1 | //
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2 | // C++ Implementation: PKSFiller
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3 | //
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4 | // Description:
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5 | //
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6 | //
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7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2010
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8 | //
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9 | // Copyright: See COPYING file that comes with this distribution
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10 | //
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11 | //
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12 | #include <casa/iostream.h>
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13 | #include <casa/iomanip.h>
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14 |
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15 | #include <casa/Exceptions.h>
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16 | #include <casa/OS/Path.h>
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17 | #include <casa/OS/File.h>
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18 | #include <casa/Quanta/Unit.h>
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19 | #include <casa/Arrays/ArrayMath.h>
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20 | #include <casa/Arrays/ArrayLogical.h>
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21 | #include <casa/Utilities/Regex.h>
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22 | #include <casa/Utilities/DataType.h>
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23 | #include <casa/Logging/LogIO.h>
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24 |
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25 | #include <casa/Containers/Record.h>
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26 | #include <measures/Measures/MDirection.h>
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27 | #include <measures/Measures/MeasConvert.h>
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28 |
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29 | #include <atnf/PKSIO/PKSrecord.h>
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30 | #include <atnf/PKSIO/PKSreader.h>
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31 |
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32 | #ifdef HAS_ALMA
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33 | #include <casa/System/ProgressMeter.h>
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34 | #endif
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35 | #include <casa/Logging/LogIO.h>
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36 |
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37 | #include <time.h>
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38 | #include <sstream>
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39 |
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40 | #include "STDefs.h"
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41 | #include "STAttr.h"
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42 |
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43 | #include "PKSFiller.h"
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44 | #include "STHeader.h"
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45 |
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46 | using namespace casa;
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47 |
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48 | namespace asap {
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49 |
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50 |
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51 | PKSFiller::PKSFiller( CountedPtr< Scantable > stbl ) :
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52 | FillerBase(stbl),
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53 | reader_(0)
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54 | {
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55 | setReferenceRegex(".*(e|w|_R)$");
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56 | }
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57 |
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58 | PKSFiller::~PKSFiller()
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59 | {
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60 | close();
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61 | }
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62 |
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63 | bool PKSFiller::open( const std::string& filename, const Record& rec)
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64 | {
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65 | Bool haveBase, haveSpectra;
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66 |
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67 | String inName(filename);
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68 | Path path(inName);
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69 | inName = path.expandedName();
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70 |
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71 | File file(inName);
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72 | filename_ = inName;
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73 |
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74 | // Create reader and fill in values for arguments
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75 | String format;
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76 | Vector<Bool> beams, ifs;
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77 | Vector<uInt> nchans,npols;
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78 |
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79 | String antenna("");
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80 | Bool getPt = False;
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81 |
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82 | // parsing MS options
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83 | if ( rec.isDefined( "ms" ) ) {
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84 | Record msrec = rec.asRecord( "ms" ) ;
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85 | //msrec.print( cout ) ;
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86 | if ( msrec.isDefined( "getpt" ) ) {
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87 | getPt = msrec.asBool( "getpt" ) ;
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88 | }
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89 | if ( msrec.isDefined( "antenna" ) ) {
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90 | if ( msrec.type( msrec.fieldNumber( "antenna" ) ) == TpInt ) {
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91 | Int antInt = msrec.asInt( "antenna" ) ;
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92 | ostringstream oss ;
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93 | oss << antInt ;
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94 | antenna = String( oss ) ;
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95 | }
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96 | else {
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97 | antenna = msrec.asString( "antenna" ) ;
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98 | }
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99 | }
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100 | }
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101 |
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102 | reader_ = getPKSreader(inName, antenna, 0, 0, format, beams, ifs,
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103 | nchans, npols, haveXPol_, haveBase, haveSpectra);
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104 | if (reader_.null() == True) {
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105 | return False;
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106 | }
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107 |
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108 | if (!haveSpectra) {
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109 | reader_ = 0;
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110 | throw(AipsError("No spectral data in file."));
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111 | }
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112 |
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113 | LogIO os( LogOrigin( "PKSFiller", "open()", WHERE ) ) ;
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114 | nBeam_ = beams.nelements();
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115 | nIF_ = ifs.nelements();
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116 | // Get basic parameters.
