[805] | 1 | //
|
---|
| 2 | // C++ Implementation: STMath
|
---|
| 3 | //
|
---|
| 4 | // Description:
|
---|
| 5 | //
|
---|
| 6 | //
|
---|
| 7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
|
---|
| 8 | //
|
---|
| 9 | // Copyright: See COPYING file that comes with this distribution
|
---|
| 10 | //
|
---|
| 11 | //
|
---|
[38] | 12 |
|
---|
[330] | 13 | #include <casa/iomanip.h>
|
---|
[805] | 14 | #include <casa/Exceptions/Error.h>
|
---|
| 15 | #include <casa/Containers/Block.h>
|
---|
[81] | 16 | #include <casa/BasicSL/String.h>
|
---|
[805] | 17 | #include <casa/Arrays/MaskArrLogi.h>
|
---|
| 18 | #include <casa/Arrays/MaskArrMath.h>
|
---|
| 19 | #include <casa/Arrays/ArrayLogical.h>
|
---|
[81] | 20 | #include <casa/Arrays/ArrayMath.h>
|
---|
[1066] | 21 | #include <casa/Arrays/Slice.h>
|
---|
| 22 | #include <casa/Arrays/Slicer.h>
|
---|
[805] | 23 | #include <casa/Containers/RecordField.h>
|
---|
| 24 | #include <tables/Tables/TableRow.h>
|
---|
| 25 | #include <tables/Tables/TableVector.h>
|
---|
[917] | 26 | #include <tables/Tables/TabVecMath.h>
|
---|
[805] | 27 | #include <tables/Tables/ExprNode.h>
|
---|
| 28 | #include <tables/Tables/TableRecord.h>
|
---|
[1140] | 29 | #include <tables/Tables/TableParse.h>
|
---|
[805] | 30 | #include <tables/Tables/ReadAsciiTable.h>
|
---|
[1140] | 31 | #include <tables/Tables/TableIter.h>
|
---|
| 32 | #include <tables/Tables/TableCopy.h>
|
---|
[1192] | 33 | #include <scimath/Mathematics/FFTServer.h>
|
---|
[2] | 34 |
|
---|
[262] | 35 | #include <lattices/Lattices/LatticeUtilities.h>
|
---|
| 36 |
|
---|
[917] | 37 | #include <coordinates/Coordinates/SpectralCoordinate.h>
|
---|
| 38 | #include <coordinates/Coordinates/CoordinateSystem.h>
|
---|
| 39 | #include <coordinates/Coordinates/CoordinateUtil.h>
|
---|
| 40 | #include <coordinates/Coordinates/FrequencyAligner.h>
|
---|
| 41 |
|
---|
[177] | 42 | #include <scimath/Mathematics/VectorKernel.h>
|
---|
| 43 | #include <scimath/Mathematics/Convolver.h>
|
---|
[234] | 44 | #include <scimath/Functionals/Polynomial.h>
|
---|
[177] | 45 |
|
---|
[38] | 46 | #include "MathUtils.h"
|
---|
[805] | 47 | #include "RowAccumulator.h"
|
---|
[878] | 48 | #include "STAttr.h"
|
---|
[805] | 49 | #include "STMath.h"
|
---|
[2] | 50 |
|
---|
[805] | 51 | using namespace casa;
|
---|
[2] | 52 |
|
---|
[83] | 53 | using namespace asap;
|
---|
[2] | 54 |
|
---|
[805] | 55 | STMath::STMath(bool insitu) :
|
---|
| 56 | insitu_(insitu)
|
---|
[716] | 57 | {
|
---|
| 58 | }
|
---|
[170] | 59 |
|
---|
| 60 |
|
---|
[805] | 61 | STMath::~STMath()
|
---|
[170] | 62 | {
|
---|
| 63 | }
|
---|
| 64 |
|
---|
[805] | 65 | CountedPtr<Scantable>
|
---|
[977] | 66 | STMath::average( const std::vector<CountedPtr<Scantable> >& in,
|
---|
[858] | 67 | const std::vector<bool>& mask,
|
---|
[805] | 68 | const std::string& weight,
|
---|
[977] | 69 | const std::string& avmode)
|
---|
[262] | 70 | {
|
---|
[977] | 71 | if ( avmode == "SCAN" && in.size() != 1 )
|
---|
[1066] | 72 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
|
---|
| 73 | "Use merge first."));
|
---|
[805] | 74 | WeightType wtype = stringToWeight(weight);
|
---|
[926] | 75 |
|
---|
[805] | 76 | // output
|
---|
| 77 | // clone as this is non insitu
|
---|
| 78 | bool insitu = insitu_;
|
---|
| 79 | setInsitu(false);
|
---|
[977] | 80 | CountedPtr< Scantable > out = getScantable(in[0], true);
|
---|
[805] | 81 | setInsitu(insitu);
|
---|
[977] | 82 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
|
---|
[862] | 83 | ++stit;
|
---|
[977] | 84 | while ( stit != in.end() ) {
|
---|
[862] | 85 | out->appendToHistoryTable((*stit)->history());
|
---|
| 86 | ++stit;
|
---|
| 87 | }
|
---|
[294] | 88 |
|
---|
[805] | 89 | Table& tout = out->table();
|
---|
[701] | 90 |
|
---|
[805] | 91 | /// @todo check if all scantables are conformant
|
---|
[294] | 92 |
|
---|
[805] | 93 | ArrayColumn<Float> specColOut(tout,"SPECTRA");
|
---|
| 94 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
|
---|
| 95 | ArrayColumn<Float> tsysColOut(tout,"TSYS");
|
---|
| 96 | ScalarColumn<Double> mjdColOut(tout,"TIME");
|
---|
| 97 | ScalarColumn<Double> intColOut(tout,"INTERVAL");
|
---|
[1008] | 98 | ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
|
---|
[1145] | 99 | ScalarColumn<uInt> scanColOut(tout,"SCANNO");
|
---|
[262] | 100 |
|
---|
[805] | 101 | // set up the output table rows. These are based on the structure of the
|
---|
[862] | 102 | // FIRST scantable in the vector
|
---|
[977] | 103 | const Table& baset = in[0]->table();
|
---|
[262] | 104 |
|
---|
[805] | 105 | Block<String> cols(3);
|
---|
| 106 | cols[0] = String("BEAMNO");
|
---|
| 107 | cols[1] = String("IFNO");
|
---|
| 108 | cols[2] = String("POLNO");
|
---|
| 109 | if ( avmode == "SOURCE" ) {
|
---|
| 110 | cols.resize(4);
|
---|
| 111 | cols[3] = String("SRCNAME");
|
---|
[488] | 112 | }
|
---|
[977] | 113 | if ( avmode == "SCAN" && in.size() == 1) {
|
---|
[805] | 114 | cols.resize(4);
|
---|
| 115 | cols[3] = String("SCANNO");
|
---|
[2] | 116 | }
|
---|
[805] | 117 | uInt outrowCount = 0;
|
---|
| 118 | TableIterator iter(baset, cols);
|
---|
| 119 | while (!iter.pastEnd()) {
|
---|
| 120 | Table subt = iter.table();
|
---|
| 121 | // copy the first row of this selection into the new table
|
---|
| 122 | tout.addRow();
|
---|
| 123 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
|
---|
[1145] | 124 | // re-index to 0
|
---|
| 125 | if ( avmode != "SCAN" && avmode != "SOURCE" ) {
|
---|
| 126 | scanColOut.put(outrowCount, uInt(0));
|
---|
| 127 | }
|
---|
[805] | 128 | ++outrowCount;
|
---|
| 129 | ++iter;
|
---|
[144] | 130 | }
|
---|
[805] | 131 | RowAccumulator acc(wtype);
|
---|
[858] | 132 | Vector<Bool> cmask(mask);
|
---|
| 133 | acc.setUserMask(cmask);
|
---|
[805] | 134 | ROTableRow row(tout);
|
---|
| 135 | ROArrayColumn<Float> specCol, tsysCol;
|
---|
| 136 | ROArrayColumn<uChar> flagCol;
|
---|
| 137 | ROScalarColumn<Double> mjdCol, intCol;
|
---|
| 138 | ROScalarColumn<Int> scanIDCol;
|
---|
[144] | 139 |
|
---|
[1333] | 140 | Vector<uInt> rowstodelete;
|
---|
| 141 |
|
---|
[805] | 142 | for (uInt i=0; i < tout.nrow(); ++i) {
|
---|
[996] | 143 | for ( int j=0; j < int(in.size()); ++j ) {
|
---|
[977] | 144 | const Table& tin = in[j]->table();
|
---|
[805] | 145 | const TableRecord& rec = row.get(i);
|
---|
| 146 | ROScalarColumn<Double> tmp(tin, "TIME");
|
---|
| 147 | Double td;tmp.get(0,td);
|
---|
| 148 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
| 149 | && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
| 150 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
|
---|
| 151 | Table subt;
|
---|
| 152 | if ( avmode == "SOURCE") {
|
---|
| 153 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
|
---|
| 154 | } else if (avmode == "SCAN") {
|
---|
| 155 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
|
---|
| 156 | } else {
|
---|
| 157 | subt = basesubt;
|
---|
| 158 | }
|
---|
| 159 | specCol.attach(subt,"SPECTRA");
|
---|
| 160 | flagCol.attach(subt,"FLAGTRA");
|
---|
| 161 | tsysCol.attach(subt,"TSYS");
|
---|
| 162 | intCol.attach(subt,"INTERVAL");
|
---|
| 163 | mjdCol.attach(subt,"TIME");
|
---|
| 164 | Vector<Float> spec,tsys;
|
---|
| 165 | Vector<uChar> flag;
|
---|
| 166 | Double inter,time;
|
---|
| 167 | for (uInt k = 0; k < subt.nrow(); ++k ) {
|
---|
| 168 | flagCol.get(k, flag);
|
---|
| 169 | Vector<Bool> bflag(flag.shape());
|
---|
| 170 | convertArray(bflag, flag);
|
---|
[1314] | 171 | /*
|
---|
[805] | 172 | if ( allEQ(bflag, True) ) {
|
---|
[1314] | 173 | continue;//don't accumulate
|
---|
[144] | 174 | }
|
---|
[1314] | 175 | */
|
---|
[805] | 176 | specCol.get(k, spec);
|
---|
| 177 | tsysCol.get(k, tsys);
|
---|
| 178 | intCol.get(k, inter);
|
---|
| 179 | mjdCol.get(k, time);
|
---|
| 180 | // spectrum has to be added last to enable weighting by the other values
|
---|
| 181 | acc.add(spec, !bflag, tsys, inter, time);
|
---|
| 182 | }
|
---|
| 183 | }
|
---|
[1333] | 184 | const Vector<Bool>& msk = acc.getMask();
|
---|
| 185 | if ( allEQ(msk, False) ) {
|
---|
| 186 | uint n = rowstodelete.nelements();
|
---|
| 187 | rowstodelete.resize(n+1, True);
|
---|
| 188 | rowstodelete[n] = i;
|
---|
| 189 | continue;
|
---|
| 190 | }
|
---|
| 191 | cout << "write "<< i << endl;
|
---|
[805] | 192 | //write out
|
---|
