[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();
|
---|
| 367 | if (errMesg == "Table column " + colName + " is unknown") {
|
---|
| 368 | table_.addColumn(ScalarColumnDesc<T>(colName));
|
---|
| 369 | col.attach(table_, colName);
|
---|
| 370 | col.fillColumn(static_cast<T>(defValue));
|
---|
| 371 | } else {
|
---|
| 372 | throw;
|
---|
| 373 | }
|
---|
| 374 | } catch (...) {
|
---|
| 375 | throw;
|
---|
| 376 | }
|
---|
| 377 | }
|
---|
| 378 |
|
---|
| 379 | template<class T, class T2>
|
---|
| 380 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
|
---|
| 381 | const String& colName,
|
---|
| 382 | const Array<T2>& defValue)
|
---|
| 383 | {
|
---|
| 384 | try {
|
---|
| 385 | col.attach(table_, colName);
|
---|
| 386 | } catch (TableError& err) {
|
---|
| 387 | String errMesg = err.getMesg();
|
---|
| 388 | if (errMesg == "Table column " + colName + " is unknown") {
|
---|
| 389 | table_.addColumn(ArrayColumnDesc<T>(colName));
|
---|
| 390 | col.attach(table_, colName);
|
---|
| 391 |
|
---|
| 392 | int size = 0;
|
---|
| 393 | ArrayIterator<T2>& it = defValue.begin();
|
---|
| 394 | while (it != defValue.end()) {
|
---|
| 395 | ++size;
|
---|
| 396 | ++it;
|
---|
| 397 | }
|
---|
| 398 | IPosition ip(1, size);
|
---|
| 399 | Array<T>& arr(ip);
|
---|
| 400 | for (int i = 0; i < size; ++i)
|
---|
| 401 | arr[i] = static_cast<T>(defValue[i]);
|
---|
| 402 |
|
---|
| 403 | col.fillColumn(arr);
|
---|
| 404 | } else {
|
---|
| 405 | throw;
|
---|
| 406 | }
|
---|
| 407 | } catch (...) {
|
---|
| 408 | throw;
|
---|
| 409 | }
|
---|
| 410 | }
|
---|
| 411 |
|
---|
[901] | 412 | void Scantable::setHeader(const STHeader& sdh)
|
---|
[206] | 413 | {
|
---|
[18] | 414 | table_.rwKeywordSet().define("nIF", sdh.nif);
|
---|
| 415 | table_.rwKeywordSet().define("nBeam", sdh.nbeam);
|
---|
| 416 | table_.rwKeywordSet().define("nPol", sdh.npol);
|
---|
| 417 | table_.rwKeywordSet().define("nChan", sdh.nchan);
|
---|
| 418 | table_.rwKeywordSet().define("Observer", sdh.observer);
|
---|
| 419 | table_.rwKeywordSet().define("Project", sdh.project);
|
---|
| 420 | table_.rwKeywordSet().define("Obstype", sdh.obstype);
|
---|
| 421 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
|
---|
| 422 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
|
---|
| 423 | table_.rwKeywordSet().define("Equinox", sdh.equinox);
|
---|
| 424 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
|
---|
| 425 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
|
---|
| 426 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
|
---|
| 427 | table_.rwKeywordSet().define("UTC", sdh.utc);
|
---|
[206] | 428 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
|
---|
| 429 | table_.rwKeywordSet().define("Epoch", sdh.epoch);
|
---|
[905] | 430 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
|
---|
[50] | 431 | }
|
---|
[21] | 432 |
|
---|
[901] | 433 | STHeader Scantable::getHeader() const
|
---|
[206] | 434 | {
|
---|
[901] | 435 | STHeader sdh;
|
---|
[21] | 436 | table_.keywordSet().get("nBeam",sdh.nbeam);
|
---|
| 437 | table_.keywordSet().get("nIF",sdh.nif);
|
---|
| 438 | table_.keywordSet().get("nPol",sdh.npol);
|
---|
| 439 | table_.keywordSet().get("nChan",sdh.nchan);
|
---|
| 440 | table_.keywordSet().get("Observer", sdh.observer);
|
---|
| 441 | table_.keywordSet().get("Project", sdh.project);
|
---|
| 442 | table_.keywordSet().get("Obstype", sdh.obstype);
|
---|
| 443 | table_.keywordSet().get("AntennaName", sdh.antennaname);
|
---|
| 444 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
|
---|
| 445 | table_.keywordSet().get("Equinox", sdh.equinox);
|
---|
| 446 | table_.keywordSet().get("FreqRefFrame", sdh.freqref);
|
---|
| 447 | table_.keywordSet().get("FreqRefVal", sdh.reffreq);
|
---|
| 448 | table_.keywordSet().get("Bandwidth", sdh.bandwidth);
|
---|
| 449 | table_.keywordSet().get("UTC", sdh.utc);
|
---|
[206] | 450 | table_.keywordSet().get("FluxUnit", sdh.fluxunit);
|
---|
| 451 | table_.keywordSet().get("Epoch", sdh.epoch);
|
---|
[905] | 452 | table_.keywordSet().get("POLTYPE", sdh.poltype);
|
---|
[21] | 453 | return sdh;
|
---|
[18] | 454 | }
|
---|
[805] | 455 |
|
---|
[1360] | 456 | void Scantable::setSourceType( int stype )
|
---|
[1068] | 457 | {
|
---|
| 458 | if ( stype < 0 || stype > 1 )
|
---|
| 459 | throw(AipsError("Illegal sourcetype."));
|
---|
| 460 | TableVector<Int> tabvec(table_, "SRCTYPE");
|
---|
| 461 | tabvec = Int(stype);
|
---|
| 462 | }
|
---|
| 463 |
|
---|
[845] | 464 | bool Scantable::conformant( const Scantable& other )
|
---|
| 465 | {
|
---|
| 466 | return this->getHeader().conformant(other.getHeader());
|
---|
| 467 | }
|
---|
| 468 |
|
---|
| 469 |
|
---|
[50] | 470 |
|
---|
[805] | 471 | std::string Scantable::formatSec(Double x) const
|
---|
[206] | 472 | {
|
---|
[105] | 473 | Double xcop = x;
|
---|
| 474 | MVTime mvt(xcop/24./3600.); // make days
|
---|
[365] | 475 |
|
---|
[105] | 476 | if (x < 59.95)
|
---|
[281] | 477 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
|
---|
[745] | 478 | else if (x < 3599.95)
|
---|
[281] | 479 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
|
---|
| 480 | else {
|
---|
| 481 | ostringstream oss;
|
---|
| 482 | oss << setw(2) << std::right << setprecision(1) << mvt.hour();
|
---|
| 483 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
|
---|
| 484 | return String(oss);
|
---|
[745] | 485 | }
|
---|
[105] | 486 | };
|
---|
| 487 |
|
---|
[805] | 488 | std::string Scantable::formatDirection(const MDirection& md) const
|
---|
[281] | 489 | {
|
---|
| 490 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
|
---|
| 491 | Int prec = 7;
|
---|
| 492 |
|
---|
| 493 | MVAngle mvLon(t[0]);
|
---|
| 494 | String sLon = mvLon.string(MVAngle::TIME,prec);
|
---|
[987] | 495 | uInt tp = md.getRef().getType();
|
---|
| 496 | if (tp == MDirection::GALACTIC ||
|
---|
| 497 | tp == MDirection::SUPERGAL ) {
|
---|
| 498 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
|
---|
| 499 | }
|
---|
[281] | 500 | MVAngle mvLat(t[1]);
|
---|
| 501 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
|
---|
[380] | 502 | return sLon + String(" ") + sLat;
|
---|
[281] | 503 | }
|
---|
| 504 |
|
---|
| 505 |
|
---|
[805] | 506 | std::string Scantable::getFluxUnit() const
|
---|
[206] | 507 | {
|
---|
[847] | 508 | return table_.keywordSet().asString("FluxUnit");
|
---|
[206] | 509 | }
|
---|
| 510 |
|
---|
[805] | 511 | void Scantable::setFluxUnit(const std::string& unit)
|
---|
[218] | 512 | {
|
---|
| 513 | String tmp(unit);
|
---|
| 514 | Unit tU(tmp);
|
---|
| 515 | if (tU==Unit("K") || tU==Unit("Jy")) {
|
---|
| 516 | table_.rwKeywordSet().define(String("FluxUnit"), tmp);
|
---|
| 517 | } else {
|
---|
| 518 | throw AipsError("Illegal unit - must be compatible with Jy or K");
|
---|
| 519 | }
|
---|
| 520 | }
|
---|
| 521 |
|
---|
[805] | 522 | void Scantable::setInstrument(const std::string& name)
|
---|
[236] | 523 | {
|
---|
[805] | 524 | bool throwIt = true;
|
---|
[996] | 525 | // create an Instrument to see if this is valid
|
---|
| 526 | STAttr::convertInstrument(name, throwIt);
|
---|
[236] | 527 | String nameU(name);
|
---|
| 528 | nameU.upcase();
|
---|
| 529 | table_.rwKeywordSet().define(String("AntennaName"), nameU);
|
---|
| 530 | }
|
---|
| 531 |
|
---|
[1189] | 532 | void Scantable::setFeedType(const std::string& feedtype)
|
---|
| 533 | {
|
---|
| 534 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
|
---|
| 535 | std::string msg = "Illegal feed type "+ feedtype;
|
---|
| 536 | throw(casa::AipsError(msg));
|
---|
| 537 | }
|
---|
| 538 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
|
---|
| 539 | }
|
---|
| 540 |
|
---|
[1743] | 541 | MPosition Scantable::getAntennaPosition() const
|
---|
[805] | 542 | {
|
---|
| 543 | Vector<Double> antpos;
|
---|
| 544 | table_.keywordSet().get("AntennaPosition", antpos);
|
---|
| 545 | MVPosition mvpos(antpos(0),antpos(1),antpos(2));
|
---|
| 546 | return MPosition(mvpos);
|
---|
| 547 | }
|
---|
[281] | 548 |
|
---|
[805] | 549 | void Scantable::makePersistent(const std::string& filename)
|
---|
| 550 | {
|
---|
| 551 | String inname(filename);
|
---|
| 552 | Path path(inname);
|
---|
[1111] | 553 | /// @todo reindex SCANNO, recompute nbeam, nif, npol
|
---|
[805] | 554 | inname = path.expandedName();
|
---|
[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 | // }
|
---|
[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");
|
---|
[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);
|
---|
| 998 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
|
---|
| 999 | << setw(15) << "IFs:" << setw(4) << nif() << endl
|
---|
[896] | 1000 | << setw(15) << "Polarisations:" << setw(4) << npol()
|
---|
| 1001 | << "(" << getPolType() << ")" << endl
|
---|
[1694] | 1002 | << setw(15) << "Channels:" << nchan() << endl;
|
---|
[805] | 1003 | String tmp;
|
---|
[860] | 1004 | oss << setw(15) << "Observer:"
|
---|
| 1005 | << table_.keywordSet().asString("Observer") << endl;
|
---|
[805] | 1006 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
|
---|
| 1007 | table_.keywordSet().get("Project", tmp);
|
---|
| 1008 | oss << setw(15) << "Project:" << tmp << endl;
|
---|
| 1009 | table_.keywordSet().get("Obstype", tmp);
|
---|
| 1010 | oss << setw(15) << "Obs. Type:" << tmp << endl;
|
---|
| 1011 | table_.keywordSet().get("AntennaName", tmp);
|
---|
| 1012 | oss << setw(15) << "Antenna Name:" << tmp << endl;
|
---|
| 1013 | table_.keywordSet().get("FluxUnit", tmp);
|
---|
| 1014 | oss << setw(15) << "Flux Unit:" << tmp << endl;
|
---|
[1819] | 1015 | //Vector<Double> vec(moleculeTable_.getRestFrequencies());
|
---|
| 1016 | int nid = moleculeTable_.nrow();
|
---|
| 1017 | Bool firstline = True;
|
---|
[805] | 1018 | oss << setw(15) << "Rest Freqs:";
|
---|
[1819] | 1019 | for (int i=0; i<nid; i++) {
|
---|
[2244] | 1020 | Table t = table_(table_.col("MOLECULE_ID") == i, 1);
|
---|
[1819] | 1021 | if (t.nrow() > 0) {
|
---|
| 1022 | Vector<Double> vec(moleculeTable_.getRestFrequency(i));
|
---|
| 1023 | if (vec.nelements() > 0) {
|
---|
| 1024 | if (firstline) {
|
---|
| 1025 | oss << setprecision(10) << vec << " [Hz]" << endl;
|
---|
| 1026 | firstline=False;
|
---|
| 1027 | }
|
---|
| 1028 | else{
|
---|
| 1029 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
|
---|
| 1030 | }
|
---|
| 1031 | } else {
|
---|
| 1032 | oss << "none" << endl;
|
---|
| 1033 | }
|
---|
| 1034 | }
|
---|
[805] | 1035 | }
|
---|
[941] | 1036 |
|
---|
| 1037 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
|
---|
[805] | 1038 | oss << selector_.print() << endl;
|
---|
[2111] | 1039 | return String(oss);
|
---|
| 1040 | }
|
---|
| 1041 |
|
---|
[2286] | 1042 | //std::string Scantable::summary( const std::string& filename )
|
---|
| 1043 | void Scantable::summary( const std::string& filename )
|
---|
[2111] | 1044 | {
|
---|
| 1045 | ostringstream oss;
|
---|
[2286] | 1046 | ofstream ofs;
|
---|
| 1047 | LogIO ols(LogOrigin("Scantable", "summary", WHERE));
|
---|
| 1048 |
|
---|
| 1049 | if (filename != "")
|
---|
| 1050 | ofs.open( filename.c_str(), ios::out );
|
---|
| 1051 |
|
---|
[805] | 1052 | oss << endl;
|
---|
[2111] | 1053 | oss << asap::SEPERATOR << endl;
|
---|
| 1054 | oss << " Scan Table Summary" << endl;
|
---|
| 1055 | oss << asap::SEPERATOR << endl;
|
---|
| 1056 |
|
---|
| 1057 | // Format header info
|
---|
[2163] | 1058 | oss << headerSummary();
|
---|
[2111] | 1059 | oss << endl;
|
---|
| 1060 |
|
---|
[805] | 1061 | // main table
|
---|
| 1062 | String dirtype = "Position ("
|
---|
[987] | 1063 | + getDirectionRefString()
|
---|
[805] | 1064 | + ")";
|
---|
[2111] | 1065 | oss.flags(std::ios_base::left);
|
---|
[941] | 1066 | oss << setw(5) << "Scan" << setw(15) << "Source"
|
---|
[2005] | 1067 | << setw(10) << "Time" << setw(18) << "Integration"
|
---|
| 1068 | << setw(15) << "Source Type" << endl;
|
---|
[941] | 1069 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
|
---|
[1694] | 1070 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
|
---|
[805] | 1071 | << setw(8) << "Frame" << setw(16)
|
---|
[1694] | 1072 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
|
---|
| 1073 | << setw(7) << "Channels"
|
---|
| 1074 | << endl;
|
---|
[805] | 1075 | oss << asap::SEPERATOR << endl;
|
---|
[2286] | 1076 |
|
---|
| 1077 | // Flush summary and clear up the string
|
---|
| 1078 | ols << String(oss) << LogIO::POST;
|
---|
| 1079 | if (ofs) ofs << String(oss) << flush;
|
---|
| 1080 | oss.str("");
|
---|
