source: trunk/src/SDMemTable.cc @ 521

Last change on this file since 521 was 521, checked in by kil064, 19 years ago

add restFreqIDs to summary listing
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  • Property svn:keywords set to Author Date Id Revision
File size: 52.4 KB
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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  //cerr << "hello from C SDMemTable @ " << this << endl;
96  attach();
97}
98
99SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
100{
101  table_ = other.table_.copyToMemoryTable(String("dummy"));
102  // clear all rows()
103  if (clear) {
104    table_.removeRow(this->table_.rowNumbers());
105    IFSel_= 0;
106    beamSel_= 0;
107    polSel_= 0;
108    chanMask_.resize(0);
109  } else {
110    IFSel_= other.IFSel_;
111    beamSel_= other.beamSel_;
112    polSel_= other.polSel_;
113    chanMask_.resize(0);
114    chanMask_ = other.chanMask_;
115  }
116
117  attach();
118  //cerr << "hello from CC SDMemTable @ " << this << endl;
119}
120
121SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
122  IFSel_(0),
123  beamSel_(0),
124  polSel_(0)
125{
126  Table t = tableCommand(exprs,tab);
127  if (t.nrow() == 0)
128      throw(AipsError("Query unsuccessful."));
129  table_ = t.copyToMemoryTable("dummy");
130  attach();
131  renumber();
132}
133
134SDMemTable::~SDMemTable()
135{
136  //cerr << "goodbye from SDMemTable @ " << this << endl;
137}
138
139SDMemTable SDMemTable::getScan(Int scanID) const
140{
141  String cond("SELECT * from $1 WHERE SCANID == ");
142  cond += String::toString(scanID);
143  return SDMemTable(table_, cond);
144}
145
146SDMemTable &SDMemTable::operator=(const SDMemTable& other)
147{
148  if (this != &other) {
149     IFSel_= other.IFSel_;
150     beamSel_= other.beamSel_;
151     polSel_= other.polSel_;
152     chanMask_.resize(0);
153     chanMask_ = other.chanMask_;
154     table_ = other.table_.copyToMemoryTable(String("dummy"));
155     attach();
156  }
157  return *this;
158}
159
160SDMemTable SDMemTable::getSource(const std::string& source) const
161{
162  String cond("SELECT * from $1 WHERE SRCNAME == ");
163  cond += source;
164  return SDMemTable(table_, cond);
165}
166
167void SDMemTable::setup()
168{
169  TableDesc td("", "1", TableDesc::Scratch);
170  td.comment() = "A SDMemTable";
171  td.rwKeywordSet().define("VERSION", Int(version_));
172
173  td.addColumn(ScalarColumnDesc<Double>("TIME"));
174  td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
175  td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
176  td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
177  td.addColumn(ArrayColumnDesc<Float>("TSYS"));
178  td.addColumn(ArrayColumnDesc<Float>("STOKES"));
179  td.addColumn(ScalarColumnDesc<Int>("SCANID"));
180  td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
181  td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
182  td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
183  td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
184  td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
185  td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
186  td.addColumn(ArrayColumnDesc<Float>("TCAL"));
187  td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
188  td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
189  td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
190  td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
191  td.addColumn(ArrayColumnDesc<Int>("FITID"));
192
193  // Now create Table SetUp from the description.
194  SetupNewTable aNewTab("dummy", td, Table::New);
195
196  // Bind the Stokes Virtual machine to the STOKES column Because we
197  // don't know how many polarizations will be in the data at this
198  // point, we must bind the Virtual Engine regardless.  The STOKES
199  // column won't be accessed if not appropriate (nPol=4)
200  SDStokesEngine::registerClass();
201  SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
202  aNewTab.bindColumn("STOKES", stokesEngine);
203 
204  // Create Table
205  table_ = Table(aNewTab, Table::Memory, 0);
206  // add subtable
207  TableDesc tdf("", "1", TableDesc::Scratch);
208  tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
209  tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
210  tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
211  tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
212  tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
213  SetupNewTable fittab("fits", tdf, Table::New);
214  Table fitTable(fittab, Table::Memory);
215  table_.rwKeywordSet().defineTable("FITS", fitTable);
216
217  TableDesc tdh("", "1", TableDesc::Scratch);
218  tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
219  SetupNewTable histtab("hist", tdh, Table::New);
220  Table histTable(histtab, Table::Memory);
221  table_.rwKeywordSet().defineTable("HISTORY", histTable);
222}
223
224void SDMemTable::attach()
225{
226  timeCol_.attach(table_, "TIME");
227  srcnCol_.attach(table_, "SRCNAME");
228  specCol_.attach(table_, "SPECTRA");
229  flagsCol_.attach(table_, "FLAGTRA");
230  tsCol_.attach(table_, "TSYS");
231  stokesCol_.attach(table_, "STOKES");
232  scanCol_.attach(table_, "SCANID");
233  integrCol_.attach(table_, "INTERVAL");
234  freqidCol_.attach(table_, "FREQID");
235  restfreqidCol_.attach(table_, "RESTFREQID");
236  dirCol_.attach(table_, "DIRECTION");
237  fldnCol_.attach(table_, "FIELDNAME");
238  tcaltCol_.attach(table_, "TCALTIME");
239  tcalCol_.attach(table_, "TCAL");
240  azCol_.attach(table_, "AZIMUTH");
241  elCol_.attach(table_, "ELEVATION");
242  paraCol_.attach(table_, "PARANGLE");
243  rbeamCol_.attach(table_, "REFBEAM");
244  fitCol_.attach(table_,"FITID");
245}
246
247
248std::string SDMemTable::getSourceName(Int whichRow) const
249{
250  String name;
251  srcnCol_.get(whichRow, name);
252  return name;
253}
254
255std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
256{
257  Double tm;
258  if (whichRow > -1) {
259    timeCol_.get(whichRow, tm);
260  } else {
261    table_.keywordSet().get("UTC",tm);
262  }
263  MVTime mvt(tm);
264  if (showDate)
265    mvt.setFormat(MVTime::YMD);
266  else
267    mvt.setFormat(MVTime::TIME);
268  ostringstream oss;
269  oss << mvt;
270  return String(oss);
271}
272
273double SDMemTable::getInterval(Int whichRow) const
274{
275  Double intval;
276  integrCol_.get(whichRow, intval);
277  return intval;
278}
279
280bool SDMemTable::setIF(Int whichIF)
281{
282  if ( whichIF >= 0 && whichIF < nIF()) {
283    IFSel_ = whichIF;
284    return true;
285  }
286  return false;
287}
288
289bool SDMemTable::setBeam(Int whichBeam)
290{
291  if ( whichBeam >= 0 && whichBeam < nBeam()) {
292    beamSel_ = whichBeam;
293    return true;
294  }
295  return false;
296}
297
298bool SDMemTable::setPol(Int whichPol)
299{
300  if ( whichPol >= 0 && whichPol < nPol()) {
