[1795] | 1 | // |
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| 2 | // C++ Implementation: PKSFiller |
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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) 2010 |
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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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| 12 | #include <casa/iostream.h> |
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| 13 | #include <casa/iomanip.h> |
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| 14 | |
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| 15 | #include <casa/Exceptions.h> |
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| 16 | #include <casa/OS/Path.h> |
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| 17 | #include <casa/OS/File.h> |
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| 18 | #include <casa/Quanta/Unit.h> |
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| 19 | #include <casa/Arrays/ArrayMath.h> |
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| 20 | #include <casa/Arrays/ArrayLogical.h> |
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| 21 | #include <casa/Utilities/Regex.h> |
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[1916] | 22 | #include <casa/Utilities/DataType.h> |
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[1816] | 23 | #include <casa/Logging/LogIO.h> |
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[1795] | 24 | |
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[1904] | 25 | #include <casa/Containers/Record.h> |
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[1795] | 26 | #include <measures/Measures/MDirection.h> |
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| 27 | #include <measures/Measures/MeasConvert.h> |
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| 28 | |
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| 29 | #include <atnf/PKSIO/PKSrecord.h> |
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| 30 | #include <atnf/PKSIO/PKSreader.h> |
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| 31 | |
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| 32 | #ifdef HAS_ALMA |
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| 33 | #include <casa/System/ProgressMeter.h> |
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| 34 | #endif |
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| 35 | #include <casa/Logging/LogIO.h> |
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| 36 | |
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| 37 | #include <time.h> |
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[1916] | 38 | #include <sstream> |
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[1795] | 39 | |
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| 40 | #include "STDefs.h" |
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| 41 | #include "STAttr.h" |
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| 42 | |
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| 43 | #include "PKSFiller.h" |
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| 44 | #include "STHeader.h" |
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| 45 | |
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| 46 | using namespace casa; |
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| 47 | |
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| 48 | namespace asap { |
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| 49 | |
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| 50 | |
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| 51 | PKSFiller::PKSFiller( CountedPtr< Scantable > stbl ) : |
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| 52 | FillerBase(stbl), |
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[1815] | 53 | reader_(0) |
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[1795] | 54 | { |
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| 55 | setReferenceRegex(".*(e|w|_R)$"); |
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| 56 | } |
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| 57 | |
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| 58 | PKSFiller::~PKSFiller() |
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| 59 | { |
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| 60 | close(); |
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| 61 | } |
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| 62 | |
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[1904] | 63 | bool PKSFiller::open( const std::string& filename, const Record& rec) |
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[1795] | 64 | { |
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| 65 | Bool haveBase, haveSpectra; |
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| 66 | |
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| 67 | String inName(filename); |
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| 68 | Path path(inName); |
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| 69 | inName = path.expandedName(); |
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| 70 | |
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| 71 | File file(inName); |
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| 72 | filename_ = inName; |
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| 73 | |
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| 74 | // Create reader and fill in values for arguments |
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| 75 | String format; |
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| 76 | Vector<Bool> beams, ifs; |
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| 77 | Vector<uInt> nchans,npols; |
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| 78 | |
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[1880] | 79 | String antenna(""); |
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[1916] | 80 | Bool getPt = False; |
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[1815] | 81 | |
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[1916] | 82 | // parsing MS options |
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| 83 | if ( rec.isDefined( "ms" ) ) { |
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| 84 | Record msrec = rec.asRecord( "ms" ) ; |
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| 85 | //msrec.print( cout ) ; |
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| 86 | if ( msrec.isDefined( "getpt" ) ) { |