| 193 | Vector<uChar> flg(msk.shape());
|
---|
| 194 | convertArray(flg, !msk);
|
---|
| 195 | flagColOut.put(i, flg);
|
---|
[1333] | 196 | specColOut.put(i, acc.getSpectrum());
|
---|
[805] | 197 | tsysColOut.put(i, acc.getTsys());
|
---|
| 198 | intColOut.put(i, acc.getInterval());
|
---|
| 199 | mjdColOut.put(i, acc.getTime());
|
---|
[1008] | 200 | // we should only have one cycle now -> reset it to be 0
|
---|
| 201 | // frequency switched data has different CYCLENO for different IFNO
|
---|
| 202 | // which requires resetting this value
|
---|
| 203 | cycColOut.put(i, uInt(0));
|
---|
[805] | 204 | acc.reset();
|
---|
[144] | 205 | }
|
---|
[1333] | 206 | if (rowstodelete.nelements() > 0) {
|
---|
| 207 | cout << rowstodelete << endl;
|
---|
| 208 | tout.removeRow(rowstodelete);
|
---|
| 209 | if (tout.nrow() == 0) {
|
---|
| 210 | throw(AipsError("Can't average fully flagged data."));
|
---|
| 211 | }
|
---|
| 212 | }
|
---|
[805] | 213 | return out;
|
---|
[2] | 214 | }
|
---|
[9] | 215 |
|
---|
[1069] | 216 | CountedPtr< Scantable >
|
---|
| 217 | STMath::averageChannel( const CountedPtr < Scantable > & in,
|
---|
[1078] | 218 | const std::string & mode,
|
---|
| 219 | const std::string& avmode )
|
---|
[1069] | 220 | {
|
---|
| 221 | // clone as this is non insitu
|
---|
| 222 | bool insitu = insitu_;
|
---|
| 223 | setInsitu(false);
|
---|
| 224 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 225 | setInsitu(insitu);
|
---|
| 226 | Table& tout = out->table();
|
---|
| 227 | ArrayColumn<Float> specColOut(tout,"SPECTRA");
|
---|
| 228 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
|
---|
| 229 | ArrayColumn<Float> tsysColOut(tout,"TSYS");
|
---|
[1140] | 230 | ScalarColumn<uInt> scanColOut(tout,"SCANNO");
|
---|
[1232] | 231 | ScalarColumn<Double> intColOut(tout, "INTERVAL");
|
---|
[1140] | 232 | Table tmp = in->table().sort("BEAMNO");
|
---|
[1069] | 233 | Block<String> cols(3);
|
---|
| 234 | cols[0] = String("BEAMNO");
|
---|
| 235 | cols[1] = String("IFNO");
|
---|
| 236 | cols[2] = String("POLNO");
|
---|
[1078] | 237 | if ( avmode == "SCAN") {
|
---|
| 238 | cols.resize(4);
|
---|
| 239 | cols[3] = String("SCANNO");
|
---|
| 240 | }
|
---|
[1069] | 241 | uInt outrowCount = 0;
|
---|
| 242 | uChar userflag = 1 << 7;
|
---|
[1140] | 243 | TableIterator iter(tmp, cols);
|
---|
[1069] | 244 | while (!iter.pastEnd()) {
|
---|
| 245 | Table subt = iter.table();
|
---|
| 246 | ROArrayColumn<Float> specCol, tsysCol;
|
---|
| 247 | ROArrayColumn<uChar> flagCol;
|
---|
[1232] | 248 | ROScalarColumn<Double> intCol(subt, "INTERVAL");
|
---|
[1069] | 249 | specCol.attach(subt,"SPECTRA");
|
---|
| 250 | flagCol.attach(subt,"FLAGTRA");
|
---|
| 251 | tsysCol.attach(subt,"TSYS");
|
---|
| 252 | tout.addRow();
|
---|
| 253 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
|
---|
[1140] | 254 | if ( avmode != "SCAN") {
|
---|
| 255 | scanColOut.put(outrowCount, uInt(0));
|
---|
| 256 | }
|
---|
[1069] | 257 | Vector<Float> tmp;
|
---|
| 258 | specCol.get(0, tmp);
|
---|
| 259 | uInt nchan = tmp.nelements();
|
---|
[1078] | 260 | // have to do channel by channel here as MaskedArrMath
|
---|
| 261 | // doesn't have partialMedians
|
---|
[1069] | 262 | Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
|
---|
| 263 | Vector<Float> outspec(nchan);
|
---|
| 264 | Vector<uChar> outflag(nchan,0);
|
---|
| 265 | Vector<Float> outtsys(1);/// @fixme when tsys is channel based
|
---|
| 266 | for (uInt i=0; i<nchan; ++i) {
|
---|
| 267 | Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
|
---|
| 268 | MaskedArray<Float> ma = maskedArray(specs,flags);
|
---|
| 269 | outspec[i] = median(ma);
|
---|
| 270 | if ( allEQ(ma.getMask(), False) )
|
---|
| 271 | outflag[i] = userflag;// flag data
|
---|
| 272 | }
|
---|
| 273 | outtsys[0] = median(tsysCol.getColumn());
|
---|
| 274 | specColOut.put(outrowCount, outspec);
|
---|
| 275 | flagColOut.put(outrowCount, outflag);
|
---|
| 276 | tsysColOut.put(outrowCount, outtsys);
|
---|
[1232] | 277 | Double intsum = sum(intCol.getColumn());
|
---|
| 278 | intColOut.put(outrowCount, intsum);
|
---|
[1069] | 279 | ++outrowCount;
|
---|
| 280 | ++iter;
|
---|
| 281 | }
|
---|
| 282 | return out;
|
---|
| 283 | }
|
---|
| 284 |
|
---|
[805] | 285 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
|
---|
| 286 | bool droprows)
|
---|
[185] | 287 | {
|
---|
[805] | 288 | if (insitu_) return in;
|
---|
| 289 | else {
|
---|
| 290 | // clone
|
---|
| 291 | Scantable* tabp = new Scantable(*in, Bool(droprows));
|
---|
| 292 | return CountedPtr<Scantable>(tabp);
|
---|
[234] | 293 | }
|
---|
[805] | 294 | }
|
---|
[234] | 295 |
|
---|
[805] | 296 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
|
---|
| 297 | float val,
|
---|
| 298 | const std::string& mode,
|
---|
| 299 | bool tsys )
|
---|
| 300 | {
|
---|
| 301 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 302 | Table& tab = out->table();
|
---|
| 303 | ArrayColumn<Float> specCol(tab,"SPECTRA");
|
---|
| 304 | ArrayColumn<Float> tsysCol(tab,"TSYS");
|
---|
| 305 | for (uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 306 | Vector<Float> spec;
|
---|
| 307 | Vector<Float> ts;
|
---|
| 308 | specCol.get(i, spec);
|
---|
| 309 | tsysCol.get(i, ts);
|
---|
[1308] | 310 | if (mode == "MUL" || mode == "DIV") {
|
---|
| 311 | if (mode == "DIV") val = 1.0/val;
|
---|
[805] | 312 | spec *= val;
|
---|
| 313 | specCol.put(i, spec);
|
---|
| 314 | if ( tsys ) {
|
---|
| 315 | ts *= val;
|
---|
| 316 | tsysCol.put(i, ts);
|
---|
| 317 | }
|
---|
[1308] | 318 | } else if ( mode == "ADD" || mode == "SUB") {
|
---|
| 319 | if (mode == "SUB") val *= -1.0;
|
---|
[805] | 320 | spec += val;
|
---|
| 321 | specCol.put(i, spec);
|
---|
| 322 | if ( tsys ) {
|
---|
| 323 | ts += val;
|
---|
| 324 | tsysCol.put(i, ts);
|
---|
| 325 | }
|
---|
| 326 | }
|
---|
[234] | 327 | }
|
---|
[805] | 328 | return out;
|
---|
| 329 | }
|
---|
[234] | 330 |
|
---|
[1308] | 331 | CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
|
---|
| 332 | const CountedPtr<Scantable>& right,
|
---|
| 333 | const std::string& mode)
|
---|
| 334 | {
|
---|
| 335 | bool insitu = insitu_;
|
---|
| 336 | if ( ! left->conformant(*right) ) {
|
---|
| 337 | throw(AipsError("'left' and 'right' scantables are not conformant."));
|
---|
| 338 | }
|
---|
| 339 | setInsitu(false);
|
---|
| 340 | CountedPtr< Scantable > out = getScantable(left, false);
|
---|
| 341 | setInsitu(insitu);
|
---|
| 342 | Table& tout = out->table();
|
---|
| 343 | Block<String> coln(5);
|
---|
| 344 | coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO";
|
---|
| 345 | coln[3] = "IFNO"; coln[4] = "POLNO";
|
---|
| 346 | Table tmpl = tout.sort(coln);
|
---|
| 347 | Table tmpr = right->table().sort(coln);
|
---|
| 348 | ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
|
---|
| 349 | ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
|
---|
| 350 | ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
|
---|
| 351 | ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
|
---|
| 352 |
|
---|
| 353 | for (uInt i=0; i<tout.nrow(); ++i) {
|
---|
| 354 | Vector<Float> lspecvec, rspecvec;
|
---|
| 355 | Vector<uChar> lflagvec, rflagvec;
|
---|
| 356 | lspecvec = lspecCol(i); rspecvec = rspecCol(i);
|
---|
| 357 | lflagvec = lflagCol(i); rflagvec = rflagCol(i);
|
---|
| 358 | MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
|
---|
| 359 | MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
|
---|
| 360 | if (mode == "ADD") {
|
---|
| 361 | mleft += mright;
|
---|
| 362 | } else if ( mode == "SUB") {
|
---|
| 363 | mleft -= mright;
|
---|
| 364 | } else if ( mode == "MUL") {
|
---|
| 365 | mleft *= mright;
|
---|
| 366 | } else if ( mode == "DIV") {
|
---|
| 367 | mleft /= mright;
|
---|
| 368 | } else {
|
---|
| 369 | throw(AipsError("Illegal binary operator"));
|
---|
| 370 | }
|
---|
| 371 | lspecCol.put(i, mleft.getArray());
|
---|
| 372 | }
|
---|
| 373 | return out;
|
---|
| 374 | }
|
---|
| 375 |
|
---|
| 376 |
|
---|
| 377 |
|
---|
[805] | 378 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
|
---|
| 379 | const Vector<uChar>& f)
|
---|
| 380 | {
|
---|
| 381 | Vector<Bool> mask;
|
---|
| 382 | mask.resize(f.shape());
|
---|
| 383 | convertArray(mask, f);
|
---|
| 384 | return MaskedArray<Float>(s,!mask);
|
---|
| 385 | }
|
---|
[248] | 386 |
