|
| 1431 | TableIterator cyciter(subt, "CYCLENO"); |
---|
| 1432 | int nint = 0; |
---|
| 1433 | while (!cyciter.pastEnd()) { |
---|
| 1434 | ++nint; |
---|
| 1435 | ++cyciter; |
---|
| 1436 | } |
---|
| 1437 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
[2005] | 1438 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
| 1439 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
[447] | 1440 | |
---|
[805] | 1441 | TableIterator biter(subt, "BEAMNO"); |
---|
| 1442 | while (!biter.pastEnd()) { |
---|
| 1443 | Table bsubt = biter.table(); |
---|
| 1444 | ROTableRow brow(bsubt); |
---|
| 1445 | const TableRecord& brec = brow.get(0); |
---|
[1000] | 1446 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
[941] | 1447 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
[987] | 1448 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
[805] | 1449 | TableIterator iiter(bsubt, "IFNO"); |
---|
| 1450 | while (!iiter.pastEnd()) { |
---|
| 1451 | Table isubt = iiter.table(); |
---|
| 1452 | ROTableRow irow(isubt); |
---|
| 1453 | const TableRecord& irec = irow.get(0); |
---|
[1694] | 1454 | oss << setw(9) << ""; |
---|
[941] | 1455 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
[1694] | 1456 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
| 1457 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
[1375] | 1458 | << endl; |
---|
[447] | 1459 | |
---|
[805] | 1460 | ++iiter; |
---|
| 1461 | } |
---|
| 1462 | ++biter; |
---|
| 1463 | } |
---|
[2286] | 1464 | // Flush summary every scan and clear up the string |
---|
| 1465 | ols << String(oss) << LogIO::POST; |
---|
| 1466 | if (ofs) ofs << String(oss) << flush; |
---|
| 1467 | oss.str(""); |
---|
| 1468 | oss.clear(); |
---|
| 1469 | |
---|
[805] | 1470 | ++iter; |
---|
[447] | 1471 | } |
---|
[2286] | 1472 | oss << asap::SEPERATOR << endl; |
---|
| 1473 | ols << String(oss) << LogIO::POST; |
---|
| 1474 | if (ofs) { |
---|
[2290] | 1475 | ofs << String(oss) << flush; |
---|
[2286] | 1476 | ofs.close(); |
---|
| 1477 | } |
---|
| 1478 | // return String(oss); |
---|
[447] | 1479 | } |
---|
| 1480 | |
---|
[1947] | 1481 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
| 1482 | // { |
---|
| 1483 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 1484 | // MEpoch me; |
---|
| 1485 | // if (whichrow > -1) { |
---|
| 1486 | // me = timeCol(uInt(whichrow)); |
---|
| 1487 | // } else { |
---|
| 1488 | // Double tm; |
---|
| 1489 | // table_.keywordSet().get("UTC",tm); |
---|
| 1490 | // me = MEpoch(MVEpoch(tm)); |
---|
| 1491 | // } |
---|
| 1492 | // return formatTime(me, showdate); |
---|
| 1493 | // } |
---|
| 1494 | |
---|
| 1495 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
[777] | 1496 | { |
---|
[805] | 1497 | MEpoch me; |
---|
[1947] | 1498 | me = getEpoch(whichrow); |
---|
| 1499 | return formatTime(me, showdate, prec); |
---|
[777] | 1500 | } |
---|
[805] | 1501 | |
---|
[1411] | 1502 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
| 1503 | { |
---|
| 1504 | if (whichrow > -1) { |
---|
| 1505 | return timeCol_(uInt(whichrow)); |
---|
| 1506 | } else { |
---|
| 1507 | Double tm; |
---|
| 1508 | table_.keywordSet().get("UTC",tm); |
---|
[1598] | 1509 | return MEpoch(MVEpoch(tm)); |
---|
[1411] | 1510 | } |
---|
| 1511 | } |
---|
| 1512 | |
---|
[1068] | 1513 | std::string Scantable::getDirectionString(int whichrow) const |
---|
| 1514 | { |
---|
| 1515 | return formatDirection(getDirection(uInt(whichrow))); |
---|
| 1516 | } |
---|
| 1517 | |
---|
[1598] | 1518 | |
---|
| 1519 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
| 1520 | const MPosition& mp = getAntennaPosition(); |
---|
| 1521 | const MDirection& md = getDirection(whichrow); |
---|
| 1522 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1523 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
| 1524 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[1598] | 1525 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
| 1526 | mfreqidCol_(whichrow)); |
---|
| 1527 | } |
---|
| 1528 | |
---|
[1360] | 1529 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
[865] | 1530 | { |
---|
[1507] | 1531 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
[865] | 1532 | std::vector<double> stlout; |
---|
| 1533 | int nchan = specCol_(whichrow).nelements(); |
---|
| 1534 | String us = freqTable_.getUnitString(); |
---|
| 1535 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
| 1536 | for (int i=0; i<nchan; ++i) { |
---|
| 1537 | stlout.push_back(double(i)); |
---|
| 1538 | } |
---|
| 1539 | return stlout; |
---|
| 1540 | } |
---|
[1598] | 1541 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
[865] | 1542 | Vector<Double> pixel(nchan); |
---|
| 1543 | Vector<Double> world; |
---|
| 1544 | indgen(pixel); |
---|
| 1545 | if ( Unit(us) == Unit("Hz") ) { |
---|
| 1546 | for ( int i=0; i < nchan; ++i) { |
---|
| 1547 | Double world; |
---|
| 1548 | spc.toWorld(world, pixel[i]); |
---|
| 1549 | stlout.push_back(double(world)); |
---|
| 1550 | } |
---|
| 1551 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
| 1552 | Vector<Double> world; |
---|
| 1553 | spc.pixelToVelocity(world, pixel); |
---|
| 1554 | world.tovector(stlout); |
---|
| 1555 | } |
---|
| 1556 | return stlout; |
---|
| 1557 | } |
---|
[1360] | 1558 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
[987] | 1559 | { |
---|
| 1560 | MDirection::Types mdt; |
---|
| 1561 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
| 1562 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1563 | } |
---|
| 1564 | if ( refstr == "" ) { |
---|
| 1565 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1566 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
| 1567 | } else { |
---|
| 1568 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
| 1569 | } |
---|
| 1570 | } |
---|
[865] | 1571 | |
---|
[1360] | 1572 | std::string Scantable::getDirectionRefString( ) const |
---|
[987] | 1573 | { |
---|
| 1574 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1575 | } |
---|
| 1576 | |
---|
| 1577 | MDirection Scantable::getDirection(int whichrow ) const |
---|
| 1578 | { |
---|
| 1579 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1580 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1581 | if ( usertype != type ) { |
---|
| 1582 | MDirection::Types mdt; |
---|
| 1583 | if (!MDirection::getType(mdt, usertype)) { |
---|
| 1584 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1585 | } |
---|
| 1586 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
| 1587 | } else { |
---|
| 1588 | return dirCol_(uInt(whichrow)); |
---|
| 1589 | } |
---|
| 1590 | } |
---|
| 1591 | |
---|
[847] | 1592 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
| 1593 | { |
---|
[996] | 1594 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
[847] | 1595 | const MPosition& mp = getAntennaPosition(); |
---|
[987] | 1596 | const MDirection& md = getDirection(whichrow); |
---|
[847] | 1597 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1598 | //const Double& rf = mmolidCol_(whichrow); |
---|
| 1599 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[847] | 1600 | SpectralCoordinate spc = |
---|
| 1601 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
| 1602 | |
---|
| 1603 | String s = "Channel"; |
---|
| 1604 | Unit u = Unit(freqTable_.getUnitString()); |
---|
| 1605 | if (u == Unit("km/s")) { |
---|
[1170] | 1606 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
[847] | 1607 | } else if (u == Unit("Hz")) { |
---|
| 1608 | Vector<String> wau(1);wau = u.getName(); |
---|
| 1609 | spc.setWorldAxisUnits(wau); |
---|
[1170] | 1610 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
[847] | 1611 | } |
---|
| 1612 | return s; |
---|
| 1613 | |
---|
| 1614 | } |
---|
| 1615 | |
---|
[1819] | 1616 | /** |
---|
| 1617 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
[1170] | 1618 | const std::string& unit ) |
---|
[1819] | 1619 | **/ |
---|
| 1620 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
| 1621 | const std::string& unit ) |
---|
| 1622 | |
---|
[847] | 1623 | { |
---|
[923] | 1624 | ///@todo lookup in line table to fill in name and formattedname |
---|
[847] | 1625 | Unit u(unit); |
---|
[1819] | 1626 | //Quantum<Double> urf(rf, u); |
---|
| 1627 | Quantum<Vector<Double> >urf(rf, u); |
---|
| 1628 | Vector<String> formattedname(0); |
---|
| 1629 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
| 1630 | |
---|
| 1631 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
| 1632 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
[847] | 1633 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
| 1634 | tabvec = id; |
---|
| 1635 | } |
---|
| 1636 | |
---|
[1819] | 1637 | /** |
---|
| 1638 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
[847] | 1639 | { |
---|
| 1640 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
| 1641 | ///@todo implement |
---|
| 1642 | } |
---|
[1819] | 1643 | **/ |
---|
[2012] | 1644 | |
---|
[1819] | 1645 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
| 1646 | { |
---|
[2163] | 1647 | (void) name; // suppress unused warning |
---|
[1819] | 1648 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
| 1649 | ///@todo implement |
---|
| 1650 | } |
---|
[847] | 1651 | |
---|
[1360] | 1652 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
[852] | 1653 | { |
---|
| 1654 | std::vector<unsigned int> stlout; |
---|
| 1655 | Vector<uInt> vec = table_.rowNumbers(); |
---|
| 1656 | vec.tovector(stlout); |
---|
| 1657 | return stlout; |
---|
| 1658 | } |
---|
| 1659 | |
---|
[865] | 1660 | |
---|
[1360] | 1661 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
[896] | 1662 | { |
---|
| 1663 | ROTableRow row(table_); |
---|
| 1664 | const TableRecord& rec = row.get(whichrow); |
---|
| 1665 | Table t = |
---|
| 1666 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
| 1667 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 1668 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 1669 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 1670 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 1671 | return speccol.getColumn(); |
---|
| 1672 | } |
---|
[865] | 1673 | |
---|
[1360] | 1674 | std::vector< std::string > Scantable::columnNames( ) const |
---|
[902] | 1675 | { |
---|
| 1676 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
| 1677 | return mathutil::tovectorstring(vec); |
---|
| 1678 | } |
---|
[896] | 1679 | |
---|
[1360] | 1680 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
[915] | 1681 | { |
---|
| 1682 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
[972] | 1683 | } |
---|
[915] | 1684 | |
---|
[1360] | 1685 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
[972] | 1686 | { |
---|
[1819] | 1687 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
| 1688 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
