source: branches/Release-1-fixes/src/SDMemTable.cc @ 586

Last change on this file since 586 was 586, checked in by mar637, 19 years ago

Fix bug asap0001
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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    chanMask_.resize(0);
108  } else {
109    IFSel_= other.IFSel_;
110    beamSel_= other.beamSel_;
111    polSel_= other.polSel_;
112    chanMask_.resize(0);
113    chanMask_ = other.chanMask_;
114  }
115
116  attach();
117}
118
119SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
120  IFSel_(0),
121  beamSel_(0),
122  polSel_(0)
123{
124  Table t = tableCommand(exprs,tab);
125  if (t.nrow() == 0)
126      throw(AipsError("Query unsuccessful."));
127  table_ = t.copyToMemoryTable("dummy");
128  attach();
129  renumber();
130}
131
132SDMemTable::~SDMemTable()
133{
134  //cerr << "goodbye from SDMemTable @ " << this << endl;
135}
136
137SDMemTable SDMemTable::getScan(Int scanID) const
138{
139  String cond("SELECT * from $1 WHERE SCANID == ");
140  cond += String::toString(scanID);
141  return SDMemTable(table_, cond);
142}
143
144SDMemTable &SDMemTable::operator=(const SDMemTable& other)
145{
146  if (this != &other) {
147     IFSel_= other.IFSel_;
148     beamSel_= other.beamSel_;
149     polSel_= other.polSel_;
150     chanMask_.resize(0);
151     chanMask_ = other.chanMask_;
152     table_ = other.table_.copyToMemoryTable(String("dummy"));
153     attach();
154  }
155  return *this;
156}
157
158SDMemTable SDMemTable::getSource(const std::string& source) const
159{
160  String cond("SELECT * from $1 WHERE SRCNAME == ");
161  cond += source;
162  return SDMemTable(table_, cond);
163}
164
165void SDMemTable::setup()
166{
167  TableDesc td("", "1", TableDesc::Scratch);
168  td.comment() = "A SDMemTable";
169  td.rwKeywordSet().define("VERSION", Int(version_));
170
171  td.addColumn(ScalarColumnDesc<Double>("TIME"));
172  td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
173  td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
174  td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
175  td.addColumn(ArrayColumnDesc<Float>("TSYS"));
176  td.addColumn(ArrayColumnDesc<Float>("STOKES"));
177  td.addColumn(ScalarColumnDesc<Int>("SCANID"));
178  td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
179  td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
180  td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
181  td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
182  td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
183  td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
184  td.addColumn(ArrayColumnDesc<Float>("TCAL"));
185  td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
186  td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
187  td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
188  td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
189  td.addColumn(ArrayColumnDesc<Int>("FITID"));
190
191  // Now create Table SetUp from the description.
192  SetupNewTable aNewTab("dummy", td, Table::New);
193
194  // Bind the Stokes Virtual machine to the STOKES column Because we
195  // don't know how many polarizations will be in the data at this
196  // point, we must bind the Virtual Engine regardless.  The STOKES
197  // column won't be accessed if not appropriate (nPol=4)
198  SDStokesEngine::registerClass();
199  SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
200  aNewTab.bindColumn("STOKES", stokesEngine);
201 
202  // Create Table
203  table_ = Table(aNewTab, Table::Memory, 0);
204  // add subtable
205  TableDesc tdf("", "1", TableDesc::Scratch);
206  tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
207  tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
208  tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
209  tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
210  tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
211  SetupNewTable fittab("fits", tdf, Table::New);
212  Table fitTable(fittab, Table::Memory);
213  table_.rwKeywordSet().defineTable("FITS", fitTable);
214
215  TableDesc tdh("", "1", TableDesc::Scratch);
216  tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
217  SetupNewTable histtab("hist", tdh, Table::New);
218  Table histTable(histtab, Table::Memory);
219  table_.rwKeywordSet().defineTable("HISTORY", histTable);
220}
221
222void SDMemTable::attach()
223{
224  timeCol_.attach(table_, "TIME");
225  srcnCol_.attach(table_, "SRCNAME");
226  specCol_.attach(table_, "SPECTRA");
227  flagsCol_.attach(table_, "FLAGTRA");
228  tsCol_.attach(table_, "TSYS");
229  stokesCol_.attach(table_, "STOKES");
230  scanCol_.attach(table_, "SCANID");
