source: trunk/src/Scantable.cpp @ 804

Last change on this file since 804 was 804, checked in by mar637, 18 years ago

File renming to reflect major changes in asap2.
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1//#---------------------------------------------------------------------------
2//# SDMemTable.cc: A MemoryTable container for single dish integrations
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//#        Internet email: Malte.Marquarding@csiro.au
23//#        Postal address: Malte Marquarding,
24//#                        Australia Telescope National Facility,
25//#                        P.O. Box 76,
26//#                        Epping, NSW, 2121,
27//#                        AUSTRALIA
28//#
29//# $Id:
30//#---------------------------------------------------------------------------
31
32#include <map>
33
34#include <casa/aips.h>
35#include <casa/iostream.h>
36#include <casa/iomanip.h>
37#include <casa/Arrays/Array.h>
38#include <casa/Arrays/ArrayMath.h>
39#include <casa/Arrays/MaskArrMath.h>
40#include <casa/Arrays/ArrayLogical.h>
41#include <casa/Arrays/ArrayAccessor.h>
42#include <casa/Arrays/VectorSTLIterator.h>
43#include <casa/Arrays/Vector.h>
44#include <casa/BasicMath/Math.h>
45#include <casa/BasicSL/Constants.h>
46#include <casa/Quanta/MVAngle.h>
47
48#include <tables/Tables/TableParse.h>
49#include <tables/Tables/TableDesc.h>
50#include <tables/Tables/TableCopy.h>
51#include <tables/Tables/SetupNewTab.h>
52#include <tables/Tables/ScaColDesc.h>
53#include <tables/Tables/ArrColDesc.h>
54
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/TableRecord.h>
57#include <measures/Measures/MFrequency.h>
58#include <measures/Measures/MeasTable.h>
59#include <coordinates/Coordinates/CoordinateUtil.h>
60#include <casa/Quanta/MVTime.h>
61#include <casa/Quanta/MVAngle.h>
62
63#include "SDDefs.h"
64#include "SDContainer.h"
65#include "MathUtils.h"
66#include "SDPol.h"
67#include "SDAttr.h"
68
69#include "SDMemTable.h"
70
71using namespace casa;
72using namespace asap;
73
74SDMemTable::SDMemTable() :
75  IFSel_(0),
76  beamSel_(0),
77  polSel_(0)
78{
79  setup();
80  attach();
81}
82
83SDMemTable::SDMemTable(const std::string& name) :
84  IFSel_(0),
85  beamSel_(0),
86  polSel_(0)
87{
88  Table tab(name);
89  Int version;
90  tab.keywordSet().get("VERSION", version);
91  if (version != version_) {
92    throw(AipsError("Unsupported version of ASAP file."));
93  }
94  table_ = tab.copyToMemoryTable("dummy");
95  attach();
96}
97
98SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
99{
100  table_ = other.table_.copyToMemoryTable(String("dummy"));
101  // clear all rows()
102  if (clear) {
103    table_.removeRow(this->table_.rowNumbers());
104    IFSel_= 0;
105    beamSel_= 0;
106    polSel_= 0;
107  } else {
108    IFSel_= other.IFSel_;
109    beamSel_= other.beamSel_;
110    polSel_= other.polSel_;
111  }
112
113  attach();
114}
115
116SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
117  IFSel_(0),
118  beamSel_(0),
119  polSel_(0)
120{
121  Table t = tableCommand(exprs,tab);
122  if (t.nrow() == 0)
123      throw(AipsError("Query unsuccessful."));
124  table_ = t.copyToMemoryTable("dummy");
125  attach();
126  renumber();
127}
128
129SDMemTable::~SDMemTable()
130{
131  //cerr << "goodbye from SDMemTable @ " << this << endl;
132}
133
134SDMemTable SDMemTable::getScan(Int scanID) const
135{
136  String cond("SELECT * from $1 WHERE SCANID == ");
137  cond += String::toString(scanID);
138  return SDMemTable(table_, cond);
139}
140
141SDMemTable &SDMemTable::operator=(const SDMemTable& other)
142{
143  if (this != &other) {
144     IFSel_= other.IFSel_;
145     beamSel_= other.beamSel_;
146     polSel_= other.polSel_;
147     table_ = other.table_.copyToMemoryTable(String("dummy"));
148     attach();
149  }
150  return *this;
151}
152
153SDMemTable SDMemTable::getSource(const std::string& source) const
154{
155  String cond("SELECT * from $1 WHERE SRCNAME == ");
156  cond += source;
157  return SDMemTable(table_, cond);
158}
159
160void SDMemTable::setup()
161{
162  TableDesc td("", "1", TableDesc::Scratch);
163  td.comment() = "A SDMemTable";
164  td.rwKeywordSet().define("VERSION", Int(version_));
165
166  td.addColumn(ScalarColumnDesc<Double>("TIME"));
167  td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
168  td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
169  td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
170  td.addColumn(ArrayColumnDesc<Float>("TSYS"));
171  td.addColumn(ArrayColumnDesc<Float>("STOKES"));
172  td.addColumn(ScalarColumnDesc<Int>("SCANID"));
173  td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
174  td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
175  td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
176  td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
177  td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
178  td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
179  td.addColumn(ArrayColumnDesc<Float>("TCAL"));
180  td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
181  td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
182  td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
183  td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
184  td.addColumn(ArrayColumnDesc<Int>("FITID"));
185
186  // Now create Table SetUp from the description.