| 1689 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
[972] | 1690 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
| 1691 | mfitidCol_.put(uInt(row), id); |
---|
| 1692 | } |
---|
[915] | 1693 | |
---|
[1360] | 1694 | void Scantable::shift(int npix) |
---|
| 1695 | { |
---|
| 1696 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
| 1697 | genSort( fids, Sort::Ascending, |
---|
| 1698 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 1699 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
[1567] | 1700 | frequencies().shiftRefPix(npix, fids[i]); |
---|
[1360] | 1701 | } |
---|
| 1702 | } |
---|
[987] | 1703 | |
---|
[1819] | 1704 | String Scantable::getAntennaName() const |
---|
[1391] | 1705 | { |
---|
| 1706 | String out; |
---|
| 1707 | table_.keywordSet().get("AntennaName", out); |
---|
[1987] | 1708 | String::size_type pos1 = out.find("@") ; |
---|
| 1709 | String::size_type pos2 = out.find("//") ; |
---|
| 1710 | if ( pos2 != String::npos ) |
---|
[2036] | 1711 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
[1987] | 1712 | else if ( pos1 != String::npos ) |
---|
| 1713 | out = out.substr(0,pos1) ; |
---|
[1391] | 1714 | return out; |
---|
[987] | 1715 | } |
---|
[1391] | 1716 | |
---|
[1730] | 1717 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
[1391] | 1718 | { |
---|
| 1719 | String tbpath; |
---|
| 1720 | int ret = 0; |
---|
| 1721 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
| 1722 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
| 1723 | Table t(tbpath,Table::Old); |
---|
| 1724 | // check each scan if other scan of the pair exist |
---|
| 1725 | int nscan = scanlist.size(); |
---|
| 1726 | for (int i = 0; i < nscan; i++) { |
---|
| 1727 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
| 1728 | if (subt.nrow()==0) { |
---|
[1819] | 1729 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
| 1730 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1731 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1732 | ret = 1; |
---|
| 1733 | break; |
---|
| 1734 | } |
---|
| 1735 | ROTableRow row(subt); |
---|
| 1736 | const TableRecord& rec = row.get(0); |
---|
| 1737 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
| 1738 | int laston1 = rec.asuInt("LASTON"); |
---|
| 1739 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
| 1740 | if ( i < nscan-1 ) { |
---|
| 1741 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
| 1742 | if ( subt2.nrow() == 0) { |
---|
[1819] | 1743 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1744 | |
---|
| 1745 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
| 1746 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1747 | ret = 1; |
---|
| 1748 | break; |
---|
| 1749 | } |
---|
| 1750 | ROTableRow row2(subt2); |
---|
| 1751 | const TableRecord& rec2 = row2.get(0); |
---|
| 1752 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
| 1753 | int laston2 = rec2.asuInt("LASTON"); |
---|
| 1754 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
| 1755 | if (laston1 == laston2) { |
---|
[1819] | 1756 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1757 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1758 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1759 | i +=1; |
---|
| 1760 | } |
---|
| 1761 | else { |
---|
[1819] | 1762 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1763 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1764 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1765 | } |
---|
| 1766 | } |
---|
| 1767 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
| 1768 | if (laston1 == laston2) { |
---|
[1819] | 1769 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1770 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
| 1771 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
[1391] | 1772 | ret = 1; |
---|
| 1773 | break; |
---|
| 1774 | } |
---|
| 1775 | } |
---|
| 1776 | else { |
---|
[1819] | 1777 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1778 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
| 1779 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
[1391] | 1780 | ret = 1; |
---|
| 1781 | break; |
---|
| 1782 | } |
---|
| 1783 | } |
---|
| 1784 | } |
---|
| 1785 | else { |
---|
[1819] | 1786 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1787 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
| 1788 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
[1391] | 1789 | } |
---|
| 1790 | //if ( i >= nscan ) break; |
---|
| 1791 | } |
---|
| 1792 | } |
---|
| 1793 | else { |
---|
[1819] | 1794 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1795 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
| 1796 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
[1391] | 1797 | ret = 1; |
---|
| 1798 | } |
---|
| 1799 | return ret; |
---|
| 1800 | } |
---|
| 1801 | |
---|
[1730] | 1802 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
[1391] | 1803 | { |
---|
| 1804 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
| 1805 | std::vector<double> dir; |
---|
| 1806 | Dir.tovector(dir); |
---|
| 1807 | return dir; |
---|
| 1808 | } |
---|
| 1809 | |
---|
[1819] | 1810 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
| 1811 | throw( casa::AipsError ) |
---|
| 1812 | { |
---|
| 1813 | // assumed that all rows have same nChan |
---|
| 1814 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1815 | int nChan = arr.nelements() ; |
---|
| 1816 | |
---|
| 1817 | // if nmin < 0 or nmax < 0, nothing to do |
---|
| 1818 | if ( nmin < 0 ) { |
---|
| 1819 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1820 | } |
---|
| 1821 | if ( nmax < 0 ) { |
---|
| 1822 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1823 | } |
---|
| 1824 | |
---|
| 1825 | // if nmin > nmax, exchange values |
---|
| 1826 | if ( nmin > nmax ) { |
---|
| 1827 | int tmp = nmax ; |
---|
| 1828 | nmax = nmin ; |
---|
| 1829 | nmin = tmp ; |
---|
| 1830 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1831 | os << "Swap values. Applied range is [" |
---|
| 1832 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
| 1833 | } |
---|
| 1834 | |
---|
| 1835 | // if nmin exceeds nChan, nothing to do |
---|
| 1836 | if ( nmin >= nChan ) { |
---|
| 1837 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
| 1838 | } |
---|
| 1839 | |
---|
| 1840 | // if nmax exceeds nChan, reset nmax to nChan |
---|
| 1841 | if ( nmax >= nChan ) { |
---|
| 1842 | if ( nmin == 0 ) { |
---|
| 1843 | // nothing to do |
---|
| 1844 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1845 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
| 1846 | return ; |
---|
| 1847 | } |
---|
| 1848 | else { |
---|
| 1849 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1850 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
| 1851 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
| 1852 | nmax = nChan - 1 ; |
---|
| 1853 | } |
---|
| 1854 | } |
---|
| 1855 | |
---|
| 1856 | // reshape specCol_ and flagCol_ |
---|
| 1857 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1858 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
| 1859 | } |
---|
| 1860 | |
---|
| 1861 | // update FREQUENCIES subtable |
---|
| 1862 | Double refpix ; |
---|
| 1863 | Double refval ; |
---|
| 1864 | Double increment ; |
---|
| 1865 | int freqnrow = freqTable_.table().nrow() ; |
---|
| 1866 | Vector<uInt> oldId( freqnrow ) ; |
---|
| 1867 | Vector<uInt> newId( freqnrow ) ; |
---|
| 1868 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
| 1869 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
| 1870 | /*** |
---|
| 1871 | * need to shift refpix to nmin |
---|
| 1872 | * note that channel nmin in old index will be channel 0 in new one |
---|
| 1873 | ***/ |
---|
| 1874 | refval = refval - ( refpix - nmin ) * increment ; |
---|
| 1875 | refpix = 0 ; |
---|
| 1876 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
| 1877 | } |
---|
| 1878 | |
---|
| 1879 | // update nchan |
---|
| 1880 | int newsize = nmax - nmin + 1 ; |
---|
| 1881 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
| 1882 | |
---|
| 1883 | // update bandwidth |
---|
| 1884 | // assumed all spectra in the scantable have same bandwidth |
---|
| 1885 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
| 1886 | |
---|
| 1887 | return ; |
---|
| 1888 | } |
---|
| 1889 | |
---|
| 1890 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
| 1891 | { |
---|
| 1892 | // reshape specCol_ and flagCol_ |
---|
| 1893 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1894 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 1895 | uInt newsize = nmax - nmin + 1 ; |
---|
| 1896 | specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ; |
---|
| 1897 | flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ; |
---|
| 1898 | |
---|
| 1899 | return ; |
---|
| 1900 | } |
---|
| 1901 | |
---|
| 1902 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
| 1903 | { |
---|
| 1904 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1905 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
| 1906 | // assumed that all rows have same nChan |
---|
| 1907 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1908 | int oldsize = arr.nelements() ; |
---|
| 1909 | |
---|
| 1910 | // if oldsize == nChan, nothing to do |
---|
| 1911 | if ( oldsize == nChan ) { |
---|
| 1912 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
| 1913 | return ; |
---|
| 1914 | } |
---|
| 1915 | |
---|
| 1916 | // if oldChan < nChan, unphysical operation |
---|
| 1917 | if ( oldsize < nChan ) { |
---|
| 1918 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
| 1919 | return ; |
---|
| 1920 | } |
---|
| 1921 | |
---|
| 1922 | // change channel number for specCol_ and flagCol_ |
---|
| 1923 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 1924 | Vector<uChar> newflag( nChan, false ) ; |
---|
| 1925 | vector<string> coordinfo = getCoordInfo() ; |
---|
| 1926 | string oldinfo = coordinfo[0] ; |
---|
| 1927 | coordinfo[0] = "Hz" ; |
---|
| 1928 | setCoordInfo( coordinfo ) ; |
---|
| 1929 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1930 | regridChannel( nChan, dnu, irow ) ; |
---|
| 1931 | } |
---|
| 1932 | coordinfo[0] = oldinfo ; |
---|
| 1933 | setCoordInfo( coordinfo ) ; |
---|
| 1934 | |
---|
| 1935 | |
---|
| 1936 | // NOTE: this method does not update metadata such as |
---|
| 1937 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
| 1938 | |
---|
| 1939 | return ; |
---|
| 1940 | } |
---|
| 1941 | |
---|
| 1942 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
| 1943 | { |
---|
| 1944 | // logging |
---|
| 1945 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
| 1946 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
| 1947 | |
---|
| 1948 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1949 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 1950 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 1951 | Vector<uChar> newflag( nChan, false ) ; |
