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