| 1081 | oss.clear();
|
---|
| 1082 |
|
---|
| 1083 | // TableIterator iter(table_, "SCANNO");
|
---|
| 1084 | // while (!iter.pastEnd()) {
|
---|
| 1085 | // Table subt = iter.table();
|
---|
| 1086 | // ROTableRow row(subt);
|
---|
| 1087 | // MEpoch::ROScalarColumn timeCol(subt,"TIME");
|
---|
| 1088 | // const TableRecord& rec = row.get(0);
|
---|
| 1089 | // oss << setw(4) << std::right << rec.asuInt("SCANNO")
|
---|
| 1090 | // << std::left << setw(1) << ""
|
---|
| 1091 | // << setw(15) << rec.asString("SRCNAME")
|
---|
| 1092 | // << setw(10) << formatTime(timeCol(0), false);
|
---|
| 1093 | // // count the cycles in the scan
|
---|
| 1094 | // TableIterator cyciter(subt, "CYCLENO");
|
---|
| 1095 | // int nint = 0;
|
---|
| 1096 | // while (!cyciter.pastEnd()) {
|
---|
| 1097 | // ++nint;
|
---|
| 1098 | // ++cyciter;
|
---|
| 1099 | // }
|
---|
| 1100 | // oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
|
---|
| 1101 | // << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
|
---|
| 1102 | // << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
|
---|
| 1103 |
|
---|
| 1104 | // TableIterator biter(subt, "BEAMNO");
|
---|
| 1105 | // while (!biter.pastEnd()) {
|
---|
| 1106 | // Table bsubt = biter.table();
|
---|
| 1107 | // ROTableRow brow(bsubt);
|
---|
| 1108 | // const TableRecord& brec = brow.get(0);
|
---|
| 1109 | // uInt row0 = bsubt.rowNumbers(table_)[0];
|
---|
| 1110 | // oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
|
---|
| 1111 | // oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
|
---|
| 1112 | // TableIterator iiter(bsubt, "IFNO");
|
---|
| 1113 | // while (!iiter.pastEnd()) {
|
---|
| 1114 | // Table isubt = iiter.table();
|
---|
| 1115 | // ROTableRow irow(isubt);
|
---|
| 1116 | // const TableRecord& irec = irow.get(0);
|
---|
| 1117 | // oss << setw(9) << "";
|
---|
| 1118 | // oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
|
---|
| 1119 | // << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
|
---|
| 1120 | // << setw(3) << "" << nchan(irec.asuInt("IFNO"))
|
---|
| 1121 | // << endl;
|
---|
| 1122 |
|
---|
| 1123 | // ++iiter;
|
---|
| 1124 | // }
|
---|
| 1125 | // ++biter;
|
---|
| 1126 | // }
|
---|
| 1127 | // ++iter;
|
---|
| 1128 | // }
|
---|
[805] | 1129 | TableIterator iter(table_, "SCANNO");
|
---|
| 1130 | while (!iter.pastEnd()) {
|
---|
| 1131 | Table subt = iter.table();
|
---|
| 1132 | ROTableRow row(subt);
|
---|
| 1133 | MEpoch::ROScalarColumn timeCol(subt,"TIME");
|
---|
| 1134 | const TableRecord& rec = row.get(0);
|
---|
| 1135 | oss << setw(4) << std::right << rec.asuInt("SCANNO")
|
---|
| 1136 | << std::left << setw(1) << ""
|
---|
| 1137 | << setw(15) << rec.asString("SRCNAME")
|
---|
| 1138 | << setw(10) << formatTime(timeCol(0), false);
|
---|
| 1139 | // count the cycles in the scan
|
---|
| 1140 | TableIterator cyciter(subt, "CYCLENO");
|
---|
| 1141 | int nint = 0;
|
---|
| 1142 | while (!cyciter.pastEnd()) {
|
---|
| 1143 | ++nint;
|
---|
| 1144 | ++cyciter;
|
---|
| 1145 | }
|
---|
| 1146 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
|
---|
[2005] | 1147 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
|
---|
| 1148 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
|
---|
[447] | 1149 |
|
---|
[805] | 1150 | TableIterator biter(subt, "BEAMNO");
|
---|
| 1151 | while (!biter.pastEnd()) {
|
---|
| 1152 | Table bsubt = biter.table();
|
---|
| 1153 | ROTableRow brow(bsubt);
|
---|
| 1154 | const TableRecord& brec = brow.get(0);
|
---|
[1000] | 1155 | uInt row0 = bsubt.rowNumbers(table_)[0];
|
---|
[941] | 1156 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
|
---|
[987] | 1157 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
|
---|
[805] | 1158 | TableIterator iiter(bsubt, "IFNO");
|
---|
| 1159 | while (!iiter.pastEnd()) {
|
---|
| 1160 | Table isubt = iiter.table();
|
---|
| 1161 | ROTableRow irow(isubt);
|
---|
| 1162 | const TableRecord& irec = irow.get(0);
|
---|
[1694] | 1163 | oss << setw(9) << "";
|
---|
[941] | 1164 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
|
---|
[1694] | 1165 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
|
---|
| 1166 | << setw(3) << "" << nchan(irec.asuInt("IFNO"))
|
---|
[1375] | 1167 | << endl;
|
---|
[447] | 1168 |
|
---|
[805] | 1169 | ++iiter;
|
---|
| 1170 | }
|
---|
| 1171 | ++biter;
|
---|
| 1172 | }
|
---|
[2286] | 1173 | // Flush summary every scan and clear up the string
|
---|
| 1174 | ols << String(oss) << LogIO::POST;
|
---|
| 1175 | if (ofs) ofs << String(oss) << flush;
|
---|
| 1176 | oss.str("");
|
---|
| 1177 | oss.clear();
|
---|
| 1178 |
|
---|
[805] | 1179 | ++iter;
|
---|
[447] | 1180 | }
|
---|
[2286] | 1181 | oss << asap::SEPERATOR << endl;
|
---|
| 1182 | ols << String(oss) << LogIO::POST;
|
---|
| 1183 | if (ofs) {
|
---|
| 1184 | //ofs << String(oss) << flush;
|
---|
| 1185 | ofs.close();
|
---|
| 1186 | }
|
---|
| 1187 | // return String(oss);
|
---|
[447] | 1188 | }
|
---|
| 1189 |
|
---|
[1947] | 1190 | // std::string Scantable::getTime(int whichrow, bool showdate) const
|
---|
| 1191 | // {
|
---|
| 1192 | // MEpoch::ROScalarColumn timeCol(table_, "TIME");
|
---|
| 1193 | // MEpoch me;
|
---|
| 1194 | // if (whichrow > -1) {
|
---|
| 1195 | // me = timeCol(uInt(whichrow));
|
---|
| 1196 | // } else {
|
---|
| 1197 | // Double tm;
|
---|
| 1198 | // table_.keywordSet().get("UTC",tm);
|
---|
| 1199 | // me = MEpoch(MVEpoch(tm));
|
---|
| 1200 | // }
|
---|
| 1201 | // return formatTime(me, showdate);
|
---|
| 1202 | // }
|
---|
| 1203 |
|
---|
| 1204 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
|
---|
[777] | 1205 | {
|
---|
[805] | 1206 | MEpoch me;
|
---|
[1947] | 1207 | me = getEpoch(whichrow);
|
---|
| 1208 | return formatTime(me, showdate, prec);
|
---|
[777] | 1209 | }
|
---|
[805] | 1210 |
|
---|
[1411] | 1211 | MEpoch Scantable::getEpoch(int whichrow) const
|
---|
| 1212 | {
|
---|
| 1213 | if (whichrow > -1) {
|
---|
| 1214 | return timeCol_(uInt(whichrow));
|
---|
| 1215 | } else {
|
---|
| 1216 | Double tm;
|
---|
| 1217 | table_.keywordSet().get("UTC",tm);
|
---|
[1598] | 1218 | return MEpoch(MVEpoch(tm));
|
---|
[1411] | 1219 | }
|
---|
| 1220 | }
|
---|
| 1221 |
|
---|
[1068] | 1222 | std::string Scantable::getDirectionString(int whichrow) const
|
---|
| 1223 | {
|
---|
| 1224 | return formatDirection(getDirection(uInt(whichrow)));
|
---|
| 1225 | }
|
---|
| 1226 |
|
---|
[1598] | 1227 |
|
---|
| 1228 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
|
---|
| 1229 | const MPosition& mp = getAntennaPosition();
|
---|
| 1230 | const MDirection& md = getDirection(whichrow);
|
---|
| 1231 | const MEpoch& me = timeCol_(whichrow);
|
---|
[1819] | 1232 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
|
---|
| 1233 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
|
---|
[1598] | 1234 | return freqTable_.getSpectralCoordinate(md, mp, me, rf,
|
---|
| 1235 | mfreqidCol_(whichrow));
|
---|
| 1236 | }
|
---|
| 1237 |
|
---|
[1360] | 1238 | std::vector< double > Scantable::getAbcissa( int whichrow ) const
|
---|
[865] | 1239 | {
|
---|
[1507] | 1240 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
|
---|
[865] | 1241 | std::vector<double> stlout;
|
---|
| 1242 | int nchan = specCol_(whichrow).nelements();
|
---|
| 1243 | String us = freqTable_.getUnitString();
|
---|
| 1244 | if ( us == "" || us == "pixel" || us == "channel" ) {
|
---|
| 1245 | for (int i=0; i<nchan; ++i) {
|
---|
| 1246 | stlout.push_back(double(i));
|
---|
| 1247 | }
|
---|
| 1248 | return stlout;
|
---|
| 1249 | }
|
---|
[1598] | 1250 | SpectralCoordinate spc = getSpectralCoordinate(whichrow);
|
---|
[865] | 1251 | Vector<Double> pixel(nchan);
|
---|
| 1252 | Vector<Double> world;
|
---|
| 1253 | indgen(pixel);
|
---|
| 1254 | if ( Unit(us) == Unit("Hz") ) {
|
---|
| 1255 | for ( int i=0; i < nchan; ++i) {
|
---|
| 1256 | Double world;
|
---|
| 1257 | spc.toWorld(world, pixel[i]);
|
---|
| 1258 | stlout.push_back(double(world));
|
---|
| 1259 | }
|
---|
| 1260 | } else if ( Unit(us) == Unit("km/s") ) {
|
---|
| 1261 | Vector<Double> world;
|
---|
| 1262 | spc.pixelToVelocity(world, pixel);
|
---|
| 1263 | world.tovector(stlout);
|
---|
| 1264 | }
|
---|
| 1265 | return stlout;
|
---|
| 1266 | }
|
---|
[1360] | 1267 | void Scantable::setDirectionRefString( const std::string & refstr )
|
---|
[987] | 1268 | {
|
---|
| 1269 | MDirection::Types mdt;
|
---|
| 1270 | if (refstr != "" && !MDirection::getType(mdt, refstr)) {
|
---|
| 1271 | throw(AipsError("Illegal Direction frame."));
|
---|
| 1272 | }
|
---|
| 1273 | if ( refstr == "" ) {
|
---|
| 1274 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
|
---|
| 1275 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
|
---|
| 1276 | } else {
|
---|
| 1277 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
|
---|
| 1278 | }
|
---|
| 1279 | }
|
---|
[865] | 1280 |
|
---|
[1360] | 1281 | std::string Scantable::getDirectionRefString( ) const
|
---|
[987] | 1282 | {
|
---|
| 1283 | return table_.keywordSet().asString("DIRECTIONREF");
|
---|
| 1284 | }
|
---|
| 1285 |
|
---|
| 1286 | MDirection Scantable::getDirection(int whichrow ) const
|
---|
| 1287 | {
|
---|
| 1288 | String usertype = table_.keywordSet().asString("DIRECTIONREF");
|
---|
| 1289 | String type = MDirection::showType(dirCol_.getMeasRef().getType());
|
---|
| 1290 | if ( usertype != type ) {
|
---|
| 1291 | MDirection::Types mdt;
|
---|
| 1292 | if (!MDirection::getType(mdt, usertype)) {
|
---|
| 1293 | throw(AipsError("Illegal Direction frame."));
|
---|
| 1294 | }
|
---|
| 1295 | return dirCol_.convert(uInt(whichrow), mdt);
|
---|
| 1296 | } else {
|
---|
| 1297 | return dirCol_(uInt(whichrow));
|
---|
| 1298 | }
|
---|
| 1299 | }
|
---|
| 1300 |
|
---|
[847] | 1301 | std::string Scantable::getAbcissaLabel( int whichrow ) const
|
---|
| 1302 | {
|
---|
[996] | 1303 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
|
---|
[847] | 1304 | const MPosition& mp = getAntennaPosition();
|
---|
[987] | 1305 | const MDirection& md = getDirection(whichrow);
|
---|
[847] | 1306 | const MEpoch& me = timeCol_(whichrow);
|
---|
[1819] | 1307 | //const Double& rf = mmolidCol_(whichrow);
|
---|
| 1308 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
|
---|
[847] | 1309 | SpectralCoordinate spc =
|
---|
| 1310 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
|
---|
| 1311 |
|
---|
| 1312 | String s = "Channel";
|
---|
| 1313 | Unit u = Unit(freqTable_.getUnitString());
|
---|
| 1314 | if (u == Unit("km/s")) {
|
---|
[1170] | 1315 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
|
---|
[847] | 1316 | } else if (u == Unit("Hz")) {
|
---|
| 1317 | Vector<String> wau(1);wau = u.getName();
|
---|
| 1318 | spc.setWorldAxisUnits(wau);
|
---|
[1170] | 1319 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
|
---|
[847] | 1320 | }
|
---|
| 1321 | return s;
|
---|
| 1322 |
|
---|
| 1323 | }
|
---|
| 1324 |
|
---|
[1819] | 1325 | /**
|
---|
| 1326 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
|
---|
[1170] | 1327 | const std::string& unit )
|
---|
[1819] | 1328 | **/
|
---|
| 1329 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
|
---|
| 1330 | const std::string& unit )
|
---|
| 1331 |
|
---|
[847] | 1332 | {
|
---|
[923] | 1333 | ///@todo lookup in line table to fill in name and formattedname
|
---|
[847] | 1334 | Unit u(unit);
|
---|
[1819] | 1335 | //Quantum<Double> urf(rf, u);
|
---|
| 1336 | Quantum<Vector<Double> >urf(rf, u);
|
---|
| 1337 | Vector<String> formattedname(0);
|
---|
| 1338 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
|
---|
| 1339 |
|
---|
| 1340 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
|
---|
| 1341 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
|
---|
[847] | 1342 | TableVector<uInt> tabvec(table_, "MOLECULE_ID");
|
---|
| 1343 | tabvec = id;
|
---|
| 1344 | }
|
---|
| 1345 |
|
---|
[1819] | 1346 | /**
|
---|
| 1347 | void asap::Scantable::setRestFrequencies( const std::string& name )
|
---|
[847] | 1348 | {
|
---|
| 1349 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
|
---|
| 1350 | ///@todo implement
|
---|
| 1351 | }
|
---|
[1819] | 1352 | **/
|
---|
[2012] | 1353 |
|
---|
[1819] | 1354 | void Scantable::setRestFrequencies( const vector<std::string>& name )
|
---|
| 1355 | {
|
---|
[2163] | 1356 | (void) name; // suppress unused warning
|
---|
[1819] | 1357 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
|
---|
| 1358 | ///@todo implement
|
---|
| 1359 | }
|
---|
[847] | 1360 |
|
