| 1 | //#---------------------------------------------------------------------------
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| 2 | //# STWriter.cc: ASAP class to write out single dish spectra.
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| 3 | //#---------------------------------------------------------------------------
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| 4 | //# Copyright (C) 2004
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| 5 | //# ATNF
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| 6 | //#
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| 7 | //# This program is free software; you can redistribute it and/or modify it
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| 8 | //# under the terms of the GNU General Public License as published by the Free
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| 9 | //# Software Foundation; either version 2 of the License, or (at your option)
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| 10 | //# any later version.
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| 11 | //#
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| 12 | //# This program is distributed in the hope that it will be useful, but
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| 13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of
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| 14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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| 15 | //# Public License for more details.
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| 16 | //#
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| 17 | //# You should have received a copy of the GNU General Public License along
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| 18 | //# with this program; if not, write to the Free Software Foundation, Inc.,
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| 19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
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| 20 | //#
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| 21 | //# Correspondence concerning this software should be addressed as follows:
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| 22 | //# Internet email: Malte.Marquarding@csiro.au
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| 23 | //# Postal address: Malte Marquarding,
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| 24 | //# Australia Telescope National Facility,
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| 25 | //# P.O. Box 76,
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| 26 | //# Epping, NSW, 2121,
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| 27 | //# AUSTRALIA
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| 28 | //#
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| 29 | //# $Id: STWriter.cpp 2007 2011-02-23 09:23:16Z TakeshiNakazato $
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| 30 | //#---------------------------------------------------------------------------
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| 31 |
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| 32 | #include <string>
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| 33 |
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| 34 | #include <casa/aips.h>
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| 35 | #include <casa/Arrays/Array.h>
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| 36 | #include <casa/Arrays/Vector.h>
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| 37 | #include <casa/BasicSL/Complex.h>
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| 38 | #include <casa/Utilities/CountedPtr.h>
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| 39 | #include <casa/Utilities/Assert.h>
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| 40 |
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| 41 | #include <atnf/PKSIO/PKSrecord.h>
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| 42 | #include <atnf/PKSIO/PKSMS2writer.h>
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| 43 | #include <atnf/PKSIO/PKSSDwriter.h>
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| 44 | #include <atnf/PKSIO/SrcType.h>
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| 45 |
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| 46 | #include <tables/Tables/Table.h>
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| 47 | #include <tables/Tables/TableIter.h>
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| 48 | #include <tables/Tables/TableRow.h>
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| 49 | #include <tables/Tables/ArrayColumn.h>
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| 50 |
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| 51 | #include "STFITSImageWriter.h"
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| 52 | #include "STAsciiWriter.h"
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| 53 | #include "STHeader.h"
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| 54 | #include "STMath.h"
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| 55 |
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| 56 |
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| 57 | #include "STWriter.h"
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| 58 |
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| 59 | using namespace casa;
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| 60 | namespace asap {
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| 61 |
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| 62 | STWriter::STWriter(const std::string &format)
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| 63 | {
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| 64 | format_ = format;
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| 65 | String t(format_);
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| 66 | t.upcase();
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| 67 | if (t == "MS2") {
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| 68 | writer_ = new PKSMS2writer();
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| 69 | } else if (t == "SDFITS") {
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| 70 | writer_ = new PKSSDwriter();
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| 71 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") {
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| 72 | writer_ = 0;
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| 73 | } else {
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| 74 | throw (AipsError("Unrecognized export format"));
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| 75 | }
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| 76 | }
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| 77 |
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| 78 | STWriter::~STWriter()
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| 79 | {
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| 80 | if (writer_) {
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| 81 | delete writer_;
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| 82 | }
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| 83 | }
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| 84 |
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| 85 | Int STWriter::setFormat(const std::string &format)
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| 86 | {
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| 87 | if (format != format_) {
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| 88 | if (writer_) delete writer_;
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| 89 | }
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| 90 |
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| 91 | format_ = format;
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| 92 | String t(format_);
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| 93 | t.upcase();
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| 94 | if (t== "MS2") {
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| 95 | writer_ = new PKSMS2writer();
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| 96 | } else if (t== "SDFITS") {
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| 97 | writer_ = new PKSSDwriter();
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| 98 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") {
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| 99 | writer_ = 0;
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| 100 | } else {
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| 101 | throw (AipsError("Unrecognized Format"));
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| 102 | }
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| 103 | return 0;
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| 104 | }
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| 105 |
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| 106 | Int STWriter::write(const CountedPtr<Scantable> in,
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| 107 | const std::string &filename)
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| 108 | {
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| 109 | // If we write out foreign formats we have to convert the frequency system
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| 110 | // into the output frame, as we do everything related to SPectarlCoordinates
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| 111 | // in asap on-the-fly.
