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 2658 2012-10-10 03:29:17Z MalteMarquarding $
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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 | #include <casa/Logging/LogIO.h>
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41 |
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42 | #include <atnf/PKSIO/PKSrecord.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 <fits/FITS/FITSSpectralUtil.h>
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52 |
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53 | #include "STFITSImageWriter.h"
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54 | #include "STAsciiWriter.h"
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55 | #include "STHeader.h"
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56 | #include "STMath.h"
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57 |
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58 |
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59 | #include "STWriter.h"
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60 |
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61 | using namespace casa;
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62 | namespace asap {
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63 |
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64 | STWriter::STWriter(const std::string &format)
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65 | {
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66 | format_ = format;
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67 | String t(format_);
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68 | t.upcase();
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69 | if (t == "MS2") {
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70 | throw (AipsError("MS2 OUTPUT FORMAT IS NO LONGER SUPPORTED"));
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71 | } else if (t == "SDFITS") {
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72 | writer_ = new PKSSDwriter();
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73 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") {
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74 | writer_ = 0;
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75 | } else {
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76 | throw (AipsError("Unrecognized export format"));
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77 | }
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78 | }
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79 |
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80 | STWriter::~STWriter()
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81 | {
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82 | if (writer_) {
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83 | delete writer_;
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84 | }
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85 | }
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86 |
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87 | Int STWriter::setFormat(const std::string &format)
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88 | {
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89 | if (format != format_) {
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90 | if (writer_) delete writer_;
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91 | }
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92 |
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93 | format_ = format;
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94 | String t(format_);
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95 | t.upcase();
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96 | if (t== "MS2") {
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97 | throw (AipsError("MS2 OUTPUT FORMAT IS NO LONGER SUPPORTED"));
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98 | } else if (t== "SDFITS") {
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99 | writer_ = new PKSSDwriter();
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100 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") {
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101 | writer_ = 0;
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102 | } else {
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103 | throw (AipsError("Unrecognized Format"));
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104 | }
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105 | return 0;
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106 | }
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107 |
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108 | Int STWriter::write(const CountedPtr<Scantable> in,
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109 | const std::string &filename)
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110 | {
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111 | // If we write out foreign formats we have to convert the frequency system
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112 | // into the output frame, as we do everything related to SPectarlCoordinates
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113 | // in asap on-the-fly.
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114 |
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115 | String freqframe;
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116 | FITSSpectralUtil::specsysFromFrame(freqframe,
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117 | in->frequencies().getFrame(true));
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118 | CountedPtr<Scantable> inst = in;
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119 | if (in->frequencies().getFrame(true) != in->frequencies().getFrame(false)) {
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120 | FITSSpectralUtil::specsysFromFrame(freqframe,
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121 | in->frequencies().getFrame(false));
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122 |
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123 | STMath stm(false);
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124 | inst = stm.frequencyAlign(in);
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125 | }
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126 |
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127 | if (format_=="ASCII") {
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128 | STAsciiWriter iw;
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129 | // ASCII calls SpectralCoordinate::toWorld so no freqAlign use 'in'
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130 | if (iw.write(*in, filename)) {
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131 | return 0;
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132 | } else {
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133 | return 1;
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134 | }
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135 | } else if ( format_ == "FITS" || format_ == "CLASS") {
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136 | STFITSImageWriter iw;
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137 | if (format_ == "CLASS") {
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138 | iw.setClass(True);
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139 | }
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140 | if (iw.write(*inst, filename)) {
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141 | return 0;
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142 | }
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143 | }
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144 |
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145 | // MS or SDFITS
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146 |
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147 | // Extract the header from the table.