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117 | if ( anyEQ(haveXPol_, True) ) {
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118 | os << "Cross polarization present" << LogIO::POST;
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119 | for (uInt i=0; i< npols.nelements();++i) {
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120 | if (npols[i] < 3) npols[i] += 2;// Convert Complex -> 2 Floats
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121 | }
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122 | }
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123 | STHeader header;
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124 | header.nchan = max(nchans);
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125 | header.npol = max(npols);
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126 | header.nbeam = nBeam_;
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127 |
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128 | Int status = reader_->getHeader(header.observer, header.project,
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129 | header.antennaname, header.antennaposition,
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130 | header.obstype,
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131 | header.fluxunit,
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132 | header.equinox,
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133 | header.freqref,
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134 | header.utc, header.reffreq,
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135 | header.bandwidth);
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136 |
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137 | if (status) {
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138 | reader_ = 0;
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139 | throw(AipsError("Failed to get header."));
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140 | }
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141 | os << "Found " << header.antennaname << " data." << LogIO::POST;
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142 | if ((header.obstype).matches("*SW*")) {
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143 | // need robust way here - probably read ahead of next timestamp
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144 | os << "Header indicates frequency switched observation.\n"
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145 | << "setting # of IFs = 1 " << LogIO::POST;
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146 |
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147 | nIF_ = 1;
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148 | header.obstype = String("fswitch");
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149 | }
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150 | // Determine Telescope and set brightness unit
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151 | Bool throwIt = False;
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152 | Instrument inst = STAttr::convertInstrument(header.antennaname, throwIt);
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153 |
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154 | if (inst==ATMOPRA || inst==TIDBINBILLA) {
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155 | header.fluxunit = "K";
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156 | } else {
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157 | // downcase for use with Quanta
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158 | if (header.fluxunit == "JY") {
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159 | header.fluxunit = "Jy";
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160 | }
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161 | }
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162 | STAttr stattr;
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163 | header.poltype = stattr.feedPolType(inst);
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164 | header.nif = nIF_;
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165 | header.epoch = "UTC";
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166 | // *** header.frequnit = "Hz"
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167 | // Apply selection criteria.
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168 | Vector<Int> ref;
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169 |
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170 | Vector<Int> start(nIF_, 1);
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171 | Vector<Int> end(nIF_, 0);
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172 | reader_->select(beams, ifs, start, end, ref, True, haveXPol_[0], False, getPt);
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173 | setHeader(header);
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174 | //For MS, add the location of POINTING of the input MS so one get
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175 | //pointing data from there, if necessary.
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176 | //Also find nrow in MS
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177 | nInDataRow = 0;
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178 | if (format == "MS2") {
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179 | Path datapath(inName);
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180 | String ptTabPath = datapath.absoluteName();
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181 | Table inMS(ptTabPath);
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182 | nInDataRow = inMS.nrow();
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183 | ptTabPath.append("/POINTING");
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184 | table_->table().rwKeywordSet().define("POINTING", ptTabPath);
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185 | if (header.antennaname.matches("GBT")) {
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186 | String GOTabPath = datapath.absoluteName();
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187 | GOTabPath.append("/GBT_GO");
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188 | table_->table().rwKeywordSet().define("GBT_GO", GOTabPath);
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189 | }
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190 | }
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191 | String freqFrame = header.freqref;
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192 | //translate frequency reference frame back to
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193 | //MS style (as PKSMS2reader converts the original frame
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194 | //in FITS standard style)
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195 | if (freqFrame == "TOPOCENT") {
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196 | freqFrame = "TOPO";
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197 | } else if (freqFrame == "GEOCENER") {
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198 | freqFrame = "GEO";
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199 | } else if (freqFrame == "BARYCENT") {
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200 | freqFrame = "BARY";
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201 | } else if (freqFrame == "GALACTOC") {