187  SetupNewTable aNewTab("dummy", td, Table::New);
188
189  // Bind the Stokes Virtual machine to the STOKES column Because we
190  // don't know how many polarizations will be in the data at this
191  // point, we must bind the Virtual Engine regardless.  The STOKES
192  // column won't be accessed if not appropriate (nPol=4)
193  SDStokesEngine::registerClass();
194  SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
195  aNewTab.bindColumn("STOKES", stokesEngine);
196
197  // Create Table
198  table_ = Table(aNewTab, Table::Memory, 0);
199  // add subtable
200  TableDesc tdf("", "1", TableDesc::Scratch);
201  tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
202  tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
203  tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
204  tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
205  tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
206  SetupNewTable fittab("fits", tdf, Table::New);
207  Table fitTable(fittab, Table::Memory);
208  table_.rwKeywordSet().defineTable("FITS", fitTable);
209
210  TableDesc tdh("", "1", TableDesc::Scratch);
211  tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
212  SetupNewTable histtab("hist", tdh, Table::New);
213  Table histTable(histtab, Table::Memory);
214  table_.rwKeywordSet().defineTable("HISTORY", histTable);
215}
216
217void SDMemTable::attach()
218{
219  timeCol_.attach(table_, "TIME");
220  srcnCol_.attach(table_, "SRCNAME");
221  specCol_.attach(table_, "SPECTRA");
222  flagsCol_.attach(table_, "FLAGTRA");
223  tsCol_.attach(table_, "TSYS");
224  stokesCol_.attach(table_, "STOKES");
225  scanCol_.attach(table_, "SCANID");
226  integrCol_.attach(table_, "INTERVAL");
227  freqidCol_.attach(table_, "FREQID");
228  restfreqidCol_.attach(table_, "RESTFREQID");
229  dirCol_.attach(table_, "DIRECTION");
230  fldnCol_.attach(table_, "FIELDNAME");
231  tcaltCol_.attach(table_, "TCALTIME");
232  tcalCol_.attach(table_, "TCAL");
233  azCol_.attach(table_, "AZIMUTH");
234  elCol_.attach(table_, "ELEVATION");
235  paraCol_.attach(table_, "PARANGLE");
236  rbeamCol_.attach(table_, "REFBEAM");
237  fitCol_.attach(table_,"FITID");
238}
239
240
241std::string SDMemTable::getSourceName(Int whichRow) const
242{
243  String name;
244  srcnCol_.get(whichRow, name);
245  return name;
246}
247
248float SDMemTable::getElevation(Int whichRow) const
249{
250  float elevation;
251  elCol_.get(whichRow, elevation);
252  return elevation;
253}
254
255float SDMemTable::getAzimuth(Int whichRow) const
256{
257  float azimuth;
258  azCol_.get(whichRow, azimuth);
259  return azimuth;
260}
261
262float SDMemTable::getParAngle(Int whichRow) const
263{
264  float parangle;
265  paraCol_.get(whichRow, parangle);
266  return parangle;
267}
268
269std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
270{
271  Double tm;
272  if (whichRow > -1) {
273    timeCol_.get(whichRow, tm);
274  } else {
275    table_.keywordSet().get("UTC",tm);
276  }
277  MVTime mvt(tm);
278  if (showDate)
279    mvt.setFormat(MVTime::YMD);
280  else
281    mvt.setFormat(MVTime::TIME);
282  ostringstream oss;
283  oss << mvt;
284  return String(oss);
285}
286
287double SDMemTable::getInterval(Int whichRow) const
288{
289  Double intval;
290  integrCol_.get(whichRow, intval);
291  return intval;
292}
293
294bool SDMemTable::setIF(Int whichIF)
295{
296  if ( whichIF >= 0 && whichIF < nIF()) {
297    IFSel_ = whichIF;
298    return true;
299  }
300  return false;
301}
302
303bool SDMemTable::setBeam(Int whichBeam)
304{
305  if ( whichBeam >= 0 && whichBeam < nBeam()) {
306    beamSel_ = whichBeam;
307    return true;
308  }
309  return false;
310}
311
312bool SDMemTable::setPol(Int whichPol)
313{
314  if ( whichPol >= 0 && whichPol < nPol()) {
315    polSel_ = whichPol;
316    return true;
317  }
318  return false;
319}
320
321void SDMemTable::resetCursor()
322{
323   polSel_ = 0;
324   IFSel_ = 0;
325   beamSel_ = 0;
326}
327
328std::vector<bool> SDMemTable::getMask(Int whichRow) const
329{
330
331  std::vector<bool> mask;
332
333  Array<uChar> arr;
334  flagsCol_.get(whichRow, arr);
335
336  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
337  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
338  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
339  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
340  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
341  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
342
343  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
344    bool out =!static_cast<bool>(*i);
345    mask.push_back(out);
346  }
347  return mask;
348}
349
350
351
352std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
353{
354  Array<Float> arr;
355  specCol_.get(whichRow, arr);
356  return getFloatSpectrum(arr);
357}
358
359
360int SDMemTable::nStokes() const
361{
362   return stokesCol_.shape(0).nelements();        // All rows same shape
363}
364
365
366std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow,
367                                                 Bool doPol) const
368  //
369  // Gets one STokes parameter depending on cursor polSel location
370  //  doPol=False  : I,Q,U,V
371  //  doPol=True   : I,P,PA,V   ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
372  //
373{
374  AlwaysAssert(asap::nAxes==4,AipsError);
375  if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
376    throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
377  }
378
379  // For full conversion we are only supporting linears at the moment
380
381  if (nPol() > 2) {
382    String antName;
383    table_.keywordSet().get("AntennaName", antName);
384    Instrument inst = SDAttr::convertInstrument (antName, True);
385    SDAttr sdAtt;
386    if (sdAtt.feedPolType(inst) != LINEAR) {
387      throw(AipsError("Only linear polarizations are supported"));
388    }
389  }
390
391  Array<Float> arr;
392  stokesCol_.get(whichRow, arr);
393
394  if (doPol && (polSel_==1 || polSel_==2)) {       //   Q,U --> P, P.A.
395
396    // Set current cursor location
397
398    const IPosition& shape = arr.shape();
399    IPosition start, end;
400    getCursorSlice(start, end, shape);
401
402    // Get Q and U slices
403
404    Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
405    Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
406
407    // Compute output
408
409    Array<Float> out;
410    if (polSel_==1) {                                        // P
411      out = SDPolUtil::polarizedIntensity(Q,U);
412    } else if (polSel_==2) {                                 // P.A.
413      out = SDPolUtil::positionAngle(Q,U);
414    }
415
416    // Copy to output
417
418    IPosition vecShape(1,shape(asap::ChanAxis));
419    Vector<Float> outV = out.reform(vecShape);
420    std::vector<float> stlout;
421    outV.tovector(stlout);
422    return stlout;
423
424  } else {
425    // Selects at the cursor location
426    return getFloatSpectrum(arr);
427  }
428}
429
430std::string SDMemTable::getPolarizationLabel(Bool linear, Bool stokes,
431                                              Bool linPol, Int polIdx) const
432{
433   uInt idx = polSel_;
434   if (polIdx >=0) idx = polIdx;
435   return SDPolUtil::polarizationLabel(idx, linear, stokes, linPol);
436}
437
438
439
440std::vector<float> SDMemTable::stokesToPolSpectrum(Int whichRow,
441                                                   Bool toLinear,
442                                                   Int polIdx) const
443//
444// polIdx
445//   0:3 -> RR,LL,Real(RL),Imag(RL)
446//          XX,YY,Real(XY),Image(XY)
447//
448// Gets only
449//  RR = I + V
450//  LL = I - V
451// at the moment
452//
453{
454  AlwaysAssert(asap::nAxes==4,AipsError);
455  if (nStokes()!=4) {
456     throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
457  }
458//
459  Array<Float> arr, out;
460  stokesCol_.get(whichRow, arr);
461
462// Set current cursor location
463
464  const IPosition& shape = arr.shape();
465  IPosition start, end;
466  getCursorSlice(start, end, shape);
467
468// Get the slice
469
470  if (toLinear) {
471     throw(AipsError("Conversion to linears not yet supported"));
472  } else {
473    uInt selection = polSel_;
474    if (polIdx > -1) selection = polIdx;
475    Bool doRR = (selection==0);
476    if (selection>1) {
477      throw(AipsError("Only conversion to RR & LL is currently supported"));
478    }
479
480    // Get I and V slices
481    Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