---|
| 1952 | |
---|
| 1953 | // regrid |
---|
| 1954 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1955 | int oldsize = abcissa.size() ; |
---|
| 1956 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
| 1957 | //int refChan = 0 ; |
---|
| 1958 | //double frac = 0.0 ; |
---|
| 1959 | //double wedge = 0.0 ; |
---|
| 1960 | //double pile = 0.0 ; |
---|
| 1961 | int ichan = 0 ; |
---|
| 1962 | double wsum = 0.0 ; |
---|
| 1963 | Vector<Float> zi( nChan+1 ) ; |
---|
| 1964 | Vector<Float> yi( oldsize + 1 ) ; |
---|
[2133] | 1965 | zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 1966 | zi[1] = zi[1] + dnu ; |
---|
[1819] | 1967 | for ( int ii = 2 ; ii < nChan ; ii++ ) |
---|
[2133] | 1968 | zi[ii] = zi[0] + dnu * ii ; |
---|
| 1969 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
[1819] | 1970 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 1971 | yi[1] = abcissa[1] + 0.5 * olddnu ; |
---|
| 1972 | for ( int ii = 2 ; ii < oldsize ; ii++ ) |
---|
| 1973 | yi[ii] = abcissa[ii-1] + olddnu ; |
---|
| 1974 | yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ; |
---|
| 1975 | if ( dnu > 0.0 ) { |
---|
| 1976 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 1977 | double zl = zi[ii] ; |
---|
| 1978 | double zr = zi[ii+1] ; |
---|
| 1979 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 1980 | double yl = yi[j] ; |
---|
| 1981 | double yr = yi[j+1] ; |
---|
| 1982 | if ( yl <= zl ) { |
---|
| 1983 | if ( yr <= zl ) { |
---|
| 1984 | continue ; |
---|
| 1985 | } |
---|
| 1986 | else if ( yr <= zr ) { |
---|
| 1987 | newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
| 1988 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1989 | wsum += ( yr - zl ) ; |
---|
| 1990 | } |
---|
| 1991 | else { |
---|
| 1992 | newspec[ii] += oldspec[j] * dnu ; |
---|
| 1993 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 1994 | wsum += dnu ; |
---|
| 1995 | ichan = j ; |
---|
| 1996 | break ; |
---|
| 1997 | } |
---|
| 1998 | } |
---|
| 1999 | else if ( yl < zr ) { |
---|
| 2000 | if ( yr <= zr ) { |
---|
| 2001 | newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
| 2002 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2003 | wsum += ( yr - yl ) ; |
---|
| 2004 | } |
---|
| 2005 | else { |
---|
| 2006 | newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
| 2007 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2008 | wsum += ( zr - yl ) ; |
---|
| 2009 | ichan = j ; |
---|
| 2010 | break ; |
---|
| 2011 | } |
---|
| 2012 | } |
---|
| 2013 | else { |
---|
| 2014 | ichan = j - 1 ; |
---|
| 2015 | break ; |
---|
| 2016 | } |
---|
| 2017 | } |
---|
[2133] | 2018 | if ( wsum != 0.0 ) |
---|
| 2019 | newspec[ii] /= wsum ; |
---|
[1819] | 2020 | wsum = 0.0 ; |
---|
| 2021 | } |
---|
| 2022 | } |
---|
| 2023 | else if ( dnu < 0.0 ) { |
---|
| 2024 | for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 2025 | double zl = zi[ii] ; |
---|
| 2026 | double zr = zi[ii+1] ; |
---|
| 2027 | for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 2028 | double yl = yi[j] ; |
---|
| 2029 | double yr = yi[j+1] ; |
---|
| 2030 | if ( yl >= zl ) { |
---|
| 2031 | if ( yr >= zl ) { |
---|
| 2032 | continue ; |
---|
| 2033 | } |
---|
| 2034 | else if ( yr >= zr ) { |
---|
| 2035 | newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
| 2036 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2037 | wsum += abs( yr - zl ) ; |
---|
| 2038 | } |
---|
| 2039 | else { |
---|
| 2040 | newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
| 2041 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2042 | wsum += abs( dnu ) ; |
---|
| 2043 | ichan = j ; |
---|
| 2044 | break ; |
---|
| 2045 | } |
---|
| 2046 | } |
---|
| 2047 | else if ( yl > zr ) { |
---|
| 2048 | if ( yr >= zr ) { |
---|
| 2049 | newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
| 2050 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2051 | wsum += abs( yr - yl ) ; |
---|
| 2052 | } |
---|
| 2053 | else { |
---|
| 2054 | newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
| 2055 | newflag[ii] = newflag[ii] || oldflag[j] ; |
---|
| 2056 | wsum += abs( zr - yl ) ; |
---|
| 2057 | ichan = j ; |
---|
| 2058 | break ; |
---|
| 2059 | } |
---|
| 2060 | } |
---|
| 2061 | else { |
---|
| 2062 | ichan = j - 1 ; |
---|
| 2063 | break ; |
---|
| 2064 | } |
---|
| 2065 | } |
---|
[2133] | 2066 | if ( wsum != 0.0 ) |
---|
| 2067 | newspec[ii] /= wsum ; |
---|
[1819] | 2068 | wsum = 0.0 ; |
---|
| 2069 | } |
---|
| 2070 | } |
---|
| 2071 | // * ichan = 0 |
---|
| 2072 | // ***/ |
---|
| 2073 | // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
| 2074 | // pile += dnu ; |
---|
| 2075 | // wedge = olddnu * ( refChan + 1 ) ; |
---|
| 2076 | // while ( wedge < pile ) { |
---|
| 2077 | // newspec[0] += olddnu * oldspec[refChan] ; |
---|
| 2078 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2079 | // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
| 2080 | // refChan++ ; |
---|
| 2081 | // wedge += olddnu ; |
---|
| 2082 | // wsum += olddnu ; |
---|
| 2083 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2084 | // } |
---|
| 2085 | // frac = ( wedge - pile ) / olddnu ; |
---|
| 2086 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2087 | // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2088 | // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2089 | // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2090 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2091 | // newspec[0] /= wsum ; |
---|
| 2092 | // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
| 2093 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2094 | |
---|
| 2095 | // /*** |
---|
| 2096 | // * ichan = 1 - nChan-2 |
---|
| 2097 | // ***/ |
---|
| 2098 | // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
| 2099 | // pile += dnu ; |
---|
| 2100 | // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
| 2101 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2102 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
| 2103 | // refChan++ ; |
---|
| 2104 | // wedge += olddnu ; |
---|
| 2105 | // wsum = frac * olddnu ; |
---|
| 2106 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2107 | // while ( wedge < pile ) { |
---|
| 2108 | // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
| 2109 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2110 | // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
| 2111 | // refChan++ ; |
---|
| 2112 | // wedge += olddnu ; |
---|
| 2113 | // wsum += olddnu ; |
---|
| 2114 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2115 | // } |
---|
| 2116 | // frac = ( wedge - pile ) / olddnu ; |
---|
| 2117 | // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2118 | // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2119 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2120 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2121 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2122 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2123 | // newspec[ichan] /= wsum ; |
---|
| 2124 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
| 2125 | // } |
---|
| 2126 | |
---|
| 2127 | // /*** |
---|
| 2128 | // * ichan = nChan-1 |
---|
| 2129 | // ***/ |
---|
| 2130 | // // NOTE: Assumed that all spectra have the same bandwidth |
---|
| 2131 | // pile += dnu ; |
---|
| 2132 | // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
| 2133 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
| 2134 | // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2135 | // refChan++ ; |
---|
| 2136 | // wedge += olddnu ; |
---|
| 2137 | // wsum = frac * olddnu ; |
---|
| 2138 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2139 | // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
| 2140 | // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
| 2141 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
| 2142 | // wsum += olddnu ; |
---|
| 2143 | // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2144 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2145 | // } |
---|
| 2146 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2147 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2148 | // newspec[nChan-1] /= wsum ; |
---|
| 2149 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
| 2150 | |
---|
| 2151 | // // ofs.close() ; |
---|
| 2152 | |
---|
[2032] | 2153 | specCol_.put( irow, newspec ) ; |
---|
| 2154 | flagsCol_.put( irow, newflag ) ; |
---|
[1819] | 2155 | |
---|
| 2156 | return ; |
---|
| 2157 | } |
---|
| 2158 | |
---|
[1730] | 2159 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
| 2160 | { |
---|
| 2161 | std::vector<float> out(5); |
---|
| 2162 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
| 2163 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
| 2164 | mweatheridCol_(uInt(whichrow))); |
---|
| 2165 | |
---|
| 2166 | |
---|
| 2167 | return out; |
---|
[1391] | 2168 | } |
---|
[1730] | 2169 | |
---|
[2047] | 2170 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
[1907] | 2171 | { |
---|
| 2172 | uChar flag; |
---|
| 2173 | Vector<uChar> flags; |
---|
[2047] | 2174 | flagsCol_.get(whichrow, flags); |
---|
[2012] | 2175 | flag = flags[0]; |
---|
[2047] | 2176 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
[2012] | 2177 | flag &= flags[i]; |
---|
| 2178 | } |
---|
| 2179 | return ((flag >> 7) == 1); |
---|
| 2180 | } |
---|
| 2181 | |
---|
[2277] | 2182 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2183 | { |
---|
[2193] | 2184 | try { |
---|
| 2185 | ofstream ofs; |
---|
| 2186 | String coordInfo = ""; |
---|
| 2187 | bool hasSameNchan = true; |
---|
| 2188 | bool outTextFile = false; |
---|
[2047] | 2189 | |
---|
[2193] | 2190 | if (blfile != "") { |
---|
| 2191 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2192 | if (ofs) outTextFile = true; |
---|
| 2193 | } |
---|
[2047] | 2194 | |
---|
[2193] | 2195 | if (outLogger || outTextFile) { |
---|
| 2196 | coordInfo = getCoordInfo()[0]; |
---|
| 2197 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2198 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2199 | } |
---|
[2047] | 2200 | |
---|
[2193] | 2201 | Fitter fitter = Fitter(); |
---|
| 2202 | fitter.setExpression("poly", order); |
---|
| 2203 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2204 | |
---|
[2193] | 2205 | int nRow = nrow(); |
---|
| 2206 | std::vector<bool> chanMask; |
---|
| 2207 | bool showProgress; |
---|
| 2208 | int minNRow; |
---|
| 2209 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2047] | 2210 | |
---|
[2193] | 2211 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2212 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2213 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2214 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2277] | 2215 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
