1 | //
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2 | // C++ Implementation: STFiller
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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) 2006-2007
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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 |
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23 | #include <casa/Containers/RecordField.h>
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24 |
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25 | #include <tables/Tables/TableRow.h>
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26 |
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27 | #include <atnf/PKSIO/PKSrecord.h>
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28 | #include <atnf/PKSIO/PKSreader.h>
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29 | #ifdef HAS_ALMA
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30 | #include <casa/System/ProgressMeter.h>
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31 | #endif
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32 |
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33 | #include "STDefs.h"
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34 | #include "STAttr.h"
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35 |
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36 | #include "STFiller.h"
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37 | #include "STHeader.h"
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38 |
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39 | using namespace casa;
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40 |
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41 | namespace asap {
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42 |
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43 | STFiller::STFiller() :
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44 | reader_(0),
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45 | header_(0),
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46 | table_(0),
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47 | refRx_(".*(e|w|_R)$")
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48 | {
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49 | }
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50 |
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51 | STFiller::STFiller( CountedPtr< Scantable > stbl ) :
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52 | reader_(0),
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53 | header_(0),
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54 | table_(stbl),
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55 | refRx_(".*(e|w|_R)$")
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56 | {
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57 | }
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58 |
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59 | STFiller::STFiller(const std::string& filename, int whichIF, int whichBeam ) :
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60 | reader_(0),
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61 | header_(0),
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62 | table_(0),
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63 | refRx_(".*(e|w|_R)$")
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64 | {
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65 | open(filename, whichIF, whichBeam);
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66 | }
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67 |
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68 | STFiller::~STFiller()
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69 | {
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70 | close();
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71 | }
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72 |
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73 | void STFiller::open( const std::string& filename, int whichIF, int whichBeam )
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74 | {
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75 | if (table_.null()) {
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76 | table_ = new Scantable();
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77 | }
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78 | if (reader_) { delete reader_; reader_ = 0; }
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79 | Bool haveBase, haveSpectra;
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80 |
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81 | String inName(filename);
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82 | Path path(inName);
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83 | inName = path.expandedName();
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84 |
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85 | File file(inName);
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86 | if ( !file.exists() ) {
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87 | throw(AipsError("File does not exist"));
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88 | }
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89 | filename_ = inName;
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90 |
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91 | // Create reader and fill in values for arguments
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92 | String format;
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93 | Vector<Bool> beams, ifs;
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94 | Vector<uInt> nchans,npols;
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95 | if ( (reader_ = getPKSreader(inName, 0, 0, format, beams, ifs,
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96 | nchans, npols, haveXPol_,haveBase, haveSpectra
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97 | )) == 0 ) {
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98 | throw(AipsError("Creation of PKSreader failed"));
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99 | }
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100 | if (!haveSpectra) {
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101 | delete reader_;
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102 | reader_ = 0;
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103 | throw(AipsError("No spectral data in file."));
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104 | return;
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105 | }
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106 | nBeam_ = beams.nelements();
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107 | nIF_ = ifs.nelements();
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108 | // Get basic parameters.