---|
[1360] | 1361 | std::vector< unsigned int > Scantable::rownumbers( ) const
|
---|
[852] | 1362 | {
|
---|
| 1363 | std::vector<unsigned int> stlout;
|
---|
| 1364 | Vector<uInt> vec = table_.rowNumbers();
|
---|
| 1365 | vec.tovector(stlout);
|
---|
| 1366 | return stlout;
|
---|
| 1367 | }
|
---|
| 1368 |
|
---|
[865] | 1369 |
|
---|
[1360] | 1370 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
|
---|
[896] | 1371 | {
|
---|
| 1372 | ROTableRow row(table_);
|
---|
| 1373 | const TableRecord& rec = row.get(whichrow);
|
---|
| 1374 | Table t =
|
---|
| 1375 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
|
---|
| 1376 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
| 1377 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
| 1378 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
|
---|
| 1379 | ROArrayColumn<Float> speccol(t, "SPECTRA");
|
---|
| 1380 | return speccol.getColumn();
|
---|
| 1381 | }
|
---|
[865] | 1382 |
|
---|
[1360] | 1383 | std::vector< std::string > Scantable::columnNames( ) const
|
---|
[902] | 1384 | {
|
---|
| 1385 | Vector<String> vec = table_.tableDesc().columnNames();
|
---|
| 1386 | return mathutil::tovectorstring(vec);
|
---|
| 1387 | }
|
---|
[896] | 1388 |
|
---|
[1360] | 1389 | MEpoch::Types Scantable::getTimeReference( ) const
|
---|
[915] | 1390 | {
|
---|
| 1391 | return MEpoch::castType(timeCol_.getMeasRef().getType());
|
---|
[972] | 1392 | }
|
---|
[915] | 1393 |
|
---|
[1360] | 1394 | void Scantable::addFit( const STFitEntry& fit, int row )
|
---|
[972] | 1395 | {
|
---|
[1819] | 1396 | //cout << mfitidCol_(uInt(row)) << endl;
|
---|
| 1397 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
|
---|
| 1398 | os << mfitidCol_(uInt(row)) << LogIO::POST ;
|
---|
[972] | 1399 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
|
---|
| 1400 | mfitidCol_.put(uInt(row), id);
|
---|
| 1401 | }
|
---|
[915] | 1402 |
|
---|
[1360] | 1403 | void Scantable::shift(int npix)
|
---|
| 1404 | {
|
---|
| 1405 | Vector<uInt> fids(mfreqidCol_.getColumn());
|
---|
| 1406 | genSort( fids, Sort::Ascending,
|
---|
| 1407 | Sort::QuickSort|Sort::NoDuplicates );
|
---|
| 1408 | for (uInt i=0; i<fids.nelements(); ++i) {
|
---|
[1567] | 1409 | frequencies().shiftRefPix(npix, fids[i]);
|
---|
[1360] | 1410 | }
|
---|
| 1411 | }
|
---|
[987] | 1412 |
|
---|
[1819] | 1413 | String Scantable::getAntennaName() const
|
---|
[1391] | 1414 | {
|
---|
| 1415 | String out;
|
---|
| 1416 | table_.keywordSet().get("AntennaName", out);
|
---|
[1987] | 1417 | String::size_type pos1 = out.find("@") ;
|
---|
| 1418 | String::size_type pos2 = out.find("//") ;
|
---|
| 1419 | if ( pos2 != String::npos )
|
---|
[2036] | 1420 | out = out.substr(pos2+2,pos1-pos2-2) ;
|
---|
[1987] | 1421 | else if ( pos1 != String::npos )
|
---|
| 1422 | out = out.substr(0,pos1) ;
|
---|
[1391] | 1423 | return out;
|
---|
[987] | 1424 | }
|
---|
[1391] | 1425 |
|
---|
[1730] | 1426 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
|
---|
[1391] | 1427 | {
|
---|
| 1428 | String tbpath;
|
---|
| 1429 | int ret = 0;
|
---|
| 1430 | if ( table_.keywordSet().isDefined("GBT_GO") ) {
|
---|
| 1431 | table_.keywordSet().get("GBT_GO", tbpath);
|
---|
| 1432 | Table t(tbpath,Table::Old);
|
---|
| 1433 | // check each scan if other scan of the pair exist
|
---|
| 1434 | int nscan = scanlist.size();
|
---|
| 1435 | for (int i = 0; i < nscan; i++) {
|
---|
| 1436 | Table subt = t( t.col("SCAN") == scanlist[i]+1 );
|
---|
| 1437 | if (subt.nrow()==0) {
|
---|
[1819] | 1438 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
|
---|
| 1439 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1440 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
|
---|
[1391] | 1441 | ret = 1;
|
---|
| 1442 | break;
|
---|
| 1443 | }
|
---|
| 1444 | ROTableRow row(subt);
|
---|
| 1445 | const TableRecord& rec = row.get(0);
|
---|
| 1446 | int scan1seqn = rec.asuInt("PROCSEQN");
|
---|
| 1447 | int laston1 = rec.asuInt("LASTON");
|
---|
| 1448 | if ( rec.asuInt("PROCSIZE")==2 ) {
|
---|
| 1449 | if ( i < nscan-1 ) {
|
---|
| 1450 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
|
---|
| 1451 | if ( subt2.nrow() == 0) {
|
---|
[1819] | 1452 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1453 |
|
---|
| 1454 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
|
---|
| 1455 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
|
---|
[1391] | 1456 | ret = 1;
|
---|
| 1457 | break;
|
---|
| 1458 | }
|
---|
| 1459 | ROTableRow row2(subt2);
|
---|
| 1460 | const TableRecord& rec2 = row2.get(0);
|
---|
| 1461 | int scan2seqn = rec2.asuInt("PROCSEQN");
|
---|
| 1462 | int laston2 = rec2.asuInt("LASTON");
|
---|
| 1463 | if (scan1seqn == 1 && scan2seqn == 2) {
|
---|
| 1464 | if (laston1 == laston2) {
|
---|
[1819] | 1465 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1466 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
|
---|
| 1467 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
|
---|
[1391] | 1468 | i +=1;
|
---|
| 1469 | }
|
---|
| 1470 | else {
|
---|
[1819] | 1471 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1472 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
|
---|
| 1473 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
|
---|
[1391] | 1474 | }
|
---|
| 1475 | }
|
---|
| 1476 | else if (scan1seqn==2 && scan2seqn == 1) {
|
---|
| 1477 | if (laston1 == laston2) {
|
---|
[1819] | 1478 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1479 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
|
---|
| 1480 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
|
---|
[1391] | 1481 | ret = 1;
|
---|
| 1482 | break;
|
---|
| 1483 | }
|
---|
| 1484 | }
|
---|
| 1485 | else {
|
---|
[1819] | 1486 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1487 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
|
---|
| 1488 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
|
---|
[1391] | 1489 | ret = 1;
|
---|
| 1490 | break;
|
---|
| 1491 | }
|
---|
| 1492 | }
|
---|
| 1493 | }
|
---|
| 1494 | else {
|
---|
[1819] | 1495 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1496 | //cerr<<"The scan does not appear to be standard obsevation."<<endl;
|
---|
| 1497 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
|
---|
[1391] | 1498 | }
|
---|
| 1499 | //if ( i >= nscan ) break;
|
---|
| 1500 | }
|
---|
| 1501 | }
|
---|
| 1502 | else {
|
---|
[1819] | 1503 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
|
---|
| 1504 | //cerr<<"No reference to GBT_GO table."<<endl;
|
---|
| 1505 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
|
---|
[1391] | 1506 | ret = 1;
|
---|
| 1507 | }
|
---|
| 1508 | return ret;
|
---|
| 1509 | }
|
---|
| 1510 |
|
---|
[1730] | 1511 | std::vector<double> Scantable::getDirectionVector(int whichrow) const
|
---|
[1391] | 1512 | {
|
---|
| 1513 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
|
---|
| 1514 | std::vector<double> dir;
|
---|
| 1515 | Dir.tovector(dir);
|
---|
| 1516 | return dir;
|
---|
| 1517 | }
|
---|
| 1518 |
|
---|
[1819] | 1519 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
|
---|
| 1520 | throw( casa::AipsError )
|
---|
| 1521 | {
|
---|
| 1522 | // assumed that all rows have same nChan
|
---|
| 1523 | Vector<Float> arr = specCol_( 0 ) ;
|
---|
| 1524 | int nChan = arr.nelements() ;
|
---|
| 1525 |
|
---|
| 1526 | // if nmin < 0 or nmax < 0, nothing to do
|
---|
| 1527 | if ( nmin < 0 ) {
|
---|
| 1528 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
|
---|
| 1529 | }
|
---|
| 1530 | if ( nmax < 0 ) {
|
---|
| 1531 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
|
---|
| 1532 | }
|
---|
| 1533 |
|
---|
| 1534 | // if nmin > nmax, exchange values
|
---|
| 1535 | if ( nmin > nmax ) {
|
---|
| 1536 | int tmp = nmax ;
|
---|
| 1537 | nmax = nmin ;
|
---|
| 1538 | nmin = tmp ;
|
---|
| 1539 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
|
---|
| 1540 | os << "Swap values. Applied range is ["
|
---|
| 1541 | << nmin << ", " << nmax << "]" << LogIO::POST ;
|
---|
| 1542 | }
|
---|
| 1543 |
|
---|
| 1544 | // if nmin exceeds nChan, nothing to do
|
---|
| 1545 | if ( nmin >= nChan ) {
|
---|
| 1546 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
|
---|
| 1547 | }
|
---|
| 1548 |
|
---|
| 1549 | // if nmax exceeds nChan, reset nmax to nChan
|
---|
| 1550 | if ( nmax >= nChan ) {
|
---|
| 1551 | if ( nmin == 0 ) {
|
---|
| 1552 | // nothing to do
|
---|
| 1553 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
|
---|
| 1554 | os << "Whole range is selected. Nothing to do." << LogIO::POST ;
|
---|
| 1555 | return ;
|
---|
| 1556 | }
|
---|
| 1557 | else {
|
---|
| 1558 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
|
---|
| 1559 | os << "Specified maximum exceeds nChan. Applied range is ["
|
---|
| 1560 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
|
---|
| 1561 | nmax = nChan - 1 ;
|
---|
| 1562 | }
|
---|
| 1563 | }
|
---|
| 1564 |
|
---|
| 1565 | // reshape specCol_ and flagCol_
|
---|
| 1566 | for ( int irow = 0 ; irow < nrow() ; irow++ ) {
|
---|
| 1567 | reshapeSpectrum( nmin, nmax, irow ) ;
|
---|
| 1568 | }
|
---|
| 1569 |
|
---|
| 1570 | // update FREQUENCIES subtable
|
---|
| 1571 | Double refpix ;
|
---|
| 1572 | Double refval ;
|
---|
| 1573 | Double increment ;
|
---|
| 1574 | int freqnrow = freqTable_.table().nrow() ;
|
---|
| 1575 | Vector<uInt> oldId( freqnrow ) ;
|
---|
| 1576 | Vector<uInt> newId( freqnrow ) ;
|
---|
| 1577 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
|
---|
| 1578 | freqTable_.getEntry( refpix, refval, increment, irow ) ;
|
---|
| 1579 | /***
|
---|
| 1580 | * need to shift refpix to nmin
|
---|
| 1581 | * note that channel nmin in old index will be channel 0 in new one
|
---|
| 1582 | ***/
|
---|
| 1583 | refval = refval - ( refpix - nmin ) * increment ;
|
---|
| 1584 | refpix = 0 ;
|
---|
| 1585 | freqTable_.setEntry( refpix, refval, increment, irow ) ;
|
---|
| 1586 | }
|
---|
| 1587 |
|
---|
| 1588 | // update nchan
|
---|
| 1589 | int newsize = nmax - nmin + 1 ;
|
---|
| 1590 | table_.rwKeywordSet().define( "nChan", newsize ) ;
|
---|
| 1591 |
|
---|
| 1592 | // update bandwidth
|
---|
| 1593 | // assumed all spectra in the scantable have same bandwidth
|
---|
| 1594 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
|
---|
| 1595 |
|
---|
| 1596 | return ;
|
---|
| 1597 | }
|
---|
| 1598 |
|
---|
| 1599 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
|
---|
| 1600 | {
|
---|
| 1601 | // reshape specCol_ and flagCol_
|
---|
| 1602 | Vector<Float> oldspec = specCol_( irow ) ;
|
---|
| 1603 | Vector<uChar> oldflag = flagsCol_( irow ) ;
|
---|
| 1604 | uInt newsize = nmax - nmin + 1 ;
|
---|
| 1605 | specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ;
|
---|
| 1606 | flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ;
|
---|
| 1607 |
|
---|
| 1608 | return ;
|
---|
| 1609 | }
|
---|
| 1610 |
|
---|
| 1611 | void asap::Scantable::regridChannel( int nChan, double dnu )
|
---|
| 1612 | {
|
---|
| 1613 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
|
---|
| 1614 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
|
---|
| 1615 | // assumed that all rows have same nChan
|
---|
| 1616 | Vector<Float> arr = specCol_( 0 ) ;
|
---|
| 1617 | int oldsize = arr.nelements() ;
|
---|
| 1618 |
|
---|
| 1619 | // if oldsize == nChan, nothing to do
|
---|
| 1620 | if ( oldsize == nChan ) {
|
---|
| 1621 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
|
---|
| 1622 | return ;
|
---|
| 1623 | }
|
---|
| 1624 |
|
---|
| 1625 | // if oldChan < nChan, unphysical operation
|
---|
| 1626 | if ( oldsize < nChan ) {
|
---|
| 1627 | os << "Unphysical operation. Nothing to do." << LogIO::POST ;
|
---|
| 1628 | return ;
|
---|
| 1629 | }
|
---|
| 1630 |
|
---|
| 1631 | // change channel number for specCol_ and flagCol_
|
---|
| 1632 | Vector<Float> newspec( nChan, 0 ) ;
|
---|
| 1633 | Vector<uChar> newflag( nChan, false ) ;
|
---|
| 1634 | vector<string> coordinfo = getCoordInfo() ;
|
---|
| 1635 | string oldinfo = coordinfo[0] ;
|
---|
| 1636 | coordinfo[0] = "Hz" ;
|
---|
| 1637 | setCoordInfo( coordinfo ) ;
|
---|
| 1638 | for ( int irow = 0 ; irow < nrow() ; irow++ ) {
|
---|
| 1639 | regridChannel( nChan, dnu, irow ) ;
|
---|
| 1640 | }
|
---|
| 1641 | coordinfo[0] = oldinfo ;
|
---|
| 1642 | setCoordInfo( coordinfo ) ;
|
---|
| 1643 |
|
---|
| 1644 |
|
---|
| 1645 | // NOTE: this method does not update metadata such as
|
---|
| 1646 | // FREQUENCIES subtable, nChan, Bandwidth, etc.