[2193] | 2216 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2217 | } |
---|
| 2218 | |
---|
| 2219 | if (outTextFile) ofs.close(); |
---|
| 2220 | |
---|
| 2221 | } catch (...) { |
---|
| 2222 | throw; |
---|
[2047] | 2223 | } |
---|
| 2224 | } |
---|
| 2225 | |
---|
[2189] | 2226 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2227 | { |
---|
[2193] | 2228 | try { |
---|
| 2229 | ofstream ofs; |
---|
| 2230 | String coordInfo = ""; |
---|
| 2231 | bool hasSameNchan = true; |
---|
| 2232 | bool outTextFile = false; |
---|
[2047] | 2233 | |
---|
[2193] | 2234 | if (blfile != "") { |
---|
| 2235 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2236 | if (ofs) outTextFile = true; |
---|
| 2237 | } |
---|
[2047] | 2238 | |
---|
[2193] | 2239 | if (outLogger || outTextFile) { |
---|
| 2240 | coordInfo = getCoordInfo()[0]; |
---|
| 2241 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2242 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2243 | } |
---|
[2047] | 2244 | |
---|
[2193] | 2245 | Fitter fitter = Fitter(); |
---|
| 2246 | fitter.setExpression("poly", order); |
---|
| 2247 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2248 | |
---|
[2193] | 2249 | int nRow = nrow(); |
---|
| 2250 | std::vector<bool> chanMask; |
---|
| 2251 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2252 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2253 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2047] | 2254 | |
---|
[2193] | 2255 | bool showProgress; |
---|
| 2256 | int minNRow; |
---|
| 2257 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2258 | |
---|
[2193] | 2259 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2047] | 2260 | |
---|
[2193] | 2261 | //------------------------------------------------------- |
---|
| 2262 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2263 | //------------------------------------------------------- |
---|
| 2264 | int edgeSize = edge.size(); |
---|
| 2265 | std::vector<int> currentEdge; |
---|
| 2266 | if (edgeSize >= 2) { |
---|
| 2267 | int idx = 0; |
---|
| 2268 | if (edgeSize > 2) { |
---|
| 2269 | if (edgeSize < minEdgeSize) { |
---|
| 2270 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2271 | } |
---|
| 2272 | idx = 2 * getIF(whichrow); |
---|
[2047] | 2273 | } |
---|
[2193] | 2274 | currentEdge.push_back(edge[idx]); |
---|
| 2275 | currentEdge.push_back(edge[idx+1]); |
---|
| 2276 | } else { |
---|
| 2277 | throw(AipsError("Wrong length of edge element")); |
---|
[2047] | 2278 | } |
---|
[2193] | 2279 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2280 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2281 | chanMask = lineFinder.getMask(); |
---|
| 2282 | //------------------------------------------------------- |
---|
| 2283 | |
---|
| 2284 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2285 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2286 | |
---|
| 2287 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
| 2288 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2047] | 2289 | } |
---|
| 2290 | |
---|
[2193] | 2291 | if (outTextFile) ofs.close(); |
---|
[2047] | 2292 | |
---|
[2193] | 2293 | } catch (...) { |
---|
| 2294 | throw; |
---|
[2047] | 2295 | } |
---|
| 2296 | } |
---|
| 2297 | |
---|
[2189] | 2298 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2081] | 2299 | { |
---|
[2193] | 2300 | try { |
---|
| 2301 | ofstream ofs; |
---|
| 2302 | String coordInfo = ""; |
---|
| 2303 | bool hasSameNchan = true; |
---|
| 2304 | bool outTextFile = false; |
---|
[2012] | 2305 | |
---|
[2193] | 2306 | if (blfile != "") { |
---|
| 2307 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2308 | if (ofs) outTextFile = true; |
---|
| 2309 | } |
---|
[2012] | 2310 | |
---|
[2193] | 2311 | if (outLogger || outTextFile) { |
---|
| 2312 | coordInfo = getCoordInfo()[0]; |
---|
| 2313 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2314 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2315 | } |
---|
[2012] | 2316 | |
---|
[2193] | 2317 | //Fitter fitter = Fitter(); |
---|
| 2318 | //fitter.setExpression("cspline", nPiece); |
---|
| 2319 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2320 | |
---|
[2193] | 2321 | int nRow = nrow(); |
---|
| 2322 | std::vector<bool> chanMask; |
---|
| 2323 | bool showProgress; |
---|
| 2324 | int minNRow; |
---|
| 2325 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2012] | 2326 | |
---|
[2193] | 2327 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2328 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2329 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2330 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2331 | std::vector<int> pieceEdges; |
---|
| 2332 | std::vector<float> params; |
---|
| 2333 | int nClipped = 0; |
---|
| 2334 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2335 | setSpectrum(res, whichrow); |
---|
| 2336 | // |
---|
[2012] | 2337 | |
---|
[2193] | 2338 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
| 2339 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2340 | } |
---|
| 2341 | |
---|
| 2342 | if (outTextFile) ofs.close(); |
---|
| 2343 | |
---|
| 2344 | } catch (...) { |
---|
| 2345 | throw; |
---|
[2012] | 2346 | } |
---|
| 2347 | } |
---|
| 2348 | |
---|
[2189] | 2349 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 2350 | { |
---|
[2193] | 2351 | try { |
---|
| 2352 | ofstream ofs; |
---|
| 2353 | String coordInfo = ""; |
---|
| 2354 | bool hasSameNchan = true; |
---|
| 2355 | bool outTextFile = false; |
---|
[2012] | 2356 | |
---|
[2193] | 2357 | if (blfile != "") { |
---|
| 2358 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2359 | if (ofs) outTextFile = true; |
---|
| 2360 | } |
---|
[2012] | 2361 | |
---|
[2193] | 2362 | if (outLogger || outTextFile) { |
---|
| 2363 | coordInfo = getCoordInfo()[0]; |
---|
| 2364 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2365 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2366 | } |
---|
[2012] | 2367 | |
---|
[2193] | 2368 | //Fitter fitter = Fitter(); |
---|
| 2369 | //fitter.setExpression("cspline", nPiece); |
---|
| 2370 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2371 | |
---|
[2193] | 2372 | int nRow = nrow(); |
---|
| 2373 | std::vector<bool> chanMask; |
---|
| 2374 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2375 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2376 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 2377 | |
---|
[2193] | 2378 | bool showProgress; |
---|
| 2379 | int minNRow; |
---|
| 2380 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2381 | |
---|
[2193] | 2382 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 2383 | |
---|
[2193] | 2384 | //------------------------------------------------------- |
---|
| 2385 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2386 | //------------------------------------------------------- |
---|
| 2387 | int edgeSize = edge.size(); |
---|
| 2388 | std::vector<int> currentEdge; |
---|
| 2389 | if (edgeSize >= 2) { |
---|
| 2390 | int idx = 0; |
---|
| 2391 | if (edgeSize > 2) { |
---|
| 2392 | if (edgeSize < minEdgeSize) { |
---|
| 2393 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2394 | } |
---|
| 2395 | idx = 2 * getIF(whichrow); |
---|
[2012] | 2396 | } |
---|
[2193] | 2397 | currentEdge.push_back(edge[idx]); |
---|
| 2398 | currentEdge.push_back(edge[idx+1]); |
---|
| 2399 | } else { |
---|
| 2400 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 2401 | } |
---|
[2193] | 2402 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2403 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2404 | chanMask = lineFinder.getMask(); |
---|
| 2405 | //------------------------------------------------------- |
---|
| 2406 | |
---|
| 2407 | |
---|
| 2408 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2409 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2410 | std::vector<int> pieceEdges; |
---|
| 2411 | std::vector<float> params; |
---|
| 2412 | int nClipped = 0; |
---|
| 2413 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2414 | setSpectrum(res, whichrow); |
---|
| 2415 | // |
---|
| 2416 | |
---|
| 2417 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
| 2418 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[1907] | 2419 | } |
---|
[2012] | 2420 | |
---|
[2193] | 2421 | if (outTextFile) ofs.close(); |
---|
[2012] | 2422 | |
---|
[2193] | 2423 | } catch (...) { |
---|
| 2424 | throw; |
---|
[2012] | 2425 | } |
---|
[1730] | 2426 | } |
---|
[1907] | 2427 | |
---|
[2193] | 2428 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 2429 | { |
---|
| 2430 | if (data.size() != mask.size()) { |
---|
| 2431 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 2432 | } |
---|
[2012] | 2433 | if (nPiece < 1) { |
---|
[2094] | 2434 | throw(AipsError("number of the sections must be one or more")); |
---|
[2012] | 2435 | } |
---|
| 2436 | |
---|
| 2437 | int nChan = data.size(); |
---|
| 2438 | std::vector<int> maskArray; |
---|
| 2439 | std::vector<int> x; |
---|
| 2440 | for (int i = 0; i < nChan; ++i) { |
---|
| 2441 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 2442 | if (mask[i]) { |
---|
| 2443 | x.push_back(i); |
---|
| 2444 | } |
---|
| 2445 | } |
---|
| 2446 | |
---|
[2081] | 2447 | int initNData = x.size(); |
---|
[2193] | 2448 | if (initNData < nPiece) { |
---|
| 2449 | throw(AipsError("too few non-flagged channels")); |
---|
| 2450 | } |
---|
[2081] | 2451 | |
---|
| 2452 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
[2064] | 2453 | std::vector<double> invEdge; |
---|
| 2454 | idxEdge.clear(); |
---|
| 2455 | idxEdge.push_back(x[0]); |
---|
[2012] | 2456 | for (int i = 1; i < nPiece; ++i) { |
---|
[2047] | 2457 | int valX = x[nElement*i]; |
---|
[2064] | 2458 | idxEdge.push_back(valX); |
---|
| 2459 | invEdge.push_back(1.0/(double)valX); |
---|
[2012] | 2460 | } |
---|
[2064] | 2461 | idxEdge.push_back(x[x.size()-1]+1); |
---|
| 2462 | |
---|
[2081] | 2463 | int nData = initNData; |
---|
| 2464 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
| 2465 | |
---|
| 2466 | std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1, residual; |
---|
[2012] | 2467 | for (int i = 0; i < nChan; ++i) { |
---|
[2064] | 2468 | double di = (double)i; |
---|
| 2469 | double dD = (double)data[i]; |
---|
| 2470 | x1.push_back(di); |
---|
| 2471 | x2.push_back(di*di); |
---|
| 2472 | x3.push_back(di*di*di); |
---|
| 2473 | z1.push_back(dD); |
---|
| 2474 | x1z1.push_back(dD*di); |
---|
| 2475 | x2z1.push_back(dD*di*di); |
---|
| 2476 | x3z1.push_back(dD*di*di*di); |
---|
[2012] | 2477 | r1.push_back(0.0); |
---|
[2081] | 2478 | residual.push_back(0.0); |
---|
[2012] | 2479 | } |
---|
| 2480 | |
---|