482    Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
483
484    // Compute output
485    out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
486  }
487
488  // Copy to output
489   IPosition vecShape(1,shape(asap::ChanAxis));
490   Vector<Float> outV = out.reform(vecShape);
491   std::vector<float> stlout;
492   outV.tovector(stlout);
493//
494   return stlout;
495}
496
497
498
499
500Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
501{
502
503// Get data
504
505  Array<Float> arr;
506  stokesCol_.get(whichRow, arr);
507
508// Set current cursor location and overwrite polarization axis
509
510  const IPosition& shape = arr.shape();
511  IPosition start(shape.nelements(),0);
512  IPosition end(shape-1);
513  if (iBeam!=-1) {
514     start(asap::BeamAxis) = iBeam;
515     end(asap::BeamAxis) = iBeam;
516  }
517  if (iIF!=-1) {
518     start(asap::IFAxis) = iIF;
519     end(asap::IFAxis) = iIF;
520  }
521
522// Get slice
523
524  return arr(start,end);
525}
526
527
528std::vector<string> SDMemTable::getCoordInfo() const
529{
530  String un;
531  Table t = table_.keywordSet().asTable("FREQUENCIES");
532  String sunit;
533  t.keywordSet().get("UNIT",sunit);
534  String dpl;
535  t.keywordSet().get("DOPPLER",dpl);
536  if (dpl == "") dpl = "RADIO";
537  String rfrm;
538  t.keywordSet().get("REFFRAME",rfrm);
539  std::vector<string> inf;
540  inf.push_back(sunit);
541  inf.push_back(rfrm);
542  inf.push_back(dpl);
543  t.keywordSet().get("BASEREFFRAME",rfrm);
544  inf.push_back(rfrm);
545  return inf;
546}
547
548void SDMemTable::setCoordInfo(std::vector<string> theinfo)
549{
550  std::vector<string>::iterator it;
551  String un,rfrm, brfrm,dpl;
552  un = theinfo[0];              // Abcissa unit
553  rfrm = theinfo[1];            // Active (or conversion) frame
554  dpl = theinfo[2];             // Doppler
555  brfrm = theinfo[3];           // Base frame
556  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
557
558  Vector<Double> rstf;
559  t.keywordSet().get("RESTFREQS",rstf);
560
561  Bool canDo = True;
562  Unit u1("km/s");Unit u2("Hz");
563  if (Unit(un) == u1) {
564    Vector<Double> rstf;
565    t.keywordSet().get("RESTFREQS",rstf);
566    if (rstf.nelements() == 0) {
567        throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
568    }
569  } else if (Unit(un) != u2 && un != "") {
570        throw(AipsError("Unit not conformant with Spectral Coordinates"));
571  }
572  t.rwKeywordSet().define("UNIT", un);
573
574  MFrequency::Types mdr;
575  if (!MFrequency::getType(mdr, rfrm)) {
576
577    Int a,b;const uInt* c;
578    const String* valid = MFrequency::allMyTypes(a, b, c);
579    String pfix = "Please specify a legal frame type. Types are\n";
580    throw(AipsError(pfix+(*valid)));
581  } else {
582    t.rwKeywordSet().define("REFFRAME",rfrm);
583  }
584
585  MDoppler::Types dtype;
586  dpl.upcase();
587  if (!MDoppler::getType(dtype, dpl)) {
588    throw(AipsError("Doppler type unknown"));
589  } else {
590    t.rwKeywordSet().define("DOPPLER",dpl);
591  }
592
593  if (!MFrequency::getType(mdr, brfrm)) {
594     Int a,b;const uInt* c;
595     const String* valid = MFrequency::allMyTypes(a, b, c);
596     String pfix = "Please specify a legal frame type. Types are\n";
597     throw(AipsError(pfix+(*valid)));
598   } else {
599    t.rwKeywordSet().define("BASEREFFRAME",brfrm);
600   }
601}
602
603
604std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
605{
606  std::vector<double> abc(nChan());
607
608  // Get header units keyword
609  Table t = table_.keywordSet().asTable("FREQUENCIES");
610  String sunit;
611  t.keywordSet().get("UNIT",sunit);
612  if (sunit == "") sunit = "pixel";
613  Unit u(sunit);
614
615  // Easy if just wanting pixels
616  if (sunit==String("pixel")) {
617    // assume channels/pixels
618    std::vector<double>::iterator it;
619    uInt i=0;
620    for (it = abc.begin(); it != abc.end(); ++it) {
621      (*it) = Double(i++);
622    }
623    return abc;
624  }
625
626  // Continue with km/s or Hz.  Get FreqIDs
627  Vector<uInt> freqIDs;
628  freqidCol_.get(whichRow, freqIDs);
629  uInt freqID = freqIDs(IFSel_);
630  restfreqidCol_.get(whichRow, freqIDs);
631  uInt restFreqID = freqIDs(IFSel_);
632
633  // Get SpectralCoordinate, set reference frame conversion,
634  // velocity conversion, and rest freq state
635
636  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
637  Vector<Double> pixel(nChan());
638  indgen(pixel);
639
640  if (u == Unit("km/s")) {
641     Vector<Double> world;
642     spc.pixelToVelocity(world,pixel);
643     std::vector<double>::iterator it;
644     uInt i = 0;
645     for (it = abc.begin(); it != abc.end(); ++it) {
646       (*it) = world[i];
647       i++;
648     }
649  } else if (u == Unit("Hz")) {
650
651    // Set world axis units
652    Vector<String> wau(1); wau = u.getName();
653    spc.setWorldAxisUnits(wau);
654
655    std::vector<double>::iterator it;
656    Double tmp;
657    uInt i = 0;
658    for (it = abc.begin(); it != abc.end(); ++it) {
659      spc.toWorld(tmp,pixel[i]);
660      (*it) = tmp;
661      i++;
662    }
663  }
664  return abc;
665}
666
667std::string SDMemTable::getAbcissaString(Int whichRow) const
668{
669  Table t = table_.keywordSet().asTable("FREQUENCIES");
670
671  String sunit;
672  t.keywordSet().get("UNIT",sunit);
673  if (sunit == "") sunit = "pixel";
674  Unit u(sunit);
675
676  Vector<uInt> freqIDs;
677  freqidCol_.get(whichRow, freqIDs);
678  uInt freqID = freqIDs(IFSel_);
679  restfreqidCol_.get(whichRow, freqIDs);
680  uInt restFreqID = freqIDs(IFSel_);
681
682  // Get SpectralCoordinate, with frame, velocity, rest freq state set
683  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
684
685  String s = "Channel";
686  if (u == Unit("km/s")) {
687    s = CoordinateUtil::axisLabel(spc,0,True,True,True);
688  } else if (u == Unit("Hz")) {
689    Vector<String> wau(1);wau = u.getName();
690    spc.setWorldAxisUnits(wau);
691
692    s = CoordinateUtil::axisLabel(spc,0,True,True,False);
693  }
694  return s;
695}
696
697void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
698{
699  Array<Float> arr;
700  specCol_.get(whichRow, arr);
701  if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
702    throw(AipsError("Attempting to set spectrum with incorrect length."));
703  }
704
705  // Setup accessors
706  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
707  aa0.reset(aa0.begin(uInt(beamSel_)));                   // Beam selection
708  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
709  aa1.reset(aa1.begin(uInt(IFSel_)));                     // IF selection
710  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
711  aa2.reset(aa2.begin(uInt(polSel_)));                    // Pol selection
712
713  // Iterate
714  std::vector<float>::iterator it = spectrum.begin();
715  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
716    (*i) = Float(*it);
717    it++;
718  }
719  specCol_.put(whichRow, arr);
720}
721
722void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
723{
724  Array<Float> arr;
725  specCol_.get(whichRow, arr);
726
727  // Iterate and extract
728  spectrum.resize(arr.shape()(3));
729  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
730  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
731  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
732  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
733  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
734  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
735
736  ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
737  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
738    (*va) = (*i);
739    va++;
740  }
741}
742
743
744/*
745void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
746  Array<uChar> arr;
747  flagsCol_.get(whichRow, arr);
748  mask.resize(arr.shape()(3));
749
750  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
751  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
752  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
753  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
754  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
755  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
756
757  Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
758
759  ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
760  std::vector<bool> tmp;
761  tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
762                   // iterator should work on chanMask_??