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148 | // this is a little different from what I have done
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149 | // before. Need to check with the Offline User Test data
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150 | STHeader hdr = inst->getHeader();
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151 | std::vector<uint> ifs = inst->getIFNos();
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152 | int nIF = inst->nif();//ifs.size();
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153 | Vector<uInt> nPol(nIF),nChan(nIF);
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154 | Vector<Bool> havexpol(nIF);
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155 | String fluxUnit = hdr.fluxunit;
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156 | fluxUnit.upcase();
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157 | nPol = 0;nChan = 0; havexpol = False;
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158 | for (uint i=0;i<ifs.size();++i) {
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159 | if ( inst->npol() > 2 ) {
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160 | havexpol(ifs[i]) = True;
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161 | nPol(ifs[i]) = 2;
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162 | } else {
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163 | nPol(ifs[i]) = inst->npol();
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164 | }
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165 | nChan(ifs[i]) = inst->nchan(ifs[i]);
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166 | }
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167 | // Vector<String> obstypes(2);
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168 | // obstypes(0) = "TR";//on
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169 | // obstypes(1) = "RF TR";//off
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170 | const Table table = inst->table();
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171 |
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172 |
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173 | // Create the output file and write static data.
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174 | Int status;
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175 | status = writer_->create(String(filename), hdr.observer, hdr.project,
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176 | inst->getAntennaName(), hdr.antennaposition,
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177 | hdr.obstype, hdr.fluxunit,
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178 | hdr.equinox, freqframe,
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179 | nChan, nPol, havexpol, False);
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180 | if ( status ) {
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181 | throw(AipsError("Failed to create output file"));
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182 | }
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183 |
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184 | Int count = 0;
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185 | PKSrecord pksrec;
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186 | pksrec.scanNo = 1;
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187 | // use spearate iterators to ensure renumbering of all numbers
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188 | TableIterator scanit(table, "SCANNO");
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189 | while (!scanit.pastEnd() ) {
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190 | Table stable = scanit.table();
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191 | TableIterator beamit(stable, "BEAMNO");
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192 | pksrec.beamNo = 1;
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193 | while (!beamit.pastEnd() ) {
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194 | Table btable = beamit.table();
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195 | //MDirection::ScalarColumn dirCol(btable, "DIRECTION");
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196 | //pksrec.direction = dirCol(0).getAngle("rad").getValue();
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197 | TableIterator cycit(btable, "CYCLENO");
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198 | ROArrayColumn<Double> srateCol(btable, "SCANRATE");
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199 | Vector<Double> sratedbl;
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200 | srateCol.get(0, sratedbl);
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201 | Vector<Float> srateflt(sratedbl.nelements());
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202 | convertArray(srateflt, sratedbl);
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203 | //pksrec.scanRate = srateflt;
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204 | pksrec.scanRate = sratedbl;
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205 | ROArrayColumn<Double> spmCol(btable, "SRCPROPERMOTION");
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206 | spmCol.get(0, pksrec.srcPM);
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207 | ROArrayColumn <Double> sdirCol(btable, "SRCDIRECTION");
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208 | sdirCol.get(0, pksrec.srcDir);
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209 | ROScalarColumn<Double> svelCol(btable, "SRCVELOCITY");
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210 | svelCol.get(0, pksrec.srcVel);
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211 | ROScalarColumn<uInt> bCol(btable, "BEAMNO");
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212 | pksrec.beamNo = bCol(0)+1;
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213 | pksrec.cycleNo = 1;
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214 | while (!cycit.pastEnd() ) {
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215 | Table ctable = cycit.table();
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216 | TableIterator typeit( ctable, "SRCTYPE" ) ;
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217 | while(!typeit.pastEnd() ) {
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218 | Table ttable = typeit.table() ;
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219 | TableIterator ifit(ttable, "IFNO",
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220 | TableIterator::Ascending, TableIterator::HeapSort);
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221 | MDirection::ScalarColumn dirCol(ctable, "DIRECTION");
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222 | pksrec.direction = dirCol(0).getAngle("rad").getValue();
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223 | pksrec.IFno = 1;
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224 | while (!ifit.pastEnd() ) {