|
---|
[805] | 387 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
|
---|
| 388 | {
|
---|
| 389 | const Vector<Bool>& m = ma.getMask();
|
---|
| 390 | Vector<uChar> flags(m.shape());
|
---|
| 391 | convertArray(flags, !m);
|
---|
| 392 | return flags;
|
---|
| 393 | }
|
---|
[234] | 394 |
|
---|
[1066] | 395 | CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
|
---|
| 396 | const std::string & mode,
|
---|
| 397 | bool preserve )
|
---|
[805] | 398 | {
|
---|
| 399 | /// @todo make other modes available
|
---|
| 400 | /// modes should be "nearest", "pair"
|
---|
| 401 | // make this operation non insitu
|
---|
| 402 | const Table& tin = in->table();
|
---|
| 403 | Table ons = tin(tin.col("SRCTYPE") == Int(0));
|
---|
| 404 | Table offs = tin(tin.col("SRCTYPE") == Int(1));
|
---|
| 405 | if ( offs.nrow() == 0 )
|
---|
| 406 | throw(AipsError("No 'off' scans present."));
|
---|
| 407 | // put all "on" scans into output table
|
---|
[701] | 408 |
|
---|
[805] | 409 | bool insitu = insitu_;
|
---|
| 410 | setInsitu(false);
|
---|
| 411 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 412 | setInsitu(insitu);
|
---|
| 413 | Table& tout = out->table();
|
---|
[248] | 414 |
|
---|
[805] | 415 | TableCopy::copyRows(tout, ons);
|
---|
| 416 | TableRow row(tout);
|
---|
| 417 | ROScalarColumn<Double> offtimeCol(offs, "TIME");
|
---|
| 418 | ArrayColumn<Float> outspecCol(tout, "SPECTRA");
|
---|
| 419 | ROArrayColumn<Float> outtsysCol(tout, "TSYS");
|
---|
| 420 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
|
---|
| 421 | for (uInt i=0; i < tout.nrow(); ++i) {
|
---|
| 422 | const TableRecord& rec = row.get(i);
|
---|
| 423 | Double ontime = rec.asDouble("TIME");
|
---|
[1321] | 424 | Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
| 425 | && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
| 426 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
|
---|
| 427 | ROScalarColumn<Double> offtimeCol(presel, "TIME");
|
---|
| 428 |
|
---|
[805] | 429 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
|
---|
[1259] | 430 | // Timestamp may vary within a cycle ???!!!
|
---|
[1321] | 431 | // increase this by 0.01 sec in case of rounding errors...
|
---|
[1259] | 432 | // There might be a better way to do this.
|
---|
[1321] | 433 | // fix to this fix. TIME is MJD, so 1.0d not 1.0s
|
---|
| 434 | mindeltat += 0.01/24./60./60.;
|
---|
| 435 | Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat);
|
---|
[780] | 436 |
|
---|
[1259] | 437 | if ( sel.nrow() < 1 ) {
|
---|
| 438 | throw(AipsError("No closest in time found... This could be a rounding "
|
---|
| 439 | "issue. Try quotient instead."));
|
---|
| 440 | }
|
---|
[805] | 441 | TableRow offrow(sel);
|
---|
| 442 | const TableRecord& offrec = offrow.get(0);//should only be one row
|
---|
| 443 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
|
---|
| 444 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
|
---|
| 445 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
|
---|
| 446 | /// @fixme this assumes tsys is a scalar not vector
|
---|
| 447 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
|
---|
| 448 | Vector<Float> specon, tsyson;
|
---|
| 449 | outtsysCol.get(i, tsyson);
|
---|
| 450 | outspecCol.get(i, specon);
|
---|
| 451 | Vector<uChar> flagon;
|
---|
| 452 | outflagCol.get(i, flagon);
|
---|
| 453 | MaskedArray<Float> mon = maskedArray(specon, flagon);
|
---|
| 454 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
|
---|
| 455 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
|
---|
| 456 | if (preserve) {
|
---|
| 457 | quot -= tsysoffscalar;
|
---|
| 458 | } else {
|
---|
| 459 | quot -= tsyson[0];
|
---|
[701] | 460 | }
|
---|
[805] | 461 | outspecCol.put(i, quot.getArray());
|
---|
| 462 | outflagCol.put(i, flagsFromMA(quot));
|
---|
| 463 | }
|
---|
[926] | 464 | // renumber scanno
|
---|
| 465 | TableIterator it(tout, "SCANNO");
|
---|
| 466 | uInt i = 0;
|
---|
| 467 | while ( !it.pastEnd() ) {
|
---|
| 468 | Table t = it.table();
|
---|
| 469 | TableVector<uInt> vec(t, "SCANNO");
|
---|
| 470 | vec = i;
|
---|
| 471 | ++i;
|
---|
| 472 | ++it;
|
---|
| 473 | }
|
---|
[805] | 474 | return out;
|
---|
| 475 | }
|
---|
[234] | 476 |
|
---|
[1066] | 477 |
|
---|
| 478 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
|
---|
| 479 | const CountedPtr< Scantable > & off,
|
---|
| 480 | bool preserve )
|
---|
| 481 | {
|
---|
| 482 | bool insitu = insitu_;
|
---|
[1069] | 483 | if ( ! on->conformant(*off) ) {
|
---|
| 484 | throw(AipsError("'on' and 'off' scantables are not conformant."));
|
---|
| 485 | }
|
---|
[1066] | 486 | setInsitu(false);
|
---|
| 487 | CountedPtr< Scantable > out = getScantable(on, false);
|
---|
| 488 | setInsitu(insitu);
|
---|
| 489 | Table& tout = out->table();
|
---|
| 490 | const Table& toff = off->table();
|
---|
| 491 | TableIterator sit(tout, "SCANNO");
|
---|
| 492 | TableIterator s2it(toff, "SCANNO");
|
---|
| 493 | while ( !sit.pastEnd() ) {
|
---|
| 494 | Table ton = sit.table();
|
---|
| 495 | TableRow row(ton);
|
---|
| 496 | Table t = s2it.table();
|
---|
| 497 | ArrayColumn<Float> outspecCol(ton, "SPECTRA");
|
---|
| 498 | ROArrayColumn<Float> outtsysCol(ton, "TSYS");
|
---|
| 499 | ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
|
---|
| 500 | for (uInt i=0; i < ton.nrow(); ++i) {
|
---|
| 501 | const TableRecord& rec = row.get(i);
|
---|
| 502 | Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
|
---|
| 503 | && t.col("IFNO") == Int(rec.asuInt("IFNO"))
|
---|
| 504 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
|
---|
[1145] | 505 | if ( offsel.nrow() == 0 )
|
---|
| 506 | throw AipsError("STMath::quotient: no matching off");
|
---|
[1066] | 507 | TableRow offrow(offsel);
|
---|
| 508 | const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
|
---|
| 509 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
|
---|
| 510 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
|
---|
| 511 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
|
---|
| 512 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
|
---|
| 513 | Vector<Float> specon, tsyson;
|
---|
| 514 | outtsysCol.get(i, tsyson);
|
---|
| 515 | outspecCol.get(i, specon);
|
---|
| 516 | Vector<uChar> flagon;
|
---|
| 517 | outflagCol.get(i, flagon);
|
---|
| 518 | MaskedArray<Float> mon = maskedArray(specon, flagon);
|
---|
| 519 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
|
---|
| 520 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
|
---|
| 521 | if (preserve) {
|
---|
| 522 | quot -= tsysoffscalar;
|
---|
| 523 | } else {
|
---|
| 524 | quot -= tsyson[0];
|
---|
| 525 | }
|
---|
| 526 | outspecCol.put(i, quot.getArray());
|
---|
| 527 | outflagCol.put(i, flagsFromMA(quot));
|
---|
| 528 | }
|
---|
| 529 | ++sit;
|
---|
| 530 | ++s2it;
|
---|
| 531 | // take the first off for each on scan which doesn't have a
|
---|
| 532 | // matching off scan
|
---|
| 533 | // non <= noff: matching pairs, non > noff matching pairs then first off
|
---|
| 534 | if ( s2it.pastEnd() ) s2it.reset();
|
---|
| 535 | }
|
---|
| 536 | return out;
|
---|
| 537 | }
|
---|
| 538 |
|
---|
| 539 |
|
---|
[805] | 540 | CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
|
---|
| 541 | {
|
---|
| 542 | // make copy or reference
|
---|
| 543 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 544 | Table& tout = out->table();
|
---|
[1008] | 545 | Block<String> cols(4);
|
---|
[805] | 546 | cols[0] = String("SCANNO");
|
---|
[1008] | 547 | cols[1] = String("CYCLENO");
|
---|
| 548 | cols[2] = String("BEAMNO");
|
---|
| 549 | cols[3] = String("POLNO");
|
---|
[805] | 550 | TableIterator iter(tout, cols);
|
---|
| 551 | while (!iter.pastEnd()) {
|
---|
| 552 | Table subt = iter.table();
|
---|
| 553 | // this should leave us with two rows for the two IFs....if not ignore
|
---|
| 554 | if (subt.nrow() != 2 ) {
|
---|
| 555 | continue;
|
---|
[701] | 556 | }
|
---|
[1008] | 557 | ArrayColumn<Float> specCol(subt, "SPECTRA");
|
---|
| 558 | ArrayColumn<Float> tsysCol(subt, "TSYS");
|
---|
| 559 | ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
|
---|
[805] | 560 | Vector<Float> onspec,offspec, ontsys, offtsys;
|
---|
| 561 | Vector<uChar> onflag, offflag;
|
---|
| 562 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
|
---|
| 563 | specCol.get(0, onspec); specCol.get(1, offspec);