301    polSel_ = whichPol;
302    return true;
303  }
304  return false;
305}
306
307void SDMemTable::resetCursor()
308{
309   polSel_ = 0;
310   IFSel_ = 0;
311   beamSel_ = 0;
312}
313
314bool SDMemTable::setMask(std::vector<int> whichChans)
315{
316  std::vector<int>::iterator it;
317  uInt n = flagsCol_.shape(0)(3);
318  if (whichChans.empty()) {
319    chanMask_ = std::vector<bool>(n,true);
320    return true;     
321  }
322  chanMask_.resize(n,true);
323  for (it = whichChans.begin(); it != whichChans.end(); ++it) {
324    if (*it < n) {
325      chanMask_[*it] = false;
326    }
327  }
328  return true;
329}
330
331std::vector<bool> SDMemTable::getMask(Int whichRow) const
332{
333
334  std::vector<bool> mask;
335
336  Array<uChar> arr;
337  flagsCol_.get(whichRow, arr);
338
339  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
340  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
341  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
342  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
343  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
344  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
345
346  Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
347
348  std::vector<bool> tmp;
349  tmp = chanMask_; // WHY the fxxx do I have to make a copy here
350  std::vector<bool>::iterator miter;
351  miter = tmp.begin();
352
353  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
354    bool out =!static_cast<bool>(*i);
355    if (useUserMask) {
356      out = out && (*miter);
357      miter++;
358    }
359    mask.push_back(out);
360  }
361  return mask;
362}
363
364
365
366std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
367{
368  Array<Float> arr;
369  specCol_.get(whichRow, arr);
370  return getFloatSpectrum(arr);
371}
372
373
374int SDMemTable::nStokes() const
375{
376   return stokesCol_.shape(0).nelements();        // All rows same shape
377}
378
379
380std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow, Bool doPol) const
381//
382// Gets one STokes parameter depending on cursor polSel location
383//  doPol=False  : I,Q,U,V
384//  doPol=True   : I,P,PA,V   ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
385//
386{
387  AlwaysAssert(asap::nAxes==4,AipsError);
388  if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
389     throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
390  }
391
392// For full conversion we are only supporting linears at the moment
393
394  if (nPol() > 2) {
395     String antName;
396     table_.keywordSet().get("AntennaName", antName);
397     Instrument inst = SDAttr::convertInstrument (antName, True);
398     SDAttr sdAtt;
399     if (sdAtt.feedPolType(inst) != LINEAR) {
400       throw(AipsError("Only linear polarizations are supported"));
401     }
402  }
403//
404  Array<Float> arr;
405  stokesCol_.get(whichRow, arr);
406//
407  if (doPol && (polSel_==1 || polSel_==2)) {       //   Q,U --> P, P.A.
408
409// Set current cursor location
410
411     const IPosition& shape = arr.shape();
412     IPosition start, end;
413     getCursorSlice(start, end, shape);
414
415// Get Q and U slices
416
417     Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
418     Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
419
420// Compute output
421
422     Array<Float> out;
423     if (polSel_==1) {                                        // P
424        out = SDPolUtil::polarizedIntensity(Q,U);
425     } else if (polSel_==2) {                                 // P.A.
426        out = SDPolUtil::positionAngle(Q,U);
427     }
428
429     // Copy to output
430
431     IPosition vecShape(1,shape(asap::ChanAxis));
432     Vector<Float> outV = out.reform(vecShape);
433     std::vector<float> stlout;
434     outV.tovector(stlout);
435     return stlout;
436
437  } else {
438
439    // Selects at the cursor location
440    return getFloatSpectrum(arr);
441  }
442}
443
444std::string SDMemTable::getPolarizationLabel (Bool linear, Bool stokes, Bool linPol, Int polIdx) const
445{
446   uInt idx = polSel_;   
447   if (polIdx >=0) idx = polIdx;
448//
449   return SDPolUtil::polarizationLabel (idx, linear, stokes, linPol);
450}
451
452
453
454std::vector<float> SDMemTable::stokesToPolSpectrum (Int whichRow, Bool toLinear, uInt polIdx) const
455//
456// polIdx
457//   0:3 -> RR,LL,Real(RL),Imag(RL)
458//          XX,YY,Real(XY),Image(XY)
459//
460// Gets only
461//  RR = I + V
462//  LL = I - V
463// at the moment
464//
465{
466  AlwaysAssert(asap::nAxes==4,AipsError);
467  if (nStokes()!=4) {
468     throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
469  }
470//
471  Array<Float> arr, out;
472  stokesCol_.get(whichRow, arr);
473
474// Set current cursor location
475
476  const IPosition& shape = arr.shape();
477  IPosition start, end;
478  getCursorSlice(start, end, shape);
479
480// Get the slice
481
482  if (toLinear) {
483     throw(AipsError("Conversion to linears not yet supported"));
484  } else {
485     Bool doRR = (polIdx==0);
486     if(polIdx>1) {
487        throw(AipsError("Only conversion to RR & LL is currently supported"));
488     }
489
490// Get I and V slices
491
492     Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
493     Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
494
495// Compute output
496
497     out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
498   }
499
500// Copy to output
501
502   IPosition vecShape(1,shape(asap::ChanAxis));
503   Vector<Float> outV = out.reform(vecShape);
504   std::vector<float> stlout;
505   outV.tovector(stlout);
506//
507   return stlout;
508}
509
510
511
512
513Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
514{
515
516// Get data
517
518  Array<Float> arr;
519  stokesCol_.get(whichRow, arr);
520
521// Set current cursor location and overwrite polarization axis
522
523  const IPosition& shape = arr.shape();
524  IPosition start(shape.nelements(),0); 
525  IPosition end(shape-1);
526  if (iBeam!=-1) {
527     start(asap::BeamAxis) = iBeam;
528     end(asap::BeamAxis) = iBeam;
529  }
530  if (iIF!=-1) {
531     start(asap::IFAxis) = iIF;
532     end(asap::IFAxis) = iIF;
533  }
534
535// Get slice
536
537  return arr(start,end);
538}
539
540
541std::vector<string> SDMemTable::getCoordInfo() const
542{
543  String un;
544  Table t = table_.keywordSet().asTable("FREQUENCIES");
545  String sunit;
546  t.keywordSet().get("UNIT",sunit);
547  String dpl;
548  t.keywordSet().get("DOPPLER",dpl);
549  if (dpl == "") dpl = "RADIO";
550  String rfrm;
551  t.keywordSet().get("REFFRAME",rfrm);
552  std::vector<string> inf;
553  inf.push_back(sunit);
554  inf.push_back(rfrm);
555  inf.push_back(dpl);
556  t.keywordSet().get("BASEREFFRAME",rfrm);
557  inf.push_back(rfrm);
558  return inf;
559}
560
561void SDMemTable::setCoordInfo(std::vector<string> theinfo)
562{
563  std::vector<string>::iterator it;