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202 | freqFrame = "GALACTO";
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203 | } else if (freqFrame == "LOCALGRP") {
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204 | freqFrame = "LGROUP";
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205 | } else if (freqFrame == "CMBDIPOL") {
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206 | freqFrame = "CMB";
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207 | } else if (freqFrame == "SOURCE") {
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208 | freqFrame = "REST";
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209 | }
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210 | // set both "FRAME" and "BASEFRAME"
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211 | table_->frequencies().setFrame(freqFrame, false);
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212 | table_->frequencies().setFrame(freqFrame, true);
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213 |
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214 | return true;
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215 | }
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216 |
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217 | void PKSFiller::close( )
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218 | {
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219 | if (reader_.null() != False) {
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220 | reader_ = 0;
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221 | }
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222 | table_ = 0;
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223 | }
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224 |
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225 | void PKSFiller::fill( )
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226 | {
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227 | int status = 0;
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228 | LogIO os( LogOrigin( "PKSFiller", "fill()", WHERE ) ) ;
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229 |
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230 | /**
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231 | Int beamNo, IFno, refBeam, scanNo, cycleNo;
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232 | Float azimuth, elevation, focusAxi, focusRot, focusTan,
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233 | humidity, parAngle, pressure, temperature, windAz, windSpeed;
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234 | Double bandwidth, freqInc, interval, mjd, refFreq, srcVel;
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235 | String fieldName, srcName, tcalTime, obsType;
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236 | Vector<Float> calFctr, sigma, tcal, tsys;
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237 | Matrix<Float> baseLin, baseSub;
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238 | Vector<Double> direction(2), scanRate(2), srcDir(2), srcPM(2), restFreq(1);
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239 | Matrix<Float> spectra;
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240 | Matrix<uChar> flagtra;
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241 | Complex xCalFctr;
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242 | Vector<Complex> xPol;
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243 | **/
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244 |
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245 | Double min = 0.0;
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246 | Double max = nInDataRow;
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247 | #ifdef HAS_ALMA
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248 | ProgressMeter fillpm(min, max, "Data importing progress");
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249 | #endif
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250 | PKSrecord pksrec;
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251 | pksrec.srcType=-1;
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252 | int n = 0;
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253 | bool isGBTFITS = false ;
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254 | if ((table_->getAntennaName().find( "GBT" ) != String::npos)
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255 | && File(filename_).isRegular()) {
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256 | FILE *fp = fopen( filename_.c_str(), "r" ) ;
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257 | fseek( fp, 640, SEEK_SET ) ;
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258 | char buf[81] ;
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259 | size_t tmp = fread( buf, 80, 1, fp ) ;
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260 | (void) tmp;
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261 | buf[80] = '\0' ;
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262 | if ( strstr( buf, "NRAO_GBT" ) != NULL ) {
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263 | isGBTFITS = true ;
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264 | }
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265 | fclose( fp ) ;
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266 | }
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267 |
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268 | while ( status == 0 ) {
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269 |
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270 | status = reader_->read(pksrec);
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271 | if ( status != 0 ) break;
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272 | n += 1;
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273 | Regex filterrx(".*[SL|PA]$");
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274 | Regex obsrx("^AT.+");
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275 | if ( table_->getAntennaName().matches(obsrx) &&
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276 | pksrec.obsType.matches(filterrx)) {
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277 | //cerr << "ignoring paddle scan" << endl;
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278 | continue;
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279 | }
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280 |
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281 | Vector<Double> sratedbl(pksrec.scanRate.nelements());
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282 | convertArray(sratedbl, pksrec.scanRate);
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283 | setScanRate(sratedbl);
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284 |
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285 | Regex rx(getReferenceRegex());
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286 | Regex rx2("_S$");
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287 | Int match = pksrec.srcName.matches(rx);
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288 | std::string srcname;
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289 | Int srctype = Int(SrcType::NOTYPE);
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290 | if (match) {
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291 | srcname = pksrec.srcName;