|
---|
| 564 | flagCol.get(0, onflag); flagCol.get(1, offflag);
|
---|
| 565 | MaskedArray<Float> on = maskedArray(onspec, onflag);
|
---|
| 566 | MaskedArray<Float> off = maskedArray(offspec, offflag);
|
---|
| 567 | MaskedArray<Float> oncopy = on.copy();
|
---|
[248] | 568 |
|
---|
[805] | 569 | on /= off; on -= 1.0f;
|
---|
| 570 | on *= ontsys[0];
|
---|
| 571 | off /= oncopy; off -= 1.0f;
|
---|
| 572 | off *= offtsys[0];
|
---|
| 573 | specCol.put(0, on.getArray());
|
---|
| 574 | const Vector<Bool>& m0 = on.getMask();
|
---|
| 575 | Vector<uChar> flags0(m0.shape());
|
---|
| 576 | convertArray(flags0, !m0);
|
---|
| 577 | flagCol.put(0, flags0);
|
---|
[234] | 578 |
|
---|
[805] | 579 | specCol.put(1, off.getArray());
|
---|
| 580 | const Vector<Bool>& m1 = off.getMask();
|
---|
| 581 | Vector<uChar> flags1(m1.shape());
|
---|
| 582 | convertArray(flags1, !m1);
|
---|
| 583 | flagCol.put(1, flags1);
|
---|
[867] | 584 | ++iter;
|
---|
[130] | 585 | }
|
---|
[780] | 586 |
|
---|
[805] | 587 | return out;
|
---|
[9] | 588 | }
|
---|
[48] | 589 |
|
---|
[805] | 590 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
|
---|
| 591 | const std::vector< bool > & mask,
|
---|
| 592 | const std::string& which )
|
---|
[130] | 593 | {
|
---|
| 594 |
|
---|
[805] | 595 | Vector<Bool> m(mask);
|
---|
| 596 | const Table& tab = in->table();
|
---|
| 597 | ROArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 598 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 599 | std::vector<float> out;
|
---|
| 600 | for (uInt i=0; i < tab.nrow(); ++i ) {
|
---|
| 601 | Vector<Float> spec; specCol.get(i, spec);
|
---|
[867] | 602 | Vector<uChar> flag; flagCol.get(i, flag);
|
---|
| 603 | MaskedArray<Float> ma = maskedArray(spec, flag);
|
---|
| 604 | float outstat = 0.0;
|
---|
[805] | 605 | if ( spec.nelements() == m.nelements() ) {
|
---|
| 606 | outstat = mathutil::statistics(which, ma(m));
|
---|
| 607 | } else {
|
---|
| 608 | outstat = mathutil::statistics(which, ma);
|
---|
| 609 | }
|
---|
| 610 | out.push_back(outstat);
|
---|
[234] | 611 | }
|
---|
[805] | 612 | return out;
|
---|
[130] | 613 | }
|
---|
| 614 |
|
---|
[805] | 615 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
|
---|
| 616 | int width )
|
---|
[144] | 617 | {
|
---|
[841] | 618 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
|
---|
[805] | 619 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 620 | Table& tout = out->table();
|
---|
| 621 | out->frequencies().rescale(width, "BIN");
|
---|
| 622 | ArrayColumn<Float> specCol(tout, "SPECTRA");
|
---|
| 623 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
|
---|
| 624 | for (uInt i=0; i < tout.nrow(); ++i ) {
|
---|
| 625 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
|
---|
| 626 | MaskedArray<Float> maout;
|
---|
| 627 | LatticeUtilities::bin(maout, main, 0, Int(width));
|
---|
| 628 | /// @todo implement channel based tsys binning
|
---|
| 629 | specCol.put(i, maout.getArray());
|
---|
| 630 | flagCol.put(i, flagsFromMA(maout));
|
---|
| 631 | // take only the first binned spectrum's length for the deprecated
|
---|
| 632 | // global header item nChan
|
---|
| 633 | if (i==0) tout.rwKeywordSet().define(String("nChan"),
|
---|
| 634 | Int(maout.getArray().nelements()));
|
---|
[169] | 635 | }
|
---|
[805] | 636 | return out;
|
---|
[146] | 637 | }
|
---|
| 638 |
|
---|
[805] | 639 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
|
---|
| 640 | const std::string& method,
|
---|
| 641 | float width )
|
---|
[299] | 642 | //
|
---|
| 643 | // Should add the possibility of width being specified in km/s. This means
|
---|
[780] | 644 | // that for each freqID (SpectralCoordinate) we will need to convert to an
|
---|
| 645 | // average channel width (say at the reference pixel). Then we would need
|
---|
| 646 | // to be careful to make sure each spectrum (of different freqID)
|
---|
[299] | 647 | // is the same length.
|
---|
| 648 | //
|
---|
| 649 | {
|
---|
[996] | 650 | //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
[805] | 651 | Int interpMethod(stringToIMethod(method));
|
---|
[299] | 652 |
|
---|
[805] | 653 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 654 | Table& tout = out->table();
|
---|
[299] | 655 |
|
---|
| 656 | // Resample SpectralCoordinates (one per freqID)
|
---|
[805] | 657 | out->frequencies().rescale(width, "RESAMPLE");
|
---|
| 658 | TableIterator iter(tout, "IFNO");
|
---|
| 659 | TableRow row(tout);
|
---|
| 660 | while ( !iter.pastEnd() ) {
|
---|
| 661 | Table tab = iter.table();
|
---|
| 662 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 663 | //ArrayColumn<Float> tsysCol(tout, "TSYS");
|
---|
| 664 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 665 | Vector<Float> spec;
|
---|
| 666 | Vector<uChar> flag;
|
---|
| 667 | specCol.get(0,spec); // the number of channels should be constant per IF
|
---|
| 668 | uInt nChanIn = spec.nelements();
|
---|
| 669 | Vector<Float> xIn(nChanIn); indgen(xIn);
|
---|
| 670 | Int fac = Int(nChanIn/width);
|
---|
| 671 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later
|
---|
| 672 | uInt k = 0;
|
---|
| 673 | Float x = 0.0;
|
---|
| 674 | while (x < Float(nChanIn) ) {
|
---|
| 675 | xOut(k) = x;
|
---|
| 676 | k++;
|
---|
| 677 | x += width;
|
---|
| 678 | }
|
---|
| 679 | uInt nChanOut = k;
|
---|
| 680 | xOut.resize(nChanOut, True);
|
---|
| 681 | // process all rows for this IFNO
|
---|
| 682 | Vector<Float> specOut;
|
---|
| 683 | Vector<Bool> maskOut;
|
---|
| 684 | Vector<uChar> flagOut;
|
---|
| 685 | for (uInt i=0; i < tab.nrow(); ++i) {
|
---|
| 686 | specCol.get(i, spec);
|
---|
| 687 | flagCol.get(i, flag);
|
---|
| 688 | Vector<Bool> mask(flag.nelements());
|
---|
| 689 | convertArray(mask, flag);
|
---|
[299] | 690 |
|
---|
[805] | 691 | IPosition shapeIn(spec.shape());
|
---|
| 692 | //sh.nchan = nChanOut;
|
---|
| 693 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
|
---|
| 694 | xIn, spec, mask,
|
---|
| 695 | interpMethod, True, True);
|
---|
| 696 | /// @todo do the same for channel based Tsys
|
---|
| 697 | flagOut.resize(maskOut.nelements());
|
---|
| 698 | convertArray(flagOut, maskOut);
|
---|
| 699 | specCol.put(i, specOut);
|
---|
| 700 | flagCol.put(i, flagOut);
|
---|
| 701 | }
|
---|
| 702 | ++iter;
|
---|
[299] | 703 | }
|
---|
| 704 |
|
---|
[805] | 705 | return out;
|
---|
| 706 | }
|
---|
[299] | 707 |
|
---|
[805] | 708 | STMath::imethod STMath::stringToIMethod(const std::string& in)
|
---|
| 709 | {
|
---|
| 710 | static STMath::imap lookup;
|
---|
[299] | 711 |
|
---|
[805] | 712 | // initialize the lookup table if necessary
|
---|
| 713 | if ( lookup.empty() ) {
|
---|
[926] | 714 | lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
|
---|
| 715 | lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
|
---|
| 716 | lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
|
---|
| 717 | lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
|
---|
[299] | 718 | }
|
---|
| 719 |
|
---|
[805] | 720 | STMath::imap::const_iterator iter = lookup.find(in);
|
---|
[299] | 721 |
|
---|
[805] | 722 | if ( lookup.end() == iter ) {
|
---|
| 723 | std::string message = in;
|
---|
| 724 | message += " is not a valid interpolation mode";
|
---|
| 725 | throw(AipsError(message));
|
---|
[299] | 726 | }
|
---|
[805] | 727 | return iter->second;
|
---|
[299] | 728 | }
|
---|
| 729 |
|
---|
[805] | 730 | WeightType STMath::stringToWeight(const std::string& in)
|
---|
[146] | 731 | {
|
---|
[805] | 732 | static std::map<std::string, WeightType> lookup;
|
---|
[434] | 733 |
|
---|
[805] | 734 | // initialize the lookup table if necessary
|
---|
| 735 | if ( lookup.empty() ) {
|
---|
| 736 | lookup["NONE"] = asap::NONE;
|
---|
| 737 | lookup["TINT"] = asap::TINT;
|
---|
| 738 | lookup["TINTSYS"] = asap::TINTSYS;
|
---|
| 739 | lookup["TSYS"] = asap::TSYS;
|
---|
| 740 | lookup["VAR"] = asap::VAR;
|
---|
| 741 | }
|
---|
[434] | 742 |
|
---|
[805] | 743 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
|
---|
[294] | 744 |
|
---|
[805] | 745 | if ( lookup.end() == iter ) {
|
---|
| 746 | std::string message = in;
|
---|
| 747 | message += " is not a valid weighting mode";
|
---|
| 748 | throw(AipsError(message));
|
---|
| 749 | }
|
---|
| 750 | return iter->second;
|
---|
[146] | 751 | }
|
---|