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| 112 |
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| 113 | CountedPtr<Scantable> inst = in;
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| 114 | if (in->frequencies().getFrame(true) != in->frequencies().getFrame(false)) {
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| 115 | STMath stm(false);
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| 116 | inst = stm.frequencyAlign(in);
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| 117 | }
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| 118 |
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| 119 | if (format_=="ASCII") {
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| 120 | STAsciiWriter iw;
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| 121 | // ASCII calls SpectralCoordinate::toWorld so no freqAlign use 'in'
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| 122 | if (iw.write(*in, filename)) {
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| 123 | return 0;
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| 124 | } else {
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| 125 | return 1;
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| 126 | }
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| 127 | } else if ( format_ == "FITS" || format_ == "CLASS") {
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| 128 | STFITSImageWriter iw;
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| 129 | if (format_ == "CLASS") {
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| 130 | iw.setClass(True);
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| 131 | }
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| 132 | if (iw.write(*inst, filename)) {
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| 133 | return 0;
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| 134 | }
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| 135 | }
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| 136 |
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| 137 | // MS or SDFITS
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| 138 |
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| 139 | // Extract the header from the table.
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| 140 | // this is a little different from what I have done
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| 141 | // before. Need to check with the Offline User Test data
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| 142 | STHeader hdr = inst->getHeader();
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| 143 | //const Int nPol = hdr.npol;
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| 144 | //const Int nChan = hdr.nchan;
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| 145 | std::vector<uint> ifs = inst->getIFNos();
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| 146 | int nIF = inst->nif();//ifs.size();
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| 147 | Vector<uInt> nPol(nIF),nChan(nIF);
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| 148 | Vector<Bool> havexpol(nIF);
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| 149 | String fluxUnit = hdr.fluxunit;
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| 150 | fluxUnit.upcase();
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| 151 | nPol = 0;nChan = 0; havexpol = False;
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| 152 | for (uint i=0;i<ifs.size();++i) {
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| 153 | nPol(ifs[i]) = inst->npol();
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| 154 | nChan(ifs[i]) = inst->nchan(ifs[i]);
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| 155 | havexpol(ifs[i]) = nPol(ifs[i]) > 2;
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| 156 | }
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| 157 | // Vector<String> obstypes(2);
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| 158 | // obstypes(0) = "TR";//on
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| 159 | // obstypes(1) = "RF TR";//off
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| 160 | const Table table = inst->table();
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| 161 |
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| 162 |
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| 163 | // Create the output file and write static data.