231  integrCol_.attach(table_, "INTERVAL");
232  freqidCol_.attach(table_, "FREQID");
233  restfreqidCol_.attach(table_, "RESTFREQID");
234  dirCol_.attach(table_, "DIRECTION");
235  fldnCol_.attach(table_, "FIELDNAME");
236  tcaltCol_.attach(table_, "TCALTIME");
237  tcalCol_.attach(table_, "TCAL");
238  azCol_.attach(table_, "AZIMUTH");
239  elCol_.attach(table_, "ELEVATION");
240  paraCol_.attach(table_, "PARANGLE");
241  rbeamCol_.attach(table_, "REFBEAM");
242  fitCol_.attach(table_,"FITID");
243}
244
245
246std::string SDMemTable::getSourceName(Int whichRow) const
247{
248  String name;
249  srcnCol_.get(whichRow, name);
250  return name;
251}
252
253std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
254{
255  Double tm;
256  if (whichRow > -1) {
257    timeCol_.get(whichRow, tm);
258  } else {
259    table_.keywordSet().get("UTC",tm);
260  }
261  MVTime mvt(tm);
262  if (showDate)
263    mvt.setFormat(MVTime::YMD);
264  else
265    mvt.setFormat(MVTime::TIME);
266  ostringstream oss;
267  oss << mvt;
268  return String(oss);
269}
270
271double SDMemTable::getInterval(Int whichRow) const
272{
273  Double intval;
274  integrCol_.get(whichRow, intval);
275  return intval;
276}
277
278bool SDMemTable::setIF(Int whichIF)
279{
280  if ( whichIF >= 0 && whichIF < nIF()) {
281    IFSel_ = whichIF;
282    return true;
283  }
284  return false;
285}
286
287bool SDMemTable::setBeam(Int whichBeam)
288{
289  if ( whichBeam >= 0 && whichBeam < nBeam()) {
290    beamSel_ = whichBeam;
291    return true;
292  }
293  return false;
294}
295
296bool SDMemTable::setPol(Int whichPol)
297{
298  if ( whichPol >= 0 && whichPol < nPol()) {
299    polSel_ = whichPol;
300    return true;
301  }
302  return false;
303}
304
305void SDMemTable::resetCursor()
306{
307   polSel_ = 0;
308   IFSel_ = 0;
309   beamSel_ = 0;
310}
311
312bool SDMemTable::setMask(std::vector<int> whichChans)
313{
314  std::vector<int>::iterator it;
315  uInt n = flagsCol_.shape(0)(3);
316  if (whichChans.empty()) {
317    chanMask_ = std::vector<bool>(n,true);
318    return true;     
319  }
320  chanMask_.resize(n,true);
321  for (it = whichChans.begin(); it != whichChans.end(); ++it) {
322    if (*it < n) {
323      chanMask_[*it] = false;
324    }
325  }
326  return true;
327}
328
329std::vector<bool> SDMemTable::getMask(Int whichRow) const
330{
331
332  std::vector<bool> mask;
333
334  Array<uChar> arr;
335  flagsCol_.get(whichRow, arr);
336
337  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
338  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
339  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
340  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
341  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
342  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
343
344  Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
345
346  std::vector<bool> tmp;
347  tmp = chanMask_; // WHY the fxxx do I have to make a copy here
348  std::vector<bool>::iterator miter;
349  miter = tmp.begin();
350
351  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
352    bool out =!static_cast<bool>(*i);
353    if (useUserMask) {
354      out = out && (*miter);
355      miter++;
356    }
357    mask.push_back(out);
358  }
359  return mask;
360}
361
362
363
364std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
365{
366  Array<Float> arr;
367  specCol_.get(whichRow, arr);
368  return getFloatSpectrum(arr);
369}
370
371
372int SDMemTable::nStokes() const
373{
374   return stokesCol_.shape(0).nelements();        // All rows same shape
375}
376
377
378std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow,
379                                                 Bool doPol) const
380  //
381  // Gets one STokes parameter depending on cursor polSel location
382  //  doPol=False  : I,Q,U,V
383  //  doPol=True   : I,P,PA,V   ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
384  //
385{
386  AlwaysAssert(asap::nAxes==4,AipsError);
387  if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
388    throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
389  }
390 
391  // For full conversion we are only supporting linears at the moment
392 
393  if (nPol() > 2) {
394    String antName;
395    table_.keywordSet().get("AntennaName", antName);
396    Instrument inst = SDAttr::convertInstrument (antName, True);
397    SDAttr sdAtt;
398    if (sdAtt.feedPolType(inst) != LINEAR) {
399      throw(AipsError("Only linear polarizations are supported"));
400    }
401  }
402
403  Array<Float> arr;
404  stokesCol_.get(whichRow, arr);
405 
406  if (doPol && (polSel_==1 || polSel_==2)) {       //   Q,U --> P, P.A.