| 752 |
|
---|
[805] | 753 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
|
---|
[867] | 754 | const vector< float > & coeff,
|
---|
[805] | 755 | const std::string & filename,
|
---|
| 756 | const std::string& method)
|
---|
[165] | 757 | {
|
---|
[805] | 758 | // Get elevation data from Scantable and convert to degrees
|
---|
| 759 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[926] | 760 | Table& tab = out->table();
|
---|
[805] | 761 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
| 762 | Vector<Float> x = elev.getColumn();
|
---|
| 763 | x *= Float(180 / C::pi); // Degrees
|
---|
[165] | 764 |
|
---|
[867] | 765 | Vector<Float> coeffs(coeff);
|
---|
[805] | 766 | const uInt nc = coeffs.nelements();
|
---|
| 767 | if ( filename.length() > 0 && nc > 0 ) {
|
---|
| 768 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
|
---|
[315] | 769 | }
|
---|
[165] | 770 |
|
---|
[805] | 771 | // Correct
|
---|
| 772 | if ( nc > 0 || filename.length() == 0 ) {
|
---|
| 773 | // Find instrument
|
---|
| 774 | Bool throwit = True;
|
---|
| 775 | Instrument inst =
|
---|
[878] | 776 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
|
---|
[805] | 777 | throwit);
|
---|
[165] | 778 |
|
---|
[805] | 779 | // Set polynomial
|
---|
| 780 | Polynomial<Float>* ppoly = 0;
|
---|
| 781 | Vector<Float> coeff;
|
---|
| 782 | String msg;
|
---|
| 783 | if ( nc > 0 ) {
|
---|
| 784 | ppoly = new Polynomial<Float>(nc);
|
---|
| 785 | coeff = coeffs;
|
---|
| 786 | msg = String("user");
|
---|
| 787 | } else {
|
---|
[878] | 788 | STAttr sdAttr;
|
---|
[805] | 789 | coeff = sdAttr.gainElevationPoly(inst);
|
---|
| 790 | ppoly = new Polynomial<Float>(3);
|
---|
| 791 | msg = String("built in");
|
---|
| 792 | }
|
---|
[532] | 793 |
|
---|
[805] | 794 | if ( coeff.nelements() > 0 ) {
|
---|
| 795 | ppoly->setCoefficients(coeff);
|
---|
| 796 | } else {
|
---|
| 797 | delete ppoly;
|
---|
| 798 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
|
---|
| 799 | }
|
---|
| 800 | ostringstream oss;
|
---|
| 801 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
|
---|
| 802 | oss << " " << coeff;
|
---|
| 803 | pushLog(String(oss));
|
---|
| 804 | const uInt nrow = tab.nrow();
|
---|
| 805 | Vector<Float> factor(nrow);
|
---|
| 806 | for ( uInt i=0; i < nrow; ++i ) {
|
---|
| 807 | factor[i] = 1.0 / (*ppoly)(x[i]);
|
---|
| 808 | }
|
---|
| 809 | delete ppoly;
|
---|
| 810 | scaleByVector(tab, factor, true);
|
---|
[532] | 811 |
|
---|
[805] | 812 | } else {
|
---|
| 813 | // Read and correct
|
---|
| 814 | pushLog("Making correction from ascii Table");
|
---|
| 815 | scaleFromAsciiTable(tab, filename, method, x, true);
|
---|
[532] | 816 | }
|
---|
[805] | 817 | return out;
|
---|
| 818 | }
|
---|
[165] | 819 |
|
---|
[805] | 820 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
|
---|
| 821 | const std::string& method,
|
---|
| 822 | const Vector<Float>& xout, bool dotsys)
|
---|
| 823 | {
|
---|
[165] | 824 |
|
---|
[805] | 825 | // Read gain-elevation ascii file data into a Table.
|
---|
[165] | 826 |
|
---|
[805] | 827 | String formatString;
|
---|
| 828 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
|
---|
| 829 | scaleFromTable(in, tbl, method, xout, dotsys);
|
---|
| 830 | }
|
---|
[165] | 831 |
|
---|
[805] | 832 | void STMath::scaleFromTable(Table& in,
|
---|
| 833 | const Table& table,
|
---|
| 834 | const std::string& method,
|
---|
| 835 | const Vector<Float>& xout, bool dotsys)
|
---|
| 836 | {
|
---|
[780] | 837 |
|
---|
[805] | 838 | ROScalarColumn<Float> geElCol(table, "ELEVATION");
|
---|
| 839 | ROScalarColumn<Float> geFacCol(table, "FACTOR");
|
---|
| 840 | Vector<Float> xin = geElCol.getColumn();
|
---|
| 841 | Vector<Float> yin = geFacCol.getColumn();
|
---|
| 842 | Vector<Bool> maskin(xin.nelements(),True);
|
---|
[165] | 843 |
|
---|
[805] | 844 | // Interpolate (and extrapolate) with desired method
|
---|
[532] | 845 |
|
---|
[996] | 846 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
|
---|
[165] | 847 |
|
---|
[805] | 848 | Vector<Float> yout;
|
---|
| 849 | Vector<Bool> maskout;
|
---|
| 850 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
|
---|
[996] | 851 | xin, yin, maskin, interp,
|
---|
[805] | 852 | True, True);
|
---|
[165] | 853 |
|
---|
[805] | 854 | scaleByVector(in, Float(1.0)/yout, dotsys);
|
---|
[165] | 855 | }
|
---|
[167] | 856 |
|
---|
[805] | 857 | void STMath::scaleByVector( Table& in,
|
---|
| 858 | const Vector< Float >& factor,
|
---|
| 859 | bool dotsys )
|
---|
[177] | 860 | {
|
---|
[805] | 861 | uInt nrow = in.nrow();
|
---|
| 862 | if ( factor.nelements() != nrow ) {
|
---|
| 863 | throw(AipsError("factors.nelements() != table.nelements()"));
|
---|
| 864 | }
|
---|
| 865 | ArrayColumn<Float> specCol(in, "SPECTRA");
|
---|
| 866 | ArrayColumn<uChar> flagCol(in, "FLAGTRA");
|
---|
| 867 | ArrayColumn<Float> tsysCol(in, "TSYS");
|
---|
| 868 | for (uInt i=0; i < nrow; ++i) {
|
---|
| 869 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
---|
| 870 | ma *= factor[i];
|
---|
| 871 | specCol.put(i, ma.getArray());
|
---|
| 872 | flagCol.put(i, flagsFromMA(ma));
|
---|
| 873 | if ( dotsys ) {
|
---|
[926] | 874 | Vector<Float> tsys = tsysCol(i);
|
---|
[805] | 875 | tsys *= factor[i];
|
---|
[926] | 876 | tsysCol.put(i,tsys);
|
---|
[805] | 877 | }
|
---|
| 878 | }
|
---|
[177] | 879 | }
|
---|
| 880 |
|
---|
[805] | 881 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
|
---|
| 882 | float d, float etaap,
|
---|
| 883 | float jyperk )
|
---|
[221] | 884 | {
|
---|
[805] | 885 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 886 | Table& tab = in->table();
|
---|
| 887 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
|
---|
[221] | 888 | Unit K(String("K"));
|
---|
| 889 | Unit JY(String("Jy"));
|
---|
[701] | 890 |
|
---|
[805] | 891 | bool tokelvin = true;
|
---|
| 892 | Double cfac = 1.0;
|
---|
[716] | 893 |
|
---|
[805] | 894 | if ( fluxUnit == JY ) {
|
---|
[716] | 895 | pushLog("Converting to K");
|
---|
[701] | 896 | Quantum<Double> t(1.0,fluxUnit);
|
---|
| 897 | Quantum<Double> t2 = t.get(JY);
|
---|
[805] | 898 | cfac = (t2 / t).getValue(); // value to Jy
|
---|
[780] | 899 |
|
---|
[805] | 900 | tokelvin = true;
|
---|
| 901 | out->setFluxUnit("K");
|
---|
| 902 | } else if ( fluxUnit == K ) {
|
---|
[716] | 903 | pushLog("Converting to Jy");
|
---|
[701] | 904 | Quantum<Double> t(1.0,fluxUnit);
|
---|
| 905 | Quantum<Double> t2 = t.get(K);
|
---|
[805] | 906 | cfac = (t2 / t).getValue(); // value to K
|
---|
[780] | 907 |
|
---|
[805] | 908 | tokelvin = false;
|
---|
| 909 | out->setFluxUnit("Jy");
|
---|
[221] | 910 | } else {
|
---|
[701] | 911 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
|
---|
[221] | 912 | }
|
---|
[701] | 913 | // Make sure input values are converted to either Jy or K first...
|
---|
[805] | 914 | Float factor = cfac;
|
---|
[221] | 915 |
|
---|
[701] | 916 | // Select method
|
---|
[805] | 917 | if (jyperk > 0.0) {
|
---|
| 918 | factor *= jyperk;
|
---|
| 919 | if ( tokelvin ) factor = 1.0 / jyperk;
|
---|
[716] | 920 | ostringstream oss;
|
---|
[805] | 921 | oss << "Jy/K = " << jyperk;
|
---|
[716] | 922 | pushLog(String(oss));
|
---|
[805] | 923 | Vector<Float> factors(tab.nrow(), factor);
|
---|
| 924 | scaleByVector(tab,factors, false);
|
---|
| 925 | } else if ( etaap > 0.0) {
|
---|
[1319] | 926 | if (d < 0) {
|
---|
| 927 | Instrument inst =
|
---|
| 928 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
|
---|
| 929 | True);
|
---|
| 930 | STAttr sda;
|
---|
| 931 | d = sda.diameter(inst);
|
---|
| 932 | }
|
---|
[996] | 933 | jyperk = STAttr::findJyPerK(etaap, d);
|
---|
[716] | 934 | ostringstream oss;
|
---|
[805] | 935 | oss << "Jy/K = " << jyperk;
|
---|
[716] | 936 | pushLog(String(oss));
|
---|
[805] | 937 | factor *= jyperk;
|
---|
| 938 | if ( tokelvin ) {
|
---|
[701] | 939 | factor = 1.0 / factor;
|
---|
| 940 | }
|
---|
[805] | 941 | Vector<Float> factors(tab.nrow(), factor);
|
---|
| 942 | scaleByVector(tab, factors, False);
|
---|
[354] | 943 | } else {
|
---|
[780] | 944 |
|
---|
[701] | 945 | // OK now we must deal with automatic look up of values.
|
---|
| 946 | // We must also deal with the fact that the factors need
|
---|
| 947 | // to be computed per IF and may be different and may
|
---|
| 948 | // change per integration.
