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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