| 2481 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2064] | 2482 | // xMatrix : horizontal concatenation of |
---|
| 2483 | // the least-sq. matrix (left) and an |
---|
| 2484 | // identity matrix (right). |
---|
| 2485 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2012] | 2486 | double xMatrix[nDOF][2*nDOF]; |
---|
| 2487 | double zMatrix[nDOF]; |
---|
| 2488 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2489 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 2490 | xMatrix[i][j] = 0.0; |
---|
| 2491 | } |
---|
| 2492 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 2493 | zMatrix[i] = 0.0; |
---|
| 2494 | } |
---|
| 2495 | |
---|
| 2496 | for (int n = 0; n < nPiece; ++n) { |
---|
[2193] | 2497 | int nUseDataInPiece = 0; |
---|
[2064] | 2498 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2499 | |
---|
[2012] | 2500 | if (maskArray[i] == 0) continue; |
---|
[2064] | 2501 | |
---|
[2012] | 2502 | xMatrix[0][0] += 1.0; |
---|
[2064] | 2503 | xMatrix[0][1] += x1[i]; |
---|
| 2504 | xMatrix[0][2] += x2[i]; |
---|
| 2505 | xMatrix[0][3] += x3[i]; |
---|
| 2506 | xMatrix[1][1] += x2[i]; |
---|
| 2507 | xMatrix[1][2] += x3[i]; |
---|
| 2508 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
| 2509 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
| 2510 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
| 2511 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
[2012] | 2512 | zMatrix[0] += z1[i]; |
---|
[2064] | 2513 | zMatrix[1] += x1z1[i]; |
---|
| 2514 | zMatrix[2] += x2z1[i]; |
---|
| 2515 | zMatrix[3] += x3z1[i]; |
---|
| 2516 | |
---|
[2012] | 2517 | for (int j = 0; j < n; ++j) { |
---|
[2064] | 2518 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
[2012] | 2519 | q = q*q*q; |
---|
| 2520 | xMatrix[0][j+4] += q; |
---|
[2064] | 2521 | xMatrix[1][j+4] += q*x1[i]; |
---|
| 2522 | xMatrix[2][j+4] += q*x2[i]; |
---|
| 2523 | xMatrix[3][j+4] += q*x3[i]; |
---|
[2012] | 2524 | for (int k = 0; k < j; ++k) { |
---|
[2064] | 2525 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
[2012] | 2526 | r = r*r*r; |
---|
| 2527 | xMatrix[k+4][j+4] += r*q; |
---|
| 2528 | } |
---|
| 2529 | xMatrix[j+4][j+4] += q*q; |
---|
| 2530 | zMatrix[j+4] += q*z1[i]; |
---|
| 2531 | } |
---|
[2064] | 2532 | |
---|
[2193] | 2533 | nUseDataInPiece++; |
---|
[2012] | 2534 | } |
---|
[2193] | 2535 | |
---|
| 2536 | if (nUseDataInPiece < 1) { |
---|
| 2537 | std::vector<string> suffixOfPieceNumber(4); |
---|
| 2538 | suffixOfPieceNumber[0] = "th"; |
---|
| 2539 | suffixOfPieceNumber[1] = "st"; |
---|
| 2540 | suffixOfPieceNumber[2] = "nd"; |
---|
| 2541 | suffixOfPieceNumber[3] = "rd"; |
---|
| 2542 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
| 2543 | ostringstream oss; |
---|
| 2544 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
| 2545 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
| 2546 | throw(AipsError(String(oss))); |
---|
| 2547 | } |
---|
[2012] | 2548 | } |
---|
| 2549 | |
---|
| 2550 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2551 | for (int j = 0; j < i; ++j) { |
---|
| 2552 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 2553 | } |
---|
| 2554 | } |
---|
| 2555 | |
---|
| 2556 | std::vector<double> invDiag; |
---|
| 2557 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2558 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 2559 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2560 | xMatrix[i][j] *= invDiag[i]; |
---|
| 2561 | } |
---|
| 2562 | } |
---|
| 2563 | |
---|
| 2564 | for (int k = 0; k < nDOF; ++k) { |
---|
| 2565 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2566 | if (i != k) { |
---|
| 2567 | double factor1 = xMatrix[k][k]; |
---|
| 2568 | double factor2 = xMatrix[i][k]; |
---|
| 2569 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2570 | xMatrix[i][j] *= factor1; |
---|
| 2571 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 2572 | xMatrix[i][j] /= factor1; |
---|
| 2573 | } |
---|
| 2574 | } |
---|
| 2575 | } |
---|
| 2576 | double xDiag = xMatrix[k][k]; |
---|
| 2577 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2578 | xMatrix[k][j] /= xDiag; |
---|
| 2579 | } |
---|
| 2580 | } |
---|
| 2581 | |
---|
| 2582 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2583 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2584 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 2585 | } |
---|
| 2586 | } |
---|
| 2587 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
| 2588 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
| 2589 | //cubic terms for the other pieces (in case nPiece>1). |
---|
| 2590 | std::vector<double> y; |
---|
[2058] | 2591 | y.clear(); |
---|
[2012] | 2592 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2593 | y.push_back(0.0); |
---|
| 2594 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2595 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 2596 | } |
---|
| 2597 | } |
---|
| 2598 | |
---|
| 2599 | double a0 = y[0]; |
---|
| 2600 | double a1 = y[1]; |
---|
| 2601 | double a2 = y[2]; |
---|
| 2602 | double a3 = y[3]; |
---|
| 2603 | params.clear(); |
---|
| 2604 | |
---|
| 2605 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 2606 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2607 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
[2081] | 2608 | residual[i] = z1[i] - r1[i]; |
---|
[2012] | 2609 | } |
---|
| 2610 | params.push_back(a0); |
---|
| 2611 | params.push_back(a1); |
---|
| 2612 | params.push_back(a2); |
---|
| 2613 | params.push_back(a3); |
---|
| 2614 | |
---|
| 2615 | if (n == nPiece-1) break; |
---|
| 2616 | |
---|
| 2617 | double d = y[4+n]; |
---|
[2064] | 2618 | double iE = invEdge[n]; |
---|
| 2619 | a0 += d; |
---|
| 2620 | a1 -= 3.0*d*iE; |
---|
| 2621 | a2 += 3.0*d*iE*iE; |
---|
| 2622 | a3 -= d*iE*iE*iE; |
---|
[2012] | 2623 | } |
---|
| 2624 | |
---|
| 2625 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 2626 | break; |
---|
| 2627 | } else { |
---|
| 2628 | double stdDev = 0.0; |
---|
| 2629 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2630 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2012] | 2631 | } |
---|
| 2632 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 2633 | |
---|
| 2634 | double thres = stdDev * thresClip; |
---|
| 2635 | int newNData = 0; |
---|
| 2636 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2637 | if (abs(residual[i]) >= thres) { |
---|
[2012] | 2638 | maskArray[i] = 0; |
---|
| 2639 | } |
---|
| 2640 | if (maskArray[i] > 0) { |
---|
| 2641 | newNData++; |
---|
| 2642 | } |
---|
| 2643 | } |
---|
[2081] | 2644 | if (newNData == nData) { |
---|
[2064] | 2645 | break; //no more flag to add. iteration stops. |
---|
[2012] | 2646 | } else { |
---|
[2081] | 2647 | nData = newNData; |
---|
[2012] | 2648 | } |
---|
| 2649 | } |
---|
| 2650 | } |
---|
| 2651 | |
---|
[2193] | 2652 | nClipped = initNData - nData; |
---|
| 2653 | |
---|
[2058] | 2654 | std::vector<float> result; |
---|
| 2655 | if (getResidual) { |
---|
| 2656 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2657 | result.push_back((float)residual[i]); |
---|
[2058] | 2658 | } |
---|
| 2659 | } else { |
---|
| 2660 | for (int i = 0; i < nChan; ++i) { |
---|
| 2661 | result.push_back((float)r1[i]); |
---|
| 2662 | } |
---|
[2012] | 2663 | } |
---|
| 2664 | |
---|
[2058] | 2665 | return result; |
---|
[2012] | 2666 | } |
---|
| 2667 | |
---|
[2186] | 2668 | void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2081] | 2669 | { |
---|
[2186] | 2670 | nWaves.clear(); |
---|
| 2671 | |
---|
| 2672 | if (applyFFT) { |
---|
| 2673 | string fftThAttr; |
---|
| 2674 | float fftThSigma; |
---|
| 2675 | int fftThTop; |
---|
| 2676 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
| 2677 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
| 2678 | } |
---|
| 2679 | |
---|
| 2680 | addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves); |
---|
| 2681 | } |
---|
| 2682 | |
---|
| 2683 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
| 2684 | { |
---|
| 2685 | uInt idxSigma = fftThresh.find("sigma"); |
---|
| 2686 | uInt idxTop = fftThresh.find("top"); |
---|
| 2687 | |
---|
| 2688 | if (idxSigma == fftThresh.size() - 5) { |
---|
| 2689 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
| 2690 | is >> fftThSigma; |
---|
| 2691 | fftThAttr = "sigma"; |
---|
| 2692 | } else if (idxTop == 0) { |
---|
| 2693 | std::istringstream is(fftThresh.substr(3)); |
---|
| 2694 | is >> fftThTop; |
---|
| 2695 | fftThAttr = "top"; |
---|
| 2696 | } else { |
---|
| 2697 | bool isNumber = true; |
---|
| 2698 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
| 2699 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
| 2700 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
| 2701 | isNumber = false; |
---|
| 2702 | break; |
---|
| 2703 | } |
---|
| 2704 | } |
---|
| 2705 | if (isNumber) { |
---|
| 2706 | std::istringstream is(fftThresh); |
---|
| 2707 | is >> fftThSigma; |
---|
| 2708 | fftThAttr = "sigma"; |
---|
| 2709 | } else { |
---|
| 2710 | throw(AipsError("fftthresh has a wrong value")); |
---|
| 2711 | } |
---|
| 2712 | } |
---|
| 2713 | } |
---|
| 2714 | |
---|
| 2715 | 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) |
---|
| 2716 | { |
---|
| 2717 | std::vector<float> fspec; |
---|
| 2718 | if (fftMethod == "fft") { |
---|
| 2719 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
| 2720 | //} else if (fftMethod == "lsp") { |
---|
| 2721 | // fspec = lombScarglePeriodogram(whichrow); |
---|
| 2722 | } |
---|
| 2723 | |
---|
| 2724 | if (fftThAttr == "sigma") { |
---|
| 2725 | float mean = 0.0; |
---|
| 2726 | float mean2 = 0.0; |
---|
| 2727 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 2728 | mean += fspec[i]; |
---|
| 2729 | mean2 += fspec[i]*fspec[i]; |
---|
| 2730 | } |
---|
| 2731 | mean /= float(fspec.size()); |
---|
| 2732 | mean2 /= float(fspec.size()); |
---|
| 2733 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
| 2734 | |
---|
| 2735 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 2736 | if (fspec[i] >= thres) { |
---|
| 2737 | nWaves.push_back(i); |
---|
| 2738 | } |
---|
| 2739 | } |
---|
| 2740 | |
---|
| 2741 | } else if (fftThAttr == "top") { |
---|
| 2742 | for (int i = 0; i < fftThTop; ++i) { |
---|
| 2743 | float max = 0.0; |
---|
| 2744 | int maxIdx = 0; |
---|
| 2745 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
| 2746 | if (fspec[j] > max) { |
---|
| 2747 | max = fspec[j]; |
---|
| 2748 | maxIdx = j; |
---|
| 2749 | } |
---|
| 2750 | } |
---|
| 2751 | nWaves.push_back(maxIdx); |
---|
| 2752 | fspec[maxIdx] = 0.0; |
---|
| 2753 | } |
---|
| 2754 | |
---|
| 2755 | } |
---|
| 2756 | |
---|
| 2757 | if (nWaves.size() > 1) { |
---|
| 2758 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2759 | } |
---|
| 2760 | } |
---|
| 2761 | |
---|
| 2762 | void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