|
---|
| 1647 |
|
---|
| 1648 | return ;
|
---|
| 1649 | }
|
---|
| 1650 |
|
---|
| 1651 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
|
---|
| 1652 | {
|
---|
| 1653 | // logging
|
---|
| 1654 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
|
---|
| 1655 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
|
---|
| 1656 |
|
---|
| 1657 | Vector<Float> oldspec = specCol_( irow ) ;
|
---|
| 1658 | Vector<uChar> oldflag = flagsCol_( irow ) ;
|
---|
| 1659 | Vector<Float> newspec( nChan, 0 ) ;
|
---|
| 1660 | Vector<uChar> newflag( nChan, false ) ;
|
---|
| 1661 |
|
---|
| 1662 | // regrid
|
---|
| 1663 | vector<double> abcissa = getAbcissa( irow ) ;
|
---|
| 1664 | int oldsize = abcissa.size() ;
|
---|
| 1665 | double olddnu = abcissa[1] - abcissa[0] ;
|
---|
| 1666 | //int refChan = 0 ;
|
---|
| 1667 | //double frac = 0.0 ;
|
---|
| 1668 | //double wedge = 0.0 ;
|
---|
| 1669 | //double pile = 0.0 ;
|
---|
| 1670 | int ichan = 0 ;
|
---|
| 1671 | double wsum = 0.0 ;
|
---|
| 1672 | Vector<Float> zi( nChan+1 ) ;
|
---|
| 1673 | Vector<Float> yi( oldsize + 1 ) ;
|
---|
[2133] | 1674 | zi[0] = abcissa[0] - 0.5 * olddnu ;
|
---|
| 1675 | zi[1] = zi[1] + dnu ;
|
---|
[1819] | 1676 | for ( int ii = 2 ; ii < nChan ; ii++ )
|
---|
[2133] | 1677 | zi[ii] = zi[0] + dnu * ii ;
|
---|
| 1678 | zi[nChan] = zi[nChan-1] + dnu ;
|
---|
[1819] | 1679 | yi[0] = abcissa[0] - 0.5 * olddnu ;
|
---|
| 1680 | yi[1] = abcissa[1] + 0.5 * olddnu ;
|
---|
| 1681 | for ( int ii = 2 ; ii < oldsize ; ii++ )
|
---|
| 1682 | yi[ii] = abcissa[ii-1] + olddnu ;
|
---|
| 1683 | yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ;
|
---|
| 1684 | if ( dnu > 0.0 ) {
|
---|
| 1685 | for ( int ii = 0 ; ii < nChan ; ii++ ) {
|
---|
| 1686 | double zl = zi[ii] ;
|
---|
| 1687 | double zr = zi[ii+1] ;
|
---|
| 1688 | for ( int j = ichan ; j < oldsize ; j++ ) {
|
---|
| 1689 | double yl = yi[j] ;
|
---|
| 1690 | double yr = yi[j+1] ;
|
---|
| 1691 | if ( yl <= zl ) {
|
---|
| 1692 | if ( yr <= zl ) {
|
---|
| 1693 | continue ;
|
---|
| 1694 | }
|
---|
| 1695 | else if ( yr <= zr ) {
|
---|
| 1696 | newspec[ii] += oldspec[j] * ( yr - zl ) ;
|
---|
| 1697 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1698 | wsum += ( yr - zl ) ;
|
---|
| 1699 | }
|
---|
| 1700 | else {
|
---|
| 1701 | newspec[ii] += oldspec[j] * dnu ;
|
---|
| 1702 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1703 | wsum += dnu ;
|
---|
| 1704 | ichan = j ;
|
---|
| 1705 | break ;
|
---|
| 1706 | }
|
---|
| 1707 | }
|
---|
| 1708 | else if ( yl < zr ) {
|
---|
| 1709 | if ( yr <= zr ) {
|
---|
| 1710 | newspec[ii] += oldspec[j] * ( yr - yl ) ;
|
---|
| 1711 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1712 | wsum += ( yr - yl ) ;
|
---|
| 1713 | }
|
---|
| 1714 | else {
|
---|
| 1715 | newspec[ii] += oldspec[j] * ( zr - yl ) ;
|
---|
| 1716 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1717 | wsum += ( zr - yl ) ;
|
---|
| 1718 | ichan = j ;
|
---|
| 1719 | break ;
|
---|
| 1720 | }
|
---|
| 1721 | }
|
---|
| 1722 | else {
|
---|
| 1723 | ichan = j - 1 ;
|
---|
| 1724 | break ;
|
---|
| 1725 | }
|
---|
| 1726 | }
|
---|
[2133] | 1727 | if ( wsum != 0.0 )
|
---|
| 1728 | newspec[ii] /= wsum ;
|
---|
[1819] | 1729 | wsum = 0.0 ;
|
---|
| 1730 | }
|
---|
| 1731 | }
|
---|
| 1732 | else if ( dnu < 0.0 ) {
|
---|
| 1733 | for ( int ii = 0 ; ii < nChan ; ii++ ) {
|
---|
| 1734 | double zl = zi[ii] ;
|
---|
| 1735 | double zr = zi[ii+1] ;
|
---|
| 1736 | for ( int j = ichan ; j < oldsize ; j++ ) {
|
---|
| 1737 | double yl = yi[j] ;
|
---|
| 1738 | double yr = yi[j+1] ;
|
---|
| 1739 | if ( yl >= zl ) {
|
---|
| 1740 | if ( yr >= zl ) {
|
---|
| 1741 | continue ;
|
---|
| 1742 | }
|
---|
| 1743 | else if ( yr >= zr ) {
|
---|
| 1744 | newspec[ii] += oldspec[j] * abs( yr - zl ) ;
|
---|
| 1745 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1746 | wsum += abs( yr - zl ) ;
|
---|
| 1747 | }
|
---|
| 1748 | else {
|
---|
| 1749 | newspec[ii] += oldspec[j] * abs( dnu ) ;
|
---|
| 1750 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1751 | wsum += abs( dnu ) ;
|
---|
| 1752 | ichan = j ;
|
---|
| 1753 | break ;
|
---|
| 1754 | }
|
---|
| 1755 | }
|
---|
| 1756 | else if ( yl > zr ) {
|
---|
| 1757 | if ( yr >= zr ) {
|
---|
| 1758 | newspec[ii] += oldspec[j] * abs( yr - yl ) ;
|
---|
| 1759 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1760 | wsum += abs( yr - yl ) ;
|
---|
| 1761 | }
|
---|
| 1762 | else {
|
---|
| 1763 | newspec[ii] += oldspec[j] * abs( zr - yl ) ;
|
---|
| 1764 | newflag[ii] = newflag[ii] || oldflag[j] ;
|
---|
| 1765 | wsum += abs( zr - yl ) ;
|
---|
| 1766 | ichan = j ;
|
---|
| 1767 | break ;
|
---|
| 1768 | }
|
---|
| 1769 | }
|
---|
| 1770 | else {
|
---|
| 1771 | ichan = j - 1 ;
|
---|
| 1772 | break ;
|
---|
| 1773 | }
|
---|
| 1774 | }
|
---|
[2133] | 1775 | if ( wsum != 0.0 )
|
---|
| 1776 | newspec[ii] /= wsum ;
|
---|
[1819] | 1777 | wsum = 0.0 ;
|
---|
| 1778 | }
|
---|
| 1779 | }
|
---|
| 1780 | // * ichan = 0
|
---|
| 1781 | // ***/
|
---|
| 1782 | // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
|
---|
| 1783 | // pile += dnu ;
|
---|
| 1784 | // wedge = olddnu * ( refChan + 1 ) ;
|
---|
| 1785 | // while ( wedge < pile ) {
|
---|
| 1786 | // newspec[0] += olddnu * oldspec[refChan] ;
|
---|
| 1787 | // newflag[0] = newflag[0] || oldflag[refChan] ;
|
---|
| 1788 | // //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
|
---|
| 1789 | // refChan++ ;
|
---|
| 1790 | // wedge += olddnu ;
|
---|
| 1791 | // wsum += olddnu ;
|
---|
| 1792 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
|
---|
| 1793 | // }
|
---|
| 1794 | // frac = ( wedge - pile ) / olddnu ;
|
---|
| 1795 | // wsum += ( 1.0 - frac ) * olddnu ;
|
---|
| 1796 | // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
|
---|
| 1797 | // newflag[0] = newflag[0] || oldflag[refChan] ;
|
---|
| 1798 | // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
|
---|
| 1799 | // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
|
---|
| 1800 | // newspec[0] /= wsum ;
|
---|
| 1801 | // //ofs << "newspec[0] = " << newspec[0] << endl ;
|
---|
| 1802 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
|
---|
| 1803 |
|
---|
| 1804 | // /***
|
---|
| 1805 | // * ichan = 1 - nChan-2
|
---|
| 1806 | // ***/
|
---|
| 1807 | // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
|
---|
| 1808 | // pile += dnu ;
|
---|
| 1809 | // newspec[ichan] += frac * olddnu * oldspec[refChan] ;
|
---|
| 1810 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
|
---|
| 1811 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
|
---|
| 1812 | // refChan++ ;
|
---|
| 1813 | // wedge += olddnu ;
|
---|
| 1814 | // wsum = frac * olddnu ;
|
---|
| 1815 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
|
---|
| 1816 | // while ( wedge < pile ) {
|
---|
| 1817 | // newspec[ichan] += olddnu * oldspec[refChan] ;
|
---|
| 1818 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
|
---|
| 1819 | // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
|
---|
| 1820 | // refChan++ ;
|
---|
| 1821 | // wedge += olddnu ;
|
---|
| 1822 | // wsum += olddnu ;
|
---|
| 1823 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
|
---|
| 1824 | // }
|
---|
| 1825 | // frac = ( wedge - pile ) / olddnu ;
|
---|
| 1826 | // wsum += ( 1.0 - frac ) * olddnu ;
|
---|
| 1827 | // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
|
---|
| 1828 | // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
|
---|
| 1829 | // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
|
---|
| 1830 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
|
---|
| 1831 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
|
---|
| 1832 | // newspec[ichan] /= wsum ;
|
---|
| 1833 | // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
|
---|
| 1834 | // }
|
---|
| 1835 |
|
---|
| 1836 | // /***
|
---|
| 1837 | // * ichan = nChan-1
|
---|
| 1838 | // ***/
|
---|
| 1839 | // // NOTE: Assumed that all spectra have the same bandwidth
|
---|
| 1840 | // pile += dnu ;
|
---|
| 1841 | // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
|
---|
| 1842 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
|
---|
| 1843 | // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
|
---|
| 1844 | // refChan++ ;
|
---|
| 1845 | // wedge += olddnu ;
|
---|
| 1846 | // wsum = frac * olddnu ;
|
---|
| 1847 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
|
---|
| 1848 | // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
|
---|
| 1849 | // newspec[nChan-1] += olddnu * oldspec[jchan] ;
|
---|
| 1850 | // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
|
---|
| 1851 | // wsum += olddnu ;
|
---|
| 1852 | // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
|
---|
| 1853 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
|
---|
| 1854 | // }
|
---|
| 1855 | // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
|
---|
| 1856 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
|
---|
| 1857 | // newspec[nChan-1] /= wsum ;
|
---|
| 1858 | // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
|
---|
| 1859 |
|
---|
| 1860 | // // ofs.close() ;
|
---|
| 1861 |
|
---|
[2032] | 1862 | specCol_.put( irow, newspec ) ;
|
---|
| 1863 | flagsCol_.put( irow, newflag ) ;
|
---|
[1819] | 1864 |
|
---|
| 1865 | return ;
|
---|
| 1866 | }
|
---|
| 1867 |
|
---|
[1730] | 1868 | std::vector<float> Scantable::getWeather(int whichrow) const
|
---|
| 1869 | {
|
---|
| 1870 | std::vector<float> out(5);
|
---|
| 1871 | //Float temperature, pressure, humidity, windspeed, windaz;
|
---|
| 1872 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
|
---|
| 1873 | mweatheridCol_(uInt(whichrow)));
|
---|
| 1874 |
|
---|
| 1875 |
|
---|
| 1876 | return out;
|
---|
[1391] | 1877 | }
|
---|
[1730] | 1878 |
|
---|
[2047] | 1879 | bool Scantable::getFlagtraFast(uInt whichrow)
|
---|
[1907] | 1880 | {
|
---|
| 1881 | uChar flag;
|
---|
| 1882 | Vector<uChar> flags;
|
---|
[2047] | 1883 | flagsCol_.get(whichrow, flags);
|
---|
[2012] | 1884 | flag = flags[0];
|
---|
[2047] | 1885 | for (uInt i = 1; i < flags.size(); ++i) {
|
---|
[2012] | 1886 | flag &= flags[i];
|
---|
| 1887 | }
|
---|
| 1888 | return ((flag >> 7) == 1);
|
---|
| 1889 | }
|
---|
| 1890 |
|
---|
[2277] | 1891 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
|
---|
[2047] | 1892 | {
|
---|
[2193] | 1893 | try {
|
---|
| 1894 | ofstream ofs;
|
---|
| 1895 | String coordInfo = "";
|
---|
| 1896 | bool hasSameNchan = true;
|
---|
| 1897 | bool outTextFile = false;
|
---|
[2047] | 1898 |
|
---|
[2193] | 1899 | if (blfile != "") {
|
---|
| 1900 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
| 1901 | if (ofs) outTextFile = true;
|
---|
| 1902 | }
|
---|
[2047] | 1903 |
|
---|
[2193] | 1904 | if (outLogger || outTextFile) {
|
---|
| 1905 | coordInfo = getCoordInfo()[0];
|
---|
| 1906 | if (coordInfo == "") coordInfo = "channel";
|
---|
| 1907 | hasSameNchan = hasSameNchanOverIFs();
|
---|
| 1908 | }
|
---|
[2047] | 1909 |
|
---|
[2193] | 1910 | Fitter fitter = Fitter();
|
---|
| 1911 | fitter.setExpression("poly", order);
|
---|
| 1912 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
[2047] | 1913 |
|
---|
[2193] | 1914 | int nRow = nrow();
|
---|
| 1915 | std::vector<bool> chanMask;
|
---|
| 1916 | bool showProgress;
|
---|
| 1917 | int minNRow;
|
---|
| 1918 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
[2047] | 1919 |
|
---|
[2193] | 1920 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
| 1921 | chanMask = getCompositeChanMask(whichrow, mask);
|
---|
| 1922 | fitBaseline(chanMask, whichrow, fitter);
|
---|
| 1923 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
[2277] | 1924 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
|
---|
[2193] | 1925 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
| 1926 | }
|
---|
| 1927 |
|
---|
| 1928 | if (outTextFile) ofs.close();
|
---|
| 1929 |
|
---|
| 1930 | } catch (...) {
|
---|
| 1931 | throw;
|
---|
[2047] | 1932 | }
|
---|
| 1933 | }
|
---|
| 1934 |
|
---|
[2189] | 1935 | 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] | 1936 | {
|
---|
[2193] | 1937 | try {
|
---|
| 1938 | ofstream ofs;
|
---|
| 1939 | String coordInfo = "";
|
---|
| 1940 | bool hasSameNchan = true;
|
---|
| 1941 | bool outTextFile = false;
|
---|
[2047] | 1942 |
|
---|
[2193] | 1943 | if (blfile != "") {
|
---|
| 1944 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
| 1945 | if (ofs) outTextFile = true;
|
---|
| 1946 | }
|
---|
[2047] | 1947 |
|
---|
[2193] | 1948 | if (outLogger || outTextFile) {
|
---|
| 1949 | coordInfo = getCoordInfo()[0];
|
---|
| 1950 | if (coordInfo == "") coordInfo = "channel";
|
---|
| 1951 | hasSameNchan = hasSameNchanOverIFs();
|
---|
| 1952 | }
|
---|
[2047] | 1953 |
|
---|
[2193] | 1954 | Fitter fitter = Fitter();
|
---|
| 1955 | fitter.setExpression("poly", order);
|
---|
| 1956 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
[2047] | 1957 |
|
---|
[2193] | 1958 | int nRow = nrow();
|
---|
| 1959 | std::vector<bool> chanMask;
|
---|
| 1960 | int minEdgeSize = getIFNos().size()*2;
|
---|
| 1961 | STLineFinder lineFinder = STLineFinder();
|
---|
| 1962 | lineFinder.setOptions(threshold, 3, chanAvgLimit);
|
---|
[2047] | 1963 |
|
---|
[2193] | 1964 | bool showProgress;
|
---|
| 1965 | int minNRow;
|
---|
| 1966 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
[2189] | 1967 |
|
---|
[2193] | 1968 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
[2047] | 1969 |
|
---|
[2193] | 1970 | //-------------------------------------------------------
|
---|
| 1971 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
|
---|
| 1972 | //-------------------------------------------------------
|
---|
| 1973 | int edgeSize = edge.size();
|
---|
| 1974 | std::vector<int> currentEdge;
|
---|
| 1975 | if (edgeSize >= 2) {
|
---|
| 1976 | int idx = 0;
|
---|
| 1977 | if (edgeSize > 2) {
|
---|
| 1978 | if (edgeSize < minEdgeSize) {
|
---|
| 1979 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
| 1980 | }
|
---|
| 1981 | idx = 2 * getIF(whichrow);
|
---|
[2047] | 1982 | }
|
---|
[2193] | 1983 | currentEdge.push_back(edge[idx]);
|
---|
| 1984 | currentEdge.push_back(edge[idx+1]);
|
---|
| 1985 | } else {
|
---|
| 1986 | throw(AipsError("Wrong length of edge element"));
|
---|
[2047] | 1987 | }
|
---|
[2193] | 1988 | lineFinder.setData(getSpectrum(whichrow));
|
---|
| 1989 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
|
---|
| 1990 | chanMask = lineFinder.getMask();
|
---|
| 1991 | //-------------------------------------------------------
|
---|
| 1992 |
|
---|
| 1993 | fitBaseline(chanMask, whichrow, fitter);
|
---|
| 1994 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