763  std::vector<bool>::iterator miter;
764  miter = tmp.begin();
765
766  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
767    bool out =!static_cast<bool>(*i);
768    if (useUserMask) {
769      out = out && (*miter);
770      miter++;
771    }
772    (*va) = out;
773    va++;
774  }
775}
776*/
777
778MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
779                                                Bool toStokes) const
780{
781  // Get flags
782  Array<uChar> farr;
783  flagsCol_.get(whichRow, farr);
784
785  // Get data and convert mask to Bool
786  Array<Float> arr;
787  Array<Bool> mask;
788  if (toStokes) {
789     stokesCol_.get(whichRow, arr);
790
791     Array<Bool> tMask(farr.shape());
792     convertArray(tMask, farr);
793     mask = SDPolUtil::stokesData (tMask, True);
794  } else {
795     specCol_.get(whichRow, arr);
796     mask.resize(farr.shape());
797     convertArray(mask, farr);
798  }
799
800  return MaskedArray<Float>(arr,!mask);
801}
802
803Float SDMemTable::getTsys(Int whichRow) const
804{
805  Array<Float> arr;
806  tsCol_.get(whichRow, arr);
807  Float out;
808
809  IPosition ip(arr.shape());
810  ip(asap::BeamAxis) = beamSel_;
811  ip(asap::IFAxis) = IFSel_;
812  ip(asap::PolAxis) = polSel_;
813  ip(asap::ChanAxis)=0;               // First channel only
814
815  out = arr(ip);
816  return out;
817}
818
819MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
820{
821  MDirection::Types mdr = getDirectionReference();
822  Array<Double> posit;
823  dirCol_.get(whichRow,posit);
824  Vector<Double> wpos(2);
825  Int rb;
826  rbeamCol_.get(whichRow,rb);
827  wpos[0] = posit(IPosition(2,beamSel_,0));
828  wpos[1] = posit(IPosition(2,beamSel_,1));
829  if (refBeam && rb > -1) {  // use refBeam instead if it exists
830    wpos[0] = posit(IPosition(2,rb,0));
831    wpos[1] = posit(IPosition(2,rb,1));
832  }
833
834  Quantum<Double> lon(wpos[0],Unit(String("rad")));
835  Quantum<Double> lat(wpos[1],Unit(String("rad")));
836  return MDirection(lon, lat, mdr);
837}
838
839MEpoch SDMemTable::getEpoch(Int whichRow) const
840{
841  MEpoch::Types met = getTimeReference();
842
843  Double obstime;
844  timeCol_.get(whichRow,obstime);
845  MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
846  return MEpoch(tm2, met);
847}
848
849MPosition SDMemTable::getAntennaPosition () const
850{
851  Vector<Double> antpos;
852  table_.keywordSet().get("AntennaPosition", antpos);
853  MVPosition mvpos(antpos(0),antpos(1),antpos(2));
854  return MPosition(mvpos);
855}
856
857
858SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
859{
860
861  Table t = table_.keywordSet().asTable("FREQUENCIES");
862  if (freqID> t.nrow() ) {
863    throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
864  }
865
866  Double rp,rv,inc;
867  String rf;
868  ROScalarColumn<Double> rpc(t, "REFPIX");
869  ROScalarColumn<Double> rvc(t, "REFVAL");
870  ROScalarColumn<Double> incc(t, "INCREMENT");
871  t.keywordSet().get("BASEREFFRAME",rf);
872
873  // Create SpectralCoordinate (units Hz)
874  MFrequency::Types mft;
875  if (!MFrequency::getType(mft, rf)) {
876    ostringstream oss;
877    pushLog("WARNING: Frequency type unknown assuming TOPO");
878    mft = MFrequency::TOPO;
879  }
880  rpc.get(freqID, rp);
881  rvc.get(freqID, rv);
882  incc.get(freqID, inc);
883
884  SpectralCoordinate spec(mft,rv,inc,rp);
885  return spec;
886}
887
888
889SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
890                                                     uInt restFreqID,
891                                                     uInt whichRow) const
892{
893
894  // Create basic SC
895  SpectralCoordinate spec = getSpectralCoordinate (freqID);
896
897  Table t = table_.keywordSet().asTable("FREQUENCIES");
898
899  // Set rest frequency
900  Vector<Double> restFreqIDs;
901  t.keywordSet().get("RESTFREQS",restFreqIDs);
902  if (restFreqID < restFreqIDs.nelements()) {    // Should always be true
903    spec.setRestFrequency(restFreqIDs(restFreqID),True);
904  }
905
906  // Set up frame conversion layer
907  String frm;
908  t.keywordSet().get("REFFRAME",frm);
909  if (frm == "") frm = "TOPO";
910  MFrequency::Types mtype;
911  if (!MFrequency::getType(mtype, frm)) {
912    // Should never happen
913    pushLog("WARNING: Frequency type unknown assuming TOPO");
914    mtype = MFrequency::TOPO;
915  }
916
917  // Set reference frame conversion  (requires row)
918  MDirection dir = getDirection(whichRow);
919  MEpoch epoch = getEpoch(whichRow);
920  MPosition pos = getAntennaPosition();
921
922  if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
923    throw(AipsError("Couldn't convert frequency frame."));
924  }
925
926  // Now velocity conversion if appropriate
927  String unitStr;
928  t.keywordSet().get("UNIT",unitStr);
929
930  String dpl;
931  t.keywordSet().get("DOPPLER",dpl);
932  MDoppler::Types dtype;
933  MDoppler::getType(dtype, dpl);
934
935  // Only set velocity unit if non-blank and non-Hz
936  if (!unitStr.empty()) {
937     Unit unitU(unitStr);
938     if (unitU==Unit("Hz")) {
939     } else {
940        spec.setVelocity(unitStr, dtype);
941     }
942  }
943
944  return spec;
945}
946
947
948Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
949                               uInt freqID) {
950  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
951  if (freqID > t.nrow() ) {
952    throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
953  }
954  ScalarColumn<Double> rpc(t, "REFPIX");
955  ScalarColumn<Double> rvc(t, "REFVAL");
956  ScalarColumn<Double> incc(t, "INCREMENT");
957
958  rpc.put(freqID, speccord.referencePixel()[0]);
959  rvc.put(freqID, speccord.referenceValue()[0]);
960  incc.put(freqID, speccord.increment()[0]);
961
962  return True;
963}
964
965Int SDMemTable::nCoordinates() const
966{
967  return table_.keywordSet().asTable("FREQUENCIES").nrow();
968}
969
970
971std::vector<double> SDMemTable::getRestFreqs() const
972{
973  Table t = table_.keywordSet().asTable("FREQUENCIES");
974  Vector<Double> tvec;
975  t.keywordSet().get("RESTFREQS",tvec);
976  std::vector<double> stlout;
977  tvec.tovector(stlout);
978  return stlout;
979}
980
981bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
982{
983  TableDesc td("", "1", TableDesc::Scratch);
984  td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
985  td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
986  td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
987  SetupNewTable aNewTab("freqs", td, Table::New);
988  Table aTable (aNewTab, Table::Memory, sdft.length());
989  ScalarColumn<Double> sc0(aTable, "REFPIX");
990  ScalarColumn<Double> sc1(aTable, "REFVAL");
991  ScalarColumn<Double> sc2(aTable, "INCREMENT");
992  for (uInt i=0; i < sdft.length(); ++i) {
993    sc0.put(i,sdft.referencePixel(i));
994    sc1.put(i,sdft.referenceValue(i));
995    sc2.put(i,sdft.increment(i));
996  }
997  String rf = sdft.refFrame();
998  if (rf.contains("TOPO")) rf = "TOPO";
999  String brf = sdft.baseRefFrame();
1000  if (brf.contains("TOPO")) brf = "TOPO";
1001
1002  aTable.rwKeywordSet().define("BASEREFFRAME", brf);
1003  aTable.rwKeywordSet().define("REFFRAME", rf);
1004  aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
1005  aTable.rwKeywordSet().define("UNIT", sdft.unit());