407   
408    // Set current cursor location
409   
410    const IPosition& shape = arr.shape();
411    IPosition start, end;
412    getCursorSlice(start, end, shape);
413   
414    // Get Q and U slices
415   
416    Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
417    Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
418   
419    // Compute output
420   
421    Array<Float> out;
422    if (polSel_==1) {                                        // P
423      out = SDPolUtil::polarizedIntensity(Q,U);
424    } else if (polSel_==2) {                                 // P.A.
425      out = SDPolUtil::positionAngle(Q,U);
426    }
427   
428    // Copy to output
429   
430    IPosition vecShape(1,shape(asap::ChanAxis));
431    Vector<Float> outV = out.reform(vecShape);
432    std::vector<float> stlout;
433    outV.tovector(stlout);
434    return stlout;
435   
436  } else {   
437    // Selects at the cursor location
438    return getFloatSpectrum(arr);
439  }
440}
441
442std::string SDMemTable::getPolarizationLabel(Bool linear, Bool stokes,
443                                              Bool linPol, Int polIdx) const
444{
445   uInt idx = polSel_;   
446   if (polIdx >=0) idx = polIdx;
447   return SDPolUtil::polarizationLabel(idx, linear, stokes, linPol);
448}
449
450
451
452std::vector<float> SDMemTable::stokesToPolSpectrum(Int whichRow,
453                                                   Bool toLinear,
454                                                   Int 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    uInt selection = polSel_;
486    if (polIdx > -1) selection = polIdx;
487    Bool doRR = (selection==0);
488    if (selection>1) {
489      throw(AipsError("Only conversion to RR & LL is currently supported"));
490    }
491   
492    // Get I and V slices   
493    Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
494    Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
495   
496    // Compute output     
497    out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
498  }
499 
500  // Copy to output
501   IPosition vecShape(1,shape(asap::ChanAxis));
502   Vector<Float> outV = out.reform(vecShape);
503   std::vector<float> stlout;
504   outV.tovector(stlout);
505//
506   return stlout;
507}
508
509
510
511
512Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
513{
514
515// Get data
516
517  Array<Float> arr;
518  stokesCol_.get(whichRow, arr);
519
520// Set current cursor location and overwrite polarization axis
521
522  const IPosition& shape = arr.shape();
523  IPosition start(shape.nelements(),0); 
524  IPosition end(shape-1);
525  if (iBeam!=-1) {
526     start(asap::BeamAxis) = iBeam;
527     end(asap::BeamAxis) = iBeam;
528  }
529  if (iIF!=-1) {
530     start(asap::IFAxis) = iIF;
531     end(asap::IFAxis) = iIF;
532  }
533
534// Get slice
535
536  return arr(start,end);
537}
538
539
540std::vector<string> SDMemTable::getCoordInfo() const
541{
542  String un;
543  Table t = table_.keywordSet().asTable("FREQUENCIES");
544  String sunit;
545  t.keywordSet().get("UNIT",sunit);
546  String dpl;
547  t.keywordSet().get("DOPPLER",dpl);
548  if (dpl == "") dpl = "RADIO";
549  String rfrm;
550  t.keywordSet().get("REFFRAME",rfrm);
551  std::vector<string> inf;
552  inf.push_back(sunit);
553  inf.push_back(rfrm);
554  inf.push_back(dpl);
555  t.keywordSet().get("BASEREFFRAME",rfrm);
556  inf.push_back(rfrm);
557  return inf;
558}
559
560void SDMemTable::setCoordInfo(std::vector<string> theinfo)