| 1995 |
|
---|
| 1996 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
|
---|
| 1997 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
[2047] | 1998 | }
|
---|
| 1999 |
|
---|
[2193] | 2000 | if (outTextFile) ofs.close();
|
---|
[2047] | 2001 |
|
---|
[2193] | 2002 | } catch (...) {
|
---|
| 2003 | throw;
|
---|
[2047] | 2004 | }
|
---|
| 2005 | }
|
---|
| 2006 |
|
---|
[2189] | 2007 | 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] | 2008 | {
|
---|
[2193] | 2009 | try {
|
---|
| 2010 | ofstream ofs;
|
---|
| 2011 | String coordInfo = "";
|
---|
| 2012 | bool hasSameNchan = true;
|
---|
| 2013 | bool outTextFile = false;
|
---|
[2012] | 2014 |
|
---|
[2193] | 2015 | if (blfile != "") {
|
---|
| 2016 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
| 2017 | if (ofs) outTextFile = true;
|
---|
| 2018 | }
|
---|
[2012] | 2019 |
|
---|
[2193] | 2020 | if (outLogger || outTextFile) {
|
---|
| 2021 | coordInfo = getCoordInfo()[0];
|
---|
| 2022 | if (coordInfo == "") coordInfo = "channel";
|
---|
| 2023 | hasSameNchan = hasSameNchanOverIFs();
|
---|
| 2024 | }
|
---|
[2012] | 2025 |
|
---|
[2193] | 2026 | //Fitter fitter = Fitter();
|
---|
| 2027 | //fitter.setExpression("cspline", nPiece);
|
---|
| 2028 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
[2012] | 2029 |
|
---|
[2193] | 2030 | int nRow = nrow();
|
---|
| 2031 | std::vector<bool> chanMask;
|
---|
| 2032 | bool showProgress;
|
---|
| 2033 | int minNRow;
|
---|
| 2034 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
[2012] | 2035 |
|
---|
[2193] | 2036 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
| 2037 | chanMask = getCompositeChanMask(whichrow, mask);
|
---|
| 2038 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
| 2039 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
| 2040 | std::vector<int> pieceEdges;
|
---|
| 2041 | std::vector<float> params;
|
---|
| 2042 | int nClipped = 0;
|
---|
| 2043 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
| 2044 | setSpectrum(res, whichrow);
|
---|
| 2045 | //
|
---|
[2012] | 2046 |
|
---|
[2193] | 2047 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
|
---|
| 2048 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
| 2049 | }
|
---|
| 2050 |
|
---|
| 2051 | if (outTextFile) ofs.close();
|
---|
| 2052 |
|
---|
| 2053 | } catch (...) {
|
---|
| 2054 | throw;
|
---|
[2012] | 2055 | }
|
---|
| 2056 | }
|
---|
| 2057 |
|
---|
[2189] | 2058 | 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] | 2059 | {
|
---|
[2193] | 2060 | try {
|
---|
| 2061 | ofstream ofs;
|
---|
| 2062 | String coordInfo = "";
|
---|
| 2063 | bool hasSameNchan = true;
|
---|
| 2064 | bool outTextFile = false;
|
---|
[2012] | 2065 |
|
---|
[2193] | 2066 | if (blfile != "") {
|
---|
| 2067 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
| 2068 | if (ofs) outTextFile = true;
|
---|
| 2069 | }
|
---|
[2012] | 2070 |
|
---|
[2193] | 2071 | if (outLogger || outTextFile) {
|
---|
| 2072 | coordInfo = getCoordInfo()[0];
|
---|
| 2073 | if (coordInfo == "") coordInfo = "channel";
|
---|
| 2074 | hasSameNchan = hasSameNchanOverIFs();
|
---|
| 2075 | }
|
---|
[2012] | 2076 |
|
---|
[2193] | 2077 | //Fitter fitter = Fitter();
|
---|
| 2078 | //fitter.setExpression("cspline", nPiece);
|
---|
| 2079 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
[2012] | 2080 |
|
---|
[2193] | 2081 | int nRow = nrow();
|
---|
| 2082 | std::vector<bool> chanMask;
|
---|
| 2083 | int minEdgeSize = getIFNos().size()*2;
|
---|
| 2084 | STLineFinder lineFinder = STLineFinder();
|
---|
| 2085 | lineFinder.setOptions(threshold, 3, chanAvgLimit);
|
---|
[2012] | 2086 |
|
---|
[2193] | 2087 | bool showProgress;
|
---|
| 2088 | int minNRow;
|
---|
| 2089 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
[2189] | 2090 |
|
---|
[2193] | 2091 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
[2012] | 2092 |
|
---|
[2193] | 2093 | //-------------------------------------------------------
|
---|
| 2094 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
|
---|
| 2095 | //-------------------------------------------------------
|
---|
| 2096 | int edgeSize = edge.size();
|
---|
| 2097 | std::vector<int> currentEdge;
|
---|
| 2098 | if (edgeSize >= 2) {
|
---|
| 2099 | int idx = 0;
|
---|
| 2100 | if (edgeSize > 2) {
|
---|
| 2101 | if (edgeSize < minEdgeSize) {
|
---|
| 2102 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
| 2103 | }
|
---|
| 2104 | idx = 2 * getIF(whichrow);
|
---|
[2012] | 2105 | }
|
---|
[2193] | 2106 | currentEdge.push_back(edge[idx]);
|
---|
| 2107 | currentEdge.push_back(edge[idx+1]);
|
---|
| 2108 | } else {
|
---|
| 2109 | throw(AipsError("Wrong length of edge element"));
|
---|
[2012] | 2110 | }
|
---|
[2193] | 2111 | lineFinder.setData(getSpectrum(whichrow));
|
---|
| 2112 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
|
---|
| 2113 | chanMask = lineFinder.getMask();
|
---|
| 2114 | //-------------------------------------------------------
|
---|
| 2115 |
|
---|
| 2116 |
|
---|
| 2117 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
| 2118 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
| 2119 | std::vector<int> pieceEdges;
|
---|
| 2120 | std::vector<float> params;
|
---|
| 2121 | int nClipped = 0;
|
---|
| 2122 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
| 2123 | setSpectrum(res, whichrow);
|
---|
| 2124 | //
|
---|
| 2125 |
|
---|
| 2126 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
|
---|
| 2127 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
[1907] | 2128 | }
|
---|
[2012] | 2129 |
|
---|
[2193] | 2130 | if (outTextFile) ofs.close();
|
---|
[2012] | 2131 |
|
---|
[2193] | 2132 | } catch (...) {
|
---|
| 2133 | throw;
|
---|
[2012] | 2134 | }
|
---|
[1730] | 2135 | }
|
---|
[1907] | 2136 |
|
---|
[2193] | 2137 | 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] | 2138 | {
|
---|
| 2139 | if (data.size() != mask.size()) {
|
---|
| 2140 | throw(AipsError("data and mask sizes are not identical"));
|
---|
| 2141 | }
|
---|
[2012] | 2142 | if (nPiece < 1) {
|
---|
[2094] | 2143 | throw(AipsError("number of the sections must be one or more"));
|
---|
[2012] | 2144 | }
|
---|
| 2145 |
|
---|
| 2146 | int nChan = data.size();
|
---|
| 2147 | std::vector<int> maskArray;
|
---|
| 2148 | std::vector<int> x;
|
---|
| 2149 | for (int i = 0; i < nChan; ++i) {
|
---|
| 2150 | maskArray.push_back(mask[i] ? 1 : 0);
|
---|
| 2151 | if (mask[i]) {
|
---|
| 2152 | x.push_back(i);
|
---|
| 2153 | }
|
---|
| 2154 | }
|
---|
| 2155 |
|
---|
[2081] | 2156 | int initNData = x.size();
|
---|
[2193] | 2157 | if (initNData < nPiece) {
|
---|
| 2158 | throw(AipsError("too few non-flagged channels"));
|
---|
| 2159 | }
|
---|
[2081] | 2160 |
|
---|
| 2161 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
|
---|
[2064] | 2162 | std::vector<double> invEdge;
|
---|
| 2163 | idxEdge.clear();
|
---|
| 2164 | idxEdge.push_back(x[0]);
|
---|
[2012] | 2165 | for (int i = 1; i < nPiece; ++i) {
|
---|
[2047] | 2166 | int valX = x[nElement*i];
|
---|
[2064] | 2167 | idxEdge.push_back(valX);
|
---|
| 2168 | invEdge.push_back(1.0/(double)valX);
|
---|
[2012] | 2169 | }
|
---|
[2064] | 2170 | idxEdge.push_back(x[x.size()-1]+1);
|
---|
| 2171 |
|
---|
[2081] | 2172 | int nData = initNData;
|
---|
| 2173 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
|
---|
| 2174 |
|
---|
| 2175 | std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1, residual;
|
---|
[2012] | 2176 | for (int i = 0; i < nChan; ++i) {
|
---|
[2064] | 2177 | double di = (double)i;
|
---|
| 2178 | double dD = (double)data[i];
|
---|
| 2179 | x1.push_back(di);
|
---|
| 2180 | x2.push_back(di*di);
|
---|
| 2181 | x3.push_back(di*di*di);
|
---|
| 2182 | z1.push_back(dD);
|
---|
| 2183 | x1z1.push_back(dD*di);
|
---|
| 2184 | x2z1.push_back(dD*di*di);
|
---|
| 2185 | x3z1.push_back(dD*di*di*di);
|
---|
[2012] | 2186 | r1.push_back(0.0);
|
---|
[2081] | 2187 | residual.push_back(0.0);
|
---|
[2012] | 2188 | }
|
---|
| 2189 |
|
---|
| 2190 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
|
---|
[2064] | 2191 | // xMatrix : horizontal concatenation of
|
---|
| 2192 | // the least-sq. matrix (left) and an
|
---|
| 2193 | // identity matrix (right).
|
---|
| 2194 | // the right part is used to calculate the inverse matrix of the left part.
|
---|
[2012] | 2195 | double xMatrix[nDOF][2*nDOF];
|
---|
| 2196 | double zMatrix[nDOF];
|
---|
| 2197 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2198 | for (int j = 0; j < 2*nDOF; ++j) {
|
---|
| 2199 | xMatrix[i][j] = 0.0;
|
---|
| 2200 | }
|
---|
| 2201 | xMatrix[i][nDOF+i] = 1.0;
|
---|
| 2202 | zMatrix[i] = 0.0;
|
---|
| 2203 | }
|
---|
| 2204 |
|
---|
| 2205 | for (int n = 0; n < nPiece; ++n) {
|
---|
[2193] | 2206 | int nUseDataInPiece = 0;
|
---|
[2064] | 2207 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
|
---|
| 2208 |
|
---|
[2012] | 2209 | if (maskArray[i] == 0) continue;
|
---|
[2064] | 2210 |
|
---|
[2012] | 2211 | xMatrix[0][0] += 1.0;
|
---|
[2064] | 2212 | xMatrix[0][1] += x1[i];
|
---|
| 2213 | xMatrix[0][2] += x2[i];
|
---|
| 2214 | xMatrix[0][3] += x3[i];
|
---|
| 2215 | xMatrix[1][1] += x2[i];
|
---|
| 2216 | xMatrix[1][2] += x3[i];
|
---|
| 2217 | xMatrix[1][3] += x2[i]*x2[i];
|
---|
| 2218 | xMatrix[2][2] += x2[i]*x2[i];
|
---|
| 2219 | xMatrix[2][3] += x3[i]*x2[i];
|
---|
| 2220 | xMatrix[3][3] += x3[i]*x3[i];
|
---|
[2012] | 2221 | zMatrix[0] += z1[i];
|
---|
[2064] | 2222 | zMatrix[1] += x1z1[i];
|
---|
| 2223 | zMatrix[2] += x2z1[i];
|
---|
| 2224 | zMatrix[3] += x3z1[i];
|
---|
| 2225 |
|
---|
[2012] | 2226 | for (int j = 0; j < n; ++j) {
|
---|
[2064] | 2227 | double q = 1.0 - x1[i]*invEdge[j];
|
---|
[2012] | 2228 | q = q*q*q;
|
---|
| 2229 | xMatrix[0][j+4] += q;
|
---|
[2064] | 2230 | xMatrix[1][j+4] += q*x1[i];
|
---|
| 2231 | xMatrix[2][j+4] += q*x2[i];
|
---|
| 2232 | xMatrix[3][j+4] += q*x3[i];
|
---|
[2012] | 2233 | for (int k = 0; k < j; ++k) {
|
---|
[2064] | 2234 | double r = 1.0 - x1[i]*invEdge[k];
|
---|
[2012] | 2235 | r = r*r*r;
|
---|
| 2236 | xMatrix[k+4][j+4] += r*q;
|
---|
| 2237 | }
|
---|
| 2238 | xMatrix[j+4][j+4] += q*q;
|
---|
| 2239 | zMatrix[j+4] += q*z1[i];
|
---|
| 2240 | }
|
---|
[2064] | 2241 |
|
---|
[2193] | 2242 | nUseDataInPiece++;
|
---|
[2012] | 2243 | }
|
---|
[2193] | 2244 |
|
---|
| 2245 | if (nUseDataInPiece < 1) {
|
---|
| 2246 | std::vector<string> suffixOfPieceNumber(4);
|
---|
| 2247 | suffixOfPieceNumber[0] = "th";
|
---|
| 2248 | suffixOfPieceNumber[1] = "st";
|
---|
| 2249 | suffixOfPieceNumber[2] = "nd";
|
---|
| 2250 | suffixOfPieceNumber[3] = "rd";
|
---|
| 2251 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
|
---|
| 2252 | ostringstream oss;
|
---|
| 2253 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
|
---|
| 2254 | oss << " piece of the spectrum. can't execute fitting anymore.";
|
---|
| 2255 | throw(AipsError(String(oss)));
|
---|
| 2256 | }
|
---|
[2012] | 2257 | }
|
---|
| 2258 |
|
---|
| 2259 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2260 | for (int j = 0; j < i; ++j) {
|
---|
| 2261 | xMatrix[i][j] = xMatrix[j][i];
|
---|
| 2262 | }
|
---|
| 2263 | }
|
---|
| 2264 |
|
---|
| 2265 | std::vector<double> invDiag;
|
---|
| 2266 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2267 | invDiag.push_back(1.0/xMatrix[i][i]);
|
---|
| 2268 | for (int j = 0; j < nDOF; ++j) {
|
---|
| 2269 | xMatrix[i][j] *= invDiag[i];
|
---|
| 2270 | }
|
---|
| 2271 | }
|
---|
| 2272 |
|
---|
| 2273 | for (int k = 0; k < nDOF; ++k) {
|
---|
| 2274 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2275 | if (i != k) {
|
---|
| 2276 | double factor1 = xMatrix[k][k];
|
---|
| 2277 | double factor2 = xMatrix[i][k];
|
---|
| 2278 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
| 2279 | xMatrix[i][j] *= factor1;
|
---|
| 2280 | xMatrix[i][j] -= xMatrix[k][j]*factor2;
|
---|
| 2281 | xMatrix[i][j] /= factor1;
|
---|
| 2282 | }
|
---|
| 2283 | }
|
---|
| 2284 | }
|
---|
| 2285 | double xDiag = xMatrix[k][k];
|
---|
| 2286 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
| 2287 | xMatrix[k][j] /= xDiag;
|
---|
| 2288 | }
|
---|
| 2289 | }
|
---|
| 2290 |
|
---|
| 2291 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2292 | for (int j = 0; j < nDOF; ++j) {
|
---|
| 2293 | xMatrix[i][nDOF+j] *= invDiag[j];
|
---|
| 2294 | }
|
---|
| 2295 | }
|
---|
| 2296 | //compute a vector y which consists of the coefficients of the best-fit spline curves
|
---|
| 2297 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
|
---|
| 2298 | //cubic terms for the other pieces (in case nPiece>1).
|
---|
| 2299 | std::vector<double> y;
|
---|
[2058] | 2300 | y.clear();
|
---|
[2012] | 2301 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2302 | y.push_back(0.0);
|
---|
| 2303 | for (int j = 0; j < nDOF; ++j) {
|
---|
| 2304 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
|
---|
| 2305 | }
|
---|
| 2306 | }
|
---|
| 2307 |
|
---|
| 2308 | double a0 = y[0];
|
---|
| 2309 | double a1 = y[1];
|
---|
| 2310 | double a2 = y[2];
|
---|
| 2311 | double a3 = y[3];
|
---|
| 2312 | params.clear();
|
---|
| 2313 |
|
---|
| 2314 | for (int n = 0; n < nPiece; ++n) {
|
---|
[2064] | 2315 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
|
---|
| 2316 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
|
---|
[2081] | 2317 | residual[i] = z1[i] - r1[i];
|
---|
[2012] | 2318 | }
|
---|
| 2319 | params.push_back(a0);
|
---|
| 2320 | params.push_back(a1);
|
---|
| 2321 | params.push_back(a2);
|
---|
| 2322 | params.push_back(a3);
|
---|
| 2323 |
|
---|
| 2324 | if (n == nPiece-1) break;
|
---|
| 2325 |
|
---|
| 2326 | double d = y[4+n];
|
---|
[2064] | 2327 | double iE = invEdge[n];
|
---|
| 2328 | a0 += d;
|
---|
| 2329 | a1 -= 3.0*d*iE;
|
---|
| 2330 | a2 += 3.0*d*iE*iE;
|
---|
| 2331 | a3 -= d*iE*iE*iE;
|
---|
[2012] | 2332 | }
|
---|
| 2333 |
|
---|
| 2334 | if ((nClip == nIterClip) || (thresClip <= 0.0)) {
|
---|
| 2335 | break;
|
---|
| 2336 | } else {
|
---|
| 2337 | double stdDev = 0.0;
|
---|
| 2338 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2339 | stdDev += residual[i]*residual[i]*(double)maskArray[i];
|
---|
[2012] | 2340 | }
|
---|
| 2341 | stdDev = sqrt(stdDev/(double)nData);
|
---|
| 2342 |
|
---|
| 2343 | double thres = stdDev * thresClip;
|
---|
| 2344 | int newNData = 0;
|
---|
| 2345 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2346 | if (abs(residual[i]) >= thres) {
|
---|
[2012] | 2347 | maskArray[i] = 0;
|
---|
| 2348 | }
|
---|
| 2349 | if (maskArray[i] > 0) {
|
---|
| 2350 | newNData++;
|
---|
| 2351 | }
|
---|
| 2352 | }
|
---|
[2081] | 2353 | if (newNData == nData) {
|
---|
[2064] | 2354 | break; //no more flag to add. iteration stops.