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| 164 | Int status;
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| 165 | status = writer_->create(String(filename), hdr.observer, hdr.project,
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| 166 | hdr.antennaname, hdr.antennaposition,
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| 167 | hdr.obstype, hdr.fluxunit,
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| 168 | hdr.equinox, hdr.freqref,
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| 169 | nChan, nPol, havexpol, False);
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| 170 | if ( status ) {
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| 171 | throw(AipsError("Failed to create output file"));
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| 172 | }
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| 173 |
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| 174 | Int count = 0;
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| 175 | PKSrecord pksrec;
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| 176 | pksrec.scanNo = 1;
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| 177 | // use spearate iterators to ensure renumbering of all numbers
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| 178 | TableIterator scanit(table, "SCANNO");
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| 179 | while (!scanit.pastEnd() ) {
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| 180 | Table stable = scanit.table();
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| 181 | TableIterator beamit(stable, "BEAMNO");
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| 182 | pksrec.beamNo = 1;
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| 183 | while (!beamit.pastEnd() ) {
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| 184 | Table btable = beamit.table();
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| 185 | //MDirection::ScalarColumn dirCol(btable, "DIRECTION");
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| 186 | //pksrec.direction = dirCol(0).getAngle("rad").getValue();
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| 187 | TableIterator cycit(btable, "CYCLENO");
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| 188 | ROArrayColumn<Double> srateCol(btable, "SCANRATE");
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| 189 | Vector<Double> sratedbl;
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| 190 | srateCol.get(0, sratedbl);
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| 191 | Vector<Float> srateflt(sratedbl.nelements());
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| 192 | convertArray(srateflt, sratedbl);
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| 193 | //pksrec.scanRate = srateflt;
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| 194 | pksrec.scanRate = sratedbl;
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| 195 | ROArrayColumn<Double> spmCol(btable, "SRCPROPERMOTION");
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| 196 | spmCol.get(0, pksrec.srcPM);
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| 197 | ROArrayColumn <Double> sdirCol(btable, "SRCDIRECTION");
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| 198 | sdirCol.get(0, pksrec.srcDir);
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| 199 | ROScalarColumn<Double> svelCol(btable, "SRCVELOCITY");
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| 200 | svelCol.get(0, pksrec.srcVel);
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| 201 | ROScalarColumn<uInt> bCol(btable, "BEAMNO");
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| 202 | pksrec.beamNo = bCol(0)+1;
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| 203 | pksrec.cycleNo = 1;
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| 204 | while (!cycit.pastEnd() ) {
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| 205 | Table ctable = cycit.table();
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| 206 | TableIterator typeit( ctable, "SRCTYPE" ) ;
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| 207 | while(!typeit.pastEnd() ) {
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| 208 | Table ttable = typeit.table() ;
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| 209 | TableIterator ifit(ttable, "IFNO", TableIterator::Ascending, TableIterator::HeapSort);
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| 210 | MDirection::ScalarColumn dirCol(ctable, "DIRECTION");
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| 211 | pksrec.direction = dirCol(0).getAngle("rad").getValue();
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| 212 | pksrec.IFno = 1;
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| 213 | while (!ifit.pastEnd() ) {
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| 214 | Table itable = ifit.table();
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| 215 | TableRow row(itable);
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| 216 | // use the first row to fill in all the "metadata"
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| 217 | const TableRecord& rec = row.get(0);
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| 218 | ROArrayColumn<Float> specCol(itable, "SPECTRA");
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| 219 | pksrec.IFno = rec.asuInt("IFNO")+1;
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| 220 | uInt nchan = specCol(0).nelements();
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| 221 | Double crval,crpix;
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| 222 | //Vector<Double> restfreq;
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| 223 | Float tmp0,tmp1,tmp2,tmp3,tmp4;
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| 224 | String tcalt;
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| 225 | Vector<String> stmp0, stmp1;
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| 226 | inst->frequencies().getEntry(crpix,crval, pksrec.freqInc,
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| 227 | rec.asuInt("FREQ_ID"));
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| 228 | inst->focus().getEntry(pksrec.parAngle, pksrec.focusAxi, pksrec.focusTan,
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| 229 | pksrec.focusRot, tmp0,tmp1,tmp2,tmp3,tmp4,
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| 230 | rec.asuInt("FOCUS_ID"));
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| 231 | inst->molecules().getEntry(pksrec.restFreq,stmp0,stmp1,
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| 232 | rec.asuInt("MOLECULE_ID"));
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| 233 | // inst->tcal().getEntry(pksrec.tcalTime, pksrec.tcal,
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| 234 | // rec.asuInt("TCAL_ID"));
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| 235 | inst->weather().getEntry(pksrec.temperature, pksrec.pressure,
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| 236 | pksrec.humidity, pksrec.windSpeed,
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| 237 | pksrec.windAz, rec.asuInt("WEATHER_ID"));