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225 | Table itable = ifit.table();
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226 | TableRow row(itable);
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227 | // use the first row to fill in all the "metadata"
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228 | const TableRecord& rec = row.get(0);
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229 | ROArrayColumn<Float> specCol(itable, "SPECTRA");
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230 | pksrec.IFno = rec.asuInt("IFNO")+1;
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231 | uInt nchan = specCol(0).nelements();
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232 | Double crval,crpix;
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233 | //Vector<Double> restfreq;
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234 | Float tmp0,tmp1,tmp2,tmp3,tmp4;
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235 | String tcalt;
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236 | Vector<String> stmp0, stmp1;
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237 | inst->frequencies().getEntry(crpix,crval, pksrec.freqInc,
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238 | rec.asuInt("FREQ_ID"));
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239 | inst->focus().getEntry(pksrec.parAngle, pksrec.focusAxi,
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240 | pksrec.focusTan,
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241 | pksrec.focusRot, tmp0,tmp1,tmp2,tmp3,tmp4,
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242 | rec.asuInt("FOCUS_ID"));
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243 | inst->molecules().getEntry(pksrec.restFreq,stmp0,stmp1,
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244 | rec.asuInt("MOLECULE_ID"));
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245 | // inst->tcal().getEntry(pksrec.tcalTime, pksrec.tcal,
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246 | // rec.asuInt("TCAL_ID"));
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247 | inst->weather().getEntry(pksrec.temperature, pksrec.pressure,
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248 | pksrec.humidity, pksrec.windSpeed,
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249 | pksrec.windAz, rec.asuInt("WEATHER_ID"));
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250 | Double pixel = Double(nchan/2);
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251 | pksrec.refFreq = (pixel-crpix)*pksrec.freqInc + crval;
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252 | // ok, now we have nrows for the n polarizations in this table
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253 | polConversion(pksrec.spectra, pksrec.flagged, pksrec.xPol, itable);
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254 | pksrec.tsys = tsysFromTable(itable);
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255 | // dummy data
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256 | uInt npol = pksrec.spectra.ncolumn();
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257 |
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258 | // TCAL
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259 | inst->tcal().getEntry( pksrec.tcalTime, pksrec.tcal,
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260 | rec.asuInt("TCAL_ID") ) ;
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261 | if ( pksrec.tcal.nelements() == 1 ) {
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262 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ;
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263 | Vector<uInt> tcalids = uintCol.getColumn() ;
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264 | pksrec.tcal.resize( npol ) ;
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265 | Vector<Float> dummyA ;
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266 | String dummyS ;
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267 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) {
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268 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ;
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269 | pksrec.tcal[ipol] = dummyA[0] ;
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270 | }
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271 | }
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272 | else if ( pksrec.tcal.nelements() == nchan ) {
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273 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ;
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274 | Vector<uInt> tcalids = uintCol.getColumn() ;
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275 | pksrec.tcal.resize( npol ) ;
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276 | Vector<Float> dummyA ;
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277 | String dummyS ;
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278 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) {
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279 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ;
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280 | pksrec.tcal[ipol] = mean( dummyA ) ;
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281 | }
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282 | }
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283 | pksrec.mjd = rec.asDouble("TIME");
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284 | pksrec.interval = rec.asDouble("INTERVAL");
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285 | pksrec.fieldName = rec.asString("FIELDNAME");
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286 | pksrec.srcName = rec.asString("SRCNAME");
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287 | //pksrec.obsType = obstypes[rec.asInt("SRCTYPE")];
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288 | pksrec.obsType = getObsTypes( rec.asInt("SRCTYPE") ) ;
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289 | pksrec.bandwidth = nchan * abs(pksrec.freqInc);
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290 | pksrec.azimuth = rec.asFloat("AZIMUTH");
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291 | pksrec.elevation = rec.asFloat("ELEVATION");
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292 | pksrec.refBeam = rec.asInt("REFBEAMNO") + 1;
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293 | pksrec.sigma.resize(npol);
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294 | pksrec.sigma = 0.0f;
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295 | pksrec.calFctr.resize(npol);
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296 | pksrec.calFctr = 0.0f;
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297 | pksrec.baseLin.resize(npol,2);
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298 | pksrec.baseLin = 0.0f;
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299 | pksrec.baseSub.resize(npol,9);
