[470] | 1 | //#--------------------------------------------------------------------------- |
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[822] | 2 | //# STWriter.cc: ASAP class to write out single dish spectra. |
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[28] | 3 | //#--------------------------------------------------------------------------- |
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| 4 | //# Copyright (C) 2004 |
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[125] | 5 | //# ATNF |
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[28] | 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 2023 2011-03-02 05:31:40Z 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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[81] | 34 | #include <casa/aips.h> |
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[470] | 35 | #include <casa/Arrays/Array.h> |
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| 36 | #include <casa/Arrays/Vector.h> |
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[81] | 37 | #include <casa/BasicSL/Complex.h> |
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| 38 | #include <casa/Utilities/CountedPtr.h> |
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[470] | 39 | #include <casa/Utilities/Assert.h> |
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[28] | 40 | |
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[1449] | 41 | #include <atnf/PKSIO/PKSrecord.h> |
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[28] | 42 | #include <atnf/PKSIO/PKSMS2writer.h> |
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| 43 | #include <atnf/PKSIO/PKSSDwriter.h> |
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[1819] | 44 | #include <atnf/PKSIO/SrcType.h> |
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[28] | 45 | |
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[827] | 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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[324] | 49 | #include <tables/Tables/ArrayColumn.h> |
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| 50 | |
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[1443] | 51 | #include "STFITSImageWriter.h" |
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[988] | 52 | #include "STAsciiWriter.h" |
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[901] | 53 | #include "STHeader.h" |
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[1575] | 54 | #include "STMath.h" |
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[324] | 55 | |
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[1575] | 56 | |
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[822] | 57 | #include "STWriter.h" |
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[28] | 58 | |
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[125] | 59 | using namespace casa; |
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[827] | 60 | namespace asap { |
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[28] | 61 | |
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[822] | 62 | STWriter::STWriter(const std::string &format) |
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[28] | 63 | { |
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[988] | 64 | format_ = format; |
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| 65 | String t(format_); |
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[450] | 66 | t.upcase(); |
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[1443] | 67 | if (t == "MS2") { |
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[988] | 68 | writer_ = new PKSMS2writer(); |
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[1443] | 69 | } else if (t == "SDFITS") { |
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[988] | 70 | writer_ = new PKSSDwriter(); |
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[1443] | 71 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") { |
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[988] | 72 | writer_ = 0; |
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[450] | 73 | } else { |
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[988] | 74 | throw (AipsError("Unrecognized export format")); |
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[28] | 75 | } |
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| 76 | } |
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| 77 | |
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[822] | 78 | STWriter::~STWriter() |
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[28] | 79 | { |
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[988] | 80 | if (writer_) { |
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| 81 | delete writer_; |
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[192] | 82 | } |
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[28] | 83 | } |
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| 84 | |
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[822] | 85 | Int STWriter::setFormat(const std::string &format) |
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[28] | 86 | { |
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[988] | 87 | if (format != format_) { |
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| 88 | if (writer_) delete writer_; |
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[450] | 89 | } |
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[827] | 90 | |
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[988] | 91 | format_ = format; |
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| 92 | String t(format_); |
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[450] | 93 | t.upcase(); |
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| 94 | if (t== "MS2") { |
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[988] | 95 | writer_ = new PKSMS2writer(); |
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[450] | 96 | } else if (t== "SDFITS") { |
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[988] | 97 | writer_ = new PKSSDwriter(); |
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[1443] | 98 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") { |
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[988] | 99 | writer_ = 0; |
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[450] | 100 | } else { |
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| 101 | throw (AipsError("Unrecognized Format")); |
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[28] | 102 | } |
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| 103 | return 0; |