|
---|
[2012] | 2355 | } else {
|
---|
[2081] | 2356 | nData = newNData;
|
---|
[2012] | 2357 | }
|
---|
| 2358 | }
|
---|
| 2359 | }
|
---|
| 2360 |
|
---|
[2193] | 2361 | nClipped = initNData - nData;
|
---|
| 2362 |
|
---|
[2058] | 2363 | std::vector<float> result;
|
---|
| 2364 | if (getResidual) {
|
---|
| 2365 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2366 | result.push_back((float)residual[i]);
|
---|
[2058] | 2367 | }
|
---|
| 2368 | } else {
|
---|
| 2369 | for (int i = 0; i < nChan; ++i) {
|
---|
| 2370 | result.push_back((float)r1[i]);
|
---|
| 2371 | }
|
---|
[2012] | 2372 | }
|
---|
| 2373 |
|
---|
[2058] | 2374 | return result;
|
---|
[2012] | 2375 | }
|
---|
| 2376 |
|
---|
[2186] | 2377 | 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] | 2378 | {
|
---|
[2186] | 2379 | nWaves.clear();
|
---|
| 2380 |
|
---|
| 2381 | if (applyFFT) {
|
---|
| 2382 | string fftThAttr;
|
---|
| 2383 | float fftThSigma;
|
---|
| 2384 | int fftThTop;
|
---|
| 2385 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
|
---|
| 2386 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
|
---|
| 2387 | }
|
---|
| 2388 |
|
---|
| 2389 | addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves);
|
---|
| 2390 | }
|
---|
| 2391 |
|
---|
| 2392 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
|
---|
| 2393 | {
|
---|
| 2394 | uInt idxSigma = fftThresh.find("sigma");
|
---|
| 2395 | uInt idxTop = fftThresh.find("top");
|
---|
| 2396 |
|
---|
| 2397 | if (idxSigma == fftThresh.size() - 5) {
|
---|
| 2398 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
|
---|
| 2399 | is >> fftThSigma;
|
---|
| 2400 | fftThAttr = "sigma";
|
---|
| 2401 | } else if (idxTop == 0) {
|
---|
| 2402 | std::istringstream is(fftThresh.substr(3));
|
---|
| 2403 | is >> fftThTop;
|
---|
| 2404 | fftThAttr = "top";
|
---|
| 2405 | } else {
|
---|
| 2406 | bool isNumber = true;
|
---|
| 2407 | for (uInt i = 0; i < fftThresh.size()-1; ++i) {
|
---|
| 2408 | char ch = (fftThresh.substr(i, 1).c_str())[0];
|
---|
| 2409 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
|
---|
| 2410 | isNumber = false;
|
---|
| 2411 | break;
|
---|
| 2412 | }
|
---|
| 2413 | }
|
---|
| 2414 | if (isNumber) {
|
---|
| 2415 | std::istringstream is(fftThresh);
|
---|
| 2416 | is >> fftThSigma;
|
---|
| 2417 | fftThAttr = "sigma";
|
---|
| 2418 | } else {
|
---|
| 2419 | throw(AipsError("fftthresh has a wrong value"));
|
---|
| 2420 | }
|
---|
| 2421 | }
|
---|
| 2422 | }
|
---|
| 2423 |
|
---|
| 2424 | 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)
|
---|
| 2425 | {
|
---|
| 2426 | std::vector<float> fspec;
|
---|
| 2427 | if (fftMethod == "fft") {
|
---|
| 2428 | fspec = execFFT(whichrow, chanMask, false, true);
|
---|
| 2429 | //} else if (fftMethod == "lsp") {
|
---|
| 2430 | // fspec = lombScarglePeriodogram(whichrow);
|
---|
| 2431 | }
|
---|
| 2432 |
|
---|
| 2433 | if (fftThAttr == "sigma") {
|
---|
| 2434 | float mean = 0.0;
|
---|
| 2435 | float mean2 = 0.0;
|
---|
| 2436 | for (uInt i = 0; i < fspec.size(); ++i) {
|
---|
| 2437 | mean += fspec[i];
|
---|
| 2438 | mean2 += fspec[i]*fspec[i];
|
---|
| 2439 | }
|
---|
| 2440 | mean /= float(fspec.size());
|
---|
| 2441 | mean2 /= float(fspec.size());
|
---|
| 2442 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
|
---|
| 2443 |
|
---|
| 2444 | for (uInt i = 0; i < fspec.size(); ++i) {
|
---|
| 2445 | if (fspec[i] >= thres) {
|
---|
| 2446 | nWaves.push_back(i);
|
---|
| 2447 | }
|
---|
| 2448 | }
|
---|
| 2449 |
|
---|
| 2450 | } else if (fftThAttr == "top") {
|
---|
| 2451 | for (int i = 0; i < fftThTop; ++i) {
|
---|
| 2452 | float max = 0.0;
|
---|
| 2453 | int maxIdx = 0;
|
---|
| 2454 | for (uInt j = 0; j < fspec.size(); ++j) {
|
---|
| 2455 | if (fspec[j] > max) {
|
---|
| 2456 | max = fspec[j];
|
---|
| 2457 | maxIdx = j;
|
---|
| 2458 | }
|
---|
| 2459 | }
|
---|
| 2460 | nWaves.push_back(maxIdx);
|
---|
| 2461 | fspec[maxIdx] = 0.0;
|
---|
| 2462 | }
|
---|
| 2463 |
|
---|
| 2464 | }
|
---|
| 2465 |
|
---|
| 2466 | if (nWaves.size() > 1) {
|
---|
| 2467 | sort(nWaves.begin(), nWaves.end());
|
---|
| 2468 | }
|
---|
| 2469 | }
|
---|
| 2470 |
|
---|
| 2471 | void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
|
---|
| 2472 | {
|
---|
| 2473 | for (uInt i = 0; i < addNWaves.size(); ++i) {
|
---|
| 2474 | bool found = false;
|
---|
| 2475 | for (uInt j = 0; j < nWaves.size(); ++j) {
|
---|
| 2476 | if (nWaves[j] == addNWaves[i]) {
|
---|
| 2477 | found = true;
|
---|
| 2478 | break;
|
---|
| 2479 | }
|
---|
| 2480 | }
|
---|
| 2481 | if (!found) nWaves.push_back(addNWaves[i]);
|
---|
| 2482 | }
|
---|
| 2483 |
|
---|
| 2484 | for (uInt i = 0; i < rejectNWaves.size(); ++i) {
|
---|
| 2485 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
|
---|
| 2486 | if (*j == rejectNWaves[i]) {
|
---|
| 2487 | j = nWaves.erase(j);
|
---|
| 2488 | } else {
|
---|
| 2489 | ++j;
|
---|
| 2490 | }
|
---|
| 2491 | }
|
---|
| 2492 | }
|
---|
| 2493 |
|
---|
| 2494 | if (nWaves.size() > 1) {
|
---|
| 2495 | sort(nWaves.begin(), nWaves.end());
|
---|
| 2496 | unique(nWaves.begin(), nWaves.end());
|
---|
| 2497 | }
|
---|
| 2498 | }
|
---|
| 2499 |
|
---|
[2189] | 2500 | 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] | 2501 | {
|
---|
[2193] | 2502 | try {
|
---|
| 2503 | ofstream ofs;
|
---|
| 2504 | String coordInfo = "";
|
---|
| 2505 | bool hasSameNchan = true;
|
---|
| 2506 | bool outTextFile = false;
|
---|
[2012] | 2507 |
|
---|
[2193] | 2508 | if (blfile != "") {
|
---|
| 2509 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
| 2510 | if (ofs) outTextFile = true;
|
---|
| 2511 | }
|
---|
[2012] | 2512 |
|
---|
[2193] | 2513 | if (outLogger || outTextFile) {
|
---|
| 2514 | coordInfo = getCoordInfo()[0];
|
---|
| 2515 | if (coordInfo == "") coordInfo = "channel";
|
---|
| 2516 | hasSameNchan = hasSameNchanOverIFs();
|
---|
| 2517 | }
|
---|
[2012] | 2518 |
|
---|
[2193] | 2519 | //Fitter fitter = Fitter();
|
---|
| 2520 | //fitter.setExpression("sinusoid", nWaves);
|
---|
| 2521 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
[2012] | 2522 |
|
---|
[2193] | 2523 | int nRow = nrow();
|
---|
| 2524 | std::vector<bool> chanMask;
|
---|
| 2525 | std::vector<int> nWaves;
|
---|
[2012] | 2526 |
|
---|
[2193] | 2527 | bool showProgress;
|
---|
| 2528 | int minNRow;
|
---|
| 2529 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
[2189] | 2530 |
|
---|
[2193] | 2531 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
| 2532 | chanMask = getCompositeChanMask(whichrow, mask);
|
---|
| 2533 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
|
---|
[2186] | 2534 |
|
---|
[2193] | 2535 | //FOR DEBUGGING------------
|
---|
| 2536 | if (whichrow < 0) {// == nRow -1) {
|
---|
| 2537 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
|
---|
| 2538 | if (applyFFT) {
|
---|
[2186] | 2539 | cout << "[ ";
|
---|
| 2540 | for (uInt j = 0; j < nWaves.size(); ++j) {
|
---|
| 2541 | cout << nWaves[j] << ", ";
|
---|
| 2542 | }
|
---|
| 2543 | cout << " ] " << endl;
|
---|
[2193] | 2544 | }
|
---|
| 2545 | cout << flush;
|
---|
[2186] | 2546 | }
|
---|
[2193] | 2547 | //-------------------------
|
---|
| 2548 |
|
---|
| 2549 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
| 2550 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
| 2551 | std::vector<float> params;
|
---|
| 2552 | int nClipped = 0;
|
---|
| 2553 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
| 2554 | setSpectrum(res, whichrow);
|
---|
| 2555 | //
|
---|
| 2556 |
|
---|
| 2557 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
|
---|
| 2558 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
[2186] | 2559 | }
|
---|
| 2560 |
|
---|
[2193] | 2561 | if (outTextFile) ofs.close();
|
---|
[2012] | 2562 |
|
---|
[2193] | 2563 | } catch (...) {
|
---|
| 2564 | throw;
|
---|
[1931] | 2565 | }
|
---|
[1907] | 2566 | }
|
---|
| 2567 |
|
---|
[2189] | 2568 | 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] | 2569 | {
|
---|
[2193] | 2570 | try {
|
---|
| 2571 | ofstream ofs;
|
---|
| 2572 | String coordInfo = "";
|
---|
| 2573 | bool hasSameNchan = true;
|
---|
| 2574 | bool outTextFile = false;
|
---|
[2012] | 2575 |
|
---|
[2193] | 2576 | if (blfile != "") {
|
---|
| 2577 | ofs.open(blfile.c_str(), ios::out | ios::app);
|
---|
| 2578 | if (ofs) outTextFile = true;
|
---|
| 2579 | }
|
---|
[2012] | 2580 |
|
---|
[2193] | 2581 | if (outLogger || outTextFile) {
|
---|
| 2582 | coordInfo = getCoordInfo()[0];
|
---|
| 2583 | if (coordInfo == "") coordInfo = "channel";
|
---|
| 2584 | hasSameNchan = hasSameNchanOverIFs();
|
---|
| 2585 | }
|
---|
[2012] | 2586 |
|
---|
[2193] | 2587 | //Fitter fitter = Fitter();
|
---|
| 2588 | //fitter.setExpression("sinusoid", nWaves);
|
---|
| 2589 | //fitter.setIterClipping(thresClip, nIterClip);
|
---|
[2012] | 2590 |
|
---|
[2193] | 2591 | int nRow = nrow();
|
---|
| 2592 | std::vector<bool> chanMask;
|
---|
| 2593 | std::vector<int> nWaves;
|
---|
[2186] | 2594 |
|
---|
[2193] | 2595 | int minEdgeSize = getIFNos().size()*2;
|
---|
| 2596 | STLineFinder lineFinder = STLineFinder();
|
---|
| 2597 | lineFinder.setOptions(threshold, 3, chanAvgLimit);
|
---|
[2012] | 2598 |
|
---|
[2193] | 2599 | bool showProgress;
|
---|
| 2600 | int minNRow;
|
---|
| 2601 | parseProgressInfo(progressInfo, showProgress, minNRow);
|
---|
[2189] | 2602 |
|
---|
[2193] | 2603 | for (int whichrow = 0; whichrow < nRow; ++whichrow) {
|
---|
[2012] | 2604 |
|
---|
[2193] | 2605 | //-------------------------------------------------------
|
---|
| 2606 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
|
---|
| 2607 | //-------------------------------------------------------
|
---|
| 2608 | int edgeSize = edge.size();
|
---|
| 2609 | std::vector<int> currentEdge;
|
---|
| 2610 | if (edgeSize >= 2) {
|
---|
| 2611 | int idx = 0;
|
---|
| 2612 | if (edgeSize > 2) {
|
---|
| 2613 | if (edgeSize < minEdgeSize) {
|
---|
| 2614 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
| 2615 | }
|
---|
| 2616 | idx = 2 * getIF(whichrow);
|
---|
[2012] | 2617 | }
|
---|
[2193] | 2618 | currentEdge.push_back(edge[idx]);
|
---|
| 2619 | currentEdge.push_back(edge[idx+1]);
|
---|
| 2620 | } else {
|
---|
| 2621 | throw(AipsError("Wrong length of edge element"));
|
---|
[2012] | 2622 | }
|
---|
[2193] | 2623 | lineFinder.setData(getSpectrum(whichrow));
|
---|
| 2624 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
|
---|
| 2625 | chanMask = lineFinder.getMask();
|
---|
| 2626 | //-------------------------------------------------------
|
---|
| 2627 |
|
---|
| 2628 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
|
---|
| 2629 |
|
---|
| 2630 | //fitBaseline(chanMask, whichrow, fitter);
|
---|
| 2631 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
|
---|
| 2632 | std::vector<float> params;
|
---|
| 2633 | int nClipped = 0;
|
---|
| 2634 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
|
---|
| 2635 | setSpectrum(res, whichrow);
|
---|
| 2636 | //
|
---|
| 2637 |
|
---|
| 2638 | outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
|
---|
| 2639 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
|
---|
[2012] | 2640 | }
|
---|
| 2641 |
|
---|
[2193] | 2642 | if (outTextFile) ofs.close();
|
---|
[2012] | 2643 |
|
---|
[2193] | 2644 | } catch (...) {
|
---|
| 2645 | throw;
|
---|
[2047] | 2646 | }
|
---|
| 2647 | }
|
---|
| 2648 |
|
---|
[2193] | 2649 | 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] | 2650 | {
|
---|
[2047] | 2651 | if (data.size() != mask.size()) {
|
---|
[2081] | 2652 | throw(AipsError("data and mask sizes are not identical"));
|
---|
[2047] | 2653 | }
|
---|
[2081] | 2654 | if (data.size() < 2) {
|
---|
| 2655 | throw(AipsError("data size is too short"));
|
---|
| 2656 | }
|
---|
| 2657 | if (waveNumbers.size() == 0) {
|
---|
[2186] | 2658 | throw(AipsError("no wave numbers given"));
|
---|
[2081] | 2659 | }
|
---|
| 2660 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers
|
---|
| 2661 | nWaves.reserve(waveNumbers.size());
|
---|
| 2662 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
|
---|
| 2663 | sort(nWaves.begin(), nWaves.end());
|
---|
| 2664 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
|
---|
| 2665 | nWaves.erase(end_it, nWaves.end());
|
---|
| 2666 |
|
---|
| 2667 | int minNWaves = nWaves[0];
|
---|
| 2668 | if (minNWaves < 0) {
|
---|
[2058] | 2669 | throw(AipsError("wave number must be positive or zero (i.e. constant)"));
|
---|
| 2670 | }
|
---|
[2081] | 2671 | bool hasConstantTerm = (minNWaves == 0);
|
---|
[2047] | 2672 |
|
---|
| 2673 | int nChan = data.size();
|
---|
| 2674 | std::vector<int> maskArray;
|
---|
| 2675 | std::vector<int> x;
|
---|
| 2676 | for (int i = 0; i < nChan; ++i) {
|
---|
| 2677 | maskArray.push_back(mask[i] ? 1 : 0);
|
---|
| 2678 | if (mask[i]) {
|
---|
| 2679 | x.push_back(i);
|
---|
| 2680 | }
|
---|
| 2681 | }
|
---|
| 2682 |
|
---|
[2081] | 2683 | int initNData = x.size();
|
---|
[2047] | 2684 |
|
---|
[2081] | 2685 | int nData = initNData;
|
---|
| 2686 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
|
---|
| 2687 |
|
---|
| 2688 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
|
---|
[2186] | 2689 | 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] | 2690 |
|
---|
| 2691 | // xArray : contains elemental values for computing the least-square matrix.