|
---|
[780] | 949 |
|
---|
[716] | 950 | pushLog("Looking up conversion factors");
|
---|
[805] | 951 | convertBrightnessUnits(out, tokelvin, cfac);
|
---|
[701] | 952 | }
|
---|
[805] | 953 |
|
---|
| 954 | return out;
|
---|
[221] | 955 | }
|
---|
| 956 |
|
---|
[805] | 957 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
|
---|
| 958 | bool tokelvin, float cfac )
|
---|
[227] | 959 | {
|
---|
[805] | 960 | Table& table = in->table();
|
---|
| 961 | Instrument inst =
|
---|
[878] | 962 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
|
---|
[805] | 963 | TableIterator iter(table, "FREQ_ID");
|
---|
| 964 | STFrequencies stfreqs = in->frequencies();
|
---|
[878] | 965 | STAttr sdAtt;
|
---|
[805] | 966 | while (!iter.pastEnd()) {
|
---|
| 967 | Table tab = iter.table();
|
---|
| 968 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 969 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 970 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
|
---|
| 971 | MEpoch::ROScalarColumn timeCol(tab, "TIME");
|
---|
[234] | 972 |
|
---|
[805] | 973 | uInt freqid; freqidCol.get(0, freqid);
|
---|
| 974 | Vector<Float> tmpspec; specCol.get(0, tmpspec);
|
---|
[878] | 975 | // STAttr.JyPerK has a Vector interface... change sometime.
|
---|
[805] | 976 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
|
---|
| 977 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 978 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
|
---|
| 979 | Float factor = cfac * jyperk;
|
---|
| 980 | if ( tokelvin ) factor = Float(1.0) / factor;
|
---|
| 981 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
---|
| 982 | ma *= factor;
|
---|
| 983 | specCol.put(i, ma.getArray());
|
---|
| 984 | flagCol.put(i, flagsFromMA(ma));
|
---|
| 985 | }
|
---|
[867] | 986 | ++iter;
|
---|
[234] | 987 | }
|
---|
[230] | 988 | }
|
---|
[227] | 989 |
|
---|
[805] | 990 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
|
---|
| 991 | float tau )
|
---|
[234] | 992 | {
|
---|
[805] | 993 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[926] | 994 |
|
---|
| 995 | Table tab = out->table();
|
---|
[234] | 996 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
[805] | 997 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 998 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 999 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 1000 | Float zdist = Float(C::pi_2) - elev(i);
|
---|
[1318] | 1001 | Float factor = exp(tau/cos(zdist));
|
---|
[926] | 1002 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
---|
[805] | 1003 | ma *= factor;
|
---|
| 1004 | specCol.put(i, ma.getArray());
|
---|
| 1005 | flagCol.put(i, flagsFromMA(ma));
|
---|
[234] | 1006 | }
|
---|
[805] | 1007 | return out;
|
---|
[234] | 1008 | }
|
---|
| 1009 |
|
---|
[805] | 1010 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
|
---|
| 1011 | const std::string& kernel, float width )
|
---|
[457] | 1012 | {
|
---|
[805] | 1013 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[1033] | 1014 | Table& table = out->table();
|
---|
[805] | 1015 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
|
---|
| 1016 | // same IFNO should have same no of channels
|
---|
| 1017 | // this saves overhead
|
---|
| 1018 | TableIterator iter(table, "IFNO");
|
---|
| 1019 | while (!iter.pastEnd()) {
|
---|
| 1020 | Table tab = iter.table();
|
---|
| 1021 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 1022 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 1023 | Vector<Float> tmpspec; specCol.get(0, tmpspec);
|
---|
| 1024 | uInt nchan = tmpspec.nelements();
|
---|
| 1025 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
|
---|
| 1026 | Convolver<Float> conv(kvec, IPosition(1,nchan));
|
---|
| 1027 | Vector<Float> spec;
|
---|
| 1028 | Vector<uChar> flag;
|
---|
| 1029 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 1030 | specCol.get(i, spec);
|
---|
| 1031 | flagCol.get(i, flag);
|
---|
| 1032 | Vector<Bool> mask(flag.nelements());
|
---|
| 1033 | convertArray(mask, flag);
|
---|
| 1034 | Vector<Float> specout;
|
---|
| 1035 | if ( type == VectorKernel::HANNING ) {
|
---|
| 1036 | Vector<Bool> maskout;
|
---|
[1033] | 1037 | mathutil::hanning(specout, maskout, spec , !mask);
|
---|
| 1038 | convertArray(flag, !maskout);
|
---|
[805] | 1039 | flagCol.put(i, flag);
|
---|
[1033] | 1040 | specCol.put(i, specout);
|
---|
| 1041 | } else {
|
---|
[805] | 1042 | mathutil::replaceMaskByZero(specout, mask);
|
---|
| 1043 | conv.linearConv(specout, spec);
|
---|
[1033] | 1044 | specCol.put(i, specout);
|
---|
[354] | 1045 | }
|
---|
[805] | 1046 | }
|
---|
[867] | 1047 | ++iter;
|
---|
[701] | 1048 | }
|
---|
[805] | 1049 | return out;
|
---|
[701] | 1050 | }
|
---|
[841] | 1051 |
|
---|
| 1052 | CountedPtr< Scantable >
|
---|
| 1053 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
|
---|
| 1054 | {
|
---|
| 1055 | if ( in.size() < 2 ) {
|
---|
[862] | 1056 | throw(AipsError("Need at least two scantables to perform a merge."));
|
---|
[841] | 1057 | }
|
---|
| 1058 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
|
---|
| 1059 | bool insitu = insitu_;
|
---|
| 1060 | setInsitu(false);
|
---|
[862] | 1061 | CountedPtr< Scantable > out = getScantable(*it, false);
|
---|
[841] | 1062 | setInsitu(insitu);
|
---|
| 1063 | Table& tout = out->table();
|
---|
| 1064 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
|
---|
[917] | 1065 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
|
---|
| 1066 | // Renumber SCANNO to be 0-based
|
---|
[926] | 1067 | Vector<uInt> scannos = scannocol.getColumn();
|
---|
| 1068 | uInt offset = min(scannos);
|
---|
[917] | 1069 | scannos -= offset;
|
---|
[926] | 1070 | scannocol.putColumn(scannos);
|
---|
| 1071 | uInt newscanno = max(scannos)+1;
|
---|
[862] | 1072 | ++it;
|
---|
[841] | 1073 | while ( it != in.end() ){
|
---|
| 1074 | if ( ! (*it)->conformant(*out) ) {
|
---|
| 1075 | // log message: "ignoring scantable i, as it isn't
|
---|
| 1076 | // conformant with the other(s)"
|
---|
| 1077 | cerr << "oh oh" << endl;
|
---|
| 1078 | ++it;
|
---|
| 1079 | continue;
|
---|
| 1080 | }
|
---|
[862] | 1081 | out->appendToHistoryTable((*it)->history());
|
---|
[841] | 1082 | const Table& tab = (*it)->table();
|
---|
| 1083 | TableIterator scanit(tab, "SCANNO");
|
---|
| 1084 | while (!scanit.pastEnd()) {
|
---|
| 1085 | TableIterator freqit(scanit.table(), "FREQ_ID");
|
---|
| 1086 | while ( !freqit.pastEnd() ) {
|
---|
| 1087 | Table thetab = freqit.table();
|
---|
| 1088 | uInt nrow = tout.nrow();
|
---|
| 1089 | //tout.addRow(thetab.nrow());
|
---|
| 1090 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
|
---|
| 1091 | ROTableRow row(thetab);
|
---|
| 1092 | for ( uInt i=0; i<thetab.nrow(); ++i) {
|
---|
| 1093 | uInt k = nrow+i;
|
---|
| 1094 | scannocol.put(k, newscanno);
|
---|
| 1095 | const TableRecord& rec = row.get(i);
|
---|
| 1096 | Double rv,rp,inc;
|
---|
| 1097 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
|
---|
| 1098 | uInt id;
|
---|
| 1099 | id = out->frequencies().addEntry(rp, rv, inc);
|
---|
| 1100 | freqidcol.put(k,id);
|
---|
| 1101 | String name,fname;Double rf;
|
---|
| 1102 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
|
---|
| 1103 | id = out->molecules().addEntry(rf, name, fname);
|
---|
| 1104 | molidcol.put(k, id);
|
---|
[961] | 1105 | Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
|
---|
| 1106 | (*it)->focus().getEntry(fax, ftan, frot, fhand,
|
---|
| 1107 | fmount,fuser, fxy, fxyp,
|
---|
| 1108 | rec.asuInt("FOCUS_ID"));
|
---|
| 1109 | id = out->focus().addEntry(fax, ftan, frot, fhand,
|
---|
| 1110 | fmount,fuser, fxy, fxyp);
|
---|
[841] | 1111 | focusidcol.put(k, id);
|
---|
| 1112 | }
|
---|
| 1113 | ++freqit;
|
---|
| 1114 | }
|
---|
| 1115 | ++newscanno;
|
---|
| 1116 | ++scanit;
|
---|
| 1117 | }
|
---|
| 1118 | ++it;
|
---|
| 1119 | }
|
---|
| 1120 | return out;
|
---|
| 1121 | }
|
---|
[896] | 1122 |
|
---|
| 1123 | CountedPtr< Scantable >
|
---|
| 1124 | STMath::invertPhase( const CountedPtr < Scantable >& in )
|
---|
| 1125 | {
|
---|
[996] | 1126 | return applyToPol(in, &STPol::invertPhase, Float(0.0));
|
---|
[896] | 1127 | }
|
---|
| 1128 |
|
---|
| 1129 | CountedPtr< Scantable >
|
---|
| 1130 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
|
---|
| 1131 | {
|
---|
| 1132 | return applyToPol(in, &STPol::rotatePhase, Float(phase));
|
---|
| 1133 | }
|
---|
| 1134 |
|
---|
| 1135 | CountedPtr< Scantable >
|
---|
| 1136 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
|
---|
| 1137 | {
|
---|
| 1138 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
|
---|
| 1139 | }
|
---|
| 1140 |
|
---|
| 1141 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