561{
562  std::vector<string>::iterator it;
563  String un,rfrm, brfrm,dpl;
564  un = theinfo[0];              // Abcissa unit
565  rfrm = theinfo[1];            // Active (or conversion) frame
566  dpl = theinfo[2];             // Doppler
567  brfrm = theinfo[3];           // Base frame
568
569  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
570
571  Vector<Double> rstf;
572  t.keywordSet().get("RESTFREQS",rstf);
573
574  Bool canDo = True;
575  Unit u1("km/s");Unit u2("Hz");
576  if (Unit(un) == u1) {
577    Vector<Double> rstf;
578    t.keywordSet().get("RESTFREQS",rstf);
579    if (rstf.nelements() == 0) {
580        throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
581    }
582  } else if (Unit(un) != u2 && un != "") {
583        throw(AipsError("Unit not conformant with Spectral Coordinates"));
584  }
585  t.rwKeywordSet().define("UNIT", un);
586
587  MFrequency::Types mdr;
588  if (!MFrequency::getType(mdr, rfrm)) {
589   
590    Int a,b;const uInt* c;
591    const String* valid = MFrequency::allMyTypes(a, b, c);
592    String pfix = "Please specify a legal frame type. Types are\n";
593    throw(AipsError(pfix+(*valid)));
594  } else {
595    t.rwKeywordSet().define("REFFRAME",rfrm);
596  }
597
598  MDoppler::Types dtype;
599  dpl.upcase();
600  if (!MDoppler::getType(dtype, dpl)) {
601    throw(AipsError("Doppler type unknown"));
602  } else {
603    t.rwKeywordSet().define("DOPPLER",dpl);
604  }
605
606  if (!MFrequency::getType(mdr, brfrm)) {
607     Int a,b;const uInt* c;
608     const String* valid = MFrequency::allMyTypes(a, b, c);
609     String pfix = "Please specify a legal frame type. Types are\n";
610     throw(AipsError(pfix+(*valid)));
611   } else {
612    t.rwKeywordSet().define("BASEREFFRAME",brfrm);
613   }
614}
615
616
617std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
618{
619  std::vector<double> abc(nChan());
620
621  // Get header units keyword
622  Table t = table_.keywordSet().asTable("FREQUENCIES");
623  String sunit;
624  t.keywordSet().get("UNIT",sunit);
625  if (sunit == "") sunit = "pixel";
626  Unit u(sunit);
627
628  // Easy if just wanting pixels
629  if (sunit==String("pixel")) {
630    // assume channels/pixels
631    std::vector<double>::iterator it;
632    uInt i=0;
633    for (it = abc.begin(); it != abc.end(); ++it) {
634      (*it) = Double(i++);
635    }
636    return abc;
637  }
638
639  // Continue with km/s or Hz.  Get FreqIDs
640  Vector<uInt> freqIDs;
641  freqidCol_.get(whichRow, freqIDs);
642  uInt freqID = freqIDs(IFSel_);
643  restfreqidCol_.get(whichRow, freqIDs);
644  uInt restFreqID = freqIDs(IFSel_);
645
646  // Get SpectralCoordinate, set reference frame conversion,
647  // velocity conversion, and rest freq state
648
649  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
650  Vector<Double> pixel(nChan());
651  indgen(pixel);
652
653  if (u == Unit("km/s")) {
654     Vector<Double> world;
655     spc.pixelToVelocity(world,pixel);
656     std::vector<double>::iterator it;
657     uInt i = 0;
658     for (it = abc.begin(); it != abc.end(); ++it) {
659       (*it) = world[i];
660       i++;
661     }
662  } else if (u == Unit("Hz")) {
663
664    // Set world axis units   
665    Vector<String> wau(1); wau = u.getName();
666    spc.setWorldAxisUnits(wau);
667
668    std::vector<double>::iterator it;
669    Double tmp;
670    uInt i = 0;
671    for (it = abc.begin(); it != abc.end(); ++it) {