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292 | srctype = Int(SrcType::PSOFF);
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293 | } else {
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294 | srcname = pksrec.srcName.before(rx2);
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295 | srctype = Int(SrcType::PSON);
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296 | }
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297 | if ( pksrec.srcType != Int(SrcType::NOTYPE)) {
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298 | srctype = pksrec.srcType ;
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299 | }
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300 | setTime(pksrec.mjd, pksrec.interval);
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301 | setSource(srcname, srctype, pksrec.fieldName,
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302 | pksrec.srcDir, pksrec.srcPM, pksrec.srcVel);
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303 |
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304 | if (nBeam_ > 1 ) {
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305 | setReferenceBeam(pksrec.refBeam-1);
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306 | }
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307 |
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308 | setMolecule(pksrec.restFreq);
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309 | setTcal(pksrec.tcalTime, pksrec.tcal);
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310 | setWeather(pksrec.temperature, pksrec.pressure,
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311 | pksrec.humidity, pksrec.windSpeed,
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312 | pksrec.windAz);
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313 | setFocus(pksrec.parAngle, pksrec.focusAxi, pksrec.focusTan,
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314 | pksrec.focusRot);
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315 | setDirection(pksrec.direction, pksrec.azimuth, pksrec.elevation);
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316 |
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317 | setFrequency(Double(pksrec.spectra.nrow()/2),
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318 | pksrec.refFreq, pksrec.freqInc);
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319 |
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320 | // Note: this is only one value for all polarisations!
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321 |
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322 | //setFlagrow(pksrec.flagrow);
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323 | // Turn the (nchan,npol) matrix and possible complex xPol vector
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324 | // into 2-4 rows in the scantable
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325 | Vector<Float> tsysvec(1);
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326 | // Why is spectra.ncolumn() == 3 for haveXPol_ == True
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327 | uInt npol = (pksrec.spectra.ncolumn()==1 ? 1: 2);
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328 | uInt polno =0;
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329 | for ( uInt i=0; i< npol; ++i ) {
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330 | tsysvec = pksrec.tsys(i);
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331 | if (isGBTFITS) {
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332 | polno = pksrec.polNo ;
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333 | } else {
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334 | polno = i;
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335 | }
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336 | setIndex(pksrec.scanNo-1, pksrec.cycleNo-1, pksrec.IFno-1, polno,
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337 | pksrec.beamNo-1);
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338 | setSpectrum(pksrec.spectra.column(i), pksrec.flagged.column(i), tsysvec);
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339 | commitRow();
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340 | }
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341 | if ( haveXPol_[0] ) {
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342 | // no tsys given for xpol, so emulate it
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343 | tsysvec = sqrt(pksrec.tsys[0]*pksrec.tsys[1]);
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344 | // add real part of cross pol
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345 | polno = 2;
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346 | Vector<Float> r(real(pksrec.xPol));
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347 | // make up flags from linears
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348 | /// @fixme this has to be a bitwise or of both pols
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349 | /// pksrec.flagged.column(0) | pksrec.flagged.column(1);
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350 |
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351 | setIndex(pksrec.scanNo-1, pksrec.cycleNo-1, pksrec.IFno-1, polno,
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352 | pksrec.beamNo-1);
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353 | setSpectrum(r, pksrec.flagged.column(0), tsysvec);
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354 | commitRow();
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355 |
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356 | // ad imaginary part of cross pol
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357 | polno = 3;
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358 | Vector<Float> im(imag(pksrec.xPol));
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359 | setIndex(pksrec.scanNo-1, pksrec.cycleNo-1, pksrec.IFno-1, polno,
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360 | pksrec.beamNo-1);
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361 | setSpectrum(im, pksrec.flagged.column(0), tsysvec);
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362 | commitRow();
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363 | }
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364 | #ifdef HAS_ALMA
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365 | fillpm._update(n);
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366 | #endif
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367 | }
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368 | if (status > 0) {
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369 | close();
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370 | throw(AipsError("Reading error occured, data possibly corrupted."));
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371 | }
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372 | #ifdef HAS_ALMA
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373 | fillpm.done();
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374 | #endif
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375 | }
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376 |
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377 | }//namespace asap
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