| 1 | //
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| 2 | // C++ Implementation: STFiller
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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) 2006-2007
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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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| 22 |
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| 23 | #include <casa/Containers/RecordField.h>
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| 24 |
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| 25 | #include <tables/Tables/TableRow.h>
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| 26 |
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| 27 | #include <atnf/PKSIO/PKSrecord.h>
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| 28 | #include <atnf/PKSIO/PKSreader.h>
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| 29 | #ifdef HAS_ALMA
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| 30 | #include <casa/System/ProgressMeter.h>
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| 31 | #endif
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| 32 |
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| 33 | #include "STDefs.h"
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| 34 | #include "STAttr.h"
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| 35 |
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| 36 | #include "STFiller.h"
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| 37 | #include "STHeader.h"
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| 38 |
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| 39 | using namespace casa;
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| 40 |
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| 41 | namespace asap {
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| 42 |
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| 43 | STFiller::STFiller() :
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| 44 | reader_(0),
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| 45 | header_(0),
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| 46 | table_(0),
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| 47 | refRx_(".*(e|w|_R)$")
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| 48 | {
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| 49 | }
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| 50 |
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| 51 | STFiller::STFiller( CountedPtr< Scantable > stbl ) :
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| 52 | reader_(0),
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| 53 | header_(0),
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| 54 | table_(stbl),
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| 55 | refRx_(".*(e|w|_R)$")
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| 56 | {
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| 57 | }
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| 58 |
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| 59 | STFiller::STFiller(const std::string& filename, int whichIF, int whichBeam ) :
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| 60 | reader_(0),
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| 61 | header_(0),
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| 62 | table_(0),
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| 63 | refRx_(".*(e|w|_R)$")
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| 64 | {
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| 65 | open(filename, whichIF, whichBeam);
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| 66 | }
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| 67 |
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| 68 | STFiller::~STFiller()
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| 69 | {
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| 70 | close();
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| 71 | }
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| 72 |
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| 73 | void STFiller::open( const std::string& filename, int whichIF, int whichBeam )
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| 74 | {
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| 75 | if (table_.null()) {
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| 76 | table_ = new Scantable();
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| 77 | }
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| 78 | if (reader_) { delete reader_; reader_ = 0; }
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| 79 | Bool haveBase, haveSpectra;
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| 80 |
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| 81 | String inName(filename);
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| 82 | Path path(inName);
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| 83 | inName = path.expandedName();
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| 84 |
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| 85 | File file(inName);
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| 86 | if ( !file.exists() ) {
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| 87 | throw(AipsError("File does not exist"));
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| 88 | }
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| 89 | filename_ = inName;
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| 90 |
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| 91 | // Create reader and fill in values for arguments
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| 92 | String format;
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| 93 | Vector<Bool> beams, ifs;
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| 94 | Vector<uInt> nchans,npols;
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| 95 | if ( (reader_ = getPKSreader(inName, 0, 0, format, beams, ifs,
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| 96 | nchans, npols, haveXPol_,haveBase, haveSpectra
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| 97 | )) == 0 ) {
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| 98 | throw(AipsError("Creation of PKSreader failed"));
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| 99 | }
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| 100 | if (!haveSpectra) {
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| 101 | delete reader_;
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| 102 | reader_ = 0;
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| 103 | throw(AipsError("No spectral data in file."));
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| 104 | return;
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| 105 | }
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| 106 | nBeam_ = beams.nelements();
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| 107 | nIF_ = ifs.nelements();
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| 108 | // Get basic parameters.