564  String un,rfrm, brfrm,dpl;
565  un = theinfo[0];              // Abcissa unit
566  rfrm = theinfo[1];            // Active (or conversion) frame
567  dpl = theinfo[2];             // Doppler
568  brfrm = theinfo[3];           // Base frame
569
570  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
571
572  Vector<Double> rstf;
573  t.keywordSet().get("RESTFREQS",rstf);
574
575  Bool canDo = True;
576  Unit u1("km/s");Unit u2("Hz");
577  if (Unit(un) == u1) {
578    Vector<Double> rstf;
579    t.keywordSet().get("RESTFREQS",rstf);
580    if (rstf.nelements() == 0) {
581        throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
582    }
583  } else if (Unit(un) != u2 && un != "") {
584        throw(AipsError("Unit not conformant with Spectral Coordinates"));
585  }
586  t.rwKeywordSet().define("UNIT", un);
587
588  MFrequency::Types mdr;
589  if (!MFrequency::getType(mdr, rfrm)) {
590   
591    Int a,b;const uInt* c;
592    const String* valid = MFrequency::allMyTypes(a, b, c);
593    String pfix = "Please specify a legal frame type. Types are\n";
594    throw(AipsError(pfix+(*valid)));
595  } else {
596    t.rwKeywordSet().define("REFFRAME",rfrm);
597  }
598
599  MDoppler::Types dtype;
600  dpl.upcase();
601  if (!MDoppler::getType(dtype, dpl)) {
602    throw(AipsError("Doppler type unknown"));
603  } else {
604    t.rwKeywordSet().define("DOPPLER",dpl);
605  }
606
607  if (!MFrequency::getType(mdr, brfrm)) {
608     Int a,b;const uInt* c;
609     const String* valid = MFrequency::allMyTypes(a, b, c);
610     String pfix = "Please specify a legal frame type. Types are\n";
611     throw(AipsError(pfix+(*valid)));
612   } else {
613    t.rwKeywordSet().define("BASEREFFRAME",brfrm);
614   }
615}
616
617
618std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
619{
620  std::vector<double> abc(nChan());
621
622  // Get header units keyword
623  Table t = table_.keywordSet().asTable("FREQUENCIES");
624  String sunit;
625  t.keywordSet().get("UNIT",sunit);
626  if (sunit == "") sunit = "pixel";
627  Unit u(sunit);
628
629  // Easy if just wanting pixels
630  if (sunit==String("pixel")) {
631    // assume channels/pixels
632    std::vector<double>::iterator it;
633    uInt i=0;
634    for (it = abc.begin(); it != abc.end(); ++it) {
635      (*it) = Double(i++);
636    }
637    return abc;
638  }
639
640  // Continue with km/s or Hz.  Get FreqIDs
641  Vector<uInt> freqIDs;
642  freqidCol_.get(whichRow, freqIDs);
643  uInt freqID = freqIDs(IFSel_);
644  restfreqidCol_.get(whichRow, freqIDs);
645  uInt restFreqID = freqIDs(IFSel_);
646
647  // Get SpectralCoordinate, set reference frame conversion,
648  // velocity conversion, and rest freq state
649
650  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
651  Vector<Double> pixel(nChan());
652  indgen(pixel);
653
654  if (u == Unit("km/s")) {
655     Vector<Double> world;
656     spc.pixelToVelocity(world,pixel);
657     std::vector<double>::iterator it;
658     uInt i = 0;
659     for (it = abc.begin(); it != abc.end(); ++it) {
660       (*it) = world[i];
661       i++;
662     }
663  } else if (u == Unit("Hz")) {
664
665    // Set world axis units   
666    Vector<String> wau(1); wau = u.getName();
667    spc.setWorldAxisUnits(wau);
668
669    std::vector<double>::iterator it;
670    Double tmp;
671    uInt i = 0;
672    for (it = abc.begin(); it != abc.end(); ++it) {
673      spc.toWorld(tmp,pixel[i]);
674      (*it) = tmp;
675      i++;
676    }
677  }
678  return abc;
679}
680
681std::string SDMemTable::getAbcissaString(Int whichRow) const
682{
683  Table t = table_.keywordSet().asTable("FREQUENCIES");
684
685  String sunit;
686  t.keywordSet().get("UNIT",sunit);
687  if (sunit == "") sunit = "pixel";
688  Unit u(sunit);
689
690  Vector<uInt> freqIDs;
691  freqidCol_.get(whichRow, freqIDs);
692  uInt freqID = freqIDs(IFSel_); 
693  restfreqidCol_.get(whichRow, freqIDs);
694  uInt restFreqID = freqIDs(IFSel_);
695
696  // Get SpectralCoordinate, with frame, velocity, rest freq state set
697  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
698
699  String s = "Channel";
700  if (u == Unit("km/s")) {
701    s = CoordinateUtil::axisLabel(spc,0,True,True,True);
702  } else if (u == Unit("Hz")) {
703    Vector<String> wau(1);wau = u.getName();
704    spc.setWorldAxisUnits(wau);
705
706    s = CoordinateUtil::axisLabel(spc,0,True,True,False);
707  }
708  return s;
709}
710
711void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
712{
713  Array<Float> arr;
714  specCol_.get(whichRow, arr);
715  if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
716    throw(AipsError("Attempting to set spectrum with incorrect length."));
717  }
718
719  // Setup accessors
720  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
721  aa0.reset(aa0.begin(uInt(beamSel_)));                   // Beam selection
722  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
723  aa1.reset(aa1.begin(uInt(IFSel_)));                     // IF selection
724  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
725  aa2.reset(aa2.begin(uInt(polSel_)));                    // Pol selection
726
727  // Iterate
728  std::vector<float>::iterator it = spectrum.begin();
729  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
730    (*i) = Float(*it);
731    it++;
732  }
733  specCol_.put(whichRow, arr);
734}
735
736void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
737{
738  Array<Float> arr;
739  specCol_.get(whichRow, arr);
740
741  // Iterate and extract
742  spectrum.resize(arr.shape()(3));
743  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
744  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
745  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
746  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
747  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
748  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
749
750  ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
751  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
752    (*va) = (*i);
753    va++;
754  }
755}
756
757
758/*
759void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
760  Array<uChar> arr;
761  flagsCol_.get(whichRow, arr);
762  mask.resize(arr.shape()(3));
763
764  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
765  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
766  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
767  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
768  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
769  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
770
771  Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
772
773  ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
774  std::vector<bool> tmp;
775  tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
776                   // iterator should work on chanMask_??