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| 238 | Double pixel = Double(nchan/2);
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| 239 | pksrec.refFreq = (pixel-crpix)*pksrec.freqInc + crval;
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| 240 | // ok, now we have nrows for the n polarizations in this table
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| 241 | polConversion(pksrec.spectra, pksrec.flagged, pksrec.xPol, itable);
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| 242 | pksrec.tsys = tsysFromTable(itable);
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| 243 | // dummy data
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| 244 | uInt npol = pksrec.spectra.ncolumn();
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| 245 |
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| 246 | // TCAL
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| 247 | inst->tcal().getEntry( pksrec.tcalTime, pksrec.tcal,
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| 248 | rec.asuInt("TCAL_ID") ) ;
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| 249 | if ( pksrec.tcal.nelements() == 1 ) {
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| 250 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ;
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| 251 | Vector<uInt> tcalids = uintCol.getColumn() ;
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| 252 | pksrec.tcal.resize( npol ) ;
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| 253 | Vector<Float> dummyA ;
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| 254 | String dummyS ;
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| 255 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) {
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| 256 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ;
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| 257 | pksrec.tcal[ipol] = dummyA[0] ;
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| 258 | }
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| 259 | }
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| 260 | else if ( pksrec.tcal.nelements() == nchan ) {
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| 261 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ;
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| 262 | Vector<uInt> tcalids = uintCol.getColumn() ;
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| 263 | pksrec.tcal.resize( npol ) ;
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| 264 | Vector<Float> dummyA ;
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| 265 | String dummyS ;
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| 266 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) {
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| 267 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ;
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| 268 | pksrec.tcal[ipol] = mean( dummyA ) ;
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| 269 | }
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| 270 | }
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| 271 | //LogIO os ;
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| 272 | //os << "npol = " << npol << " pksrec.tcal = " << pksrec.tcal << LogIO::POST ;
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| 273 |
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| 274 | pksrec.mjd = rec.asDouble("TIME");
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| 275 | pksrec.interval = rec.asDouble("INTERVAL");
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| 276 | pksrec.fieldName = rec.asString("FIELDNAME");
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| 277 | pksrec.srcName = rec.asString("SRCNAME");
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| 278 | //pksrec.obsType = obstypes[rec.asInt("SRCTYPE")];
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| 279 | pksrec.obsType = getObsTypes( rec.asInt("SRCTYPE") ) ;
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| 280 | pksrec.bandwidth = nchan * abs(pksrec.freqInc);
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| 281 | pksrec.azimuth = rec.asFloat("AZIMUTH");
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| 282 | pksrec.elevation = rec.asFloat("ELEVATION");
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| 283 | pksrec.refBeam = rec.asInt("REFBEAMNO") + 1;
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| 284 | pksrec.sigma.resize(npol);
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| 285 | pksrec.sigma = 0.0f;
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| 286 | pksrec.calFctr.resize(npol);
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| 287 | pksrec.calFctr = 0.0f;
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| 288 | pksrec.baseLin.resize(npol,2);
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| 289 | pksrec.baseLin = 0.0f;
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| 290 | pksrec.baseSub.resize(npol,9);
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| 291 | pksrec.baseSub = 0.0f;
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| 292 | pksrec.xCalFctr = 0.0;
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| 293 | pksrec.flagrow = rec.asuInt("FLAGROW");
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| 294 |
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| 295 | status = writer_->write(pksrec);
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| 296 | if ( status ) {
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| 297 | writer_->close();
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| 298 | throw(AipsError("STWriter: Failed to export Scantable."));
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| 299 | }
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| 300 | ++count;
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| 301 | //++pksrec.IFno;
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| 302 | ++ifit;
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| 303 | }
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| 304 | ++typeit ;
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| 305 | }
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| 306 | ++pksrec.cycleNo;
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| 307 | ++cycit;
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| 308 | }
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| 309 | //++pksrec.beamNo;
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| 310 | ++beamit;
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| 311 | }
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| 312 | ++pksrec.scanNo;
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| 313 | ++scanit;
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| 314 | }
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| 315 | ostringstream oss;
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| 316 | oss << "STWriter: wrote " << count << " rows to " << filename;