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| 104 | } |
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| 105 | |
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[827] | 106 | Int STWriter::write(const CountedPtr<Scantable> in, |
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| 107 | const std::string &filename) |
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[28] | 108 | { |
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[1575] | 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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[192] | 112 | |
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[1575] | 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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[1280] | 119 | if (format_=="ASCII") { |
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| 120 | STAsciiWriter iw; |
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[1575] | 121 | // ASCII calls SpectralCoordinate::toWorld so no freqAlign use 'in' |
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[1280] | 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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[1443] | 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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[1575] | 132 | if (iw.write(*inst, filename)) { |
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[1443] | 133 | return 0; |
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| 134 | } |
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[199] | 135 | } |
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[192] | 136 | |
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[827] | 137 | // MS or SDFITS |
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[192] | 138 | |
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[28] | 139 | // Extract the header from the table. |
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[1391] | 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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[1575] | 142 | STHeader hdr = inst->getHeader(); |
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[1060] | 143 | //const Int nPol = hdr.npol; |
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| 144 | //const Int nChan = hdr.nchan; |
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[1575] | 145 | std::vector<uint> ifs = inst->getIFNos(); |
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| 146 | int nIF = inst->nif();//ifs.size(); |
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[1060] | 147 | Vector<uInt> nPol(nIF),nChan(nIF); |
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| 148 | Vector<Bool> havexpol(nIF); |
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[1391] | 149 | String fluxUnit = hdr.fluxunit; |
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[1688] | 150 | fluxUnit.upcase(); |
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[1295] | 151 | nPol = 0;nChan = 0; havexpol = False; |
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[1305] | 152 | for (uint i=0;i<ifs.size();++i) { |
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[1575] | 153 | nPol(ifs[i]) = inst->npol(); |
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| 154 | nChan(ifs[i]) = inst->nchan(ifs[i]); |
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[1295] | 155 | havexpol(ifs[i]) = nPol(ifs[i]) > 2; |
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[1060] | 156 | } |
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[1819] | 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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[1575] | 160 | const Table table = inst->table(); |
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[324] | 161 | |
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[1663] | 162 | |
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[28] | 163 | // Create the output file and write static data. |
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| 164 | Int status; |
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[2023] | 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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[1060] | 170 | status = writer_->create(String(filename), hdr.observer, hdr.project, |
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[2023] | 171 | inst->getAntennaName(), hdr.antennaposition, |
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[1410] | 172 | hdr.obstype, hdr.fluxunit, |
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| 173 | hdr.equinox, hdr.freqref, |
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| 174 | nChan, nPol, havexpol, False); |
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[996] | 175 | if ( status ) { |
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[717] | 176 | throw(AipsError("Failed to create output file")); |
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[28] | 177 | } |
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| 178 | |
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| 179 | Int count = 0; |
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[1449] | 180 | PKSrecord pksrec; |
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| 181 | pksrec.scanNo = 1; |
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[822] | 182 | // use spearate iterators to ensure renumbering of all numbers |
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| 183 | TableIterator scanit(table, "SCANNO"); |
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| 184 | while (!scanit.pastEnd() ) { |
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| 185 | Table stable = scanit.table(); |
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[988] | 186 | TableIterator beamit(stable, "BEAMNO"); |
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[1449] | 187 | pksrec.beamNo = 1; |
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[822] | 188 | while (!beamit.pastEnd() ) { |
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| 189 | Table btable = beamit.table(); |
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[1819] | 190 | //MDirection::ScalarColumn dirCol(btable, "DIRECTION"); |
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| 191 | //pksrec.direction = dirCol(0).getAngle("rad").getValue(); |
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[988] | 192 | TableIterator cycit(btable, "CYCLENO"); |
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[999] | 193 | ROArrayColumn<Double> srateCol(btable, "SCANRATE"); |
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[1462] | 194 | Vector<Double> sratedbl; |