777  std::vector<bool>::iterator miter;
778  miter = tmp.begin();
779
780  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
781    bool out =!static_cast<bool>(*i);
782    if (useUserMask) {
783      out = out && (*miter);
784      miter++;
785    }
786    (*va) = out;
787    va++;
788  }
789}
790*/
791
792MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
793                                                Bool toStokes) const
794{
795  // Get flags
796  Array<uChar> farr;
797  flagsCol_.get(whichRow, farr);
798
799  // Get data and convert mask to Bool
800  Array<Float> arr;
801  Array<Bool> mask;
802  if (toStokes) {
803     stokesCol_.get(whichRow, arr);
804
805     Array<Bool> tMask(farr.shape());
806     convertArray(tMask, farr);
807     mask = SDPolUtil::stokesData (tMask, True);
808  } else {
809     specCol_.get(whichRow, arr);
810     mask.resize(farr.shape());
811     convertArray(mask, farr);
812  }
813
814  return MaskedArray<Float>(arr,!mask);
815}
816
817Float SDMemTable::getTsys(Int whichRow) const
818{
819  Array<Float> arr;
820  tsCol_.get(whichRow, arr);
821  Float out;
822
823  IPosition ip(arr.shape());
824  ip(asap::BeamAxis) = beamSel_;
825  ip(asap::IFAxis) = IFSel_;
826  ip(asap::PolAxis) = polSel_;
827  ip(asap::ChanAxis)=0;               // First channel only
828
829  out = arr(ip);
830  return out;
831}
832
833MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
834{
835  MDirection::Types mdr = getDirectionReference();
836  Array<Double> posit;
837  dirCol_.get(whichRow,posit);
838  Vector<Double> wpos(2);
839  Int rb;
840  rbeamCol_.get(whichRow,rb);
841  wpos[0] = posit(IPosition(2,beamSel_,0));
842  wpos[1] = posit(IPosition(2,beamSel_,1));
843  if (refBeam && rb > -1) {  // use refBeam instead if it exists
844    wpos[0] = posit(IPosition(2,rb,0));
845    wpos[1] = posit(IPosition(2,rb,1));
846  }
847
848  Quantum<Double> lon(wpos[0],Unit(String("rad")));
849  Quantum<Double> lat(wpos[1],Unit(String("rad")));
850  return MDirection(lon, lat, mdr);
851}
852
853MEpoch SDMemTable::getEpoch(Int whichRow) const
854{
855  MEpoch::Types met = getTimeReference();
856
857  Double obstime;
858  timeCol_.get(whichRow,obstime);
859  MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
860  return MEpoch(tm2, met);
861}
862
863MPosition SDMemTable::getAntennaPosition () const
864{
865  Vector<Double> antpos;
866  table_.keywordSet().get("AntennaPosition", antpos);
867  MVPosition mvpos(antpos(0),antpos(1),antpos(2));
868  return MPosition(mvpos);
869}
870
871
872SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
873{
874 
875  Table t = table_.keywordSet().asTable("FREQUENCIES");
876  if (freqID> t.nrow() ) {
877    throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
878  }
879
880  Double rp,rv,inc;
881  String rf;
882  ROScalarColumn<Double> rpc(t, "REFPIX");
883  ROScalarColumn<Double> rvc(t, "REFVAL");
884  ROScalarColumn<Double> incc(t, "INCREMENT");
885  t.keywordSet().get("BASEREFFRAME",rf);
886
887  // Create SpectralCoordinate (units Hz)
888  MFrequency::Types mft;
889  if (!MFrequency::getType(mft, rf)) {
890    cerr << "Frequency type unknown assuming TOPO" << endl;
891    mft = MFrequency::TOPO;
892  }
893  rpc.get(freqID, rp);
894  rvc.get(freqID, rv);
895  incc.get(freqID, inc);
896
897  SpectralCoordinate spec(mft,rv,inc,rp);
898  return spec;
899}
900
901
902SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
903                                                     uInt restFreqID,
904                                                     uInt whichRow) const
905{
906 
907  // Create basic SC
908  SpectralCoordinate spec = getSpectralCoordinate (freqID);
909
910  Table t = table_.keywordSet().asTable("FREQUENCIES");
911
912  // Set rest frequency
913  Vector<Double> restFreqIDs;
914  t.keywordSet().get("RESTFREQS",restFreqIDs);
915  if (restFreqID < restFreqIDs.nelements()) {    // Should always be true
916    spec.setRestFrequency(restFreqIDs(restFreqID),True);
917  }
918
919  // Set up frame conversion layer
920  String frm;
921  t.keywordSet().get("REFFRAME",frm);
922  if (frm == "") frm = "TOPO";
923  MFrequency::Types mtype;
924  if (!MFrequency::getType(mtype, frm)) {
925    // Should never happen
926    cerr << "Frequency type unknown assuming TOPO" << endl;
927    mtype = MFrequency::TOPO;
928  }
929
930  // Set reference frame conversion  (requires row)
931  MDirection dir = getDirection(whichRow);
932  MEpoch epoch = getEpoch(whichRow);
933  MPosition pos = getAntennaPosition();
934
935  if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
936    throw(AipsError("Couldn't convert frequency frame."));
937  }
938
939  // Now velocity conversion if appropriate
940  String unitStr;
941  t.keywordSet().get("UNIT",unitStr);
942
943  String dpl;
944  t.keywordSet().get("DOPPLER",dpl);
945  MDoppler::Types dtype;
946  MDoppler::getType(dtype, dpl);
947
948  // Only set velocity unit if non-blank and non-Hz
949  if (!unitStr.empty()) {
950     Unit unitU(unitStr);
951     if (unitU==Unit("Hz")) {
952     } else {
953        spec.setVelocity(unitStr, dtype);
954     }
955  }
956
957  return spec;
958}
959
960
961Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
962                               uInt freqID) {
963  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
964  if (freqID > t.nrow() ) {
965    throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
966  }
967  ScalarColumn<Double> rpc(t, "REFPIX");
968  ScalarColumn<Double> rvc(t, "REFVAL");
969  ScalarColumn<Double> incc(t, "INCREMENT");
970
971  rpc.put(freqID, speccord.referencePixel()[0]);
972  rvc.put(freqID, speccord.referenceValue()[0]);
973  incc.put(freqID, speccord.increment()[0]);
974
975  return True;
976}
977
978Int SDMemTable::nCoordinates() const
979{
980  return table_.keywordSet().asTable("FREQUENCIES").nrow();
981}
982
983
984std::vector<double> SDMemTable::getRestFreqs() const
985{
986  Table t = table_.keywordSet().asTable("FREQUENCIES");
987  Vector<Double> tvec;
988  t.keywordSet().get("RESTFREQS",tvec);
989  std::vector<double> stlout;
990  tvec.tovector(stlout);
991  return stlout; 
992}
993
994bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
995{
996  TableDesc td("", "1", TableDesc::Scratch);
997  td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
998  td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
999  td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
1000  SetupNewTable aNewTab("freqs", td, Table::New);
1001  Table aTable (aNewTab, Table::Memory, sdft.length());
1002  ScalarColumn<Double> sc0(aTable, "REFPIX");
1003  ScalarColumn<Double> sc1(aTable, "REFVAL");
1004  ScalarColumn<Double> sc2(aTable, "INCREMENT");
1005  for (uInt i=0; i < sdft.length(); ++i) {
1006    sc0.put(i,sdft.referencePixel(i));
1007    sc1.put(i,sdft.referenceValue(i));
1008    sc2.put(i,sdft.increment(i));
1009  }
1010  String rf = sdft.refFrame();
1011  if (rf.contains("TOPO")) rf = "TOPO";
1012
1013  aTable.rwKeywordSet().define("BASEREFFRAME", rf);
1014  aTable.rwKeywordSet().define("REFFRAME", rf);
1015  aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
1016  aTable.rwKeywordSet().define("UNIT", String(""));
1017  aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