1006  aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
1007  Vector<Double> rfvec;
1008  String rfunit;
1009  sdft.restFrequencies(rfvec,rfunit);
1010  Quantum<Vector<Double> > q(rfvec, rfunit);
1011  rfvec.resize();
1012  rfvec = q.getValue("Hz");
1013  aTable.rwKeywordSet().define("RESTFREQS", rfvec);
1014  table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
1015  return true;
1016}
1017
1018bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
1019{
1020  TableDesc td("", "1", TableDesc::Scratch);
1021  td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1022  td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1023  td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1024  td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1025  td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1026  SetupNewTable aNewTab("fits", td, Table::New);
1027  Table aTable(aNewTab, Table::Memory);
1028  ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1029  ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1030  ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1031  ArrayColumn<Bool> sc3(aTable, "PARMASK");
1032  ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1033  for (uInt i; i<sdft.length(); ++i) {
1034    const Vector<Double>& parms = sdft.getParameters(i);
1035    const Vector<Bool>& parmask = sdft.getParameterMask(i);
1036    const Vector<String>& funcs = sdft.getFunctions(i);
1037    const Vector<Int>& comps = sdft.getComponents(i);
1038    const Vector<String>& finfo = sdft.getFrameInfo(i);
1039    sc0.put(i,funcs);
1040    sc1.put(i,comps);
1041    sc3.put(i,parmask);
1042    sc2.put(i,parms);
1043    sc4.put(i,finfo);
1044  }
1045  table_.rwKeywordSet().defineTable("FITS", aTable);
1046  return true;
1047}
1048
1049SDFitTable SDMemTable::getSDFitTable() const
1050{
1051  const Table& t = table_.keywordSet().asTable("FITS");
1052  Vector<Double> parms;
1053  Vector<Bool> parmask;
1054  Vector<String> funcs;
1055  Vector<String> finfo;
1056  Vector<Int> comps;
1057  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1058  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1059  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1060  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1061  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1062  uInt n = t.nrow();
1063  SDFitTable sdft;
1064  for (uInt i=0; i<n; ++i) {
1065    parmaskCol.get(i, parmask);
1066    parmsCol.get(i, parms);
1067    funcsCol.get(i, funcs);
1068    compsCol.get(i, comps);
1069    finfoCol.get(i, finfo);
1070    sdft.addFit(parms, parmask, funcs, comps, finfo);
1071  }
1072  return sdft;
1073}
1074
1075SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1076  const Table& t = table_.keywordSet().asTable("FITS");
1077  if (t.nrow() == 0 || whichRow >= t.nrow()) return SDFitTable();
1078  Array<Int> fitid;
1079  fitCol_.get(whichRow, fitid);
1080  if (fitid.nelements() == 0) return SDFitTable();
1081
1082  IPosition shp = fitid.shape();
1083  IPosition start(4, beamSel_, IFSel_, polSel_,0);
1084  IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1085
1086  // reform the output array slice to be of dim=1
1087  Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1088
1089  Vector<Double> parms;
1090  Vector<Bool> parmask;
1091  Vector<String> funcs;
1092  Vector<String> finfo;
1093  Vector<Int> comps;
1094  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1095  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1096  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1097  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1098  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1099  SDFitTable sdft;
1100  Int k=-1;
1101  for (uInt i=0; i< tmp.nelements(); ++i) {
1102    k = tmp[i];
1103    if ( k > -1 && k < t.nrow() ) {
1104      parms.resize();
1105      parmsCol.get(k, parms);
1106      parmask.resize();
1107      parmaskCol.get(k, parmask);
1108      funcs.resize();
1109      funcsCol.get(k, funcs);
1110      comps.resize();
1111      compsCol.get(k, comps);
1112      finfo.resize();
1113      finfoCol.get(k, finfo);
1114      sdft.addFit(parms, parmask, funcs, comps, finfo);
1115    }
1116  }
1117  return sdft;
1118}
1119
1120void SDMemTable::addFit(uInt whichRow,
1121                        const Vector<Double>& p, const Vector<Bool>& m,
1122                        const Vector<String>& f, const Vector<Int>& c)
1123{
1124  if (whichRow >= nRow()) {
1125    throw(AipsError("Specified row out of range"));
1126  }
1127  Table t = table_.keywordSet().asTable("FITS");
1128  uInt nrow = t.nrow();
1129  t.addRow();
1130  ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1131  ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1132  ArrayColumn<Int> compsCol(t, "COMPONENTS");
1133  ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1134  ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1135  parmsCol.put(nrow, p);
1136  parmaskCol.put(nrow, m);
1137  compsCol.put(nrow, c);
1138  funcsCol.put(nrow, f);
1139  Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1140  finfoCol.put(nrow, fi);
1141
1142  Array<Int> fitarr;
1143  fitCol_.get(whichRow, fitarr);
1144
1145  Array<Int> newarr;               // The new Array containing the fitid
1146  Int pos =-1;                     // The fitid position in the array
1147  if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1148    Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1149    arr = -1;
1150    newarr.reference(arr);
1151    pos = 0;
1152  } else {
1153    IPosition shp = fitarr.shape();
1154    IPosition start(4, beamSel_, IFSel_, polSel_,0);
1155    IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1156    // reform the output array slice to be of dim=1
1157    Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1158    const Vector<Int>& fits = tmp;
1159    VectorSTLIterator<Int> it(fits);
1160    Int i = 0;
1161    while (it != fits.end()) {
1162      if (*it == -1) {
1163        pos = i;
1164        break;
1165      }
1166      ++i;
1167      ++it;
1168    };
1169  }
1170  if (pos == -1) {
1171      mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1172      pos = fitarr.shape()[3];     // the new element position
1173  } else {
1174    if (fitarr.nelements() > 0)
1175      newarr = fitarr;
1176  }
1177  newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1178  fitCol_.put(whichRow, newarr);
1179
1180}
1181
1182SDFrequencyTable SDMemTable::getSDFreqTable() const
1183{
1184  const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1185  SDFrequencyTable sdft;
1186
1187  // Add refpix/refval/incr.  What are the units ? Hz I suppose
1188  // but it's nowhere described...
1189  Vector<Double> refPix, refVal, incr;
1190  ScalarColumn<Double> refPixCol(t, "REFPIX");
1191  ScalarColumn<Double> refValCol(t, "REFVAL");
1192  ScalarColumn<Double> incrCol(t, "INCREMENT");
1193  refPix = refPixCol.getColumn();
1194  refVal = refValCol.getColumn();
1195  incr = incrCol.getColumn();
1196
1197  uInt n = refPix.nelements();
1198  for (uInt i=0; i<n; i++) {
1199     sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1200  }
1201
1202  // Frequency reference frame.  I don't know if this
1203  // is the correct frame.  It might be 'REFFRAME'
1204  // rather than 'BASEREFFRAME' ?