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109 | if ( anyEQ(haveXPol_, True) ) {
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110 | pushLog("Cross polarization present");
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111 | for (uInt i=0; i< npols.nelements();++i) {
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112 | if (npols[i] < 3) npols[i] += 2;// Convert Complex -> 2 Floats
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113 | }
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114 | }
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115 | if (header_) delete header_;
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116 | header_ = new STHeader();
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117 | header_->nchan = max(nchans);
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118 | header_->npol = max(npols);
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119 | header_->nbeam = nBeam_;
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120 |
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121 | Int status = reader_->getHeader(header_->observer, header_->project,
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122 | header_->antennaname, header_->antennaposition,
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123 | header_->obstype,
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124 | header_->fluxunit,
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125 | header_->equinox,
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126 | header_->freqref,
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127 | header_->utc, header_->reffreq,
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128 | header_->bandwidth);
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129 |
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130 | if (status) {
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131 | delete reader_;
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132 | reader_ = 0;
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133 | delete header_;
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134 | header_ = 0;
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135 | throw(AipsError("Failed to get header."));
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136 | }
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137 | if ((header_->obstype).matches("*SW*")) {
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138 | // need robust way here - probably read ahead of next timestamp
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139 | pushLog("Header indicates frequency switched observation.\n"
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140 | "setting # of IFs = 1 ");
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141 | nIF_ = 1;
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142 | header_->obstype = String("fswitch");
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143 | }
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144 | // Determine Telescope and set brightness unit
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145 |
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146 |
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147 | Bool throwIt = False;
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148 | Instrument inst = STAttr::convertInstrument(header_->antennaname, throwIt);
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149 |
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150 | if (inst==ATMOPRA || inst==TIDBINBILLA) {
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151 | header_->fluxunit = "K";
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152 | } else {
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153 | // downcase for use with Quanta
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154 | if (header_->fluxunit == "JY") {
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155 | header_->fluxunit = "Jy";
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156 | }
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157 | }
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158 | STAttr stattr;
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159 | header_->poltype = stattr.feedPolType(inst);
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160 | header_->nif = nIF_;
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161 | header_->epoch = "UTC";
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162 | // *** header_->frequnit = "Hz"
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163 | // Apply selection criteria.
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164 | Vector<Int> ref;
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165 | ifOffset_ = 0;
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166 | if (whichIF>=0) {
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167 | if (whichIF>=0 && whichIF<nIF_) {
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168 | ifs = False;
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169 | ifs(whichIF) = True;
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170 | header_->nif = 1;
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171 | nIF_ = 1;
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172 | ifOffset_ = whichIF;
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173 | } else {
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174 | delete reader_;
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175 | reader_ = 0;
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176 | delete header_;
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177 | header_ = 0;
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178 | throw(AipsError("Illegal IF selection"));
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179 | }
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180 | }
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181 | beamOffset_ = 0;
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182 | if (whichBeam>=0) {
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183 | if (whichBeam>=0 && whichBeam<nBeam_) {
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184 | beams = False;
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185 | beams(whichBeam) = True;
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186 | header_->nbeam = 1;
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187 | nBeam_ = 1;
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188 | beamOffset_ = whichBeam;
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189 | } else {
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190 | delete reader_;
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191 | reader_ = 0;
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192 | delete header_;
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193 | header_ = 0;
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194 | throw(AipsError("Illegal Beam selection"));
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195 | }
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196 | }
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197 | Vector<Int> start(nIF_, 1);
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198 | Vector<Int> end(nIF_, 0);
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199 | reader_->select(beams, ifs, start, end, ref, True, haveXPol_[0]);
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200 | table_->setHeader(*header_);
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201 | //For MS, add the location of POINTING of the input MS so one get
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202 | //pointing data from there, if necessary.
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203 | //Also find nrow in MS
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204 | nInDataRow = 0;