1018  Vector<Double> rfvec;
1019  String rfunit;
1020  sdft.restFrequencies(rfvec,rfunit);
1021  Quantum<Vector<Double> > q(rfvec, rfunit);
1022  rfvec.resize();
1023  rfvec = q.getValue("Hz");
1024  aTable.rwKeywordSet().define("RESTFREQS", rfvec);
1025  table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
1026  return true;
1027}
1028
1029bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
1030{
1031  TableDesc td("", "1", TableDesc::Scratch);
1032  td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1033  td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1034  td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1035  td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1036  td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1037  SetupNewTable aNewTab("fits", td, Table::New);
1038  Table aTable(aNewTab, Table::Memory);
1039  ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1040  ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1041  ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1042  ArrayColumn<Bool> sc3(aTable, "PARMASK");
1043  ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1044  for (uInt i; i<sdft.length(); ++i) {
1045    const Vector<Double>& parms = sdft.getParameters(i);
1046    const Vector<Bool>& parmask = sdft.getParameterMask(i);
1047    const Vector<String>& funcs = sdft.getFunctions(i);
1048    const Vector<Int>& comps = sdft.getComponents(i);
1049    const Vector<String>& finfo = sdft.getFrameInfo(i);
1050    sc0.put(i,funcs);
1051    sc1.put(i,comps);
1052    sc3.put(i,parmask);
1053    sc2.put(i,parms);
1054    sc4.put(i,finfo);
1055  }
1056  table_.rwKeywordSet().defineTable("FITS", aTable);
1057  return true;
1058}
1059
1060SDFitTable SDMemTable::getSDFitTable() const
1061{
1062  const Table& t = table_.keywordSet().asTable("FITS");
1063  Vector<Double> parms;
1064  Vector<Bool> parmask;
1065  Vector<String> funcs;
1066  Vector<String> finfo;
1067  Vector<Int> comps; 
1068  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1069  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1070  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1071  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1072  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1073  uInt n = t.nrow();
1074  SDFitTable sdft;
1075  for (uInt i=0; i<n; ++i) {
1076    parmaskCol.get(i, parmask);
1077    parmsCol.get(i, parms);
1078    funcsCol.get(i, funcs);
1079    compsCol.get(i, comps);
1080    finfoCol.get(i, finfo);
1081    sdft.addFit(parms, parmask, funcs, comps, finfo);
1082  }
1083  return sdft;
1084}
1085
1086SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1087  Array<Int> fitid;
1088  fitCol_.get(whichRow, fitid);
1089  if (fitid.nelements() == 0) return SDFitTable();
1090
1091  IPosition shp = fitid.shape();
1092  IPosition start(4, beamSel_, IFSel_, polSel_,0);
1093  IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1094
1095  // reform the output array slice to be of dim=1
1096  Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1097
1098  const Table& t = table_.keywordSet().asTable("FITS");
1099  Vector<Double> parms;
1100  Vector<Bool> parmask;
1101  Vector<String> funcs;
1102  Vector<String> finfo;
1103  Vector<Int> comps;   
1104  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1105  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1106  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1107  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1108  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1109  if (t.nrow() == 0) return SDFitTable();
1110  SDFitTable sdft;
1111  Int k=-1;
1112  for (uInt i=0; i< tmp.nelements(); ++i) {
1113    k = tmp[i];
1114    if ( k > -1 && k < t.nrow() ) {
1115      parms.resize();
1116      parmsCol.get(k, parms);
1117      parmask.resize();
1118      parmaskCol.get(k, parmask);
1119      funcs.resize();
1120      funcsCol.get(k, funcs);
1121      comps.resize();
1122      compsCol.get(k, comps);
1123      finfo.resize();
1124      finfoCol.get(k, finfo);
1125      sdft.addFit(parms, parmask, funcs, comps, finfo);
1126    }
1127  }
1128  return sdft;
1129}
1130
1131void SDMemTable::addFit(uInt whichRow,
1132                        const Vector<Double>& p, const Vector<Bool>& m,
1133                        const Vector<String>& f, const Vector<Int>& c)
1134{
1135  if (whichRow >= nRow()) {
1136    throw(AipsError("Specified row out of range"));
1137  }
1138  Table t = table_.keywordSet().asTable("FITS");
1139  uInt nrow = t.nrow(); 
1140  t.addRow();
1141  ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1142  ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1143  ArrayColumn<Int> compsCol(t, "COMPONENTS");
1144  ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1145  ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1146  parmsCol.put(nrow, p);
1147  parmaskCol.put(nrow, m);
1148  compsCol.put(nrow, c);
1149  funcsCol.put(nrow, f);
1150  Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1151  finfoCol.put(nrow, fi);
1152
1153  Array<Int> fitarr;
1154  fitCol_.get(whichRow, fitarr);
1155
1156  Array<Int> newarr;               // The new Array containing the fitid
1157  Int pos =-1;                     // The fitid position in the array
1158  if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1159    Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1160    arr = -1;
1161    newarr.reference(arr);
1162    pos = 0;     
1163  } else {
1164    IPosition shp = fitarr.shape();
1165    IPosition start(4, beamSel_, IFSel_, polSel_,0);
1166    IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1167    // reform the output array slice to be of dim=1
1168    Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1169    const Vector<Int>& fits = tmp;
1170    VectorSTLIterator<Int> it(fits);
1171    Int i = 0;
1172    while (it != fits.end()) {
1173      if (*it == -1) {
1174        pos = i;
1175        break;
1176      }
1177      ++i;
1178      ++it;
1179    };
1180  }
1181  if (pos == -1) {
1182      mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1183      pos = fitarr.shape()[3];     // the new element position
1184  } else {
1185    if (fitarr.nelements() > 0)
1186      newarr = fitarr;
1187  }
1188  newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1189  fitCol_.put(whichRow, newarr);
1190
1191}
1192
1193SDFrequencyTable SDMemTable::getSDFreqTable() const
1194{
1195  const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1196  SDFrequencyTable sdft;
1197
1198  // Add refpix/refval/incr.  What are the units ? Hz I suppose
1199  // but it's nowhere described...
1200  Vector<Double> refPix, refVal, incr;
1201  ScalarColumn<Double> refPixCol(t, "REFPIX");
1202  ScalarColumn<Double> refValCol(t, "REFVAL");
1203  ScalarColumn<Double> incrCol(t, "INCREMENT");
1204  refPix = refPixCol.getColumn();
1205  refVal = refValCol.getColumn();
1206  incr = incrCol.getColumn();
1207
1208  uInt n = refPix.nelements();
1209  for (uInt i=0; i<n; i++) {
1210     sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1211  }
1212
1213  // Frequency reference frame.  I don't know if this
1214  // is the correct frame.  It might be 'REFFRAME'
1215  // rather than 'BASEREFFRAME' ?