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| 195 | srateCol.get(0, sratedbl); |
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[1477] | 196 | Vector<Float> srateflt(sratedbl.nelements()); |
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[1462] | 197 | convertArray(srateflt, sratedbl); |
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[1819] | 198 | //pksrec.scanRate = srateflt; |
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| 199 | pksrec.scanRate = sratedbl; |
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[999] | 200 | ROArrayColumn<Double> spmCol(btable, "SRCPROPERMOTION"); |
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[1449] | 201 | spmCol.get(0, pksrec.srcPM); |
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[999] | 202 | ROArrayColumn <Double> sdirCol(btable, "SRCDIRECTION"); |
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[1449] | 203 | sdirCol.get(0, pksrec.srcDir); |
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[999] | 204 | ROScalarColumn<Double> svelCol(btable, "SRCVELOCITY"); |
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[1449] | 205 | svelCol.get(0, pksrec.srcVel); |
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[1295] | 206 | ROScalarColumn<uInt> bCol(btable, "BEAMNO"); |
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[1449] | 207 | pksrec.beamNo = bCol(0)+1; |
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| 208 | pksrec.cycleNo = 1; |
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[988] | 209 | while (!cycit.pastEnd() ) { |
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| 210 | Table ctable = cycit.table(); |
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[2006] | 211 | TableIterator typeit( ctable, "SRCTYPE" ) ; |
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| 212 | while(!typeit.pastEnd() ) { |
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| 213 | Table ttable = typeit.table() ; |
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[2007] | 214 | TableIterator ifit(ttable, "IFNO", TableIterator::Ascending, TableIterator::HeapSort); |
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[2006] | 215 | MDirection::ScalarColumn dirCol(ctable, "DIRECTION"); |
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| 216 | pksrec.direction = dirCol(0).getAngle("rad").getValue(); |
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| 217 | pksrec.IFno = 1; |
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| 218 | while (!ifit.pastEnd() ) { |
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| 219 | Table itable = ifit.table(); |
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| 220 | TableRow row(itable); |
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| 221 | // use the first row to fill in all the "metadata" |
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| 222 | const TableRecord& rec = row.get(0); |
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| 223 | ROArrayColumn<Float> specCol(itable, "SPECTRA"); |
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| 224 | pksrec.IFno = rec.asuInt("IFNO")+1; |
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| 225 | uInt nchan = specCol(0).nelements(); |
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| 226 | Double crval,crpix; |
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| 227 | //Vector<Double> restfreq; |
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| 228 | Float tmp0,tmp1,tmp2,tmp3,tmp4; |
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| 229 | String tcalt; |
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| 230 | Vector<String> stmp0, stmp1; |
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| 231 | inst->frequencies().getEntry(crpix,crval, pksrec.freqInc, |
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| 232 | rec.asuInt("FREQ_ID")); |
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| 233 | inst->focus().getEntry(pksrec.parAngle, pksrec.focusAxi, pksrec.focusTan, |
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| 234 | pksrec.focusRot, tmp0,tmp1,tmp2,tmp3,tmp4, |
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| 235 | rec.asuInt("FOCUS_ID")); |
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| 236 | inst->molecules().getEntry(pksrec.restFreq,stmp0,stmp1, |
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| 237 | rec.asuInt("MOLECULE_ID")); |
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| 238 | // inst->tcal().getEntry(pksrec.tcalTime, pksrec.tcal, |
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| 239 | // rec.asuInt("TCAL_ID")); |
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| 240 | inst->weather().getEntry(pksrec.temperature, pksrec.pressure, |
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| 241 | pksrec.humidity, pksrec.windSpeed, |
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| 242 | pksrec.windAz, rec.asuInt("WEATHER_ID")); |
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| 243 | Double pixel = Double(nchan/2); |
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| 244 | pksrec.refFreq = (pixel-crpix)*pksrec.freqInc + crval; |
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| 245 | // ok, now we have nrows for the n polarizations in this table |
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| 246 | polConversion(pksrec.spectra, pksrec.flagged, pksrec.xPol, itable); |
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| 247 | pksrec.tsys = tsysFromTable(itable); |
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| 248 | // dummy data |
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| 249 | uInt npol = pksrec.spectra.ncolumn(); |
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| 250 | |
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| 251 | // TCAL |
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| 252 | inst->tcal().getEntry( pksrec.tcalTime, pksrec.tcal, |
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| 253 | rec.asuInt("TCAL_ID") ) ; |
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| 254 | if ( pksrec.tcal.nelements() == 1 ) { |
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| 255 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ; |
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| 256 | Vector<uInt> tcalids = uintCol.getColumn() ; |
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| 257 | pksrec.tcal.resize( npol ) ; |
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| 258 | Vector<Float> dummyA ; |
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| 259 | String dummyS ; |