672      spc.toWorld(tmp,pixel[i]);
673      (*it) = tmp;
674      i++;
675    }
676  }
677  return abc;
678}
679
680std::string SDMemTable::getAbcissaString(Int whichRow) const
681{
682  Table t = table_.keywordSet().asTable("FREQUENCIES");
683
684  String sunit;
685  t.keywordSet().get("UNIT",sunit);
686  if (sunit == "") sunit = "pixel";
687  Unit u(sunit);
688
689  Vector<uInt> freqIDs;
690  freqidCol_.get(whichRow, freqIDs);
691  uInt freqID = freqIDs(IFSel_); 
692  restfreqidCol_.get(whichRow, freqIDs);
693  uInt restFreqID = freqIDs(IFSel_);
694
695  // Get SpectralCoordinate, with frame, velocity, rest freq state set
696  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
697
698  String s = "Channel";
699  if (u == Unit("km/s")) {
700    s = CoordinateUtil::axisLabel(spc,0,True,True,True);
701  } else if (u == Unit("Hz")) {
702    Vector<String> wau(1);wau = u.getName();
703    spc.setWorldAxisUnits(wau);
704
705    s = CoordinateUtil::axisLabel(spc,0,True,True,False);
706  }
707  return s;
708}
709
710void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
711{
712  Array<Float> arr;
713  specCol_.get(whichRow, arr);
714  if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
715    throw(AipsError("Attempting to set spectrum with incorrect length."));
716  }
717
718  // Setup accessors
719  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
720  aa0.reset(aa0.begin(uInt(beamSel_)));                   // Beam selection
721  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
722  aa1.reset(aa1.begin(uInt(IFSel_)));                     // IF selection
723  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
724  aa2.reset(aa2.begin(uInt(polSel_)));                    // Pol selection
725
726  // Iterate
727  std::vector<float>::iterator it = spectrum.begin();
728  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
729    (*i) = Float(*it);
730    it++;
731  }
732  specCol_.put(whichRow, arr);
733}
734
735void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
736{
737  Array<Float> arr;
738  specCol_.get(whichRow, arr);
739
740  // Iterate and extract
741  spectrum.resize(arr.shape()(3));
742  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
743  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
744  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
745  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
746  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
747  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
748
749  ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
750  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
751    (*va) = (*i);
752    va++;
753  }
754}
755
756
757/*
758void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
759  Array<uChar> arr;
760  flagsCol_.get(whichRow, arr);
761  mask.resize(arr.shape()(3));
762
763  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
764  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
765  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
766  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
767  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
768  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
769
770  Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
771
772  ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
773  std::vector<bool> tmp;
774  tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
775                   // iterator should work on chanMask_??