|
---|
| 1142 | STPol::polOperation fptr,
|
---|
| 1143 | Float phase )
|
---|
| 1144 | {
|
---|
| 1145 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 1146 | Table& tout = out->table();
|
---|
| 1147 | Block<String> cols(4);
|
---|
| 1148 | cols[0] = String("SCANNO");
|
---|
| 1149 | cols[1] = String("BEAMNO");
|
---|
| 1150 | cols[2] = String("IFNO");
|
---|
| 1151 | cols[3] = String("CYCLENO");
|
---|
| 1152 | TableIterator iter(tout, cols);
|
---|
[1015] | 1153 | STPol* stpol = STPol::getPolClass(out->factories_, out->getPolType() );
|
---|
[896] | 1154 | while (!iter.pastEnd()) {
|
---|
| 1155 | Table t = iter.table();
|
---|
| 1156 | ArrayColumn<Float> speccol(t, "SPECTRA");
|
---|
[1015] | 1157 | ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
|
---|
| 1158 | ScalarColumn<Float> parancol(t, "PARANGLE");
|
---|
[896] | 1159 | Matrix<Float> pols = speccol.getColumn();
|
---|
| 1160 | try {
|
---|
| 1161 | stpol->setSpectra(pols);
|
---|
[1015] | 1162 | Float fang,fhand,parang;
|
---|
| 1163 | fang = in->focusTable_.getTotalFeedAngle(focidcol(0));
|
---|
| 1164 | fhand = in->focusTable_.getFeedHand(focidcol(0));
|
---|
| 1165 | parang = parancol(0);
|
---|
| 1166 | /// @todo re-enable this
|
---|
| 1167 | // disable total feed angle to support paralactifying Caswell style
|
---|
| 1168 | stpol->setPhaseCorrections(parang, -parang, fhand);
|
---|
[896] | 1169 | (stpol->*fptr)(phase);
|
---|
| 1170 | speccol.putColumn(stpol->getSpectra());
|
---|
[1015] | 1171 | Matrix<Float> tmp = stpol->getSpectra();
|
---|
[896] | 1172 | } catch (AipsError& e) {
|
---|
| 1173 | delete stpol;stpol=0;
|
---|
| 1174 | throw(e);
|
---|
| 1175 | }
|
---|
| 1176 | ++iter;
|
---|
| 1177 | }
|
---|
[934] | 1178 | delete stpol;stpol=0;
|
---|
[896] | 1179 | return out;
|
---|
| 1180 | }
|
---|
| 1181 |
|
---|
| 1182 | CountedPtr< Scantable >
|
---|
| 1183 | STMath::swapPolarisations( const CountedPtr< Scantable > & in )
|
---|
| 1184 | {
|
---|
| 1185 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 1186 | Table& tout = out->table();
|
---|
| 1187 | Table t0 = tout(tout.col("POLNO") == 0);
|
---|
| 1188 | Table t1 = tout(tout.col("POLNO") == 1);
|
---|
| 1189 | if ( t0.nrow() != t1.nrow() )
|
---|
| 1190 | throw(AipsError("Inconsistent number of polarisations"));
|
---|
| 1191 | ArrayColumn<Float> speccol0(t0, "SPECTRA");
|
---|
| 1192 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
|
---|
| 1193 | ArrayColumn<Float> speccol1(t1, "SPECTRA");
|
---|
| 1194 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
|
---|
| 1195 | Matrix<Float> s0 = speccol0.getColumn();
|
---|
| 1196 | Matrix<uChar> f0 = flagcol0.getColumn();
|
---|
| 1197 | speccol0.putColumn(speccol1.getColumn());
|
---|
| 1198 | flagcol0.putColumn(flagcol1.getColumn());
|
---|
| 1199 | speccol1.putColumn(s0);
|
---|
| 1200 | flagcol1.putColumn(f0);
|
---|
| 1201 | return out;
|
---|
| 1202 | }
|
---|
[917] | 1203 |
|
---|
| 1204 | CountedPtr< Scantable >
|
---|
[940] | 1205 | STMath::averagePolarisations( const CountedPtr< Scantable > & in,
|
---|
| 1206 | const std::vector<bool>& mask,
|
---|
| 1207 | const std::string& weight )
|
---|
| 1208 | {
|
---|
[1232] | 1209 | if (in->npol() < 2 )
|
---|
| 1210 | throw(AipsError("averagePolarisations can only be applied to two or more"
|
---|
| 1211 | "polarisations"));
|
---|
[1010] | 1212 | bool insitu = insitu_;
|
---|
| 1213 | setInsitu(false);
|
---|
[1232] | 1214 | CountedPtr< Scantable > pols = getScantable(in, true);
|
---|
[1010] | 1215 | setInsitu(insitu);
|
---|
| 1216 | Table& tout = pols->table();
|
---|
[1232] | 1217 | std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
|
---|
| 1218 | Table tab = tableCommand(taql, in->table());
|
---|
| 1219 | if (tab.nrow() == 0 )
|
---|
| 1220 | throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
|
---|
| 1221 | TableCopy::copyRows(tout, tab);
|
---|
[1145] | 1222 | TableVector<uInt> vec(tout, "POLNO");
|
---|
[940] | 1223 | vec = 0;
|
---|
[1145] | 1224 | pols->table_.rwKeywordSet().define("nPol", Int(1));
|
---|
[1232] | 1225 | pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
|
---|
[1010] | 1226 | std::vector<CountedPtr<Scantable> > vpols;
|
---|
| 1227 | vpols.push_back(pols);
|
---|
[1232] | 1228 | CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
|
---|
[940] | 1229 | return out;
|
---|
| 1230 | }
|
---|
| 1231 |
|
---|
[1145] | 1232 | CountedPtr< Scantable >
|
---|
| 1233 | STMath::averageBeams( const CountedPtr< Scantable > & in,
|
---|
| 1234 | const std::vector<bool>& mask,
|
---|
| 1235 | const std::string& weight )
|
---|
| 1236 | {
|
---|
| 1237 | bool insitu = insitu_;
|
---|
| 1238 | setInsitu(false);
|
---|
| 1239 | CountedPtr< Scantable > beams = getScantable(in, false);
|
---|
| 1240 | setInsitu(insitu);
|
---|
| 1241 | Table& tout = beams->table();
|
---|
| 1242 | // give all rows the same BEAMNO
|
---|
| 1243 | TableVector<uInt> vec(tout, "BEAMNO");
|
---|
| 1244 | vec = 0;
|
---|
| 1245 | beams->table_.rwKeywordSet().define("nBeam", Int(1));
|
---|
| 1246 | std::vector<CountedPtr<Scantable> > vbeams;
|
---|
| 1247 | vbeams.push_back(beams);
|
---|
[1232] | 1248 | CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
|
---|
[1145] | 1249 | return out;
|
---|
| 1250 | }
|
---|
[940] | 1251 |
|
---|
[1145] | 1252 |
|
---|
[940] | 1253 | CountedPtr< Scantable >
|
---|
[917] | 1254 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
|
---|
| 1255 | const std::string & refTime,
|
---|
[926] | 1256 | const std::string & method)
|
---|
[917] | 1257 | {
|
---|
[940] | 1258 | // clone as this is not working insitu
|
---|
| 1259 | bool insitu = insitu_;
|
---|
| 1260 | setInsitu(false);
|
---|
[917] | 1261 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[940] | 1262 | setInsitu(insitu);
|
---|
[917] | 1263 | Table& tout = out->table();
|
---|
| 1264 | // Get reference Epoch to time of first row or given String
|
---|
| 1265 | Unit DAY(String("d"));
|
---|
| 1266 | MEpoch::Ref epochRef(in->getTimeReference());
|
---|
| 1267 | MEpoch refEpoch;
|
---|
| 1268 | if (refTime.length()>0) {
|
---|
| 1269 | Quantum<Double> qt;
|
---|
| 1270 | if (MVTime::read(qt,refTime)) {
|
---|
| 1271 | MVEpoch mv(qt);
|
---|
| 1272 | refEpoch = MEpoch(mv, epochRef);
|
---|
| 1273 | } else {
|
---|
| 1274 | throw(AipsError("Invalid format for Epoch string"));
|
---|
| 1275 | }
|
---|
| 1276 | } else {
|
---|
| 1277 | refEpoch = in->timeCol_(0);
|
---|
| 1278 | }
|
---|
| 1279 | MPosition refPos = in->getAntennaPosition();
|
---|
[940] | 1280 |
|
---|
[996] | 1281 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
|
---|
[917] | 1282 | // test if user frame is different to base frame
|
---|
| 1283 | if ( in->frequencies().getFrameString(true)
|
---|
| 1284 | == in->frequencies().getFrameString(false) ) {
|
---|
[985] | 1285 | throw(AipsError("Can't convert as no output frame has been set"
|
---|
| 1286 | " (use set_freqframe) or it is aligned already."));
|
---|
[917] | 1287 | }
|
---|
| 1288 | MFrequency::Types system = in->frequencies().getFrame();
|
---|
[940] | 1289 | MVTime mvt(refEpoch.getValue());
|
---|
| 1290 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
|
---|
| 1291 | ostringstream oss;
|
---|
| 1292 | oss << "Aligned at reference Epoch " << epochout
|
---|
| 1293 | << " in frame " << MFrequency::showType(system);
|
---|
| 1294 | pushLog(String(oss));
|
---|
[917] | 1295 | // set up the iterator
|
---|
[926] | 1296 | Block<String> cols(4);
|
---|
| 1297 | // select by constant direction
|
---|
[917] | 1298 | cols[0] = String("SRCNAME");
|
---|
| 1299 | cols[1] = String("BEAMNO");
|
---|
| 1300 | // select by IF ( no of channels varies over this )
|
---|
| 1301 | cols[2] = String("IFNO");
|
---|
[926] | 1302 | // select by restfrequency
|
---|
| 1303 | cols[3] = String("MOLECULE_ID");
|
---|
[917] | 1304 | TableIterator iter(tout, cols);
|
---|
[926] | 1305 | while ( !iter.pastEnd() ) {
|
---|
[917] | 1306 | Table t = iter.table();
|
---|
| 1307 | MDirection::ROScalarColumn dirCol(t, "DIRECTION");
|
---|
[926] | 1308 | TableIterator fiter(t, "FREQ_ID");
|
---|
[917] | 1309 | // determine nchan from the first row. This should work as
|
---|
[926] | 1310 | // we are iterating over BEAMNO and IFNO // we should have constant direction
|
---|
| 1311 |
|
---|
[917] | 1312 | ROArrayColumn<Float> sCol(t, "SPECTRA");
|
---|
[926] | 1313 | MDirection direction = dirCol(0);
|
---|
[917] | 1314 | uInt nchan = sCol(0).nelements();
|
---|
[926] | 1315 | while ( !fiter.pastEnd() ) {
|
---|
| 1316 | Table ftab = fiter.table();
|
---|
| 1317 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
|
---|