1216  String baseFrame;
1217  t.keywordSet().get("BASEREFFRAME",baseFrame);
1218  sdft.setRefFrame(baseFrame);
1219
1220  // Equinox 
1221  Float equinox;
1222  t.keywordSet().get("EQUINOX", equinox);
1223  sdft.setEquinox(equinox);
1224
1225  // Rest Frequency
1226  Vector<Double> restFreqs;
1227  t.keywordSet().get("RESTFREQS", restFreqs);
1228  for (uInt i=0; i<restFreqs.nelements(); i++) {
1229     sdft.addRestFrequency(restFreqs[i]);
1230  }
1231  sdft.setRestFrequencyUnit(String("Hz"));
1232
1233  return sdft;
1234}
1235
1236bool SDMemTable::putSDContainer(const SDContainer& sdc)
1237{
1238  uInt rno = table_.nrow();
1239  table_.addRow();
1240
1241  timeCol_.put(rno, sdc.timestamp);
1242  srcnCol_.put(rno, sdc.sourcename);
1243  fldnCol_.put(rno, sdc.fieldname);
1244  specCol_.put(rno, sdc.getSpectrum());
1245  flagsCol_.put(rno, sdc.getFlags());
1246  tsCol_.put(rno, sdc.getTsys());
1247  scanCol_.put(rno, sdc.scanid);
1248  integrCol_.put(rno, sdc.interval);
1249  freqidCol_.put(rno, sdc.getFreqMap());
1250  restfreqidCol_.put(rno, sdc.getRestFreqMap());
1251  dirCol_.put(rno, sdc.getDirection());
1252  rbeamCol_.put(rno, sdc.refbeam);
1253  tcalCol_.put(rno, sdc.tcal);
1254  tcaltCol_.put(rno, sdc.tcaltime);
1255  azCol_.put(rno, sdc.azimuth);
1256  elCol_.put(rno, sdc.elevation);
1257  paraCol_.put(rno, sdc.parangle);
1258  fitCol_.put(rno, sdc.getFitMap());
1259  return true;
1260}
1261
1262SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1263{
1264  SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1265  timeCol_.get(whichRow, sdc.timestamp);
1266  srcnCol_.get(whichRow, sdc.sourcename);
1267  integrCol_.get(whichRow, sdc.interval);
1268  scanCol_.get(whichRow, sdc.scanid);
1269  fldnCol_.get(whichRow, sdc.fieldname);
1270  rbeamCol_.get(whichRow, sdc.refbeam);
1271  azCol_.get(whichRow, sdc.azimuth);
1272  elCol_.get(whichRow, sdc.elevation);
1273  paraCol_.get(whichRow, sdc.parangle);
1274  Vector<Float> tc;
1275  tcalCol_.get(whichRow, tc);
1276  sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1277  tcaltCol_.get(whichRow, sdc.tcaltime);
1278
1279  Array<Float> spectrum;
1280  Array<Float> tsys;
1281  Array<uChar> flagtrum;
1282  Vector<uInt> fmap;
1283  Array<Double> direction;
1284  Array<Int> fits;
1285 
1286  specCol_.get(whichRow, spectrum);
1287  sdc.putSpectrum(spectrum);
1288  flagsCol_.get(whichRow, flagtrum);
1289  sdc.putFlags(flagtrum);
1290  tsCol_.get(whichRow, tsys);
1291  sdc.putTsys(tsys);
1292  freqidCol_.get(whichRow, fmap);
1293  sdc.putFreqMap(fmap);
1294  restfreqidCol_.get(whichRow, fmap);
1295  sdc.putRestFreqMap(fmap);
1296  dirCol_.get(whichRow, direction);
1297  sdc.putDirection(direction);
1298  fitCol_.get(whichRow, fits);
1299  sdc.putFitMap(fits);
1300  return sdc;
1301}
1302
1303bool SDMemTable::putSDHeader(const SDHeader& sdh)
1304{
1305  table_.rwKeywordSet().define("nIF", sdh.nif);
1306  table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1307  table_.rwKeywordSet().define("nPol", sdh.npol);
1308  table_.rwKeywordSet().define("nChan", sdh.nchan);
1309  table_.rwKeywordSet().define("Observer", sdh.observer);
1310  table_.rwKeywordSet().define("Project", sdh.project);
1311  table_.rwKeywordSet().define("Obstype", sdh.obstype);
1312  table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1313  table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1314  table_.rwKeywordSet().define("Equinox", sdh.equinox);
1315  table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1316  table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1317  table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1318  table_.rwKeywordSet().define("UTC", sdh.utc);
1319  table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1320  table_.rwKeywordSet().define("Epoch", sdh.epoch);
1321  return true;
1322}
1323
1324SDHeader SDMemTable::getSDHeader() const
1325{
1326  SDHeader sdh;
1327  table_.keywordSet().get("nBeam",sdh.nbeam);
1328  table_.keywordSet().get("nIF",sdh.nif);
1329  table_.keywordSet().get("nPol",sdh.npol);
1330  table_.keywordSet().get("nChan",sdh.nchan);
1331  table_.keywordSet().get("Observer", sdh.observer);
1332  table_.keywordSet().get("Project", sdh.project);
1333  table_.keywordSet().get("Obstype", sdh.obstype);
1334  table_.keywordSet().get("AntennaName", sdh.antennaname);
1335  table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1336  table_.keywordSet().get("Equinox", sdh.equinox);
1337  table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1338  table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1339  table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1340  table_.keywordSet().get("UTC", sdh.utc);
1341  table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1342  table_.keywordSet().get("Epoch", sdh.epoch);
1343  return sdh;
1344}
1345void SDMemTable::makePersistent(const std::string& filename)
1346{ 
1347  table_.deepCopy(filename,Table::New);
1348
1349}
1350
1351Int SDMemTable::nScan() const {
1352  Int n = 0;
1353  Int previous = -1;Int current=0;
1354  for (uInt i=0; i< scanCol_.nrow();i++) {
1355    scanCol_.getScalar(i,current);
1356    if (previous != current) {
1357      previous = current;
1358      n++;
1359    }
1360  }
1361  return n;
1362}
1363
1364String SDMemTable::formatSec(Double x) const
1365{
1366  Double xcop = x;
1367  MVTime mvt(xcop/24./3600.);  // make days
1368
1369  if (x < 59.95)
1370    return  String("      ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1371  else if (x < 3599.95)
1372    return String("   ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1373  else {
1374    ostringstream oss;
1375    oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1376    oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1377    return String(oss);
1378  }   
1379};
1380
1381String SDMemTable::formatDirection(const MDirection& md) const
1382{
1383  Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1384  Int prec = 7;
1385
1386  MVAngle mvLon(t[0]);
1387  String sLon = mvLon.string(MVAngle::TIME,prec);
1388  MVAngle mvLat(t[1]);
1389  String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1390  return sLon + String(" ") + sLat;
1391}
1392
1393
1394std::string SDMemTable::getFluxUnit() const
1395{
1396  String tmp;
1397  table_.keywordSet().get("FluxUnit", tmp);
1398  return tmp;
1399}
1400
1401void SDMemTable::setFluxUnit(const std::string& unit)
1402{
1403  String tmp(unit);
1404  Unit tU(tmp);
1405  if (tU==Unit("K") || tU==Unit("Jy")) {
1406     table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1407  } else {
1408     throw AipsError("Illegal unit - must be compatible with Jy or K");
1409  }
1410}
1411
1412
1413void SDMemTable::setInstrument(const std::string& name)
1414{
1415  Bool throwIt = True;
1416  Instrument ins = SDAttr::convertInstrument(name, throwIt);
1417  String nameU(name);
1418  nameU.upcase();
1419  table_.rwKeywordSet().define(String("AntennaName"), nameU);
1420}
1421
1422std::string SDMemTable::summary(bool verbose) const  {
1423
1424  // Format header info
1425  ostringstream oss;
1426  oss << endl;
1427  oss << "--------------------------------------------------------------------------------" << endl;
1428  oss << " Scan Table Summary" << endl;