776  std::vector<bool>::iterator miter;
777  miter = tmp.begin();
778
779  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
780    bool out =!static_cast<bool>(*i);
781    if (useUserMask) {
782      out = out && (*miter);
783      miter++;
784    }
785    (*va) = out;
786    va++;
787  }
788}
789*/
790
791MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
792                                                Bool toStokes) const
793{
794  // Get flags
795  Array<uChar> farr;
796  flagsCol_.get(whichRow, farr);
797
798  // Get data and convert mask to Bool
799  Array<Float> arr;
800  Array<Bool> mask;
801  if (toStokes) {
802     stokesCol_.get(whichRow, arr);
803
804     Array<Bool> tMask(farr.shape());
805     convertArray(tMask, farr);
806     mask = SDPolUtil::stokesData (tMask, True);
807  } else {
808     specCol_.get(whichRow, arr);
809     mask.resize(farr.shape());
810     convertArray(mask, farr);
811  }
812
813  return MaskedArray<Float>(arr,!mask);
814}
815
816Float SDMemTable::getTsys(Int whichRow) const
817{
818  Array<Float> arr;
819  tsCol_.get(whichRow, arr);
820  Float out;
821
822  IPosition ip(arr.shape());
823  ip(asap::BeamAxis) = beamSel_;
824  ip(asap::IFAxis) = IFSel_;
825  ip(asap::PolAxis) = polSel_;
826  ip(asap::ChanAxis)=0;               // First channel only
827
828  out = arr(ip);
829  return out;
830}
831
832MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
833{
834  MDirection::Types mdr = getDirectionReference();
835  Array<Double> posit;
836  dirCol_.get(whichRow,posit);
837  Vector<Double> wpos(2);
838  Int rb;
839  rbeamCol_.get(whichRow,rb);
840  wpos[0] = posit(IPosition(2,beamSel_,0));
841  wpos[1] = posit(IPosition(2,beamSel_,1));
842  if (refBeam && rb > -1) {  // use refBeam instead if it exists
843    wpos[0] = posit(IPosition(2,rb,0));
844    wpos[1] = posit(IPosition(2,rb,1));
845  }
846
847  Quantum<Double> lon(wpos[0],Unit(String("rad")));
848  Quantum<Double> lat(wpos[1],Unit(String("rad")));
849  return MDirection(lon, lat, mdr);
850}
851
852MEpoch SDMemTable::getEpoch(Int whichRow) const
853{
854  MEpoch::Types met = getTimeReference();
855
856  Double obstime;
857  timeCol_.get(whichRow,obstime);
858  MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
859  return MEpoch(tm2, met);
860}
861
862MPosition SDMemTable::getAntennaPosition () const
863{
864  Vector<Double> antpos;
865  table_.keywordSet().get("AntennaPosition", antpos);
866  MVPosition mvpos(antpos(0),antpos(1),antpos(2));
867  return MPosition(mvpos);
868}
869
870
871SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
872{
873 
874  Table t = table_.keywordSet().asTable("FREQUENCIES");
875  if (freqID> t.nrow() ) {
876    throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
877  }
878
879  Double rp,rv,inc;
880  String rf;
881  ROScalarColumn<Double> rpc(t, "REFPIX");
882  ROScalarColumn<Double> rvc(t, "REFVAL");
883  ROScalarColumn<Double> incc(t, "INCREMENT");
884  t.keywordSet().get("BASEREFFRAME",rf);
885
886  // Create SpectralCoordinate (units Hz)
887  MFrequency::Types mft;
888  if (!MFrequency::getType(mft, rf)) {
889    cerr << "Frequency type unknown assuming TOPO" << endl;
890    mft = MFrequency::TOPO;
891  }
892  rpc.get(freqID, rp);
893  rvc.get(freqID, rv);
894  incc.get(freqID, inc);
895
896  SpectralCoordinate spec(mft,rv,inc,rp);
897  return spec;
898}
899
900
901SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
902                                                     uInt restFreqID,
903                                                     uInt whichRow) const
904{
905 
906  // Create basic SC
907  SpectralCoordinate spec = getSpectralCoordinate (freqID);
908
909  Table t = table_.keywordSet().asTable("FREQUENCIES");
910
911  // Set rest frequency
912  Vector<Double> restFreqIDs;
913  t.keywordSet().get("RESTFREQS",restFreqIDs);
914  if (restFreqID < restFreqIDs.nelements()) {    // Should always be true
915    spec.setRestFrequency(restFreqIDs(restFreqID),True);
916  }
917
918  // Set up frame conversion layer
919  String frm;
920  t.keywordSet().get("REFFRAME",frm);