| 2763 | { |
---|
| 2764 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
| 2765 | bool found = false; |
---|
| 2766 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
| 2767 | if (nWaves[j] == addNWaves[i]) { |
---|
| 2768 | found = true; |
---|
| 2769 | break; |
---|
| 2770 | } |
---|
| 2771 | } |
---|
| 2772 | if (!found) nWaves.push_back(addNWaves[i]); |
---|
| 2773 | } |
---|
| 2774 | |
---|
| 2775 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
| 2776 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
| 2777 | if (*j == rejectNWaves[i]) { |
---|
| 2778 | j = nWaves.erase(j); |
---|
| 2779 | } else { |
---|
| 2780 | ++j; |
---|
| 2781 | } |
---|
| 2782 | } |
---|
| 2783 | } |
---|
| 2784 | |
---|
| 2785 | if (nWaves.size() > 1) { |
---|
| 2786 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2787 | unique(nWaves.begin(), nWaves.end()); |
---|
| 2788 | } |
---|
| 2789 | } |
---|
| 2790 | |
---|
[2189] | 2791 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2186] | 2792 | { |
---|
[2193] | 2793 | try { |
---|
| 2794 | ofstream ofs; |
---|
| 2795 | String coordInfo = ""; |
---|
| 2796 | bool hasSameNchan = true; |
---|
| 2797 | bool outTextFile = false; |
---|
[2012] | 2798 | |
---|
[2193] | 2799 | if (blfile != "") { |
---|
| 2800 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2801 | if (ofs) outTextFile = true; |
---|
| 2802 | } |
---|
[2012] | 2803 | |
---|
[2193] | 2804 | if (outLogger || outTextFile) { |
---|
| 2805 | coordInfo = getCoordInfo()[0]; |
---|
| 2806 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2807 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2808 | } |
---|
[2012] | 2809 | |
---|
[2193] | 2810 | //Fitter fitter = Fitter(); |
---|
| 2811 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 2812 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2813 | |
---|
[2193] | 2814 | int nRow = nrow(); |
---|
| 2815 | std::vector<bool> chanMask; |
---|
| 2816 | std::vector<int> nWaves; |
---|
[2012] | 2817 | |
---|
[2193] | 2818 | bool showProgress; |
---|
| 2819 | int minNRow; |
---|
| 2820 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2821 | |
---|
[2193] | 2822 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2823 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2824 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
[2186] | 2825 | |
---|
[2193] | 2826 | //FOR DEBUGGING------------ |
---|
| 2827 | if (whichrow < 0) {// == nRow -1) { |
---|
| 2828 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow); |
---|
| 2829 | if (applyFFT) { |
---|
[2186] | 2830 | cout << "[ "; |
---|
| 2831 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
| 2832 | cout << nWaves[j] << ", "; |
---|
| 2833 | } |
---|
| 2834 | cout << " ] " << endl; |
---|
[2193] | 2835 | } |
---|
| 2836 | cout << flush; |
---|
[2186] | 2837 | } |
---|
[2193] | 2838 | //------------------------- |
---|
| 2839 | |
---|
| 2840 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2841 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2842 | std::vector<float> params; |
---|
| 2843 | int nClipped = 0; |
---|
| 2844 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2845 | setSpectrum(res, whichrow); |
---|
| 2846 | // |
---|
| 2847 | |
---|
| 2848 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped); |
---|
| 2849 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2186] | 2850 | } |
---|
| 2851 | |
---|
[2193] | 2852 | if (outTextFile) ofs.close(); |
---|
[2012] | 2853 | |
---|
[2193] | 2854 | } catch (...) { |
---|
| 2855 | throw; |
---|
[1931] | 2856 | } |
---|
[1907] | 2857 | } |
---|
| 2858 | |
---|
[2189] | 2859 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 2860 | { |
---|
[2193] | 2861 | try { |
---|
| 2862 | ofstream ofs; |
---|
| 2863 | String coordInfo = ""; |
---|
| 2864 | bool hasSameNchan = true; |
---|
| 2865 | bool outTextFile = false; |
---|
[2012] | 2866 | |
---|
[2193] | 2867 | if (blfile != "") { |
---|
| 2868 | ofs.open(blfile.c_str(), ios::out | ios::app); |
---|
| 2869 | if (ofs) outTextFile = true; |
---|
| 2870 | } |
---|
[2012] | 2871 | |
---|
[2193] | 2872 | if (outLogger || outTextFile) { |
---|
| 2873 | coordInfo = getCoordInfo()[0]; |
---|
| 2874 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2875 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2876 | } |
---|
[2012] | 2877 | |
---|
[2193] | 2878 | //Fitter fitter = Fitter(); |
---|
| 2879 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 2880 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2881 | |
---|
[2193] | 2882 | int nRow = nrow(); |
---|
| 2883 | std::vector<bool> chanMask; |
---|
| 2884 | std::vector<int> nWaves; |
---|
[2186] | 2885 | |
---|
[2193] | 2886 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2887 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2888 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 2889 | |
---|
[2193] | 2890 | bool showProgress; |
---|
| 2891 | int minNRow; |
---|
| 2892 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2893 | |
---|
[2193] | 2894 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 2895 | |
---|
[2193] | 2896 | //------------------------------------------------------- |
---|
| 2897 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2898 | //------------------------------------------------------- |
---|
| 2899 | int edgeSize = edge.size(); |
---|
| 2900 | std::vector<int> currentEdge; |
---|
| 2901 | if (edgeSize >= 2) { |
---|
| 2902 | int idx = 0; |
---|
| 2903 | if (edgeSize > 2) { |
---|
| 2904 | if (edgeSize < minEdgeSize) { |
---|
| 2905 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2906 | } |
---|
| 2907 | idx = 2 * getIF(whichrow); |
---|
[2012] | 2908 | } |
---|
[2193] | 2909 | currentEdge.push_back(edge[idx]); |
---|
| 2910 | currentEdge.push_back(edge[idx+1]); |
---|
| 2911 | } else { |
---|
| 2912 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 2913 | } |
---|
[2193] | 2914 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2915 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2916 | chanMask = lineFinder.getMask(); |
---|
| 2917 | //------------------------------------------------------- |
---|
| 2918 | |
---|
| 2919 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
| 2920 | |
---|
| 2921 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2922 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2923 | std::vector<float> params; |
---|
| 2924 | int nClipped = 0; |
---|
| 2925 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2926 | setSpectrum(res, whichrow); |
---|
| 2927 | // |
---|
| 2928 | |
---|
| 2929 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped); |
---|
| 2930 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2012] | 2931 | } |
---|
| 2932 | |
---|
[2193] | 2933 | if (outTextFile) ofs.close(); |
---|
[2012] | 2934 | |
---|
[2193] | 2935 | } catch (...) { |
---|
| 2936 | throw; |
---|
[2047] | 2937 | } |
---|
| 2938 | } |
---|
| 2939 | |
---|
[2193] | 2940 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 2941 | { |
---|
[2047] | 2942 | if (data.size() != mask.size()) { |
---|
[2081] | 2943 | throw(AipsError("data and mask sizes are not identical")); |
---|
[2047] | 2944 | } |
---|
[2081] | 2945 | if (data.size() < 2) { |
---|
| 2946 | throw(AipsError("data size is too short")); |
---|
| 2947 | } |
---|
| 2948 | if (waveNumbers.size() == 0) { |
---|
[2186] | 2949 | throw(AipsError("no wave numbers given")); |
---|
[2081] | 2950 | } |
---|
| 2951 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
| 2952 | nWaves.reserve(waveNumbers.size()); |
---|
| 2953 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
| 2954 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2955 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
| 2956 | nWaves.erase(end_it, nWaves.end()); |
---|
| 2957 | |
---|
| 2958 | int minNWaves = nWaves[0]; |
---|
| 2959 | if (minNWaves < 0) { |
---|
[2058] | 2960 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
| 2961 | } |
---|
[2081] | 2962 | bool hasConstantTerm = (minNWaves == 0); |
---|
[2047] | 2963 | |
---|
| 2964 | int nChan = data.size(); |
---|
| 2965 | std::vector<int> maskArray; |
---|
| 2966 | std::vector<int> x; |
---|
| 2967 | for (int i = 0; i < nChan; ++i) { |
---|
| 2968 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 2969 | if (mask[i]) { |
---|
| 2970 | x.push_back(i); |
---|
| 2971 | } |
---|
| 2972 | } |
---|
| 2973 | |
---|
[2081] | 2974 | int initNData = x.size(); |
---|
[2047] | 2975 | |
---|
[2081] | 2976 | int nData = initNData; |
---|
| 2977 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
| 2978 | |
---|
| 2979 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
[2186] | 2980 | double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK) |
---|
[2081] | 2981 | |
---|
| 2982 | // xArray : contains elemental values for computing the least-square matrix. |
---|
| 2983 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
| 2984 | // Each xArray element are as follows: |
---|
| 2985 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
| 2986 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])}, |
---|
| 2987 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])}, |
---|
| 2988 | // where (1 <= n <= nMaxWavesInSW), |
---|
| 2989 | // or, |
---|
| 2990 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])}, |
---|
| 2991 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])}, |
---|
| 2992 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
| 2993 | std::vector<std::vector<double> > xArray; |
---|
| 2994 | if (hasConstantTerm) { |
---|
| 2995 | std::vector<double> xu; |
---|
| 2996 | for (int j = 0; j < nChan; ++j) { |
---|
| 2997 | xu.push_back(1.0); |
---|
| 2998 | } |
---|
| 2999 | xArray.push_back(xu); |
---|
| 3000 | } |
---|
| 3001 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
| 3002 | double xFactor = baseXFactor*(double)nWaves[i]; |
---|
| 3003 | std::vector<double> xs, xc; |
---|
| 3004 | xs.clear(); |
---|
| 3005 | xc.clear(); |
---|
| 3006 | for (int j = 0; j < nChan; ++j) { |
---|
| 3007 | xs.push_back(sin(xFactor*(double)j)); |
---|
| 3008 | xc.push_back(cos(xFactor*(double)j)); |
---|
| 3009 | } |
---|
| 3010 | xArray.push_back(xs); |
---|
| 3011 | xArray.push_back(xc); |
---|
| 3012 | } |
---|
| 3013 | |
---|
| 3014 | std::vector<double> z1, r1, residual; |
---|
[2047] | 3015 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3016 | z1.push_back((double)data[i]); |
---|
[2047] | 3017 | r1.push_back(0.0); |
---|
[2081] | 3018 | residual.push_back(0.0); |
---|
[2047] | 3019 | } |
---|
| 3020 | |
---|
| 3021 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2081] | 3022 | // xMatrix : horizontal concatenation of |
---|
| 3023 | // the least-sq. matrix (left) and an |
---|
| 3024 | // identity matrix (right). |
---|