1429  oss << "--------------------------------------------------------------------------------" << endl;
1430  oss.flags(std::ios_base::left);
1431  oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1432      << setw(15) << "IFs:" << setw(4) << nIF() << endl
1433      << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1434      << setw(15) << "Channels:"  << setw(4) << nChan() << endl;
1435  oss << endl;
1436  String tmp;
1437  table_.keywordSet().get("Observer", tmp);
1438  oss << setw(15) << "Observer:" << tmp << endl;
1439  oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1440  table_.keywordSet().get("Project", tmp);
1441  oss << setw(15) << "Project:" << tmp << endl;
1442  table_.keywordSet().get("Obstype", tmp);
1443  oss << setw(15) << "Obs. Type:" << tmp << endl;
1444  table_.keywordSet().get("AntennaName", tmp);
1445  oss << setw(15) << "Antenna Name:" << tmp << endl;
1446  table_.keywordSet().get("FluxUnit", tmp);
1447  oss << setw(15) << "Flux Unit:" << tmp << endl;
1448  Table t = table_.keywordSet().asTable("FREQUENCIES");
1449  Vector<Double> vec;
1450  t.keywordSet().get("RESTFREQS",vec);
1451  oss << setw(15) << "Rest Freqs:";
1452  if (vec.nelements() > 0) {
1453      oss << setprecision(0) << vec << " [Hz]" << endl;
1454  } else {
1455      oss << "None set" << endl;
1456  }
1457  oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1458  oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1459      << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1460  oss << endl;
1461
1462  String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1463  oss << setw(5) << "Scan"
1464      << setw(15) << "Source"
1465      << setw(24) << dirtype
1466      << setw(10) << "Time"
1467      << setw(18) << "Integration"
1468      << setw(7) << "FreqIDs" << endl;
1469  oss << "--------------------------------------------------------------------------------" << endl;
1470 
1471  // Generate list of scan start and end integrations
1472  Vector<Int> scanIDs = scanCol_.getColumn();
1473  Vector<uInt> startInt, endInt;
1474  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1475
1476  const uInt nScans = startInt.nelements();
1477  String name;
1478  Vector<uInt> freqIDs, listFQ;
1479  Vector<uInt> restFreqIDs, listRestFQ;
1480  uInt nInt;
1481
1482  for (uInt i=0; i<nScans; i++) {
1483    // Get things from first integration of scan
1484    String time = getTime(startInt(i),False);
1485    String tInt = formatSec(Double(getInterval(startInt(i))));
1486    String posit = formatDirection(getDirection(startInt(i),True));
1487    srcnCol_.getScalar(startInt(i),name);
1488
1489    // Find all the FreqIDs in this scan
1490    listFQ.resize(0);     
1491    listRestFQ.resize(0);     
1492    for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1493      freqidCol_.get(j, freqIDs);
1494      for (uInt k=0; k<freqIDs.nelements(); k++) {
1495        mathutil::addEntry(listFQ, freqIDs(k));
1496      }
1497//
1498      restfreqidCol_.get(j, restFreqIDs);
1499      for (uInt k=0; k<restFreqIDs.nelements(); k++) {
1500        mathutil::addEntry(listRestFQ, restFreqIDs(k));
1501      }
1502    }
1503
1504    nInt = endInt(i) - startInt(i) + 1;
1505    oss << setw(3) << std::right << i << std::left << setw(2) << "  "
1506        << setw(15) << name
1507        << setw(24) << posit
1508        << setw(10) << time
1509        << setw(3) << std::right << nInt  << setw(3) << " x " << std::left
1510        << setw(6) <<  tInt
1511        << " " << listFQ << " " << listRestFQ << endl;
1512  }
1513  oss << endl;
1514  oss << "Table contains " << table_.nrow() << " integration(s) in "
1515      << nScans << " scan(s)." << endl;
1516
1517  // Frequency Table
1518  if (verbose) {
1519    std::vector<string> info = getCoordInfo();
1520    SDFrequencyTable sdft = getSDFreqTable();
1521    oss << endl << endl;
1522    oss << "FreqID  Frame   RefFreq(Hz)     RefPix   Increment(Hz)" << endl;
1523    oss << "--------------------------------------------------------------------------------" << endl;
1524    for (uInt i=0; i<sdft.length(); i++) {
1525      oss << setw(8) << i << setw(8)
1526          << info[3] << setw(16) << setprecision(8)
1527          << sdft.referenceValue(i) << setw(10)
1528          << sdft.referencePixel(i) << setw(12)
1529          << sdft.increment(i) << endl;
1530    }
1531    oss << "--------------------------------------------------------------------------------" << endl;
1532  }
1533  return String(oss);
1534}
1535/*
1536std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1537  ostringstream oss;
1538  Vector<Int> scanIDs = scanCol_.getColumn();
1539  Vector<uInt> startInt, endInt;
1540  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1541  const uInt nScans = startInt.nelements();
1542  std::vector<int>::const_iterator it(whichScans);
1543  return String(oss);
1544}
1545*/
1546Int SDMemTable::nBeam() const
1547{
1548  Int n;
1549  table_.keywordSet().get("nBeam",n);
1550  return n;
1551}
1552
1553Int SDMemTable::nIF() const {
1554  Int n;
1555  table_.keywordSet().get("nIF",n);
1556  return n;
1557}
1558
1559Int SDMemTable::nPol() const {
1560  Int n;
1561  table_.keywordSet().get("nPol",n);
1562  return n;
1563}
1564
1565Int SDMemTable::nChan() const {
1566  Int n;
1567  table_.keywordSet().get("nChan",n);
1568  return n;
1569}
1570
1571Table SDMemTable::getHistoryTable() const
1572{
1573  return table_.keywordSet().asTable("HISTORY");
1574}
1575
1576void SDMemTable::appendToHistoryTable(const Table& otherHist)
1577{
1578  Table t = table_.rwKeywordSet().asTable("HISTORY");
1579  const String sep = "--------------------------------------------------------------------------------";
1580  addHistory(sep);
1581  TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1582  addHistory(sep);
1583}
1584
1585void SDMemTable::addHistory(const std::string& hist)
1586{
1587  Table t = table_.rwKeywordSet().asTable("HISTORY");
1588  uInt nrow = t.nrow(); 
1589  t.addRow();
1590  ScalarColumn<String> itemCol(t, "ITEM");
1591  itemCol.put(nrow, hist);
1592}
1593
1594std::vector<std::string> SDMemTable::getHistory() const
1595{
1596  Vector<String> history;
1597  const Table& t = table_.keywordSet().asTable("HISTORY");
1598  uInt nrow = t.nrow(); 
1599  ROScalarColumn<String> itemCol(t, "ITEM");
1600  std::vector<std::string> stlout;
1601  String hist;
1602  for (uInt i=0; i<nrow; ++i) {
1603    itemCol.get(i, hist);
1604    stlout.push_back(hist);
1605  }
1606  return stlout;
1607}
1608
1609
1610/*
1611  void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1612
1613  std::vector<int>::iterator it;
1614  ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1615  for (it = whichChans.begin(); it != whichChans.end(); it++) {
1616    j.reset(j.begin(uInt(*it)));
1617    for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1618      for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1619        for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1620             iii != iii.end(); ++iii) {
1621          (*iii) =
1622        }
1623      }
1624    }
1625  }
1626
1627}
1628*/
1629void SDMemTable::flag(int whichRow)
1630  {
1631  Array<uChar> arr;
1632  flagsCol_.get(whichRow, arr);
1633