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| 260 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) { |
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| 261 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ; |
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| 262 | pksrec.tcal[ipol] = dummyA[0] ; |
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| 263 | } |
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[2004] | 264 | } |
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[2006] | 265 | else if ( pksrec.tcal.nelements() == nchan ) { |
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| 266 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ; |
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| 267 | Vector<uInt> tcalids = uintCol.getColumn() ; |
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| 268 | pksrec.tcal.resize( npol ) ; |
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| 269 | Vector<Float> dummyA ; |
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| 270 | String dummyS ; |
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| 271 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) { |
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| 272 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ; |
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| 273 | pksrec.tcal[ipol] = mean( dummyA ) ; |
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| 274 | } |
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[2004] | 275 | } |
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[2006] | 276 | //LogIO os ; |
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| 277 | //os << "npol = " << npol << " pksrec.tcal = " << pksrec.tcal << LogIO::POST ; |
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| 278 | |
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| 279 | pksrec.mjd = rec.asDouble("TIME"); |
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| 280 | pksrec.interval = rec.asDouble("INTERVAL"); |
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| 281 | pksrec.fieldName = rec.asString("FIELDNAME"); |
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| 282 | pksrec.srcName = rec.asString("SRCNAME"); |
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| 283 | //pksrec.obsType = obstypes[rec.asInt("SRCTYPE")]; |
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| 284 | pksrec.obsType = getObsTypes( rec.asInt("SRCTYPE") ) ; |
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| 285 | pksrec.bandwidth = nchan * abs(pksrec.freqInc); |
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| 286 | pksrec.azimuth = rec.asFloat("AZIMUTH"); |
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| 287 | pksrec.elevation = rec.asFloat("ELEVATION"); |
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| 288 | pksrec.refBeam = rec.asInt("REFBEAMNO") + 1; |
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| 289 | pksrec.sigma.resize(npol); |
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| 290 | pksrec.sigma = 0.0f; |
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| 291 | pksrec.calFctr.resize(npol); |
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| 292 | pksrec.calFctr = 0.0f; |
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| 293 | pksrec.baseLin.resize(npol,2); |
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| 294 | pksrec.baseLin = 0.0f; |
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| 295 | pksrec.baseSub.resize(npol,9); |
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| 296 | pksrec.baseSub = 0.0f; |
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| 297 | pksrec.xCalFctr = 0.0; |
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| 298 | pksrec.flagrow = rec.asuInt("FLAGROW"); |
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| 299 | |
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| 300 | status = writer_->write(pksrec); |
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| 301 | if ( status ) { |
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| 302 | writer_->close(); |
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| 303 | throw(AipsError("STWriter: Failed to export Scantable.")); |
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| 304 | } |
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| 305 | ++count; |
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| 306 | //++pksrec.IFno; |
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| 307 | ++ifit; |
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[2004] | 308 | } |
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[2006] | 309 | ++typeit ; |
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[470] | 310 | } |
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[1449] | 311 | ++pksrec.cycleNo; |
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[988] | 312 | ++cycit; |
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[28] | 313 | } |
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[1449] | 314 | //++pksrec.beamNo; |
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[822] | 315 | ++beamit; |
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[28] | 316 | } |
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[1449] | 317 | ++pksrec.scanNo; |
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[822] | 318 | ++scanit; |
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[28] | 319 | } |
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[717] | 320 | ostringstream oss; |
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[999] | 321 | oss << "STWriter: wrote " << count << " rows to " << filename; |
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[717] | 322 | pushLog(String(oss)); |
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[2006] | 323 | |
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[988] | 324 | writer_->close(); |
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[1391] | 325 | //if MS2 delete POINTING table exists and copy the one in the keyword |
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| 326 | if ( format_ == "MS2" ) { |
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| 327 | replacePtTab(table, filename); |
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| 328 | } |
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[28] | 329 | return 0; |
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| 330 | } |
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[470] | 331 | |