| 3025 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2047] | 3026 | double xMatrix[nDOF][2*nDOF]; |
---|
| 3027 | double zMatrix[nDOF]; |
---|
| 3028 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3029 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 3030 | xMatrix[i][j] = 0.0; |
---|
[2012] | 3031 | } |
---|
[2047] | 3032 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 3033 | zMatrix[i] = 0.0; |
---|
| 3034 | } |
---|
| 3035 | |
---|
[2193] | 3036 | int nUseData = 0; |
---|
[2081] | 3037 | for (int k = 0; k < nChan; ++k) { |
---|
| 3038 | if (maskArray[k] == 0) continue; |
---|
| 3039 | |
---|
| 3040 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3041 | for (int j = i; j < nDOF; ++j) { |
---|
| 3042 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
| 3043 | } |
---|
| 3044 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
| 3045 | } |
---|
[2193] | 3046 | |
---|
| 3047 | nUseData++; |
---|
[2047] | 3048 | } |
---|
| 3049 | |
---|
[2193] | 3050 | if (nUseData < 1) { |
---|
| 3051 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
| 3052 | } |
---|
| 3053 | |
---|
[2047] | 3054 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3055 | for (int j = 0; j < i; ++j) { |
---|
| 3056 | xMatrix[i][j] = xMatrix[j][i]; |
---|
[2012] | 3057 | } |
---|
| 3058 | } |
---|
| 3059 | |
---|
[2047] | 3060 | std::vector<double> invDiag; |
---|
| 3061 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3062 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 3063 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3064 | xMatrix[i][j] *= invDiag[i]; |
---|
| 3065 | } |
---|
| 3066 | } |
---|
| 3067 | |
---|
| 3068 | for (int k = 0; k < nDOF; ++k) { |
---|
| 3069 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3070 | if (i != k) { |
---|
| 3071 | double factor1 = xMatrix[k][k]; |
---|
| 3072 | double factor2 = xMatrix[i][k]; |
---|
| 3073 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3074 | xMatrix[i][j] *= factor1; |
---|
| 3075 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 3076 | xMatrix[i][j] /= factor1; |
---|
| 3077 | } |
---|
| 3078 | } |
---|
| 3079 | } |
---|
| 3080 | double xDiag = xMatrix[k][k]; |
---|
| 3081 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3082 | xMatrix[k][j] /= xDiag; |
---|
| 3083 | } |
---|
| 3084 | } |
---|
| 3085 | |
---|
| 3086 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3087 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3088 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 3089 | } |
---|
| 3090 | } |
---|
| 3091 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
[2081] | 3092 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
| 3093 | //and cosine functions, respectively. |
---|
[2047] | 3094 | std::vector<double> y; |
---|
[2081] | 3095 | params.clear(); |
---|
[2047] | 3096 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3097 | y.push_back(0.0); |
---|
| 3098 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3099 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 3100 | } |
---|
[2081] | 3101 | params.push_back(y[i]); |
---|
[2047] | 3102 | } |
---|
| 3103 | |
---|
| 3104 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3105 | r1[i] = y[0]; |
---|
| 3106 | for (int j = 1; j < nDOF; ++j) { |
---|
| 3107 | r1[i] += y[j]*xArray[j][i]; |
---|
| 3108 | } |
---|
| 3109 | residual[i] = z1[i] - r1[i]; |
---|
[2047] | 3110 | } |
---|
| 3111 | |
---|
| 3112 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 3113 | break; |
---|
| 3114 | } else { |
---|
| 3115 | double stdDev = 0.0; |
---|
| 3116 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3117 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2047] | 3118 | } |
---|
| 3119 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 3120 | |
---|
| 3121 | double thres = stdDev * thresClip; |
---|
| 3122 | int newNData = 0; |
---|
| 3123 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3124 | if (abs(residual[i]) >= thres) { |
---|
[2047] | 3125 | maskArray[i] = 0; |
---|
| 3126 | } |
---|
| 3127 | if (maskArray[i] > 0) { |
---|
| 3128 | newNData++; |
---|
| 3129 | } |
---|
| 3130 | } |
---|
[2081] | 3131 | if (newNData == nData) { |
---|
| 3132 | break; //no more flag to add. iteration stops. |
---|
[2047] | 3133 | } else { |
---|
[2081] | 3134 | nData = newNData; |
---|
[2047] | 3135 | } |
---|
| 3136 | } |
---|
[2012] | 3137 | } |
---|
| 3138 | |
---|
[2193] | 3139 | nClipped = initNData - nData; |
---|
| 3140 | |
---|
[2058] | 3141 | std::vector<float> result; |
---|
| 3142 | if (getResidual) { |
---|
| 3143 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3144 | result.push_back((float)residual[i]); |
---|
[2058] | 3145 | } |
---|
| 3146 | } else { |
---|
| 3147 | for (int i = 0; i < nChan; ++i) { |
---|
| 3148 | result.push_back((float)r1[i]); |
---|
| 3149 | } |
---|
[2047] | 3150 | } |
---|
| 3151 | |
---|
[2058] | 3152 | return result; |
---|
[2012] | 3153 | } |
---|
| 3154 | |
---|
[2047] | 3155 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
| 3156 | { |
---|
[2081] | 3157 | std::vector<double> dAbcissa = getAbcissa(whichrow); |
---|
| 3158 | std::vector<float> abcissa; |
---|
| 3159 | for (uInt i = 0; i < dAbcissa.size(); ++i) { |
---|
| 3160 | abcissa.push_back((float)dAbcissa[i]); |
---|
[2047] | 3161 | } |
---|
| 3162 | std::vector<float> spec = getSpectrum(whichrow); |
---|
[2012] | 3163 | |
---|
[2081] | 3164 | fitter.setData(abcissa, spec, mask); |
---|
[2047] | 3165 | fitter.lfit(); |
---|
| 3166 | } |
---|
| 3167 | |
---|
| 3168 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
| 3169 | { |
---|
[2186] | 3170 | std::vector<bool> mask = getMask(whichrow); |
---|
| 3171 | uInt maskSize = mask.size(); |
---|
| 3172 | if (maskSize != inMask.size()) { |
---|
| 3173 | throw(AipsError("mask sizes are not the same.")); |
---|
[2047] | 3174 | } |
---|
[2186] | 3175 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 3176 | mask[i] = mask[i] && inMask[i]; |
---|
[2047] | 3177 | } |
---|
| 3178 | |
---|
[2186] | 3179 | return mask; |
---|
[2047] | 3180 | } |
---|
| 3181 | |
---|
| 3182 | /* |
---|
| 3183 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
| 3184 | { |
---|
| 3185 | int edgeSize = edge.size(); |
---|
| 3186 | std::vector<int> currentEdge; |
---|
| 3187 | if (edgeSize >= 2) { |
---|
| 3188 | int idx = 0; |
---|
| 3189 | if (edgeSize > 2) { |
---|
| 3190 | if (edgeSize < minEdgeSize) { |
---|
| 3191 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3192 | } |
---|
| 3193 | idx = 2 * getIF(whichrow); |
---|
| 3194 | } |
---|
| 3195 | currentEdge.push_back(edge[idx]); |
---|
| 3196 | currentEdge.push_back(edge[idx+1]); |
---|
| 3197 | } else { |
---|
| 3198 | throw(AipsError("Wrong length of edge element")); |
---|
| 3199 | } |
---|
| 3200 | |
---|
| 3201 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 3202 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
| 3203 | |
---|
| 3204 | return lineFinder.getMask(); |
---|
| 3205 | } |
---|
| 3206 | */ |
---|
| 3207 | |
---|
| 3208 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
[2186] | 3209 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter) |
---|
| 3210 | { |
---|
[2047] | 3211 | if (outLogger || outTextFile) { |
---|
| 3212 | std::vector<float> params = fitter.getParameters(); |
---|
| 3213 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
| 3214 | float rms = getRms(chanMask, whichrow); |
---|
| 3215 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 3216 | |
---|
| 3217 | if (outLogger) { |
---|
| 3218 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2193] | 3219 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 3220 | } |
---|
| 3221 | if (outTextFile) { |
---|
[2193] | 3222 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush; |
---|
[2047] | 3223 | } |
---|
| 3224 | } |
---|
| 3225 | } |
---|
| 3226 | |
---|
| 3227 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
[2193] | 3228 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped) |
---|
[2186] | 3229 | { |
---|
[2047] | 3230 | if (outLogger || outTextFile) { |
---|
| 3231 | float rms = getRms(chanMask, whichrow); |
---|
| 3232 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 3233 | std::vector<bool> fixed; |
---|
| 3234 | fixed.clear(); |
---|
[2047] | 3235 | |
---|
| 3236 | if (outLogger) { |
---|
| 3237 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2193] | 3238 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 3239 | } |
---|
| 3240 | if (outTextFile) { |
---|
[2193] | 3241 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush; |
---|
[2047] | 3242 | } |
---|
| 3243 | } |
---|
| 3244 | } |
---|
| 3245 | |
---|
| 3246 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */ |
---|
[2193] | 3247 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped) |
---|
[2186] | 3248 | { |
---|
[2047] | 3249 | if (outLogger || outTextFile) { |
---|
| 3250 | float rms = getRms(chanMask, whichrow); |
---|
| 3251 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 3252 | std::vector<bool> fixed; |
---|
| 3253 | fixed.clear(); |
---|
[2047] | 3254 | |
---|
| 3255 | if (outLogger) { |
---|
| 3256 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2193] | 3257 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ; |
---|
[2047] | 3258 | } |
---|
| 3259 | if (outTextFile) { |
---|
[2193] | 3260 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush; |
---|
[2047] | 3261 | } |
---|
| 3262 | } |
---|
| 3263 | } |
---|
| 3264 | |
---|
[2189] | 3265 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
[2186] | 3266 | { |
---|
[2189] | 3267 | int idxDelimiter = progressInfo.find(","); |
---|
| 3268 | if (idxDelimiter < 0) { |
---|
| 3269 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
| 3270 | } |
---|
| 3271 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
| 3272 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
| 3273 | is >> minNRow; |
---|
| 3274 | } |
---|
| 3275 | |
---|
| 3276 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
| 3277 | { |
---|
| 3278 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
[2186] | 3279 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
| 3280 | if (nInterval == 0) nInterval++; |
---|
| 3281 | |
---|
[2193] | 3282 | if (nProcessed % nInterval == 0) { |
---|
[2189] | 3283 | printf("\r"); //go to the head of line |
---|
[2186] | 3284 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
[2189] | 3285 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
| 3286 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
[2186] | 3287 | fflush(NULL); |
---|
| 3288 | } |
---|
[2193] | 3289 | |
---|
[2186] | 3290 | if (nProcessed == nTotal - 1) { |
---|
| 3291 | printf("\r\x1b[K"); //clear |
---|
| 3292 | fflush(NULL); |
---|
| 3293 | } |
---|
[2193] | 3294 | |
---|
[2186] | 3295 | } |
---|
| 3296 | } |
---|
| 3297 | |
---|
| 3298 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