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| 109 | if ( anyEQ(haveXPol_, True) ) {
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| 110 | pushLog("Cross polarization present");
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| 111 | for (uInt i=0; i< npols.nelements();++i) {
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| 112 | if (npols[i] < 3) npols[i] += 2;// Convert Complex -> 2 Floats
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| 113 | }
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| 114 | }
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| 115 | if (header_) delete header_;
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| 116 | header_ = new STHeader();
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| 117 | header_->nchan = max(nchans);
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| 118 | header_->npol = max(npols);
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| 119 | header_->nbeam = nBeam_;
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| 120 |
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| 121 | Int status = reader_->getHeader(header_->observer, header_->project,
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| 122 | header_->antennaname, header_->antennaposition,
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| 123 | header_->obstype,
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| 124 | header_->fluxunit,
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| 125 | header_->equinox,
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| 126 | header_->freqref,
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| 127 | header_->utc, header_->reffreq,
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| 128 | header_->bandwidth);
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| 129 |
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| 130 | if (status) {
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| 131 | delete reader_;
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| 132 | reader_ = 0;
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| 133 | delete header_;
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| 134 | header_ = 0;
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| 135 | throw(AipsError("Failed to get header."));
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| 136 | }
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| 137 | if ((header_->obstype).matches("*SW*")) {
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| 138 | // need robust way here - probably read ahead of next timestamp
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| 139 | pushLog("Header indicates frequency switched observation.\n"
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| 140 | "setting # of IFs = 1 ");
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| 141 | nIF_ = 1;
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| 142 | header_->obstype = String("fswitch");
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| 143 | }
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| 144 | // Determine Telescope and set brightness unit
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| 145 |
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| 146 |
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| 147 | Bool throwIt = False;
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| 148 | Instrument inst = STAttr::convertInstrument(header_->antennaname, throwIt);
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| 149 |
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| 150 | if (inst==ATMOPRA || inst==TIDBINBILLA) {
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| 151 | header_->fluxunit = "K";
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| 152 | } else {
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| 153 | // downcase for use with Quanta
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| 154 | if (header_->fluxunit == "JY") {
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| 155 | header_->fluxunit = "Jy";
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| 156 | }
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| 157 | }
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| 158 | STAttr stattr;
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| 159 | header_->poltype = stattr.feedPolType(inst);
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| 160 | header_->nif = nIF_;
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| 161 | header_->epoch = "UTC";
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| 162 | // *** header_->frequnit = "Hz"
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| 163 | // Apply selection criteria.
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| 164 | Vector<Int> ref;
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| 165 | ifOffset_ = 0;
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| 166 | if (whichIF>=0) {
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| 167 | if (whichIF>=0 && whichIF<nIF_) {
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| 168 | ifs = False;
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| 169 | ifs(whichIF) = True;
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| 170 | header_->nif = 1;
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| 171 | nIF_ = 1;
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| 172 | ifOffset_ = whichIF;
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| 173 | } else {
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| 174 | delete reader_;
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| 175 | reader_ = 0;
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| 176 | delete header_;
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| 177 | header_ = 0;
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| 178 | throw(AipsError("Illegal IF selection"));
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| 179 | }
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| 180 | }
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| 181 | beamOffset_ = 0;
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| 182 | if (whichBeam>=0) {
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| 183 | if (whichBeam>=0 && whichBeam<nBeam_) {
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| 184 | beams = False;
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| 185 | beams(whichBeam) = True;
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| 186 | header_->nbeam = 1;
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| 187 | nBeam_ = 1;
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| 188 | beamOffset_ = whichBeam;
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| 189 | } else {
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| 190 | delete reader_;
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| 191 | reader_ = 0;
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| 192 | delete header_;
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| 193 | header_ = 0;
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| 194 | throw(AipsError("Illegal Beam selection"));
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| 195 | }
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| 196 | }
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| 197 | Vector<Int> start(nIF_, 1);
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| 198 | Vector<Int> end(nIF_, 0);
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| 199 | reader_->select(beams, ifs, start, end, ref, True, haveXPol_[0]);
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| 200 | table_->setHeader(*header_);
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| 201 | //For MS, add the location of POINTING of the input MS so one get
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| 202 | //pointing data from there, if necessary.