1205  String frame;
1206  t.keywordSet().get("REFFRAME",frame);
1207  sdft.setRefFrame(frame);
1208  t.keywordSet().get("BASEREFFRAME",frame);
1209  sdft.setBaseRefFrame(frame);
1210
1211  // Equinox
1212  Float equinox;
1213  t.keywordSet().get("EQUINOX", equinox);
1214  sdft.setEquinox(equinox);
1215
1216  String unit;
1217  t.keywordSet().get("UNIT", unit);
1218  sdft.setUnit(unit);
1219
1220  // Rest Frequency
1221  Vector<Double> restFreqs;
1222  t.keywordSet().get("RESTFREQS", restFreqs);
1223  for (uInt i=0; i<restFreqs.nelements(); i++) {
1224     sdft.addRestFrequency(restFreqs[i]);
1225  }
1226  sdft.setRestFrequencyUnit(String("Hz"));
1227
1228  return sdft;
1229}
1230
1231bool SDMemTable::putSDContainer(const SDContainer& sdc)
1232{
1233  uInt rno = table_.nrow();
1234  table_.addRow();
1235
1236  timeCol_.put(rno, sdc.timestamp);
1237  srcnCol_.put(rno, sdc.sourcename);
1238  fldnCol_.put(rno, sdc.fieldname);
1239  specCol_.put(rno, sdc.getSpectrum());
1240  flagsCol_.put(rno, sdc.getFlags());
1241  tsCol_.put(rno, sdc.getTsys());
1242  scanCol_.put(rno, sdc.scanid);
1243  integrCol_.put(rno, sdc.interval);
1244  freqidCol_.put(rno, sdc.getFreqMap());
1245  restfreqidCol_.put(rno, sdc.getRestFreqMap());
1246  dirCol_.put(rno, sdc.getDirection());
1247  rbeamCol_.put(rno, sdc.refbeam);
1248  tcalCol_.put(rno, sdc.tcal);
1249  tcaltCol_.put(rno, sdc.tcaltime);
1250  azCol_.put(rno, sdc.azimuth);
1251  elCol_.put(rno, sdc.elevation);
1252  paraCol_.put(rno, sdc.parangle);
1253  fitCol_.put(rno, sdc.getFitMap());
1254  return true;
1255}
1256
1257SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1258{
1259  SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1260  timeCol_.get(whichRow, sdc.timestamp);
1261  srcnCol_.get(whichRow, sdc.sourcename);
1262  integrCol_.get(whichRow, sdc.interval);
1263  scanCol_.get(whichRow, sdc.scanid);
1264  fldnCol_.get(whichRow, sdc.fieldname);
1265  rbeamCol_.get(whichRow, sdc.refbeam);
1266  azCol_.get(whichRow, sdc.azimuth);
1267  elCol_.get(whichRow, sdc.elevation);
1268  paraCol_.get(whichRow, sdc.parangle);
1269  Vector<Float> tc;
1270  tcalCol_.get(whichRow, tc);
1271  sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1272  tcaltCol_.get(whichRow, sdc.tcaltime);
1273
1274  Array<Float> spectrum;
1275  Array<Float> tsys;
1276  Array<uChar> flagtrum;
1277  Vector<uInt> fmap;
1278  Array<Double> direction;
1279  Array<Int> fits;
1280
1281  specCol_.get(whichRow, spectrum);
1282  sdc.putSpectrum(spectrum);
1283  flagsCol_.get(whichRow, flagtrum);
1284  sdc.putFlags(flagtrum);
1285  tsCol_.get(whichRow, tsys);
1286  sdc.putTsys(tsys);
1287  freqidCol_.get(whichRow, fmap);
1288  sdc.putFreqMap(fmap);
1289  restfreqidCol_.get(whichRow, fmap);
1290  sdc.putRestFreqMap(fmap);
1291  dirCol_.get(whichRow, direction);
1292  sdc.putDirection(direction);
1293  fitCol_.get(whichRow, fits);
1294  sdc.putFitMap(fits);
1295  return sdc;
1296}
1297
1298bool SDMemTable::putSDHeader(const SDHeader& sdh)
1299{
1300  table_.rwKeywordSet().define("nIF", sdh.nif);
1301  table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1302  table_.rwKeywordSet().define("nPol", sdh.npol);
1303  table_.rwKeywordSet().define("nChan", sdh.nchan);
1304  table_.rwKeywordSet().define("Observer", sdh.observer);
1305  table_.rwKeywordSet().define("Project", sdh.project);
1306  table_.rwKeywordSet().define("Obstype", sdh.obstype);
1307  table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1308  table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1309  table_.rwKeywordSet().define("Equinox", sdh.equinox);
1310  table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1311  table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1312  table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1313  table_.rwKeywordSet().define("UTC", sdh.utc);
1314  table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1315  table_.rwKeywordSet().define("Epoch", sdh.epoch);
1316  return true;
1317}
1318
1319SDHeader SDMemTable::getSDHeader() const
1320{
1321  SDHeader sdh;
1322  table_.keywordSet().get("nBeam",sdh.nbeam);
1323  table_.keywordSet().get("nIF",sdh.nif);
1324  table_.keywordSet().get("nPol",sdh.npol);
1325  table_.keywordSet().get("nChan",sdh.nchan);
1326  table_.keywordSet().get("Observer", sdh.observer);
1327  table_.keywordSet().get("Project", sdh.project);
1328  table_.keywordSet().get("Obstype", sdh.obstype);
1329  table_.keywordSet().get("AntennaName", sdh.antennaname);
1330  table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1331  table_.keywordSet().get("Equinox", sdh.equinox);
1332  table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1333  table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1334  table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1335  table_.keywordSet().get("UTC", sdh.utc);
1336  table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1337  table_.keywordSet().get("Epoch", sdh.epoch);
1338  return sdh;
1339}
1340void SDMemTable::makePersistent(const std::string& filename)
1341{
1342  table_.deepCopy(filename,Table::New);
1343
1344}
1345
1346Int SDMemTable::nScan() const {
1347  Int n = 0;
1348  Int previous = -1;Int current=0;
1349  for (uInt i=0; i< scanCol_.nrow();i++) {
1350    scanCol_.getScalar(i,current);
1351    if (previous != current) {
1352      previous = current;
1353      n++;
1354    }
1355  }
1356  return n;
1357}
1358
1359String SDMemTable::formatSec(Double x) const
1360{
1361  Double xcop = x;
1362  MVTime mvt(xcop/24./3600.);  // make days
1363
1364  if (x < 59.95)
1365    return  String("      ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1366  else if (x < 3599.95)
1367    return String("   ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1368  else {
1369    ostringstream oss;
1370    oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1371    oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1372    return String(oss);
1373  }
1374};
1375
1376String SDMemTable::formatDirection(const MDirection& md) const
1377{
1378  Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1379  Int prec = 7;
1380
1381  MVAngle mvLon(t[0]);
1382  String sLon = mvLon.string(MVAngle::TIME,prec);
1383  MVAngle mvLat(t[1]);
1384  String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1385  return sLon + String(" ") + sLat;
1386}
1387
1388
1389std::string SDMemTable::getFluxUnit() const
1390{
1391  String tmp;
1392  table_.keywordSet().get("FluxUnit", tmp);
1393  return tmp;
1394}
1395
1396void SDMemTable::setFluxUnit(const std::string& unit)
1397{
1398  String tmp(unit);
1399  Unit tU(tmp);
1400  if (tU==Unit("K") || tU==Unit("Jy")) {
1401     table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1402  } else {
1403     throw AipsError("Illegal unit - must be compatible with Jy or K");
1404  }
1405}
1406
1407
1408void SDMemTable::setInstrument(const std::string& name)
1409{
1410  Bool throwIt = True;
1411  Instrument ins = SDAttr::convertInstrument(name, throwIt);
1412  String nameU(name);
1413  nameU.upcase();
1414  table_.rwKeywordSet().define(String("AntennaName"), nameU);
1415}
1416
1417std::string SDMemTable::summary(bool verbose) const  {
1418
1419  // Format header info
1420  ostringstream oss;
1421  oss << endl;
1422  oss << "--------------------------------------------------------------------------------" << endl;
1423  oss << " Scan Table Summary" << endl;
1424  oss << "--------------------------------------------------------------------------------" << endl;
1425  oss.flags(std::ios_base::left);
1426  oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1427      << setw(15) << "IFs:" << setw(4) << nIF() << endl