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| 87 | getPt = msrec.asBool( "getpt" ) ; |
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| 88 | } |
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| 89 | if ( msrec.isDefined( "antenna" ) ) { |
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| 90 | if ( msrec.type( msrec.fieldNumber( "antenna" ) ) == TpInt ) { |
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| 91 | Int antInt = msrec.asInt( "antenna" ) ; |
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| 92 | ostringstream oss ; |
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| 93 | oss << antInt ; |
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| 94 | antenna = String( oss ) ; |
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| 95 | } |
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| 96 | else { |
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| 97 | antenna = msrec.asString( "antenna" ) ; |
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| 98 | } |
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| 99 | } |
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| 100 | } |
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| 101 | |
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[1815] | 102 | reader_ = getPKSreader(inName, antenna, 0, 0, format, beams, ifs, |
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| 103 | nchans, npols, haveXPol_, haveBase, haveSpectra); |
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| 104 | if (reader_.null() == True) { |
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[1795] | 105 | return False; |
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| 106 | } |
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| 107 | |
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| 108 | if (!haveSpectra) { |
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| 109 | reader_ = 0; |
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| 110 | throw(AipsError("No spectral data in file.")); |
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| 111 | } |
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[1816] | 112 | |
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| 113 | LogIO os( LogOrigin( "PKSFiller", "open()", WHERE ) ) ; |
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[1795] | 114 | nBeam_ = beams.nelements(); |
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| 115 | nIF_ = ifs.nelements(); |
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| 116 | // Get basic parameters. |
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| 117 | if ( anyEQ(haveXPol_, True) ) { |
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| 118 | os << "Cross polarization present" << LogIO::POST; |
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| 119 | for (uInt i=0; i< npols.nelements();++i) { |
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| 120 | if (npols[i] < 3) npols[i] += 2;// Convert Complex -> 2 Floats |
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| 121 | } |
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| 122 | } |
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[1815] | 123 | STHeader header; |
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| 124 | header.nchan = max(nchans); |
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| 125 | header.npol = max(npols); |
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| 126 | header.nbeam = nBeam_; |
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[1795] | 127 | |
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[1815] | 128 | Int status = reader_->getHeader(header.observer, header.project, |
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| 129 | header.antennaname, header.antennaposition, |
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| 130 | header.obstype, |
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| 131 | header.fluxunit, |
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| 132 | header.equinox, |
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| 133 | header.freqref, |
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| 134 | header.utc, header.reffreq, |
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| 135 | header.bandwidth); |
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[1795] | 136 | |
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| 137 | if (status) { |
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| 138 | reader_ = 0; |
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| 139 | throw(AipsError("Failed to get header.")); |
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| 140 | } |
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[1816] | 141 | os << "Found " << header.antennaname << " data." << LogIO::POST; |
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[1815] | 142 | if ((header.obstype).matches("*SW*")) { |
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[1795] | 143 | // need robust way here - probably read ahead of next timestamp |
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| 144 | os << "Header indicates frequency switched observation.\n" |
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| 145 | << "setting # of IFs = 1 " << LogIO::POST; |
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| 146 | |
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| 147 | nIF_ = 1; |
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[1815] | 148 | header.obstype = String("fswitch"); |
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[1795] | 149 | } |
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| 150 | // Determine Telescope and set brightness unit |
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| 151 | Bool throwIt = False; |
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[1815] | 152 | Instrument inst = STAttr::convertInstrument(header.antennaname, throwIt); |
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[1795] | 153 | |
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| 154 | if (inst==ATMOPRA || inst==TIDBINBILLA) { |
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[1815] | 155 | header.fluxunit = "K"; |
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[1795] | 156 | } else { |
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| 157 | // downcase for use with Quanta |
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[1815] | 158 | if (header.fluxunit == "JY") { |
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| 159 | header.fluxunit = "Jy"; |