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| 203 | //Also find nrow in MS
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| 204 | nInDataRow = 0;
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| 205 | if (format == "MS2") {
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| 206 | Path datapath(inName);
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| 207 | String ptTabPath = datapath.absoluteName();
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| 208 | Table inMS(ptTabPath);
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| 209 | nInDataRow = inMS.nrow();
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| 210 | ptTabPath.append("/POINTING");
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| 211 | table_->table().rwKeywordSet().define("POINTING", ptTabPath);
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| 212 | if ((header_->antennaname).matches("GBT")) {
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| 213 | String GOTabPath = datapath.absoluteName();
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| 214 | GOTabPath.append("/GBT_GO");
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| 215 | table_->table().rwKeywordSet().define("GBT_GO", GOTabPath);
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| 216 | }
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| 217 | }
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| 218 | //table_->focus().setParallactify(true);
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| 219 | }
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| 220 |
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| 221 | void STFiller::close( )
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| 222 | {
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| 223 | delete reader_;reader_=0;
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| 224 | delete header_;header_=0;
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| 225 | table_ = 0;
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| 226 | }
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| 227 |
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| 228 | int asap::STFiller::read( )
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| 229 | {
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| 230 | int status = 0;
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| 231 |
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| 232 | Double min = 0.0;
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| 233 | Double max = nInDataRow;
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| 234 | #ifdef HAS_ALMA
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| 235 | ProgressMeter fillpm(min, max, "Data importing progress");
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| 236 | #endif
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| 237 | PKSrecord pksrec;
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| 238 | int n = 0;
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| 239 | while ( status == 0 ) {
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| 240 | status = reader_->read(pksrec);
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| 241 | if ( status != 0 ) break;
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| 242 | n += 1;
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| 243 | Regex filterrx(".*[SL|PA]$");
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| 244 | Regex obsrx("^AT.+");
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| 245 | if ( header_->antennaname.matches(obsrx) &&
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| 246 | pksrec.obsType.matches(filterrx)) {
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| 247 | //cerr << "ignoring paddle scan" << endl;
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| 248 | continue;
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| 249 | }
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| 250 | TableRow row(table_->table());
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| 251 | TableRecord& rec = row.record();
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| 252 | // fields that don't get used and are just passed through asap
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| 253 | RecordFieldPtr<Array<Double> > srateCol(rec, "SCANRATE");
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| 254 | // MRC changed type from double to float
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| 255 | Vector<Double> sratedbl(pksrec.scanRate.nelements());
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| 256 | convertArray(sratedbl, pksrec.scanRate);
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| 257 | *srateCol = sratedbl;
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| 258 | RecordFieldPtr<Array<Double> > spmCol(rec, "SRCPROPERMOTION");
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| 259 | *spmCol = pksrec.srcPM;
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| 260 | RecordFieldPtr<Array<Double> > sdirCol(rec, "SRCDIRECTION");
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| 261 | *sdirCol = pksrec.srcDir;
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| 262 | RecordFieldPtr<Double> svelCol(rec, "SRCVELOCITY");
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| 263 | *svelCol = pksrec.srcVel;
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| 264 | // the real stuff
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| 265 | RecordFieldPtr<Int> fitCol(rec, "FIT_ID");
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| 266 | *fitCol = -1;
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| 267 | RecordFieldPtr<uInt> scanoCol(rec, "SCANNO");
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| 268 | *scanoCol = pksrec.scanNo-1;
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| 269 | RecordFieldPtr<uInt> cyclenoCol(rec, "CYCLENO");
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| 270 | *cyclenoCol = pksrec.cycleNo-1;
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| 271 | RecordFieldPtr<Double> mjdCol(rec, "TIME");
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| 272 | *mjdCol = pksrec.mjd;
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| 273 | RecordFieldPtr<Double> intCol(rec, "INTERVAL");
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| 274 | *intCol = pksrec.interval;
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| 275 | RecordFieldPtr<String> srcnCol(rec, "SRCNAME");
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| 276 | RecordFieldPtr<Int> srctCol(rec, "SRCTYPE");
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| 277 | RecordFieldPtr<String> fieldnCol(rec, "FIELDNAME");
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| 278 | *fieldnCol = pksrec.fieldName;
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| 279 | // try to auto-identify if it is on or off.
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| 280 | Regex rx(refRx_);
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| 281 | Regex rx2("_S$");
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| 282 | Int match = pksrec.srcName.matches(rx);
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| 283 | if (match) {
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| 284 | *srcnCol = pksrec.srcName;
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| 285 | } else {
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| 286 | *srcnCol = pksrec.srcName.before(rx2);
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| 287 | }
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| 288 | //*srcnCol = pksrec.srcName;//.before(rx2);
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| 289 | *srctCol = match;
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| 290 | RecordFieldPtr<uInt> beamCol(rec, "BEAMNO");
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| 291 | *beamCol = pksrec.beamNo-beamOffset_-1;
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| 292 | RecordFieldPtr<Int> rbCol(rec, "REFBEAMNO");
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| 293 | Int rb = -1;