1634  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1635  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1636  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1637  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1638  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1639  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1640
1641  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1642    (*i) = uChar(True);
1643  }
1644
1645  flagsCol_.put(whichRow, arr);
1646}
1647
1648MDirection::Types SDMemTable::getDirectionReference() const
1649{ 
1650  Float eq;
1651  table_.keywordSet().get("Equinox",eq);
1652  std::map<float,string> mp;
1653  mp[2000.0] = "J2000";
1654  mp[1950.0] = "B1950";
1655  MDirection::Types mdr;
1656  if (!MDirection::getType(mdr, mp[eq])) {   
1657    mdr = MDirection::J2000;
1658    cerr  << "Unknown equinox using J2000" << endl;
1659  }
1660
1661  return mdr;
1662}
1663
1664MEpoch::Types SDMemTable::getTimeReference() const
1665{
1666  MEpoch::Types met;
1667  String ep;
1668  table_.keywordSet().get("Epoch",ep);
1669  if (!MEpoch::getType(met, ep)) {
1670    cerr << "Epoch type unknown - using UTC" << endl;
1671    met = MEpoch::UTC;
1672  }
1673
1674  return met;
1675}
1676
1677
1678Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1679                              const String& sUnit,
1680                              const vector<string>& lines,
1681                              const String& source,
1682                              Int whichIF)
1683{
1684   const Int nIFs = nIF();
1685   if (whichIF>=nIFs) {
1686      throw(AipsError("Illegal IF index"));
1687   }
1688
1689   // Find vector of restfrequencies
1690   // Double takes precedence over String
1691   Unit unit;
1692   Vector<Double> restFreqs;
1693   if (restFreqsIn.nelements()>0) {
1694      restFreqs.resize(restFreqsIn.nelements());
1695      restFreqs = restFreqsIn;
1696      unit = Unit(sUnit);
1697   } else if (lines.size()>0) {
1698      const uInt nLines = lines.size();
1699      unit = Unit("Hz");
1700      restFreqs.resize(nLines);
1701      MFrequency lineFreq;
1702      for (uInt i=0; i<nLines; i++) {
1703         String tS(lines[i]);
1704         tS.upcase();
1705         if (MeasTable::Line(lineFreq, tS)) {
1706            restFreqs[i] = lineFreq.getValue().getValue();          // Hz
1707         } else {
1708            String s = String(lines[i]) +
1709              String(" is an unrecognized spectral line");
1710            throw(AipsError(s));
1711         }
1712      }
1713   } else {
1714      throw(AipsError("You have not specified any rest frequencies or lines"));
1715   }
1716
1717   // If multiple restfreqs, must be length nIF. In this
1718   // case we will just replace the rest frequencies
1719   // We can't disinguish scalar and vector of length 1
1720   const uInt nRestFreqs = restFreqs.nelements();
1721   Int idx = -1;
1722   SDFrequencyTable sdft = getSDFreqTable();
1723
1724   if (nRestFreqs>1) {
1725     // Replace restFreqs, one per IF
1726      if (nRestFreqs != nIFs) {
1727         throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1728      }
1729      cout << "Replacing rest frequencies, one per IF, with given list : " << restFreqs << endl;
1730      sdft.deleteRestFrequencies();
1731      for (uInt i=0; i<nRestFreqs; i++) {
1732         Quantum<Double> rf(restFreqs[i], unit);
1733         sdft.addRestFrequency(rf.getValue("Hz"));
1734      }
1735   } else {
1736
1737     // Add new rest freq
1738      Quantum<Double> rf(restFreqs[0], unit);
1739      idx = sdft.addRestFrequency(rf.getValue("Hz"));
1740      if (whichIF>=0) {
1741         cout << "Selecting given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1742      } else {
1743         cout << "Selecting given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1744      }
1745   }
1746   
1747   // Replace
1748   Bool empty = source.empty();
1749   Bool ok = False;
1750   if (putSDFreqTable(sdft)) {
1751      const uInt nRow = table_.nrow();
1752      String srcName;
1753      Vector<uInt> restFreqIDs;
1754      for (uInt i=0; i<nRow; i++) {
1755         srcnCol_.get(i, srcName);
1756         restfreqidCol_.get(i,restFreqIDs);       
1757         if (idx==-1) {
1758           // Replace vector of restFreqs; one per IF.
1759           // No selection possible
1760            for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1761         } else {
1762           // Set RestFreqID for selected data
1763            if (empty || source==srcName) {
1764               if (whichIF<0) {
1765                  restFreqIDs = idx;
1766               } else {             
1767                  restFreqIDs[whichIF] = idx;
1768               }
1769            }
1770         }
1771         restfreqidCol_.put(i,restFreqIDs);       
1772      }
1773      ok = True;
1774   } else {
1775     ok = False;
1776   }
1777
1778   return ok;
1779}
1780
1781void SDMemTable::spectralLines() const
1782{
1783   Vector<String> lines = MeasTable::Lines();
1784   MFrequency lineFreq;
1785   Double freq;
1786
1787   cout.flags(std::ios_base::left);
1788   cout << "Line      Frequency (Hz)" << endl;
1789   cout << "-----------------------" << endl;
1790   for (uInt i=0; i<lines.nelements(); i++) {
1791     MeasTable::Line(lineFreq, lines[i]);
1792     freq = lineFreq.getValue().getValue();          // Hz
1793     cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1794   }
1795}
1796
1797void SDMemTable::renumber()
1798{
1799  uInt nRow = scanCol_.nrow();
1800  Int newscanid = 0;
1801  Int cIdx;// the current scanid
1802  // get the first scanid
1803  scanCol_.getScalar(0,cIdx);
1804  Int pIdx = cIdx;// the scanid of the previous row
1805  for (uInt i=0; i<nRow;++i) {
1806    scanCol_.getScalar(i,cIdx);
1807    if (pIdx == cIdx) {
1808      // renumber
1809      scanCol_.put(i,newscanid);
1810    } else {
1811      ++newscanid;
1812      pIdx = cIdx;   // store scanid
1813      --i;           // don't increment next loop
1814    }
1815  }
1816}
1817
1818
1819void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1820                                const IPosition& shape) const
1821{
1822  const uInt nDim = shape.nelements();
1823  start.resize(nDim);
1824  end.resize(nDim);
1825 
1826  start(asap::BeamAxis) = beamSel_;
1827  end(asap::BeamAxis) = beamSel_;
1828  start(asap::IFAxis) = IFSel_;
1829  end(asap::IFAxis) = IFSel_;
1830
1831  start(asap::PolAxis) = polSel_;
1832  end(asap::PolAxis) = polSel_;
1833
1834  start(asap::ChanAxis) = 0;
1835  end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1836}
1837
1838
1839std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1840  // Get spectrum at cursor location
1841{
1842
1843  // Setup accessors
1844  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1845  aa0.reset(aa0.begin(uInt(beamSel_)));                    // Beam selection
1846
1847  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1848  aa1.reset(aa1.begin(uInt(IFSel_)));                      // IF selection
1849
1850  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1851  aa2.reset(aa2.begin(uInt(polSel_)));                     // Pol selection
1852 
1853  std::vector<float> spectrum;
1854  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1855    spectrum.push_back(*i);
1856  }
1857  return spectrum;
1858}
1859
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