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[1795] | 160 | } |
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| 161 | } |
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| 162 | STAttr stattr; |
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[1815] | 163 | header.poltype = stattr.feedPolType(inst); |
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| 164 | header.nif = nIF_; |
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| 165 | header.epoch = "UTC"; |
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| 166 | // *** header.frequnit = "Hz" |
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[1795] | 167 | // Apply selection criteria. |
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| 168 | Vector<Int> ref; |
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| 169 | |
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| 170 | Vector<Int> start(nIF_, 1); |
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| 171 | Vector<Int> end(nIF_, 0); |
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| 172 | reader_->select(beams, ifs, start, end, ref, True, haveXPol_[0], False, getPt); |
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[1815] | 173 | setHeader(header); |
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[1795] | 174 | //For MS, add the location of POINTING of the input MS so one get |
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| 175 | //pointing data from there, if necessary. |
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| 176 | //Also find nrow in MS |
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| 177 | nInDataRow = 0; |
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| 178 | if (format == "MS2") { |
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| 179 | Path datapath(inName); |
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| 180 | String ptTabPath = datapath.absoluteName(); |
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| 181 | Table inMS(ptTabPath); |
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| 182 | nInDataRow = inMS.nrow(); |
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| 183 | ptTabPath.append("/POINTING"); |
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| 184 | table_->table().rwKeywordSet().define("POINTING", ptTabPath); |
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[1815] | 185 | if (header.antennaname.matches("GBT")) { |
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[1795] | 186 | String GOTabPath = datapath.absoluteName(); |
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| 187 | GOTabPath.append("/GBT_GO"); |
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| 188 | table_->table().rwKeywordSet().define("GBT_GO", GOTabPath); |
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| 189 | } |
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| 190 | } |
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[1815] | 191 | String freqFrame = header.freqref; |
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[1795] | 192 | //translate frequency reference frame back to |
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| 193 | //MS style (as PKSMS2reader converts the original frame |
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| 194 | //in FITS standard style) |
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| 195 | if (freqFrame == "TOPOCENT") { |
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| 196 | freqFrame = "TOPO"; |
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| 197 | } else if (freqFrame == "GEOCENER") { |
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| 198 | freqFrame = "GEO"; |
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| 199 | } else if (freqFrame == "BARYCENT") { |
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| 200 | freqFrame = "BARY"; |
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| 201 | } else if (freqFrame == "GALACTOC") { |
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| 202 | freqFrame = "GALACTO"; |
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| 203 | } else if (freqFrame == "LOCALGRP") { |
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| 204 | freqFrame = "LGROUP"; |
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| 205 | } else if (freqFrame == "CMBDIPOL") { |
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| 206 | freqFrame = "CMB"; |
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| 207 | } else if (freqFrame == "SOURCE") { |
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| 208 | freqFrame = "REST"; |
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| 209 | } |
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| 210 | // set both "FRAME" and "BASEFRAME" |
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| 211 | table_->frequencies().setFrame(freqFrame, false); |
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[1815] | 212 | table_->frequencies().setFrame(freqFrame, true); |
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[1795] | 213 | |
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| 214 | return true; |
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| 215 | } |
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| 216 | |
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| 217 | void PKSFiller::close( ) |
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| 218 | { |
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[1815] | 219 | if (reader_.null() != False) { |
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| 220 | reader_ = 0; |
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[1795] | 221 | } |
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| 222 | table_ = 0; |
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| 223 | } |
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| 224 | |
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| 225 | void PKSFiller::fill( ) |
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| 226 | { |
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| 227 | int status = 0; |
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[1816] | 228 | LogIO os( LogOrigin( "PKSFiller", "fill()", WHERE ) ) ; |
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[1795] | 229 | |
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| 230 | /** |
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| 231 | Int beamNo, IFno, refBeam, scanNo, cycleNo; |
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| 232 | Float azimuth, elevation, focusAxi, focusRot, focusTan, |