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| 317 | pushLog(String(oss));
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| 318 |
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| 319 | writer_->close();
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| 320 | //if MS2 delete POINTING table exists and copy the one in the keyword
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| 321 | if ( format_ == "MS2" ) {
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| 322 | replacePtTab(table, filename);
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| 323 | }
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| 324 | return 0;
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| 325 | }
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| 326 |
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| 327 | Vector<Float> STWriter::tsysFromTable(const Table& tab)
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| 328 | {
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| 329 | ROArrayColumn<Float> tsysCol(tab, "TSYS");
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| 330 | Vector<Float> out(tab.nrow());
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| 331 | Vector<Float> tmp;
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| 332 | for (uInt i=0; i<tab.nrow(); ++i) {
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| 333 | tmp.resize();
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| 334 | tmp = tsysCol(i);
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| 335 | out[i] = tmp[0];
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| 336 | }
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| 337 | return out;
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| 338 | }
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| 339 |
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| 340 | void STWriter::polConversion( Matrix< Float >& specs, Matrix< uChar >& flags,
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| 341 | Vector< Complex > & xpol, const Table & tab )
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| 342 | {
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| 343 | String poltype = tab.keywordSet().asString("POLTYPE");
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| 344 | // Full stokes is not supported. Just allow stokes I
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| 345 | if ( poltype == "stokes" && tab.nrow() != 1) {
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| 346 | String msg = "poltype = " + poltype + " not yet supported in output.";
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| 347 | throw(AipsError(msg));
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| 348 | }
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| 349 | ROArrayColumn<Float> specCol(tab, "SPECTRA");
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| 350 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
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| 351 | uInt nchan = specCol(0).nelements();
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| 352 | uInt ncol = (tab.nrow()==1 ? 1: 2 );
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| 353 | specs.resize(nchan, ncol);
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| 354 | flags.resize(nchan, ncol);
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| 355 | // the linears
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| 356 | for (uInt i=0; i<ncol; ++i) {
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| 357 | specs.column(i) = specCol(i);
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| 358 | flags.column(i) = flagCol(i);
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| 359 | }
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| 360 | // now the complex if exists
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| 361 | Bool hasxpol = False;
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| 362 | xpol.resize();
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| 363 | if ( tab.nrow() == 4 ) {
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| 364 | hasxpol = True;
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| 365 | xpol.resize(nchan);
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| 366 | Vector<Float> reals, imags;
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| 367 | reals = specCol(2); imags = specCol(3);
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| 368 | for (uInt k=0; k < nchan; ++k) {
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| 369 | xpol[k] = Complex(reals[k], imags[k]);
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| 370 | }
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| 371 | }
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| 372 | }
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| 373 |
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| 374 | // For writing MS data, if there is the reference to
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| 375 | // original pointing table it replace it by it.
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| 376 | void STWriter::replacePtTab (const Table& tab, const std::string& fname)
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| 377 | {
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| 378 | String oldPtTabName = fname;
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| 379 | oldPtTabName.append("/POINTING");
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| 380 | if ( tab.keywordSet().isDefined("POINTING") ) {
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| 381 | String PointingTab = tab.keywordSet().asString("POINTING");
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| 382 | if ( Table::isReadable(PointingTab) ) {
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| 383 | Table newPtTab(PointingTab, Table::Old);
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| 384 | newPtTab.copy(oldPtTabName, Table::New);
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| 385 | ostringstream oss;
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| 386 | oss << "STWriter: copied " <<PointingTab << " to " << fname;
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| 387 | pushLog(String(oss));
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| 388 | }
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| 389 | }
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| 390 | }
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| 391 |
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| 392 | // get obsType string from SRCTYPE value
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| 393 | String STWriter::getObsTypes( Int srctype )
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| 394 | {
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| 395 | return SrcType::getName(srctype) ;
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| 396 | }
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| 397 |
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| 398 | }
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