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[827] | 332 | Vector<Float> STWriter::tsysFromTable(const Table& tab) |
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| 333 | { |
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| 334 | ROArrayColumn<Float> tsysCol(tab, "TSYS"); |
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| 335 | Vector<Float> out(tab.nrow()); |
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| 336 | Vector<Float> tmp; |
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| 337 | for (uInt i=0; i<tab.nrow(); ++i) { |
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[988] | 338 | tmp.resize(); |
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[827] | 339 | tmp = tsysCol(i); |
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| 340 | out[i] = tmp[0]; |
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| 341 | } |
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[988] | 342 | return out; |
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[827] | 343 | } |
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| 344 | |
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| 345 | void STWriter::polConversion( Matrix< Float >& specs, Matrix< uChar >& flags, |
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[822] | 346 | Vector< Complex > & xpol, const Table & tab ) |
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| 347 | { |
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| 348 | String poltype = tab.keywordSet().asString("POLTYPE"); |
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[1664] | 349 | // Full stokes is not supported. Just allow stokes I |
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| 350 | if ( poltype == "stokes" && tab.nrow() != 1) { |
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[822] | 351 | String msg = "poltype = " + poltype + " not yet supported in output."; |
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[988] | 352 | throw(AipsError(msg)); |
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| 353 | } |
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[827] | 354 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
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| 355 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
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[822] | 356 | uInt nchan = specCol(0).nelements(); |
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[988] | 357 | uInt ncol = (tab.nrow()==1 ? 1: 2 ); |
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| 358 | specs.resize(nchan, ncol); |
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| 359 | flags.resize(nchan, ncol); |
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[822] | 360 | // the linears |
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[988] | 361 | for (uInt i=0; i<ncol; ++i) { |
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[822] | 362 | specs.column(i) = specCol(i); |
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| 363 | flags.column(i) = flagCol(i); |
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| 364 | } |
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| 365 | // now the complex if exists |
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| 366 | Bool hasxpol = False; |
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| 367 | xpol.resize(); |
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[827] | 368 | if ( tab.nrow() == 4 ) { |
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[822] | 369 | hasxpol = True; |
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| 370 | xpol.resize(nchan); |
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| 371 | Vector<Float> reals, imags; |
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| 372 | reals = specCol(2); imags = specCol(3); |
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| 373 | for (uInt k=0; k < nchan; ++k) { |
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[827] | 374 | xpol[k] = Complex(reals[k], imags[k]); |
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[822] | 375 | } |
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| 376 | } |
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| 377 | } |
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[827] | 378 | |
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[1391] | 379 | // For writing MS data, if there is the reference to |
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| 380 | // original pointing table it replace it by it. |
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| 381 | void STWriter::replacePtTab (const Table& tab, const std::string& fname) |
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| 382 | { |
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| 383 | String oldPtTabName = fname; |
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| 384 | oldPtTabName.append("/POINTING"); |
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| 385 | if ( tab.keywordSet().isDefined("POINTING") ) { |
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| 386 | String PointingTab = tab.keywordSet().asString("POINTING"); |
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| 387 | if ( Table::isReadable(PointingTab) ) { |
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| 388 | Table newPtTab(PointingTab, Table::Old); |
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| 389 | newPtTab.copy(oldPtTabName, Table::New); |
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| 390 | ostringstream oss; |
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| 391 | oss << "STWriter: copied " <<PointingTab << " to " << fname; |
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| 392 | pushLog(String(oss)); |
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| 393 | } |
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| 394 | } |
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| 395 | } |
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[827] | 396 | |
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[1819] | 397 | // get obsType string from SRCTYPE value |
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| 398 | String STWriter::getObsTypes( Int srctype ) |
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| 399 | { |
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[2005] | 400 | return SrcType::getName(srctype) ; |
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[827] | 401 | } |
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[1819] | 402 | |
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| 403 | } |
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