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| 233 | humidity, parAngle, pressure, temperature, windAz, windSpeed; |
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| 234 | Double bandwidth, freqInc, interval, mjd, refFreq, srcVel; |
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| 235 | String fieldName, srcName, tcalTime, obsType; |
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| 236 | Vector<Float> calFctr, sigma, tcal, tsys; |
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| 237 | Matrix<Float> baseLin, baseSub; |
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| 238 | Vector<Double> direction(2), scanRate(2), srcDir(2), srcPM(2), restFreq(1); |
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| 239 | Matrix<Float> spectra; |
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| 240 | Matrix<uChar> flagtra; |
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| 241 | Complex xCalFctr; |
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| 242 | Vector<Complex> xPol; |
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| 243 | **/ |
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| 244 | |
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| 245 | Double min = 0.0; |
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| 246 | Double max = nInDataRow; |
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| 247 | #ifdef HAS_ALMA |
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| 248 | ProgressMeter fillpm(min, max, "Data importing progress"); |
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| 249 | #endif |
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| 250 | PKSrecord pksrec; |
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| 251 | pksrec.srcType=-1; |
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| 252 | int n = 0; |
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| 253 | bool isGBTFITS = false ; |
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[1815] | 254 | if ((table_->getAntennaName().find( "GBT" ) != String::npos) |
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[1795] | 255 | && File(filename_).isRegular()) { |
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| 256 | FILE *fp = fopen( filename_.c_str(), "r" ) ; |
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| 257 | fseek( fp, 640, SEEK_SET ) ; |
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| 258 | char buf[81] ; |
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[2163] | 259 | size_t tmp = fread( buf, 80, 1, fp ) ; |
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| 260 | (void) tmp; |
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[1795] | 261 | buf[80] = '\0' ; |
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| 262 | if ( strstr( buf, "NRAO_GBT" ) != NULL ) { |
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| 263 | isGBTFITS = true ; |
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| 264 | } |
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| 265 | fclose( fp ) ; |
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| 266 | } |
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| 267 | |
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| 268 | while ( status == 0 ) { |
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| 269 | |
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| 270 | status = reader_->read(pksrec); |
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| 271 | if ( status != 0 ) break; |
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| 272 | n += 1; |
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| 273 | Regex filterrx(".*[SL|PA]$"); |
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| 274 | Regex obsrx("^AT.+"); |
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[1815] | 275 | if ( table_->getAntennaName().matches(obsrx) && |
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[1795] | 276 | pksrec.obsType.matches(filterrx)) { |
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| 277 | //cerr << "ignoring paddle scan" << endl; |
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| 278 | continue; |
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| 279 | } |
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| 280 | |
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| 281 | Vector<Double> sratedbl(pksrec.scanRate.nelements()); |
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| 282 | convertArray(sratedbl, pksrec.scanRate); |
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[1816] | 283 | setScanRate(sratedbl); |
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[1795] | 284 | |
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| 285 | Regex rx(getReferenceRegex()); |
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| 286 | Regex rx2("_S$"); |
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| 287 | Int match = pksrec.srcName.matches(rx); |
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| 288 | std::string srcname; |
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[1872] | 289 | Int srctype = Int(SrcType::NOTYPE); |
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[1795] | 290 | if (match) { |
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| 291 | srcname = pksrec.srcName; |
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[1872] | 292 | srctype = Int(SrcType::PSOFF); |
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[1795] | 293 | } else { |
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| 294 | srcname = pksrec.srcName.before(rx2); |
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[1872] | 295 | srctype = Int(SrcType::PSON); |
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[1795] | 296 | } |
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[1872] | 297 | if ( pksrec.srcType != Int(SrcType::NOTYPE)) { |
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[1795] | 298 | srctype = pksrec.srcType ; |
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| 299 | } |
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| 300 | setTime(pksrec.mjd, pksrec.interval); |
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| 301 | setSource(srcname, srctype, pksrec.fieldName, |
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| 302 | pksrec.srcDir, pksrec.srcPM, pksrec.srcVel); |
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| 303 | |
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| 304 | if (nBeam_ > 1 ) { |
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| 305 | setReferenceBeam(pksrec.refBeam-1); |