921  if (frm == "") frm = "TOPO";
922  MFrequency::Types mtype;
923  if (!MFrequency::getType(mtype, frm)) {
924    // Should never happen
925    cerr << "Frequency type unknown assuming TOPO" << endl;
926    mtype = MFrequency::TOPO;
927  }
928
929  // Set reference frame conversion  (requires row)
930  MDirection dir = getDirection(whichRow);
931  MEpoch epoch = getEpoch(whichRow);
932  MPosition pos = getAntennaPosition();
933
934  if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
935    throw(AipsError("Couldn't convert frequency frame."));
936  }
937
938  // Now velocity conversion if appropriate
939  String unitStr;
940  t.keywordSet().get("UNIT",unitStr);
941
942  String dpl;
943  t.keywordSet().get("DOPPLER",dpl);
944  MDoppler::Types dtype;
945  MDoppler::getType(dtype, dpl);
946
947  // Only set velocity unit if non-blank and non-Hz
948  if (!unitStr.empty()) {
949     Unit unitU(unitStr);
950     if (unitU==Unit("Hz")) {
951     } else {
952        spec.setVelocity(unitStr, dtype);
953     }
954  }
955
956  return spec;
957}
958
959
960Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
961                               uInt freqID) {
962  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
963  if (freqID > t.nrow() ) {
964    throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
965  }
966  ScalarColumn<Double> rpc(t, "REFPIX");
967  ScalarColumn<Double> rvc(t, "REFVAL");
968  ScalarColumn<Double> incc(t, "INCREMENT");
969
970  rpc.put(freqID, speccord.referencePixel()[0]);
971  rvc.put(freqID, speccord.referenceValue()[0]);
972  incc.put(freqID, speccord.increment()[0]);
973
974  return True;
975}
976
977Int SDMemTable::nCoordinates() const
978{
979  return table_.keywordSet().asTable("FREQUENCIES").nrow();
980}
981
982
983std::vector<double> SDMemTable::getRestFreqs() const
984{
985  Table t = table_.keywordSet().asTable("FREQUENCIES");
986  Vector<Double> tvec;
987  t.keywordSet().get("RESTFREQS",tvec);
988  std::vector<double> stlout;
989  tvec.tovector(stlout);
990  return stlout; 
991}
992
993bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
994{
995  TableDesc td("", "1", TableDesc::Scratch);
996  td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
997  td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
998  td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
999  SetupNewTable aNewTab("freqs", td, Table::New);
1000  Table aTable (aNewTab, Table::Memory, sdft.length());
1001  ScalarColumn<Double> sc0(aTable, "REFPIX");
1002  ScalarColumn<Double> sc1(aTable, "REFVAL");
1003  ScalarColumn<Double> sc2(aTable, "INCREMENT");
1004  for (uInt i=0; i < sdft.length(); ++i) {
1005    sc0.put(i,sdft.referencePixel(i));
1006    sc1.put(i,sdft.referenceValue(i));
1007    sc2.put(i,sdft.increment(i));
1008  }
1009  String rf = sdft.refFrame();
1010  if (rf.contains("TOPO")) rf = "TOPO";
1011
1012  aTable.rwKeywordSet().define("BASEREFFRAME", rf);
1013  aTable.rwKeywordSet().define("REFFRAME", rf);
1014  aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
1015  aTable.rwKeywordSet().define("UNIT", String(""));
1016  aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
1017  Vector<Double> rfvec;
1018  String rfunit;
1019  sdft.restFrequencies(rfvec,rfunit);
1020  Quantum<Vector<Double> > q(rfvec, rfunit);
1021  rfvec.resize();
1022  rfvec = q.getValue("Hz");
1023  aTable.rwKeywordSet().define("RESTFREQS", rfvec);
1024  table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
1025  return true;
1026}
1027
1028bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
1029{
1030  TableDesc td("", "1", TableDesc::Scratch);
1031  td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1032  td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1033  td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1034  td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1035  td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1036  SetupNewTable aNewTab("fits", td, Table::New);
1037  Table aTable(aNewTab, Table::Memory);