| 3299 | { |
---|
| 3300 | std::vector<bool> mask = getMask(whichrow); |
---|
| 3301 | |
---|
| 3302 | if (inMask.size() > 0) { |
---|
| 3303 | uInt maskSize = mask.size(); |
---|
| 3304 | if (maskSize != inMask.size()) { |
---|
| 3305 | throw(AipsError("mask sizes are not the same.")); |
---|
| 3306 | } |
---|
| 3307 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 3308 | mask[i] = mask[i] && inMask[i]; |
---|
| 3309 | } |
---|
| 3310 | } |
---|
| 3311 | |
---|
| 3312 | Vector<Float> spec = getSpectrum(whichrow); |
---|
| 3313 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
| 3314 | |
---|
| 3315 | FFTServer<Float,Complex> ffts; |
---|
| 3316 | Vector<Complex> fftres; |
---|
| 3317 | ffts.fft0(fftres, spec); |
---|
| 3318 | |
---|
| 3319 | std::vector<float> res; |
---|
| 3320 | float norm = float(2.0/double(spec.size())); |
---|
| 3321 | |
---|
| 3322 | if (getRealImag) { |
---|
| 3323 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 3324 | res.push_back(real(fftres[i])*norm); |
---|
| 3325 | res.push_back(imag(fftres[i])*norm); |
---|
| 3326 | } |
---|
| 3327 | } else { |
---|
| 3328 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 3329 | res.push_back(abs(fftres[i])*norm); |
---|
| 3330 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
| 3331 | } |
---|
| 3332 | } |
---|
| 3333 | |
---|
| 3334 | return res; |
---|
| 3335 | } |
---|
| 3336 | |
---|
| 3337 | |
---|
| 3338 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
| 3339 | { |
---|
[2012] | 3340 | Vector<Float> spec; |
---|
| 3341 | specCol_.get(whichrow, spec); |
---|
| 3342 | |
---|
| 3343 | float mean = 0.0; |
---|
| 3344 | float smean = 0.0; |
---|
| 3345 | int n = 0; |
---|
[2047] | 3346 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
[2012] | 3347 | if (mask[i]) { |
---|
| 3348 | mean += spec[i]; |
---|
| 3349 | smean += spec[i]*spec[i]; |
---|
| 3350 | n++; |
---|
| 3351 | } |
---|
| 3352 | } |
---|
| 3353 | |
---|
| 3354 | mean /= (float)n; |
---|
| 3355 | smean /= (float)n; |
---|
| 3356 | |
---|
| 3357 | return sqrt(smean - mean*mean); |
---|
| 3358 | } |
---|
| 3359 | |
---|
| 3360 | |
---|
[2186] | 3361 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const |
---|
[2012] | 3362 | { |
---|
| 3363 | ostringstream oss; |
---|
| 3364 | |
---|
| 3365 | if (verbose) { |
---|
| 3366 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
| 3367 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
| 3368 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
| 3369 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
| 3370 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
| 3371 | oss << "Fitter range = " << masklist << endl; |
---|
| 3372 | oss << "Baseline parameters" << endl; |
---|
| 3373 | oss << flush; |
---|
| 3374 | } |
---|
| 3375 | |
---|
| 3376 | return String(oss); |
---|
| 3377 | } |
---|
| 3378 | |
---|
[2193] | 3379 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const |
---|
[2012] | 3380 | { |
---|
| 3381 | ostringstream oss; |
---|
| 3382 | |
---|
| 3383 | if (verbose) { |
---|
| 3384 | oss << "Results of baseline fit" << endl; |
---|
| 3385 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
[2193] | 3386 | if (nClipped >= 0) { |
---|
| 3387 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
| 3388 | } |
---|
[2094] | 3389 | for (int i = 0; i < 60; ++i) { |
---|
| 3390 | oss << "-"; |
---|
| 3391 | } |
---|
[2131] | 3392 | oss << endl; |
---|
[2094] | 3393 | oss << flush; |
---|
[2012] | 3394 | } |
---|
| 3395 | |
---|
| 3396 | return String(oss); |
---|
| 3397 | } |
---|
| 3398 | |
---|
[2186] | 3399 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
| 3400 | const std::vector<bool>& fixed, |
---|
| 3401 | float rms, |
---|
[2193] | 3402 | int nClipped, |
---|
[2186] | 3403 | const std::string& masklist, |
---|
| 3404 | int whichrow, |
---|
| 3405 | bool verbose, |
---|
| 3406 | int start, int count, |
---|
| 3407 | bool resetparamid) const |
---|
[2047] | 3408 | { |
---|
[2064] | 3409 | int nParam = (int)(params.size()); |
---|
[2047] | 3410 | |
---|
[2064] | 3411 | if (nParam < 1) { |
---|
| 3412 | return(" Not fitted"); |
---|
| 3413 | } else { |
---|
| 3414 | |
---|
| 3415 | ostringstream oss; |
---|
| 3416 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
| 3417 | |
---|
| 3418 | if (start < 0) start = 0; |
---|
| 3419 | if (count < 0) count = nParam; |
---|
| 3420 | int end = start + count; |
---|
| 3421 | if (end > nParam) end = nParam; |
---|
| 3422 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
| 3423 | |
---|
| 3424 | for (int i = start; i < end; ++i) { |
---|
| 3425 | if (i > start) { |
---|
[2047] | 3426 | oss << ","; |
---|
| 3427 | } |
---|
[2064] | 3428 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
| 3429 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
[2047] | 3430 | } |
---|
[2064] | 3431 | |
---|
| 3432 | oss << endl; |
---|
[2193] | 3433 | oss << formatBaselineParamsFooter(rms, nClipped, verbose); |
---|
[2064] | 3434 | |
---|
| 3435 | return String(oss); |
---|
[2047] | 3436 | } |
---|
| 3437 | |
---|
| 3438 | } |
---|
| 3439 | |
---|
[2193] | 3440 | std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose) const |
---|
[2012] | 3441 | { |
---|
[2064] | 3442 | int nOutParam = (int)(params.size()); |
---|
| 3443 | int nPiece = (int)(ranges.size()) - 1; |
---|
[2012] | 3444 | |
---|
[2064] | 3445 | if (nOutParam < 1) { |
---|
| 3446 | return(" Not fitted"); |
---|
| 3447 | } else if (nPiece < 0) { |
---|
[2193] | 3448 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose); |
---|
[2064] | 3449 | } else if (nPiece < 1) { |
---|
| 3450 | return(" Bad count of the piece edge info"); |
---|
| 3451 | } else if (nOutParam % nPiece != 0) { |
---|
| 3452 | return(" Bad count of the output baseline parameters"); |
---|
| 3453 | } else { |
---|
| 3454 | |
---|
| 3455 | int nParam = nOutParam / nPiece; |
---|
| 3456 | |
---|
| 3457 | ostringstream oss; |
---|
| 3458 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose); |
---|
| 3459 | |
---|
| 3460 | stringstream ss; |
---|
| 3461 | ss << ranges[nPiece] << flush; |
---|
| 3462 | int wRange = ss.str().size() * 2 + 5; |
---|
| 3463 | |
---|
| 3464 | for (int i = 0; i < nPiece; ++i) { |
---|
[2047] | 3465 | ss.str(""); |
---|
[2064] | 3466 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
| 3467 | oss << left << setw(wRange) << ss.str(); |
---|
[2193] | 3468 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true); |
---|
[2012] | 3469 | } |
---|
[2064] | 3470 | |
---|
[2193] | 3471 | oss << formatBaselineParamsFooter(rms, nClipped, verbose); |
---|
[2064] | 3472 | |
---|
| 3473 | return String(oss); |
---|
[2012] | 3474 | } |
---|
| 3475 | |
---|
| 3476 | } |
---|
| 3477 | |
---|
[2047] | 3478 | bool Scantable::hasSameNchanOverIFs() |
---|
[2012] | 3479 | { |
---|
[2047] | 3480 | int nIF = nif(-1); |
---|
| 3481 | int nCh; |
---|
| 3482 | int totalPositiveNChan = 0; |
---|
| 3483 | int nPositiveNChan = 0; |
---|
[2012] | 3484 | |
---|
[2047] | 3485 | for (int i = 0; i < nIF; ++i) { |
---|
| 3486 | nCh = nchan(i); |
---|
| 3487 | if (nCh > 0) { |
---|
| 3488 | totalPositiveNChan += nCh; |
---|
| 3489 | nPositiveNChan++; |
---|
[2012] | 3490 | } |
---|
| 3491 | } |
---|
| 3492 | |
---|
[2047] | 3493 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
[2012] | 3494 | } |
---|
| 3495 | |
---|
[2047] | 3496 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
[2012] | 3497 | { |
---|
| 3498 | if (mask.size() < 2) { |
---|
| 3499 | throw(AipsError("The mask elements should be > 1")); |
---|
| 3500 | } |
---|
[2047] | 3501 | int IF = getIF(whichrow); |
---|
| 3502 | if (mask.size() != (uInt)nchan(IF)) { |
---|
[2012] | 3503 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
| 3504 | } |
---|
| 3505 | |
---|
[2047] | 3506 | if (verbose) { |
---|
[2012] | 3507 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
| 3508 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
| 3509 | if (!hasSameNchan) { |
---|
[2047] | 3510 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
[2012] | 3511 | } |
---|
| 3512 | logOs << LogIO::POST; |
---|
| 3513 | } |
---|
| 3514 | |
---|
| 3515 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
[2047] | 3516 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
| 3517 | |
---|
[2012] | 3518 | ostringstream oss; |
---|
| 3519 | oss.setf(ios::fixed); |
---|
| 3520 | oss << setprecision(1) << "["; |
---|
[2047] | 3521 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
[2012] | 3522 | if (i > 0) oss << ","; |
---|
[2047] | 3523 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
[2012] | 3524 | } |
---|
| 3525 | oss << "]" << flush; |
---|
| 3526 | |
---|
| 3527 | return String(oss); |
---|
| 3528 | } |
---|
| 3529 | |
---|
[2047] | 3530 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
[2012] | 3531 | { |
---|
[2047] | 3532 | if (mask.size() < 2) { |
---|
| 3533 | throw(AipsError("The mask elements should be > 1")); |
---|
[2012] | 3534 | } |
---|
| 3535 | |
---|
[2047] | 3536 | std::vector<int> out, startIndices, endIndices; |
---|
| 3537 | int maskSize = mask.size(); |
---|
[2012] | 3538 | |
---|
[2047] | 3539 | startIndices.clear(); |
---|
| 3540 | endIndices.clear(); |
---|
| 3541 | |
---|
| 3542 | if (mask[0]) { |
---|
| 3543 | startIndices.push_back(0); |
---|
[2012] | 3544 | } |
---|
[2047] | 3545 | for (int i = 1; i < maskSize; ++i) { |
---|
| 3546 | if ((!mask[i-1]) && mask[i]) { |
---|
| 3547 | startIndices.push_back(i); |
---|
| 3548 | } else if (mask[i-1] && (!mask[i])) { |
---|
| 3549 | endIndices.push_back(i-1); |
---|
| 3550 | } |
---|
[2012] | 3551 | } |
---|
[2047] | 3552 | if (mask[maskSize-1]) { |
---|
| 3553 | endIndices.push_back(maskSize-1); |
---|
| 3554 | } |
---|
[2012] | 3555 | |
---|
[2047] | 3556 | if (startIndices.size() != endIndices.size()) { |
---|
| 3557 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
| 3558 | } |
---|
| 3559 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 3560 | if (startIndices[i] > endIndices[i]) { |
---|
| 3561 | throw(AipsError("Mask start index > mask end index")); |
---|
[2012] | 3562 | } |
---|
| 3563 | } |
---|
| 3564 | |
---|
[2047] | 3565 | out.clear(); |
---|
| 3566 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 3567 | out.push_back(startIndices[i]); |
---|
| 3568 | out.push_back(endIndices[i]); |
---|
| 3569 | } |
---|
| 3570 | |
---|
[2012] | 3571 | return out; |
---|
| 3572 | } |
---|
| 3573 | |
---|
[2161] | 3574 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
| 3575 | { |
---|
| 3576 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
| 3577 | vector<float> stlTsys ; |
---|
| 3578 | tsys.tovector( stlTsys ) ; |
---|
| 3579 | return stlTsys ; |
---|
| 3580 | } |
---|
[2012] | 3581 | |
---|
| 3582 | |
---|
[1907] | 3583 | } |
---|
[1819] | 3584 | //namespace asap |
---|