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| 306 | } |
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[1805] | 307 | |
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[1795] | 308 | setMolecule(pksrec.restFreq); |
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| 309 | setTcal(pksrec.tcalTime, pksrec.tcal); |
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| 310 | setWeather(pksrec.temperature, pksrec.pressure, |
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| 311 | pksrec.humidity, pksrec.windSpeed, |
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| 312 | pksrec.windAz); |
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| 313 | setFocus(pksrec.parAngle, pksrec.focusAxi, pksrec.focusTan, |
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| 314 | pksrec.focusRot); |
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| 315 | setDirection(pksrec.direction, pksrec.azimuth, pksrec.elevation); |
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| 316 | |
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[1805] | 317 | setFrequency(Double(pksrec.spectra.nrow()/2), |
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| 318 | pksrec.refFreq, pksrec.freqInc); |
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| 319 | |
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[1816] | 320 | // Note: this is only one value for all polarisations! |
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[2268] | 321 | |
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| 322 | //setFlagrow(pksrec.flagrow); |
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[1795] | 323 | // Turn the (nchan,npol) matrix and possible complex xPol vector |
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| 324 | // into 2-4 rows in the scantable |
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| 325 | Vector<Float> tsysvec(1); |
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| 326 | // Why is spectra.ncolumn() == 3 for haveXPol_ == True |
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| 327 | uInt npol = (pksrec.spectra.ncolumn()==1 ? 1: 2); |
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| 328 | uInt polno =0; |
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| 329 | for ( uInt i=0; i< npol; ++i ) { |
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| 330 | tsysvec = pksrec.tsys(i); |
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| 331 | if (isGBTFITS) { |
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| 332 | polno = pksrec.polNo ; |
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| 333 | } else { |
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| 334 | polno = i; |
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| 335 | } |
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[1828] | 336 | setIndex(pksrec.scanNo-1, pksrec.cycleNo-1, pksrec.IFno-1, polno, |
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| 337 | pksrec.beamNo-1); |
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[1795] | 338 | setSpectrum(pksrec.spectra.column(i), pksrec.flagged.column(i), tsysvec); |
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| 339 | commitRow(); |
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| 340 | } |
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| 341 | if ( haveXPol_[0] ) { |
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| 342 | // no tsys given for xpol, so emulate it |
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| 343 | tsysvec = sqrt(pksrec.tsys[0]*pksrec.tsys[1]); |
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| 344 | // add real part of cross pol |
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| 345 | polno = 2; |
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| 346 | Vector<Float> r(real(pksrec.xPol)); |
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| 347 | // make up flags from linears |
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| 348 | /// @fixme this has to be a bitwise or of both pols |
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| 349 | /// pksrec.flagged.column(0) | pksrec.flagged.column(1); |
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| 350 | |
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[1831] | 351 | setIndex(pksrec.scanNo-1, pksrec.cycleNo-1, pksrec.IFno-1, polno, |
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| 352 | pksrec.beamNo-1); |
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[1795] | 353 | setSpectrum(r, pksrec.flagged.column(0), tsysvec); |
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| 354 | commitRow(); |
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| 355 | |
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| 356 | // ad imaginary part of cross pol |
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| 357 | polno = 3; |
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| 358 | Vector<Float> im(imag(pksrec.xPol)); |
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[1830] | 359 | setIndex(pksrec.scanNo-1, pksrec.cycleNo-1, pksrec.IFno-1, polno, |
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| 360 | pksrec.beamNo-1); |
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[1795] | 361 | setSpectrum(im, pksrec.flagged.column(0), tsysvec); |
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| 362 | commitRow(); |
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| 363 | } |
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| 364 | #ifdef HAS_ALMA |
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| 365 | fillpm._update(n); |
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| 366 | #endif |
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| 367 | } |
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| 368 | if (status > 0) { |
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| 369 | close(); |
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| 370 | throw(AipsError("Reading error occured, data possibly corrupted.")); |
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| 371 | } |
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| 372 | #ifdef HAS_ALMA |
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| 373 | fillpm.done(); |
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| 374 | #endif |
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| 375 | } |
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| 376 | |
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| 377 | }//namespace asap |
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