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300 | pksrec.baseSub = 0.0f;
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301 | pksrec.xCalFctr = 0.0;
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302 | pksrec.flagrow = rec.asuInt("FLAGROW");
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303 |
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304 | status = writer_->write(pksrec);
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305 | if ( status ) {
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306 | writer_->close();
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307 | throw(AipsError("STWriter: Failed to export Scantable."));
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308 | }
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309 | ++count;
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310 | //++pksrec.IFno;
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311 | ++ifit;
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312 | }
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313 | ++typeit ;
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314 | }
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315 | ++pksrec.cycleNo;
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316 | ++cycit;
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317 | }
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318 | //++pksrec.beamNo;
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319 | ++beamit;
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320 | }
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321 | ++pksrec.scanNo;
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322 | ++scanit;
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323 | }
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324 | LogIO os( casa::LogOrigin("STWriter"));
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325 | os << "STWriter: wrote " << count << " rows to " << filename
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326 | << casa::LogIO::POST;
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327 |
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328 | writer_->close();
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329 |
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330 | return 0;
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331 | }
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332 |
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333 | Vector<Float> STWriter::tsysFromTable(const Table& tab)
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334 | {
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335 | ROArrayColumn<Float> tsysCol(tab, "TSYS");
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336 | Vector<Float> out(tab.nrow());
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337 | Vector<Float> tmp;
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338 | for (uInt i=0; i<tab.nrow(); ++i) {
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339 | tmp.resize();
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340 | tmp = tsysCol(i);
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341 | out[i] = tmp[0];
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342 | }
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343 | return out;
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344 | }
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345 |
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346 | void STWriter::polConversion( Matrix< Float >& specs, Matrix< uChar >& flags,
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347 | Vector< Complex > & xpol, const Table & tab )
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348 | {
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349 | String poltype = tab.keywordSet().asString("POLTYPE");
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350 | // Full stokes is not supported. Just allow stokes I
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351 | if ( poltype == "stokes" && tab.nrow() != 1) {
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352 | String msg = "poltype = " + poltype + " not yet supported in output.";
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353 | throw(AipsError(msg));
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354 | }
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355 | ROArrayColumn<Float> specCol(tab, "SPECTRA");
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356 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
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357 | uInt nchan = specCol(0).nelements();
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358 | uInt ncol = (tab.nrow()==1 ? 1: 2 );
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359 | specs.resize(nchan, ncol);
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360 | flags.resize(nchan, ncol);
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361 | // the linears
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362 | for (uInt i=0; i<ncol; ++i) {
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363 | specs.column(i) = specCol(i);
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364 | flags.column(i) = flagCol(i);
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365 | }
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366 | // now the complex if exists
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367 | Bool hasxpol = False;
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368 | xpol.resize();
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369 | if ( tab.nrow() == 4 ) {
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370 | hasxpol = True;
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371 | xpol.resize(nchan);
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372 | Vector<Float> reals, imags;
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373 | reals = specCol(2); imags = specCol(3);
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374 | for (uInt k=0; k < nchan; ++k) {
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375 | xpol[k] = Complex(reals[k], imags[k]);
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376 | }
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377 | }
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378 | }
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379 |
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380 |
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381 | // get obsType string from SRCTYPE value
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382 | String STWriter::getObsTypes( Int srctype )
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383 | {
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384 | return SrcType::getName(srctype) ;
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385 | }
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386 |
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387 | }
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