| 1318 | // get the SpectralCoordinate for the freqid, which we are iterating over
|
---|
| 1319 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
|
---|
| 1320 | FrequencyAligner<Float> fa( sC, nchan, refEpoch,
|
---|
| 1321 | direction, refPos, system );
|
---|
| 1322 | // realign the SpectralCoordinate and put into the output Scantable
|
---|
| 1323 | Vector<String> units(1);
|
---|
| 1324 | units = String("Hz");
|
---|
| 1325 | Bool linear=True;
|
---|
| 1326 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
|
---|
| 1327 | sc2.setWorldAxisUnits(units);
|
---|
[934] | 1328 | uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
|
---|
| 1329 | sc2.referenceValue()[0],
|
---|
| 1330 | sc2.increment()[0]);
|
---|
| 1331 | TableVector<uInt> tvec(ftab, "FREQ_ID");
|
---|
| 1332 | tvec = id;
|
---|
[926] | 1333 | // create the "global" abcissa for alignment with same FREQ_ID
|
---|
| 1334 | Vector<Double> abc(nchan);
|
---|
[917] | 1335 | Double w;
|
---|
| 1336 | for (uInt i=0; i<nchan; i++) {
|
---|
| 1337 | sC.toWorld(w,Double(i));
|
---|
| 1338 | abc[i] = w;
|
---|
| 1339 | }
|
---|
[926] | 1340 | // cache abcissa for same time stamps, so iterate over those
|
---|
| 1341 | TableIterator timeiter(ftab, "TIME");
|
---|
| 1342 | while ( !timeiter.pastEnd() ) {
|
---|
| 1343 | Table tab = timeiter.table();
|
---|
| 1344 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 1345 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 1346 | MEpoch::ROScalarColumn timeCol(tab, "TIME");
|
---|
| 1347 | // use align abcissa cache after the first row
|
---|
| 1348 | bool first = true;
|
---|
| 1349 | // these rows should be just be POLNO
|
---|
[996] | 1350 | for (int i=0; i<int(tab.nrow()); ++i) {
|
---|
[926] | 1351 | // input values
|
---|
| 1352 | Vector<uChar> flag = flagCol(i);
|
---|
| 1353 | Vector<Bool> mask(flag.shape());
|
---|
| 1354 | Vector<Float> specOut, spec;
|
---|
| 1355 | spec = specCol(i);
|
---|
| 1356 | Vector<Bool> maskOut;Vector<uChar> flagOut;
|
---|
| 1357 | convertArray(mask, flag);
|
---|
| 1358 | // alignment
|
---|
| 1359 | Bool ok = fa.align(specOut, maskOut, abc, spec,
|
---|
| 1360 | mask, timeCol(i), !first,
|
---|
| 1361 | interp, False);
|
---|
| 1362 | // back into scantable
|
---|
| 1363 | flagOut.resize(maskOut.nelements());
|
---|
| 1364 | convertArray(flagOut, maskOut);
|
---|
| 1365 | flagCol.put(i, flagOut);
|
---|
| 1366 | specCol.put(i, specOut);
|
---|
| 1367 | // start abcissa caching
|
---|
| 1368 | first = false;
|
---|
[917] | 1369 | }
|
---|
[926] | 1370 | // next timestamp
|
---|
| 1371 | ++timeiter;
|
---|
[917] | 1372 | }
|
---|
[940] | 1373 | // next FREQ_ID
|
---|
[926] | 1374 | ++fiter;
|
---|
[917] | 1375 | }
|
---|
| 1376 | // next aligner
|
---|
| 1377 | ++iter;
|
---|
| 1378 | }
|
---|
[940] | 1379 | // set this afterwards to ensure we are doing insitu correctly.
|
---|
| 1380 | out->frequencies().setFrame(system, true);
|
---|
[917] | 1381 | return out;
|
---|
| 1382 | }
|
---|
[992] | 1383 |
|
---|
| 1384 | CountedPtr<Scantable>
|
---|
| 1385 | asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
|
---|
| 1386 | const std::string & newtype )
|
---|
| 1387 | {
|
---|
| 1388 | if (in->npol() != 2 && in->npol() != 4)
|
---|
| 1389 | throw(AipsError("Can only convert two or four polarisations."));
|
---|
| 1390 | if ( in->getPolType() == newtype )
|
---|
| 1391 | throw(AipsError("No need to convert."));
|
---|
[1000] | 1392 | if ( ! in->selector_.empty() )
|
---|
| 1393 | throw(AipsError("Can only convert whole scantable. Unset the selection."));
|
---|
[992] | 1394 | bool insitu = insitu_;
|
---|
| 1395 | setInsitu(false);
|
---|
| 1396 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 1397 | setInsitu(insitu);
|
---|
| 1398 | Table& tout = out->table();
|
---|
| 1399 | tout.rwKeywordSet().define("POLTYPE", String(newtype));
|
---|
| 1400 |
|
---|
| 1401 | Block<String> cols(4);
|
---|
| 1402 | cols[0] = "SCANNO";
|
---|
| 1403 | cols[1] = "CYCLENO";
|
---|
| 1404 | cols[2] = "BEAMNO";
|
---|
| 1405 | cols[3] = "IFNO";
|
---|
| 1406 | TableIterator it(in->originalTable_, cols);
|
---|
| 1407 | String basetype = in->getPolType();
|
---|
| 1408 | STPol* stpol = STPol::getPolClass(in->factories_, basetype);
|
---|
| 1409 | try {
|
---|
| 1410 | while ( !it.pastEnd() ) {
|
---|
| 1411 | Table tab = it.table();
|
---|
| 1412 | uInt row = tab.rowNumbers()[0];
|
---|
| 1413 | stpol->setSpectra(in->getPolMatrix(row));
|
---|
| 1414 | Float fang,fhand,parang;
|
---|
| 1415 | fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row));
|
---|
| 1416 | fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
|
---|
| 1417 | parang = in->paraCol_(row);
|
---|
| 1418 | /// @todo re-enable this
|
---|
| 1419 | // disable total feed angle to support paralactifying Caswell style
|
---|
| 1420 | stpol->setPhaseCorrections(parang, -parang, fhand);
|
---|
| 1421 | Int npolout = 0;
|
---|
| 1422 | for (uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 1423 | Vector<Float> outvec = stpol->getSpectrum(i, newtype);
|
---|
| 1424 | if ( outvec.nelements() > 0 ) {
|
---|
| 1425 | tout.addRow();
|
---|
| 1426 | TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
|
---|
| 1427 | ArrayColumn<Float> sCol(tout,"SPECTRA");
|
---|
| 1428 | ScalarColumn<uInt> pCol(tout,"POLNO");
|
---|
| 1429 | sCol.put(tout.nrow()-1 ,outvec);
|
---|
| 1430 | pCol.put(tout.nrow()-1 ,uInt(npolout));
|
---|
| 1431 | npolout++;
|
---|
| 1432 | }
|
---|
| 1433 | }
|
---|
| 1434 | tout.rwKeywordSet().define("nPol", npolout);
|
---|
| 1435 | ++it;
|
---|
| 1436 | }
|
---|
| 1437 | } catch (AipsError& e) {
|
---|
| 1438 | delete stpol;
|
---|
| 1439 | throw(e);
|
---|
| 1440 | }
|
---|
| 1441 | delete stpol;
|
---|
| 1442 | return out;
|
---|
| 1443 | }
|
---|
[1066] | 1444 |
|
---|
[1143] | 1445 | CountedPtr< Scantable >
|
---|
[1140] | 1446 | asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
|
---|
| 1447 | const std::string & scantype )
|
---|
| 1448 | {
|
---|
| 1449 | bool insitu = insitu_;
|
---|
| 1450 | setInsitu(false);
|
---|
| 1451 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 1452 | setInsitu(insitu);
|
---|
| 1453 | Table& tout = out->table();
|
---|
| 1454 | std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
|
---|
| 1455 | if (scantype == "on") {
|
---|
| 1456 | taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
|
---|
| 1457 | }
|
---|
| 1458 | Table tab = tableCommand(taql, in->table());
|
---|
| 1459 | TableCopy::copyRows(tout, tab);
|
---|
| 1460 | if (scantype == "on") {
|
---|
[1143] | 1461 | // re-index SCANNO to 0
|
---|
[1140] | 1462 | TableVector<uInt> vec(tout, "SCANNO");
|
---|
| 1463 | vec = 0;
|
---|
| 1464 | }
|
---|
| 1465 | return out;
|
---|
| 1466 | }
|
---|
[1192] | 1467 |
|
---|
| 1468 | CountedPtr< Scantable >
|
---|
| 1469 | asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
|
---|
[1200] | 1470 | double frequency, double width )
|
---|
[1192] | 1471 | {
|
---|
| 1472 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 1473 | Table& tout = out->table();
|
---|
| 1474 | TableIterator iter(tout, "FREQ_ID");
|
---|
| 1475 | FFTServer<Float,Complex> ffts;
|
---|
| 1476 | while ( !iter.pastEnd() ) {
|
---|
| 1477 | Table tab = iter.table();
|
---|
| 1478 | Double rp,rv,inc;
|
---|
| 1479 | ROTableRow row(tab);
|
---|
| 1480 | const TableRecord& rec = row.get(0);
|
---|
| 1481 | uInt freqid = rec.asuInt("FREQ_ID");
|
---|
| 1482 | out->frequencies().getEntry(rp, rv, inc, freqid);
|
---|
| 1483 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 1484 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 1485 | for (int i=0; i<int(tab.nrow()); ++i) {
|
---|
| 1486 | Vector<Float> spec = specCol(i);
|
---|
| 1487 | Vector<uChar> flag = flagCol(i);
|
---|
[1200] | 1488 | Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5);
|
---|
| 1489 | Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5);
|
---|
[1192] | 1490 | for (int k=0; k < flag.nelements(); ++k ) {
|
---|
| 1491 | if (flag[k] > 0) {
|
---|
| 1492 | spec[k] = 0.0;
|
---|
| 1493 | }
|
---|
| 1494 | }
|
---|
| 1495 | Vector<Complex> lags;
|
---|
[1203] | 1496 | ffts.fft0(lags, spec);
|
---|
[1200] | 1497 | Int start = max(0, lag0);
|
---|
| 1498 | Int end = min(Int(lags.nelements()-1), lag1);
|
---|
[1192] | 1499 | if (start == end) {
|
---|
| 1500 | lags[start] = Complex(0.0);
|
---|
| 1501 | } else {
|
---|
| 1502 | for (int j=start; j <=end ;++j) {
|
---|
| 1503 | lags[j] = Complex(0.0);
|
---|
| 1504 | }
|
---|
| 1505 | }
|
---|
[1203] | 1506 | ffts.fft0(spec, lags);
|
---|
[1192] | 1507 | specCol.put(i, spec);
|
---|
| 1508 | }
|
---|
| 1509 | ++iter;
|
---|
| 1510 | }
|
---|
| 1511 | return out;
|
---|
| 1512 | }
|
---|