1428      << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1429      << setw(15) << "Channels:"  << setw(4) << nChan() << endl;
1430  oss << endl;
1431  String tmp;
1432  table_.keywordSet().get("Observer", tmp);
1433  oss << setw(15) << "Observer:" << tmp << endl;
1434  oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1435  table_.keywordSet().get("Project", tmp);
1436  oss << setw(15) << "Project:" << tmp << endl;
1437  table_.keywordSet().get("Obstype", tmp);
1438  oss << setw(15) << "Obs. Type:" << tmp << endl;
1439  table_.keywordSet().get("AntennaName", tmp);
1440  oss << setw(15) << "Antenna Name:" << tmp << endl;
1441  table_.keywordSet().get("FluxUnit", tmp);
1442  oss << setw(15) << "Flux Unit:" << tmp << endl;
1443  Table t = table_.keywordSet().asTable("FREQUENCIES");
1444  Vector<Double> vec;
1445  t.keywordSet().get("RESTFREQS",vec);
1446  oss << setw(15) << "Rest Freqs:";
1447  if (vec.nelements() > 0) {
1448      oss << setprecision(10) << vec << " [Hz]" << endl;
1449  } else {
1450      oss << "None set" << endl;
1451  }
1452  oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1453  oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1454      << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1455  oss << endl;
1456
1457  String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1458  oss << setw(5) << "Scan"
1459      << setw(15) << "Source"
1460      << setw(24) << dirtype
1461      << setw(10) << "Time"
1462      << setw(18) << "Integration"
1463      << setw(7) << "FreqIDs" << endl;
1464  oss << "--------------------------------------------------------------------------------" << endl;
1465
1466  // Generate list of scan start and end integrations
1467  Vector<Int> scanIDs = scanCol_.getColumn();
1468  Vector<uInt> startInt, endInt;
1469  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1470
1471  const uInt nScans = startInt.nelements();
1472  String name;
1473  Vector<uInt> freqIDs, listFQ;
1474  Vector<uInt> restFreqIDs, listRestFQ;
1475  uInt nInt;
1476
1477  for (uInt i=0; i<nScans; i++) {
1478    // Get things from first integration of scan
1479    String time = getTime(startInt(i),False);
1480    String tInt = formatSec(Double(getInterval(startInt(i))));
1481    String posit = formatDirection(getDirection(startInt(i),True));
1482    srcnCol_.getScalar(startInt(i),name);
1483
1484    // Find all the FreqIDs in this scan
1485    listFQ.resize(0);
1486    listRestFQ.resize(0);
1487    for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1488      freqidCol_.get(j, freqIDs);
1489      for (uInt k=0; k<freqIDs.nelements(); k++) {
1490        mathutil::addEntry(listFQ, freqIDs(k));
1491      }
1492//
1493      restfreqidCol_.get(j, restFreqIDs);
1494      for (uInt k=0; k<restFreqIDs.nelements(); k++) {
1495        mathutil::addEntry(listRestFQ, restFreqIDs(k));
1496      }
1497    }
1498
1499    nInt = endInt(i) - startInt(i) + 1;
1500    oss << setw(3) << std::right << i << std::left << setw(2) << "  "
1501        << setw(15) << name
1502        << setw(24) << posit
1503        << setw(10) << time
1504        << setw(3) << std::right << nInt  << setw(3) << " x " << std::left
1505        << setw(6) <<  tInt
1506        << " " << listFQ << " " << listRestFQ << endl;
1507  }
1508  oss << endl;
1509  oss << "Table contains " << table_.nrow() << " integration(s) in "
1510      << nScans << " scan(s)." << endl;
1511
1512  // Frequency Table
1513  if (verbose) {
1514    std::vector<string> info = getCoordInfo();
1515    SDFrequencyTable sdft = getSDFreqTable();
1516    oss << endl << endl;
1517    oss << "FreqID  Frame   RefFreq(Hz)     RefPix   Increment(Hz)" << endl;
1518    oss << "--------------------------------------------------------------------------------" << endl;
1519    for (uInt i=0; i<sdft.length(); i++) {
1520      oss << setw(8) << i << setw(8)
1521          << info[3] << setw(16) << setprecision(8)
1522          << sdft.referenceValue(i) << setw(10)
1523          << sdft.referencePixel(i) << setw(12)
1524          << sdft.increment(i) << endl;
1525    }
1526    oss << "--------------------------------------------------------------------------------" << endl;
1527  }
1528  return String(oss);
1529}
1530/*
1531std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1532  ostringstream oss;
1533  Vector<Int> scanIDs = scanCol_.getColumn();
1534  Vector<uInt> startInt, endInt;
1535  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1536  const uInt nScans = startInt.nelements();
1537  std::vector<int>::const_iterator it(whichScans);
1538  return String(oss);
1539}
1540*/
1541Int SDMemTable::nBeam() const
1542{
1543  Int n;
1544  table_.keywordSet().get("nBeam",n);
1545  return n;
1546}
1547
1548Int SDMemTable::nIF() const {
1549  Int n;
1550  table_.keywordSet().get("nIF",n);
1551  return n;
1552}
1553
1554Int SDMemTable::nPol() const {
1555  Int n;
1556  table_.keywordSet().get("nPol",n);
1557  return n;
1558}
1559
1560Int SDMemTable::nChan() const {
1561  Int n;
1562  table_.keywordSet().get("nChan",n);
1563  return n;
1564}
1565
1566Table SDMemTable::getHistoryTable() const
1567{
1568  return table_.keywordSet().asTable("HISTORY");
1569}
1570
1571void SDMemTable::appendToHistoryTable(const Table& otherHist)
1572{
1573  Table t = table_.rwKeywordSet().asTable("HISTORY");
1574  const String sep = "--------------------------------------------------------------------------------";
1575  addHistory(sep);
1576  TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1577  addHistory(sep);
1578}
1579
1580void SDMemTable::addHistory(const std::string& hist)
1581{
1582  Table t = table_.rwKeywordSet().asTable("HISTORY");
1583  uInt nrow = t.nrow();
1584  t.addRow();
1585  ScalarColumn<String> itemCol(t, "ITEM");
1586  itemCol.put(nrow, hist);
1587}
1588
1589std::vector<std::string> SDMemTable::getHistory() const
1590{
1591  Vector<String> history;
1592  const Table& t = table_.keywordSet().asTable("HISTORY");
1593  uInt nrow = t.nrow();
1594  ROScalarColumn<String> itemCol(t, "ITEM");
1595  std::vector<std::string> stlout;
1596  String hist;
1597  for (uInt i=0; i<nrow; ++i) {
1598    itemCol.get(i, hist);
1599    stlout.push_back(hist);
1600  }
1601  return stlout;
1602}
1603
1604
1605/*
1606  void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1607
1608  std::vector<int>::iterator it;
1609  ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1610  for (it = whichChans.begin(); it != whichChans.end(); it++) {
1611    j.reset(j.begin(uInt(*it)));
1612    for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1613      for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1614        for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1615             iii != iii.end(); ++iii) {
1616          (*iii) =
1617        }
1618      }
1619    }
1620  }
1621
1622}
1623*/
1624void SDMemTable::flag(int whichRow)
1625  {
1626  Array<uChar> arr;
1627  flagsCol_.get(whichRow, arr);
1628
1629  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1630  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1631  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1632  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1633  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1634  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1635
1636  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1637    (*i) = uChar(True);
1638  }
1639
1640  flagsCol_.put(whichRow, arr);
1641}
1642
1643MDirection::Types SDMemTable::getDirectionReference() const
1644{
1645  Float eq;
1646  table_.keywordSet().get("Equinox",eq);
1647  std::map<float,string> mp;
1648  mp[2000.0] = "J2000";
1649  mp[1950.0] = "B1950";