|
---|
| 2692 | // xArray.size() is nDOF and xArray[*].size() is nChan.
|
---|
| 2693 | // Each xArray element are as follows:
|
---|
| 2694 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
|
---|
| 2695 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
|
---|
| 2696 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
|
---|
| 2697 | // where (1 <= n <= nMaxWavesInSW),
|
---|
| 2698 | // or,
|
---|
| 2699 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
|
---|
| 2700 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
|
---|
| 2701 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
|
---|
| 2702 | std::vector<std::vector<double> > xArray;
|
---|
| 2703 | if (hasConstantTerm) {
|
---|
| 2704 | std::vector<double> xu;
|
---|
| 2705 | for (int j = 0; j < nChan; ++j) {
|
---|
| 2706 | xu.push_back(1.0);
|
---|
| 2707 | }
|
---|
| 2708 | xArray.push_back(xu);
|
---|
| 2709 | }
|
---|
| 2710 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
|
---|
| 2711 | double xFactor = baseXFactor*(double)nWaves[i];
|
---|
| 2712 | std::vector<double> xs, xc;
|
---|
| 2713 | xs.clear();
|
---|
| 2714 | xc.clear();
|
---|
| 2715 | for (int j = 0; j < nChan; ++j) {
|
---|
| 2716 | xs.push_back(sin(xFactor*(double)j));
|
---|
| 2717 | xc.push_back(cos(xFactor*(double)j));
|
---|
| 2718 | }
|
---|
| 2719 | xArray.push_back(xs);
|
---|
| 2720 | xArray.push_back(xc);
|
---|
| 2721 | }
|
---|
| 2722 |
|
---|
| 2723 | std::vector<double> z1, r1, residual;
|
---|
[2047] | 2724 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2725 | z1.push_back((double)data[i]);
|
---|
[2047] | 2726 | r1.push_back(0.0);
|
---|
[2081] | 2727 | residual.push_back(0.0);
|
---|
[2047] | 2728 | }
|
---|
| 2729 |
|
---|
| 2730 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
|
---|
[2081] | 2731 | // xMatrix : horizontal concatenation of
|
---|
| 2732 | // the least-sq. matrix (left) and an
|
---|
| 2733 | // identity matrix (right).
|
---|
| 2734 | // the right part is used to calculate the inverse matrix of the left part.
|
---|
[2047] | 2735 | double xMatrix[nDOF][2*nDOF];
|
---|
| 2736 | double zMatrix[nDOF];
|
---|
| 2737 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2738 | for (int j = 0; j < 2*nDOF; ++j) {
|
---|
| 2739 | xMatrix[i][j] = 0.0;
|
---|
[2012] | 2740 | }
|
---|
[2047] | 2741 | xMatrix[i][nDOF+i] = 1.0;
|
---|
| 2742 | zMatrix[i] = 0.0;
|
---|
| 2743 | }
|
---|
| 2744 |
|
---|
[2193] | 2745 | int nUseData = 0;
|
---|
[2081] | 2746 | for (int k = 0; k < nChan; ++k) {
|
---|
| 2747 | if (maskArray[k] == 0) continue;
|
---|
| 2748 |
|
---|
| 2749 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2750 | for (int j = i; j < nDOF; ++j) {
|
---|
| 2751 | xMatrix[i][j] += xArray[i][k] * xArray[j][k];
|
---|
| 2752 | }
|
---|
| 2753 | zMatrix[i] += z1[k] * xArray[i][k];
|
---|
| 2754 | }
|
---|
[2193] | 2755 |
|
---|
| 2756 | nUseData++;
|
---|
[2047] | 2757 | }
|
---|
| 2758 |
|
---|
[2193] | 2759 | if (nUseData < 1) {
|
---|
| 2760 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
|
---|
| 2761 | }
|
---|
| 2762 |
|
---|
[2047] | 2763 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2764 | for (int j = 0; j < i; ++j) {
|
---|
| 2765 | xMatrix[i][j] = xMatrix[j][i];
|
---|
[2012] | 2766 | }
|
---|
| 2767 | }
|
---|
| 2768 |
|
---|
[2047] | 2769 | std::vector<double> invDiag;
|
---|
| 2770 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2771 | invDiag.push_back(1.0/xMatrix[i][i]);
|
---|
| 2772 | for (int j = 0; j < nDOF; ++j) {
|
---|
| 2773 | xMatrix[i][j] *= invDiag[i];
|
---|
| 2774 | }
|
---|
| 2775 | }
|
---|
| 2776 |
|
---|
| 2777 | for (int k = 0; k < nDOF; ++k) {
|
---|
| 2778 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2779 | if (i != k) {
|
---|
| 2780 | double factor1 = xMatrix[k][k];
|
---|
| 2781 | double factor2 = xMatrix[i][k];
|
---|
| 2782 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
| 2783 | xMatrix[i][j] *= factor1;
|
---|
| 2784 | xMatrix[i][j] -= xMatrix[k][j]*factor2;
|
---|
| 2785 | xMatrix[i][j] /= factor1;
|
---|
| 2786 | }
|
---|
| 2787 | }
|
---|
| 2788 | }
|
---|
| 2789 | double xDiag = xMatrix[k][k];
|
---|
| 2790 | for (int j = k; j < 2*nDOF; ++j) {
|
---|
| 2791 | xMatrix[k][j] /= xDiag;
|
---|
| 2792 | }
|
---|
| 2793 | }
|
---|
| 2794 |
|
---|
| 2795 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2796 | for (int j = 0; j < nDOF; ++j) {
|
---|
| 2797 | xMatrix[i][nDOF+j] *= invDiag[j];
|
---|
| 2798 | }
|
---|
| 2799 | }
|
---|
| 2800 | //compute a vector y which consists of the coefficients of the sinusoids forming the
|
---|
[2081] | 2801 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
|
---|
| 2802 | //and cosine functions, respectively.
|
---|
[2047] | 2803 | std::vector<double> y;
|
---|
[2081] | 2804 | params.clear();
|
---|
[2047] | 2805 | for (int i = 0; i < nDOF; ++i) {
|
---|
| 2806 | y.push_back(0.0);
|
---|
| 2807 | for (int j = 0; j < nDOF; ++j) {
|
---|
| 2808 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
|
---|
| 2809 | }
|
---|
[2081] | 2810 | params.push_back(y[i]);
|
---|
[2047] | 2811 | }
|
---|
| 2812 |
|
---|
| 2813 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2814 | r1[i] = y[0];
|
---|
| 2815 | for (int j = 1; j < nDOF; ++j) {
|
---|
| 2816 | r1[i] += y[j]*xArray[j][i];
|
---|
| 2817 | }
|
---|
| 2818 | residual[i] = z1[i] - r1[i];
|
---|
[2047] | 2819 | }
|
---|
| 2820 |
|
---|
| 2821 | if ((nClip == nIterClip) || (thresClip <= 0.0)) {
|
---|
| 2822 | break;
|
---|
| 2823 | } else {
|
---|
| 2824 | double stdDev = 0.0;
|
---|
| 2825 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2826 | stdDev += residual[i]*residual[i]*(double)maskArray[i];
|
---|
[2047] | 2827 | }
|
---|
| 2828 | stdDev = sqrt(stdDev/(double)nData);
|
---|
| 2829 |
|
---|
| 2830 | double thres = stdDev * thresClip;
|
---|
| 2831 | int newNData = 0;
|
---|
| 2832 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2833 | if (abs(residual[i]) >= thres) {
|
---|
[2047] | 2834 | maskArray[i] = 0;
|
---|
| 2835 | }
|
---|
| 2836 | if (maskArray[i] > 0) {
|
---|
| 2837 | newNData++;
|
---|
| 2838 | }
|
---|
| 2839 | }
|
---|
[2081] | 2840 | if (newNData == nData) {
|
---|
| 2841 | break; //no more flag to add. iteration stops.
|
---|
[2047] | 2842 | } else {
|
---|
[2081] | 2843 | nData = newNData;
|
---|
[2047] | 2844 | }
|
---|
| 2845 | }
|
---|
[2012] | 2846 | }
|
---|
| 2847 |
|
---|
[2193] | 2848 | nClipped = initNData - nData;
|
---|
| 2849 |
|
---|
[2058] | 2850 | std::vector<float> result;
|
---|
| 2851 | if (getResidual) {
|
---|
| 2852 | for (int i = 0; i < nChan; ++i) {
|
---|
[2081] | 2853 | result.push_back((float)residual[i]);
|
---|
[2058] | 2854 | }
|
---|
| 2855 | } else {
|
---|
| 2856 | for (int i = 0; i < nChan; ++i) {
|
---|
| 2857 | result.push_back((float)r1[i]);
|
---|
| 2858 | }
|
---|
[2047] | 2859 | }
|
---|
| 2860 |
|
---|
[2058] | 2861 | return result;
|
---|
[2012] | 2862 | }
|
---|
| 2863 |
|
---|
[2047] | 2864 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
|
---|
| 2865 | {
|
---|
[2081] | 2866 | std::vector<double> dAbcissa = getAbcissa(whichrow);
|
---|
| 2867 | std::vector<float> abcissa;
|
---|
| 2868 | for (uInt i = 0; i < dAbcissa.size(); ++i) {
|
---|
| 2869 | abcissa.push_back((float)dAbcissa[i]);
|
---|
[2047] | 2870 | }
|
---|
| 2871 | std::vector<float> spec = getSpectrum(whichrow);
|
---|
[2012] | 2872 |
|
---|
[2081] | 2873 | fitter.setData(abcissa, spec, mask);
|
---|
[2047] | 2874 | fitter.lfit();
|
---|
| 2875 | }
|
---|
| 2876 |
|
---|
| 2877 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
|
---|
| 2878 | {
|
---|
[2186] | 2879 | std::vector<bool> mask = getMask(whichrow);
|
---|
| 2880 | uInt maskSize = mask.size();
|
---|
| 2881 | if (maskSize != inMask.size()) {
|
---|
| 2882 | throw(AipsError("mask sizes are not the same."));
|
---|
[2047] | 2883 | }
|
---|
[2186] | 2884 | for (uInt i = 0; i < maskSize; ++i) {
|
---|
| 2885 | mask[i] = mask[i] && inMask[i];
|
---|
[2047] | 2886 | }
|
---|
| 2887 |
|
---|
[2186] | 2888 | return mask;
|
---|
[2047] | 2889 | }
|
---|
| 2890 |
|
---|
| 2891 | /*
|
---|
| 2892 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
|
---|
| 2893 | {
|
---|
| 2894 | int edgeSize = edge.size();
|
---|
| 2895 | std::vector<int> currentEdge;
|
---|
| 2896 | if (edgeSize >= 2) {
|
---|
| 2897 | int idx = 0;
|
---|
| 2898 | if (edgeSize > 2) {
|
---|
| 2899 | if (edgeSize < minEdgeSize) {
|
---|
| 2900 | throw(AipsError("Length of edge element info is less than that of IFs"));
|
---|
| 2901 | }
|
---|
| 2902 | idx = 2 * getIF(whichrow);
|
---|
| 2903 | }
|
---|
| 2904 | currentEdge.push_back(edge[idx]);
|
---|
| 2905 | currentEdge.push_back(edge[idx+1]);
|
---|
| 2906 | } else {
|
---|
| 2907 | throw(AipsError("Wrong length of edge element"));
|
---|
| 2908 | }
|
---|
| 2909 |
|
---|
| 2910 | lineFinder.setData(getSpectrum(whichrow));
|
---|
| 2911 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
|
---|
| 2912 |
|
---|
| 2913 | return lineFinder.getMask();
|
---|
| 2914 | }
|
---|
| 2915 | */
|
---|
| 2916 |
|
---|
| 2917 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
|
---|
[2186] | 2918 | 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)
|
---|
| 2919 | {
|
---|
[2047] | 2920 | if (outLogger || outTextFile) {
|
---|
| 2921 | std::vector<float> params = fitter.getParameters();
|
---|
| 2922 | std::vector<bool> fixed = fitter.getFixedParameters();
|
---|
| 2923 | float rms = getRms(chanMask, whichrow);
|
---|
| 2924 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
|
---|
| 2925 |
|
---|
| 2926 | if (outLogger) {
|
---|
| 2927 | LogIO ols(LogOrigin("Scantable", funcName, WHERE));
|
---|
[2193] | 2928 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ;
|
---|
[2047] | 2929 | }
|
---|
| 2930 | if (outTextFile) {
|
---|
[2193] | 2931 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush;
|
---|
[2047] | 2932 | }
|
---|
| 2933 | }
|
---|
| 2934 | }
|
---|
| 2935 |
|
---|
| 2936 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
|
---|
[2193] | 2937 | 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] | 2938 | {
|
---|
[2047] | 2939 | if (outLogger || outTextFile) {
|
---|
| 2940 | float rms = getRms(chanMask, whichrow);
|
---|
| 2941 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
|
---|
[2081] | 2942 | std::vector<bool> fixed;
|
---|
| 2943 | fixed.clear();
|
---|
[2047] | 2944 |
|
---|
| 2945 | if (outLogger) {
|
---|
| 2946 | LogIO ols(LogOrigin("Scantable", funcName, WHERE));
|
---|
[2193] | 2947 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
|
---|
[2047] | 2948 | }
|
---|
| 2949 | if (outTextFile) {
|
---|
[2193] | 2950 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
|
---|
[2047] | 2951 | }
|
---|
| 2952 | }
|
---|
| 2953 | }
|
---|
| 2954 |
|
---|
| 2955 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
|
---|
[2193] | 2956 | 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] | 2957 | {
|
---|
[2047] | 2958 | if (outLogger || outTextFile) {
|
---|
| 2959 | float rms = getRms(chanMask, whichrow);
|
---|
| 2960 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
|
---|
[2081] | 2961 | std::vector<bool> fixed;
|
---|
| 2962 | fixed.clear();
|
---|
[2047] | 2963 |
|
---|
| 2964 | if (outLogger) {
|
---|
| 2965 | LogIO ols(LogOrigin("Scantable", funcName, WHERE));
|
---|
[2193] | 2966 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
|
---|
[2047] | 2967 | }
|
---|
| 2968 | if (outTextFile) {
|
---|
[2193] | 2969 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
|
---|
[2047] | 2970 | }
|
---|
| 2971 | }
|
---|
| 2972 | }
|
---|
| 2973 |
|
---|
[2189] | 2974 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
|
---|
[2186] | 2975 | {
|
---|
[2189] | 2976 | int idxDelimiter = progressInfo.find(",");
|
---|
| 2977 | if (idxDelimiter < 0) {
|
---|
| 2978 | throw(AipsError("wrong value in 'showprogress' parameter")) ;
|
---|
| 2979 | }
|
---|
| 2980 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
|
---|
| 2981 | std::istringstream is(progressInfo.substr(idxDelimiter+1));
|
---|
| 2982 | is >> minNRow;
|
---|