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205 | if (format == "MS2") {
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206 | Path datapath(inName);
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207 | String ptTabPath = datapath.absoluteName();
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208 | Table inMS(ptTabPath);
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209 | nInDataRow = inMS.nrow();
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210 | ptTabPath.append("/POINTING");
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211 | table_->table().rwKeywordSet().define("POINTING", ptTabPath);
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212 | if ((header_->antennaname).matches("GBT")) {
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213 | String GOTabPath = datapath.absoluteName();
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214 | GOTabPath.append("/GBT_GO");
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215 | table_->table().rwKeywordSet().define("GBT_GO", GOTabPath);
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216 | }
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217 | }
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218 | //table_->focus().setParallactify(true);
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219 | }
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220 |
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221 | void STFiller::close( )
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222 | {
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223 | delete reader_;reader_=0;
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224 | delete header_;header_=0;
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225 | table_ = 0;
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226 | }
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227 |
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228 | int asap::STFiller::read( )
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229 | {
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230 | int status = 0;
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231 |
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232 | Double min = 0.0;
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233 | Double max = nInDataRow;
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234 | #ifdef HAS_ALMA
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235 | ProgressMeter fillpm(min, max, "Data importing progress");
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236 | #endif
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237 | PKSrecord pksrec;
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238 | int n = 0;
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239 | while ( status == 0 ) {
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240 | status = reader_->read(pksrec);
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241 | if ( status != 0 ) break;
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242 | n += 1;
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243 |
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244 | Regex filterrx(".*[SL|PA]$");
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245 | Regex obsrx("^AT.+");
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246 | if ( header_->antennaname.matches(obsrx) &&
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247 | pksrec.obsType.matches(filterrx)) {
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248 | //cerr << "ignoring paddle scan" << endl;
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249 | continue;
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250 | }
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251 | TableRow row(table_->table());
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252 | TableRecord& rec = row.record();
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253 | // fields that don't get used and are just passed through asap
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254 | RecordFieldPtr<Array<Double> > srateCol(rec, "SCANRATE");
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255 | // MRC changed type from double to float
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256 | Vector<Double> sratedbl(pksrec.scanRate.nelements());
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257 | convertArray(sratedbl, pksrec.scanRate);
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258 | *srateCol = sratedbl;
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259 | RecordFieldPtr<Array<Double> > spmCol(rec, "SRCPROPERMOTION");
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260 | *spmCol = pksrec.srcPM;
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261 | RecordFieldPtr<Array<Double> > sdirCol(rec, "SRCDIRECTION");
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262 | *sdirCol = pksrec.srcDir;
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263 | RecordFieldPtr<Double> svelCol(rec, "SRCVELOCITY");
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264 | *svelCol = pksrec.srcVel;
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265 | // the real stuff
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266 | RecordFieldPtr<Int> fitCol(rec, "FIT_ID");
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267 | *fitCol = -1;
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268 | RecordFieldPtr<uInt> scanoCol(rec, "SCANNO");
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269 | *scanoCol = pksrec.scanNo-1;
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270 | RecordFieldPtr<uInt> cyclenoCol(rec, "CYCLENO");
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271 | *cyclenoCol = pksrec.cycleNo-1;
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272 | RecordFieldPtr<Double> mjdCol(rec, "TIME");
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273 | *mjdCol = pksrec.mjd;
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274 | RecordFieldPtr<Double> intCol(rec, "INTERVAL");
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275 | *intCol = pksrec.interval;
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276 | RecordFieldPtr<String> srcnCol(rec, "SRCNAME");
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277 | RecordFieldPtr<Int> srctCol(rec, "SRCTYPE");
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278 | RecordFieldPtr<String> fieldnCol(rec, "FIELDNAME");
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279 | *fieldnCol = pksrec.fieldName;
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280 | // try to auto-identify if it is on or off.
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281 | Regex rx(refRx_);
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282 | Regex rx2("_S$");
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283 | Int match = pksrec.srcName.matches(rx);
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284 | if (match) {
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285 | *srcnCol = pksrec.srcName;
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286 | } else {
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287 | *srcnCol = pksrec.srcName.before(rx2);
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288 | }
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289 | //*srcnCol = pksrec.srcName;//.before(rx2);
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290 | *srctCol = match;
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291 | RecordFieldPtr<uInt> beamCol(rec, "BEAMNO");
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292 | *beamCol = pksrec.beamNo-beamOffset_-1;
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293 | RecordFieldPtr<Int> rbCol(rec, "REFBEAMNO");
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294 | Int rb = -1;
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295 | if (nBeam_ > 1 ) rb = pksrec.refBeam-1;