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| 294 | if (nBeam_ > 1 ) rb = pksrec.refBeam-1;
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| 295 | *rbCol = rb;
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| 296 | RecordFieldPtr<uInt> ifCol(rec, "IFNO");
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| 297 | *ifCol = pksrec.IFno-ifOffset_- 1;
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| 298 | uInt id;
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| 299 | /// @todo this has to change when nchan isn't global anymore
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| 300 | id = table_->frequencies().addEntry(Double(header_->nchan/2),
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| 301 | pksrec.refFreq, pksrec.freqInc);
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| 302 | RecordFieldPtr<uInt> mfreqidCol(rec, "FREQ_ID");
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| 303 | *mfreqidCol = id;
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| 304 |
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| 305 | id = table_->molecules().addEntry(pksrec.restFreq);
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| 306 | RecordFieldPtr<uInt> molidCol(rec, "MOLECULE_ID");
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| 307 | *molidCol = id;
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| 308 |
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| 309 | id = table_->tcal().addEntry(pksrec.tcalTime, pksrec.tcal);
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| 310 | RecordFieldPtr<uInt> mcalidCol(rec, "TCAL_ID");
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| 311 | *mcalidCol = id;
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| 312 | id = table_->weather().addEntry(pksrec.temperature, pksrec.pressure,
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| 313 | pksrec.humidity, pksrec.windSpeed,
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| 314 | pksrec.windAz);
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| 315 | RecordFieldPtr<uInt> mweatheridCol(rec, "WEATHER_ID");
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| 316 | *mweatheridCol = id;
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| 317 |
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| 318 | RecordFieldPtr<uInt> mfocusidCol(rec, "FOCUS_ID");
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| 319 | id = table_->focus().addEntry(pksrec.parAngle, pksrec.focusAxi,
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| 320 | pksrec.focusTan, pksrec.focusRot);
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| 321 | *mfocusidCol = id;
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| 322 | RecordFieldPtr<Array<Double> > dirCol(rec, "DIRECTION");
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| 323 | *dirCol = pksrec.direction;
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| 324 | RecordFieldPtr<Float> azCol(rec, "AZIMUTH");
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| 325 | *azCol = pksrec.azimuth;
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| 326 | RecordFieldPtr<Float> elCol(rec, "ELEVATION");
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| 327 | *elCol = pksrec.elevation;
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| 328 |
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| 329 | RecordFieldPtr< Array<Float> > specCol(rec, "SPECTRA");
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| 330 | RecordFieldPtr< Array<uChar> > flagCol(rec, "FLAGTRA");
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| 331 | RecordFieldPtr< uInt > polnoCol(rec, "POLNO");
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| 332 |
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| 333 | RecordFieldPtr< Array<Float> > tsysCol(rec, "TSYS");
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| 334 | // Turn the (nchan,npol) matrix and possible complex xPol vector
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| 335 | // into 2-4 rows in the scantable
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| 336 | Vector<Float> tsysvec(1);
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| 337 | // Why is pksrec.spectra.ncolumn() == 3 for haveXPol_ == True
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| 338 | uInt npol = (pksrec.spectra.ncolumn()==1 ? 1: 2);
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| 339 | for ( uInt i=0; i< npol; ++i ) {
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| 340 | tsysvec = pksrec.tsys(i);
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| 341 | *tsysCol = tsysvec;
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| 342 | *polnoCol = i;
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| 343 |
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| 344 | *specCol = pksrec.spectra.column(i);
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| 345 | *flagCol = pksrec.flagged.column(i);
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| 346 | table_->table().addRow();
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| 347 | row.put(table_->table().nrow()-1, rec);
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| 348 | }
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| 349 | if ( haveXPol_[0] ) {
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| 350 | // no tsys given for xpol, so emulate it
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| 351 | tsysvec = sqrt(pksrec.tsys[0]*pksrec.tsys[1]);
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| 352 | *tsysCol = tsysvec;
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| 353 | // add real part of cross pol
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| 354 | *polnoCol = 2;
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| 355 | Vector<Float> r(real(pksrec.xPol));
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| 356 | *specCol = r;
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| 357 | // make up flags from linears
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| 358 | /// @fixme this has to be a bitwise or of both pols
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| 359 | *flagCol = pksrec.flagged.column(0);// | pksrec.flagged.column(1);
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| 360 | table_->table().addRow();
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| 361 | row.put(table_->table().nrow()-1, rec);
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| 362 | // ad imaginary part of cross pol
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| 363 | *polnoCol = 3;
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| 364 | Vector<Float> im(imag(pksrec.xPol));
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| 365 | *specCol = im;
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| 366 | table_->table().addRow();
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| 367 | row.put(table_->table().nrow()-1, rec);
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| 368 | }
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| 369 | #ifdef HAS_ALMA
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| 370 | fillpm._update(n);
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| 371 | #endif
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| 372 | }
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| 373 | if (status > 0) {
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| 374 | close();
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| 375 | throw(AipsError("Reading error occured, data possibly corrupted."));
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| 376 | }
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| 377 | #ifdef HAS_ALMA
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| 378 | fillpm.done();
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| 379 | #endif
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| 380 | return status;
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| 381 | }
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| 382 |
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| 383 | }//namespace asap
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