| 2983 | }
|
---|
| 2984 |
|
---|
| 2985 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
|
---|
| 2986 | {
|
---|
| 2987 | if (showProgress && (nTotal >= nTotalThreshold)) {
|
---|
[2186] | 2988 | int nInterval = int(floor(double(nTotal)/100.0));
|
---|
| 2989 | if (nInterval == 0) nInterval++;
|
---|
| 2990 |
|
---|
[2193] | 2991 | if (nProcessed % nInterval == 0) {
|
---|
[2189] | 2992 | printf("\r"); //go to the head of line
|
---|
[2186] | 2993 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted
|
---|
[2189] | 2994 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
|
---|
| 2995 | printf("\x1b[39m\x1b[0m"); //set default attributes
|
---|
[2186] | 2996 | fflush(NULL);
|
---|
| 2997 | }
|
---|
[2193] | 2998 |
|
---|
[2186] | 2999 | if (nProcessed == nTotal - 1) {
|
---|
| 3000 | printf("\r\x1b[K"); //clear
|
---|
| 3001 | fflush(NULL);
|
---|
| 3002 | }
|
---|
[2193] | 3003 |
|
---|
[2186] | 3004 | }
|
---|
| 3005 | }
|
---|
| 3006 |
|
---|
| 3007 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
|
---|
| 3008 | {
|
---|
| 3009 | std::vector<bool> mask = getMask(whichrow);
|
---|
| 3010 |
|
---|
| 3011 | if (inMask.size() > 0) {
|
---|
| 3012 | uInt maskSize = mask.size();
|
---|
| 3013 | if (maskSize != inMask.size()) {
|
---|
| 3014 | throw(AipsError("mask sizes are not the same."));
|
---|
| 3015 | }
|
---|
| 3016 | for (uInt i = 0; i < maskSize; ++i) {
|
---|
| 3017 | mask[i] = mask[i] && inMask[i];
|
---|
| 3018 | }
|
---|
| 3019 | }
|
---|
| 3020 |
|
---|
| 3021 | Vector<Float> spec = getSpectrum(whichrow);
|
---|
| 3022 | mathutil::doZeroOrderInterpolation(spec, mask);
|
---|
| 3023 |
|
---|
| 3024 | FFTServer<Float,Complex> ffts;
|
---|
| 3025 | Vector<Complex> fftres;
|
---|
| 3026 | ffts.fft0(fftres, spec);
|
---|
| 3027 |
|
---|
| 3028 | std::vector<float> res;
|
---|
| 3029 | float norm = float(2.0/double(spec.size()));
|
---|
| 3030 |
|
---|
| 3031 | if (getRealImag) {
|
---|
| 3032 | for (uInt i = 0; i < fftres.size(); ++i) {
|
---|
| 3033 | res.push_back(real(fftres[i])*norm);
|
---|
| 3034 | res.push_back(imag(fftres[i])*norm);
|
---|
| 3035 | }
|
---|
| 3036 | } else {
|
---|
| 3037 | for (uInt i = 0; i < fftres.size(); ++i) {
|
---|
| 3038 | res.push_back(abs(fftres[i])*norm);
|
---|
| 3039 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
|
---|
| 3040 | }
|
---|
| 3041 | }
|
---|
| 3042 |
|
---|
| 3043 | return res;
|
---|
| 3044 | }
|
---|
| 3045 |
|
---|
| 3046 |
|
---|
| 3047 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
|
---|
| 3048 | {
|
---|
[2012] | 3049 | Vector<Float> spec;
|
---|
| 3050 | specCol_.get(whichrow, spec);
|
---|
| 3051 |
|
---|
| 3052 | float mean = 0.0;
|
---|
| 3053 | float smean = 0.0;
|
---|
| 3054 | int n = 0;
|
---|
[2047] | 3055 | for (uInt i = 0; i < spec.nelements(); ++i) {
|
---|
[2012] | 3056 | if (mask[i]) {
|
---|
| 3057 | mean += spec[i];
|
---|
| 3058 | smean += spec[i]*spec[i];
|
---|
| 3059 | n++;
|
---|
| 3060 | }
|
---|
| 3061 | }
|
---|
| 3062 |
|
---|
| 3063 | mean /= (float)n;
|
---|
| 3064 | smean /= (float)n;
|
---|
| 3065 |
|
---|
| 3066 | return sqrt(smean - mean*mean);
|
---|
| 3067 | }
|
---|
| 3068 |
|
---|
| 3069 |
|
---|
[2186] | 3070 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
|
---|
[2012] | 3071 | {
|
---|
| 3072 | ostringstream oss;
|
---|
| 3073 |
|
---|
| 3074 | if (verbose) {
|
---|
| 3075 | oss << " Scan[" << getScan(whichrow) << "]";
|
---|
| 3076 | oss << " Beam[" << getBeam(whichrow) << "]";
|
---|
| 3077 | oss << " IF[" << getIF(whichrow) << "]";
|
---|
| 3078 | oss << " Pol[" << getPol(whichrow) << "]";
|
---|
| 3079 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
|
---|
| 3080 | oss << "Fitter range = " << masklist << endl;
|
---|
| 3081 | oss << "Baseline parameters" << endl;
|
---|
| 3082 | oss << flush;
|
---|
| 3083 | }
|
---|
| 3084 |
|
---|
| 3085 | return String(oss);
|
---|
| 3086 | }
|
---|
| 3087 |
|
---|
[2193] | 3088 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const
|
---|
[2012] | 3089 | {
|
---|
| 3090 | ostringstream oss;
|
---|
| 3091 |
|
---|
| 3092 | if (verbose) {
|
---|
| 3093 | oss << "Results of baseline fit" << endl;
|
---|
| 3094 | oss << " rms = " << setprecision(6) << rms << endl;
|
---|
[2193] | 3095 | if (nClipped >= 0) {
|
---|
| 3096 | oss << " Number of clipped channels = " << nClipped << endl;
|
---|
| 3097 | }
|
---|
[2094] | 3098 | for (int i = 0; i < 60; ++i) {
|
---|
| 3099 | oss << "-";
|
---|
| 3100 | }
|
---|
[2131] | 3101 | oss << endl;
|
---|
[2094] | 3102 | oss << flush;
|
---|
[2012] | 3103 | }
|
---|
| 3104 |
|
---|
| 3105 | return String(oss);
|
---|
| 3106 | }
|
---|
| 3107 |
|
---|
[2186] | 3108 | std::string Scantable::formatBaselineParams(const std::vector<float>& params,
|
---|
| 3109 | const std::vector<bool>& fixed,
|
---|
| 3110 | float rms,
|
---|
[2193] | 3111 | int nClipped,
|
---|
[2186] | 3112 | const std::string& masklist,
|
---|
| 3113 | int whichrow,
|
---|
| 3114 | bool verbose,
|
---|
| 3115 | int start, int count,
|
---|
| 3116 | bool resetparamid) const
|
---|
[2047] | 3117 | {
|
---|
[2064] | 3118 | int nParam = (int)(params.size());
|
---|
[2047] | 3119 |
|
---|
[2064] | 3120 | if (nParam < 1) {
|
---|
| 3121 | return(" Not fitted");
|
---|
| 3122 | } else {
|
---|
| 3123 |
|
---|
| 3124 | ostringstream oss;
|
---|
| 3125 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
|
---|
| 3126 |
|
---|
| 3127 | if (start < 0) start = 0;
|
---|
| 3128 | if (count < 0) count = nParam;
|
---|
| 3129 | int end = start + count;
|
---|
| 3130 | if (end > nParam) end = nParam;
|
---|
| 3131 | int paramidoffset = (resetparamid) ? (-start) : 0;
|
---|
| 3132 |
|
---|
| 3133 | for (int i = start; i < end; ++i) {
|
---|
| 3134 | if (i > start) {
|
---|
[2047] | 3135 | oss << ",";
|
---|
| 3136 | }
|
---|
[2064] | 3137 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
|
---|
| 3138 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
|
---|
[2047] | 3139 | }
|
---|
[2064] | 3140 |
|
---|
| 3141 | oss << endl;
|
---|
[2193] | 3142 | oss << formatBaselineParamsFooter(rms, nClipped, verbose);
|
---|
[2064] | 3143 |
|
---|
| 3144 | return String(oss);
|
---|
[2047] | 3145 | }
|
---|
| 3146 |
|
---|
| 3147 | }
|
---|
| 3148 |
|
---|
[2193] | 3149 | 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] | 3150 | {
|
---|
[2064] | 3151 | int nOutParam = (int)(params.size());
|
---|
| 3152 | int nPiece = (int)(ranges.size()) - 1;
|
---|
[2012] | 3153 |
|
---|
[2064] | 3154 | if (nOutParam < 1) {
|
---|
| 3155 | return(" Not fitted");
|
---|
| 3156 | } else if (nPiece < 0) {
|
---|
[2193] | 3157 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose);
|
---|
[2064] | 3158 | } else if (nPiece < 1) {
|
---|
| 3159 | return(" Bad count of the piece edge info");
|
---|
| 3160 | } else if (nOutParam % nPiece != 0) {
|
---|
| 3161 | return(" Bad count of the output baseline parameters");
|
---|
| 3162 | } else {
|
---|
| 3163 |
|
---|
| 3164 | int nParam = nOutParam / nPiece;
|
---|
| 3165 |
|
---|
| 3166 | ostringstream oss;
|
---|
| 3167 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
|
---|
| 3168 |
|
---|
| 3169 | stringstream ss;
|
---|
| 3170 | ss << ranges[nPiece] << flush;
|
---|
| 3171 | int wRange = ss.str().size() * 2 + 5;
|
---|
| 3172 |
|
---|
| 3173 | for (int i = 0; i < nPiece; ++i) {
|
---|
[2047] | 3174 | ss.str("");
|
---|
[2064] | 3175 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
|
---|
| 3176 | oss << left << setw(wRange) << ss.str();
|
---|
[2193] | 3177 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true);
|
---|
[2012] | 3178 | }
|
---|
[2064] | 3179 |
|
---|
[2193] | 3180 | oss << formatBaselineParamsFooter(rms, nClipped, verbose);
|
---|
[2064] | 3181 |
|
---|
| 3182 | return String(oss);
|
---|
[2012] | 3183 | }
|
---|
| 3184 |
|
---|
| 3185 | }
|
---|
| 3186 |
|
---|
[2047] | 3187 | bool Scantable::hasSameNchanOverIFs()
|
---|
[2012] | 3188 | {
|
---|
[2047] | 3189 | int nIF = nif(-1);
|
---|
| 3190 | int nCh;
|
---|
| 3191 | int totalPositiveNChan = 0;
|
---|
| 3192 | int nPositiveNChan = 0;
|
---|
[2012] | 3193 |
|
---|
[2047] | 3194 | for (int i = 0; i < nIF; ++i) {
|
---|
| 3195 | nCh = nchan(i);
|
---|
| 3196 | if (nCh > 0) {
|
---|
| 3197 | totalPositiveNChan += nCh;
|
---|
| 3198 | nPositiveNChan++;
|
---|
[2012] | 3199 | }
|
---|
| 3200 | }
|
---|
| 3201 |
|
---|
[2047] | 3202 | return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
|
---|
[2012] | 3203 | }
|
---|
| 3204 |
|
---|
[2047] | 3205 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
|
---|
[2012] | 3206 | {
|
---|
| 3207 | if (mask.size() < 2) {
|
---|
| 3208 | throw(AipsError("The mask elements should be > 1"));
|
---|
| 3209 | }
|
---|
[2047] | 3210 | int IF = getIF(whichrow);
|
---|
| 3211 | if (mask.size() != (uInt)nchan(IF)) {
|
---|
[2012] | 3212 | throw(AipsError("Number of channels in scantable != number of mask elements"));
|
---|
| 3213 | }
|
---|
| 3214 |
|
---|
[2047] | 3215 | if (verbose) {
|
---|
[2012] | 3216 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
|
---|
| 3217 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
|
---|
| 3218 | if (!hasSameNchan) {
|
---|
[2047] | 3219 | logOs << endl << "This mask is only valid for IF=" << IF;
|
---|
[2012] | 3220 | }
|
---|
| 3221 | logOs << LogIO::POST;
|
---|
| 3222 | }
|
---|
| 3223 |
|
---|
| 3224 | std::vector<double> abcissa = getAbcissa(whichrow);
|
---|
[2047] | 3225 | std::vector<int> edge = getMaskEdgeIndices(mask);
|
---|
| 3226 |
|
---|
[2012] | 3227 | ostringstream oss;
|
---|
| 3228 | oss.setf(ios::fixed);
|
---|
| 3229 | oss << setprecision(1) << "[";
|
---|
[2047] | 3230 | for (uInt i = 0; i < edge.size(); i+=2) {
|
---|
[2012] | 3231 | if (i > 0) oss << ",";
|
---|
[2047] | 3232 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
|
---|
[2012] | 3233 | }
|
---|
| 3234 | oss << "]" << flush;
|
---|
| 3235 |
|
---|
| 3236 | return String(oss);
|
---|
| 3237 | }
|
---|
| 3238 |
|
---|
[2047] | 3239 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
|
---|
[2012] | 3240 | {
|
---|
[2047] | 3241 | if (mask.size() < 2) {
|
---|
| 3242 | throw(AipsError("The mask elements should be > 1"));
|
---|
[2012] | 3243 | }
|
---|
| 3244 |
|
---|
[2047] | 3245 | std::vector<int> out, startIndices, endIndices;
|
---|
| 3246 | int maskSize = mask.size();
|
---|
[2012] | 3247 |
|
---|
[2047] | 3248 | startIndices.clear();
|
---|
| 3249 | endIndices.clear();
|
---|
| 3250 |
|
---|
| 3251 | if (mask[0]) {
|
---|
| 3252 | startIndices.push_back(0);
|
---|
[2012] | 3253 | }
|
---|
[2047] | 3254 | for (int i = 1; i < maskSize; ++i) {
|
---|
| 3255 | if ((!mask[i-1]) && mask[i]) {
|
---|
| 3256 | startIndices.push_back(i);
|
---|
| 3257 | } else if (mask[i-1] && (!mask[i])) {
|
---|
| 3258 | endIndices.push_back(i-1);
|
---|
| 3259 | }
|
---|
[2012] | 3260 | }
|
---|
[2047] | 3261 | if (mask[maskSize-1]) {
|
---|
| 3262 | endIndices.push_back(maskSize-1);
|
---|
| 3263 | }
|
---|
[2012] | 3264 |
|
---|
[2047] | 3265 | if (startIndices.size() != endIndices.size()) {
|
---|
| 3266 | throw(AipsError("Inconsistent Mask Size: bad data?"));
|
---|
| 3267 | }
|
---|
| 3268 | for (uInt i = 0; i < startIndices.size(); ++i) {
|
---|
| 3269 | if (startIndices[i] > endIndices[i]) {
|
---|
| 3270 | throw(AipsError("Mask start index > mask end index"));
|
---|
[2012] | 3271 | }
|
---|
| 3272 | }
|
---|
| 3273 |
|
---|
[2047] | 3274 | out.clear();
|
---|
| 3275 | for (uInt i = 0; i < startIndices.size(); ++i) {
|
---|
| 3276 | out.push_back(startIndices[i]);
|
---|
| 3277 | out.push_back(endIndices[i]);
|
---|
| 3278 | }
|
---|
| 3279 |
|
---|
[2012] | 3280 | return out;
|
---|
| 3281 | }
|
---|
| 3282 |
|
---|
[2161] | 3283 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const
|
---|
| 3284 | {
|
---|
| 3285 | Vector<Float> tsys( tsysCol_(whichrow) ) ;
|
---|
| 3286 | vector<float> stlTsys ;
|
---|
| 3287 | tsys.tovector( stlTsys ) ;
|
---|
| 3288 | return stlTsys ;
|
---|
| 3289 | }
|
---|
[2012] | 3290 |
|
---|
| 3291 |
|
---|
[1907] | 3292 | }
|
---|
[1819] | 3293 | //namespace asap
|
---|