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296 | *rbCol = rb;
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297 | RecordFieldPtr<uInt> ifCol(rec, "IFNO");
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298 | *ifCol = pksrec.IFno-ifOffset_- 1;
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299 | uInt id;
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300 | /// @todo this has to change when nchan isn't global anymore
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301 | id = table_->frequencies().addEntry(Double(header_->nchan/2),
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302 | pksrec.refFreq, pksrec.freqInc);
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303 | RecordFieldPtr<uInt> mfreqidCol(rec, "FREQ_ID");
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304 | *mfreqidCol = id;
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305 |
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306 | id = table_->molecules().addEntry(pksrec.restFreq);
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307 | RecordFieldPtr<uInt> molidCol(rec, "MOLECULE_ID");
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308 | *molidCol = id;
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309 |
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310 | id = table_->tcal().addEntry(pksrec.tcalTime, pksrec.tcal);
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311 | RecordFieldPtr<uInt> mcalidCol(rec, "TCAL_ID");
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312 | *mcalidCol = id;
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313 | id = table_->weather().addEntry(pksrec.temperature, pksrec.pressure,
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314 | pksrec.humidity, pksrec.windSpeed,
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315 | pksrec.windAz);
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316 | RecordFieldPtr<uInt> mweatheridCol(rec, "WEATHER_ID");
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317 | *mweatheridCol = id;
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318 |
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319 | RecordFieldPtr<uInt> mfocusidCol(rec, "FOCUS_ID");
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320 | id = table_->focus().addEntry(pksrec.parAngle, pksrec.focusAxi,
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321 | pksrec.focusTan, pksrec.focusRot);
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322 | *mfocusidCol = id;
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323 | RecordFieldPtr<Array<Double> > dirCol(rec, "DIRECTION");
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324 | *dirCol = pksrec.direction;
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325 | RecordFieldPtr<Float> azCol(rec, "AZIMUTH");
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326 | *azCol = pksrec.azimuth;
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327 | RecordFieldPtr<Float> elCol(rec, "ELEVATION");
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328 | *elCol = pksrec.elevation;
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329 |
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330 | RecordFieldPtr< Array<Float> > specCol(rec, "SPECTRA");
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331 | RecordFieldPtr< Array<uChar> > flagCol(rec, "FLAGTRA");
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332 | RecordFieldPtr< uInt > polnoCol(rec, "POLNO");
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333 |
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334 | RecordFieldPtr< Array<Float> > tsysCol(rec, "TSYS");
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335 | // Turn the (nchan,npol) matrix and possible complex xPol vector
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336 | // into 2-4 rows in the scantable
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337 | Vector<Float> tsysvec(1);
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338 | // Why is pksrec.spectra.ncolumn() == 3 for haveXPol_ == True
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339 | uInt npol = (pksrec.spectra.ncolumn()==1 ? 1: 2);
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340 | for ( uInt i=0; i< npol; ++i ) {
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341 | tsysvec = pksrec.tsys(i);
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342 | *tsysCol = tsysvec;
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343 | *polnoCol = i;
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344 |
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345 | *specCol = pksrec.spectra.column(i);
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346 | *flagCol = pksrec.flagged.column(i);
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347 | table_->table().addRow();
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348 | row.put(table_->table().nrow()-1, rec);
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349 | }
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350 | if ( haveXPol_[0] ) {
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351 | // no tsys given for xpol, so emulate it
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352 | tsysvec = sqrt(pksrec.tsys[0]*pksrec.tsys[1]);
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353 | *tsysCol = tsysvec;
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354 | // add real part of cross pol
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355 | *polnoCol = 2;
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356 | Vector<Float> r(real(pksrec.xPol));
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357 | *specCol = r;
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358 | // make up flags from linears
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359 | /// @fixme this has to be a bitwise or of both pols
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360 | *flagCol = pksrec.flagged.column(0);// | pksrec.flagged.column(1);
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361 | table_->table().addRow();
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362 | row.put(table_->table().nrow()-1, rec);
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363 | // ad imaginary part of cross pol
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364 | *polnoCol = 3;
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365 | Vector<Float> im(imag(pksrec.xPol));
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366 | *specCol = im;
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367 | table_->table().addRow();
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368 | row.put(table_->table().nrow()-1, rec);
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369 | }
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370 | #ifdef HAS_ALMA
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371 | fillpm._update(n);
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372 | #endif
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373 | }
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374 | if (status > 0) {
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375 | close();
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376 | throw(AipsError("Reading error occured, data possibly corrupted."));
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377 | }
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378 | #ifdef HAS_ALMA
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379 | fillpm.done();
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380 | #endif
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381 | return status;
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382 | }
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383 |
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384 | }//namespace asap
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