1650  MDirection::Types mdr;
1651  if (!MDirection::getType(mdr, mp[eq])) {
1652    mdr = MDirection::J2000;
1653    pushLog("WARNING: Unknown equinox using J2000");
1654  }
1655
1656  return mdr;
1657}
1658
1659MEpoch::Types SDMemTable::getTimeReference() const
1660{
1661  MEpoch::Types met;
1662  String ep;
1663  table_.keywordSet().get("Epoch",ep);
1664  if (!MEpoch::getType(met, ep)) {
1665     pushLog("WARNING: Epoch type unknown - using UTC");
1666    met = MEpoch::UTC;
1667  }
1668
1669  return met;
1670}
1671
1672
1673Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1674                              const String& sUnit,
1675                              const vector<string>& lines,
1676                              const String& source,
1677                              Int whichIF)
1678{
1679   const Int nIFs = nIF();
1680   if (whichIF>=nIFs) {
1681      throw(AipsError("Illegal IF index"));
1682   }
1683
1684   // Find vector of restfrequencies
1685   // Double takes precedence over String
1686   Unit unit;
1687   Vector<Double> restFreqs;
1688   if (restFreqsIn.nelements()>0) {
1689      restFreqs.resize(restFreqsIn.nelements());
1690      restFreqs = restFreqsIn;
1691      unit = Unit(sUnit);
1692   } else if (lines.size()>0) {
1693      const uInt nLines = lines.size();
1694      unit = Unit("Hz");
1695      restFreqs.resize(nLines);
1696      MFrequency lineFreq;
1697      for (uInt i=0; i<nLines; i++) {
1698         String tS(lines[i]);
1699         tS.upcase();
1700         if (MeasTable::Line(lineFreq, tS)) {
1701            restFreqs[i] = lineFreq.getValue().getValue();          // Hz
1702         } else {
1703            String s = String(lines[i]) +
1704              String(" is an unrecognized spectral line");
1705            throw(AipsError(s));
1706         }
1707      }
1708   } else {
1709      throw(AipsError("You have not specified any rest frequencies or lines"));
1710   }
1711
1712   // If multiple restfreqs, must be length nIF. In this
1713   // case we will just replace the rest frequencies
1714   // We can't disinguish scalar and vector of length 1
1715   const uInt nRestFreqs = restFreqs.nelements();
1716   Int idx = -1;
1717   SDFrequencyTable sdft = getSDFreqTable();
1718
1719   ostringstream oss;
1720   if (nRestFreqs>1) {
1721     // Replace restFreqs, one per IF
1722     if (nRestFreqs != nIFs) {
1723       throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1724     }
1725     ostringstream oss;
1726     oss << "Replaced rest frequencies, one per IF, with given list : " << restFreqs;
1727     sdft.deleteRestFrequencies();
1728     for (uInt i=0; i<nRestFreqs; i++) {
1729       Quantum<Double> rf(restFreqs[i], unit);
1730       sdft.addRestFrequency(rf.getValue("Hz"));
1731     }
1732   } else {
1733
1734     // Add new rest freq
1735      Quantum<Double> rf(restFreqs[0], unit);
1736      idx = sdft.addRestFrequency(rf.getValue("Hz"));
1737      if (whichIF>=0) {
1738         oss << "Selected given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1739      } else {
1740         oss << "Selected given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1741      }
1742   }
1743   pushLog(String(oss));
1744   // Replace
1745   Bool empty = source.empty();
1746   Bool ok = False;
1747   if (putSDFreqTable(sdft)) {
1748      const uInt nRow = table_.nrow();
1749      String srcName;
1750      Vector<uInt> restFreqIDs;
1751      for (uInt i=0; i<nRow; i++) {
1752         srcnCol_.get(i, srcName);
1753         restfreqidCol_.get(i,restFreqIDs);
1754         if (idx==-1) {
1755           // Replace vector of restFreqs; one per IF.
1756           // No selection possible
1757            for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1758         } else {
1759           // Set RestFreqID for selected data
1760            if (empty || source==srcName) {
1761               if (whichIF<0) {
1762                  restFreqIDs = idx;
1763               } else {
1764                  restFreqIDs[whichIF] = idx;
1765               }
1766            }
1767         }
1768         restfreqidCol_.put(i,restFreqIDs);
1769      }
1770      ok = True;
1771   } else {
1772     ok = False;
1773   }
1774
1775   return ok;
1776}
1777
1778std::string SDMemTable::spectralLines() const
1779{
1780   Vector<String> lines = MeasTable::Lines();
1781   MFrequency lineFreq;
1782   Double freq;
1783   ostringstream oss;
1784
1785   oss.flags(std::ios_base::left);
1786   oss << "Line      Frequency (Hz)" << endl;
1787   oss << "-----------------------" << endl;
1788   for (uInt i=0; i<lines.nelements(); i++) {
1789     MeasTable::Line(lineFreq, lines[i]);
1790     freq = lineFreq.getValue().getValue();          // Hz
1791     oss << setw(11) << lines[i] << setprecision(10) << freq << endl;
1792   }
1793   return String(oss);
1794}
1795
1796void SDMemTable::renumber()
1797{
1798  uInt nRow = scanCol_.nrow();
1799  Int newscanid = 0;
1800  Int cIdx;// the current scanid
1801  // get the first scanid
1802  scanCol_.getScalar(0,cIdx);
1803  Int pIdx = cIdx;// the scanid of the previous row
1804  for (uInt i=0; i<nRow;++i) {
1805    scanCol_.getScalar(i,cIdx);
1806    if (pIdx == cIdx) {
1807      // renumber
1808      scanCol_.put(i,newscanid);
1809    } else {
1810      ++newscanid;
1811      pIdx = cIdx;   // store scanid
1812      --i;           // don't increment next loop
1813    }
1814  }
1815}
1816
1817
1818void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1819                                const IPosition& shape) const
1820{
1821  const uInt nDim = shape.nelements();
1822  start.resize(nDim);
1823  end.resize(nDim);
1824
1825  start(asap::BeamAxis) = beamSel_;
1826  end(asap::BeamAxis) = beamSel_;
1827  start(asap::IFAxis) = IFSel_;
1828  end(asap::IFAxis) = IFSel_;
1829
1830  start(asap::PolAxis) = polSel_;
1831  end(asap::PolAxis) = polSel_;
1832
1833  start(asap::ChanAxis) = 0;
1834  end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1835}
1836
1837
1838std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1839  // Get spectrum at cursor location
1840{
1841
1842  // Setup accessors
1843  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1844  aa0.reset(aa0.begin(uInt(beamSel_)));                    // Beam selection
1845
1846  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1847  aa1.reset(aa1.begin(uInt(IFSel_)));                      // IF selection
1848
1849  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1850  aa2.reset(aa2.begin(uInt(polSel_)));                     // Pol selection
1851
1852  std::vector<float> spectrum;
1853  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1854    spectrum.push_back(*i);
1855  }
1856  return spectrum;
1857}
1858
1859void SDMemTable::calculateAZEL()
1860{
1861  MPosition mp = getAntennaPosition();
1862  ostringstream oss;
1863  oss << "Computed azimuth/elevation using " << endl
1864      << mp << endl;
1865  for (uInt i=0; i<nRow();++i) {
1866    MEpoch me = getEpoch(i);
1867    MDirection md = getDirection(i,False);
1868    oss  << " Time: " << getTime(i,False) << " Direction: " << formatDirection(md)
1869         << endl << "     => ";
1870    MeasFrame frame(mp, me);
1871    Vector<Double> azel =
1872        MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
1873                                                frame)
1874                            )().getAngle("rad").getValue();
1875    azCol_.put(i,azel[0]);
1876    elCol_.put(i,azel[1]);
1877    oss << "azel: " << azel[0]/C::pi*180.0 << " "
1878        << azel[1]/C::pi*180.0 << " (deg)" << endl;
1879  }
1880  pushLog(String(oss));
1881}
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