1038  ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1039  ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1040  ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1041  ArrayColumn<Bool> sc3(aTable, "PARMASK");
1042  ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1043  for (uInt i; i<sdft.length(); ++i) {
1044    const Vector<Double>& parms = sdft.getParameters(i);
1045    const Vector<Bool>& parmask = sdft.getParameterMask(i);
1046    const Vector<String>& funcs = sdft.getFunctions(i);
1047    const Vector<Int>& comps = sdft.getComponents(i);
1048    const Vector<String>& finfo = sdft.getFrameInfo(i);
1049    sc0.put(i,funcs);
1050    sc1.put(i,comps);
1051    sc3.put(i,parmask);
1052    sc2.put(i,parms);
1053    sc4.put(i,finfo);
1054  }
1055  table_.rwKeywordSet().defineTable("FITS", aTable);
1056  return true;
1057}
1058
1059SDFitTable SDMemTable::getSDFitTable() const
1060{
1061  const Table& t = table_.keywordSet().asTable("FITS");
1062  Vector<Double> parms;
1063  Vector<Bool> parmask;
1064  Vector<String> funcs;
1065  Vector<String> finfo;
1066  Vector<Int> comps; 
1067  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1068  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1069  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1070  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1071  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1072  uInt n = t.nrow();
1073  SDFitTable sdft;
1074  for (uInt i=0; i<n; ++i) {
1075    parmaskCol.get(i, parmask);
1076    parmsCol.get(i, parms);
1077    funcsCol.get(i, funcs);
1078    compsCol.get(i, comps);
1079    finfoCol.get(i, finfo);
1080    sdft.addFit(parms, parmask, funcs, comps, finfo);
1081  }
1082  return sdft;
1083}
1084
1085SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1086  const Table& t = table_.keywordSet().asTable("FITS");
1087  if (t.nrow() == 0 || whichRow >= t.nrow()) return SDFitTable();
1088  Array<Int> fitid;
1089  fitCol_.get(whichRow, fitid);
1090  if (fitid.nelements() == 0) return SDFitTable();
1091
1092  IPosition shp = fitid.shape();
1093  IPosition start(4, beamSel_, IFSel_, polSel_,0);
1094  IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1095
1096  // reform the output array slice to be of dim=1
1097  Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1098
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  SDFitTable sdft;
1110  Int k=-1;
1111  for (uInt i=0; i< tmp.nelements(); ++i) {
1112    k = tmp[i];
1113    if ( k > -1 && k < t.nrow() ) {
1114      parms.resize();
1115      parmsCol.get(k, parms);
1116      parmask.resize();
1117      parmaskCol.get(k, parmask);
1118      funcs.resize();
1119      funcsCol.get(k, funcs);
1120      comps.resize();
1121      compsCol.get(k, comps);
1122      finfo.resize();
1123      finfoCol.get(k, finfo);
1124      sdft.addFit(parms, parmask, funcs, comps, finfo);
1125    }
1126  }
1127  return sdft;
1128}
1129
1130void SDMemTable::addFit(uInt whichRow,
1131                        const Vector<Double>& p, const Vector<Bool>& m,
1132                        const Vector<String>& f, const Vector<Int>& c)
1133{
1134  if (whichRow >= nRow()) {
1135    throw(AipsError("Specified row out of range"));
1136  }
1137  Table t = table_.keywordSet().asTable("FITS");
1138  uInt nrow = t.nrow(); 
1139  t.addRow();
1140  ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1141  ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1142  ArrayColumn<Int> compsCol(t, "COMPONENTS");
1143  ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1144  ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1145  parmsCol.put(nrow, p);
1146  parmaskCol.put(nrow, m);
1147  compsCol.put(nrow, c);
1148  funcsCol.put(nrow, f);
1149  Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1150  finfoCol.put(nrow, fi);
1151
1152  Array<Int> fitarr;
1153  fitCol_.get(whichRow, fitarr);
1154
1155  Array<Int> newarr;               // The new Array containing the fitid
1156  Int pos =-1;                     // The fitid position in the array
1157  if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1158    Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1159    arr = -1;
1160    newarr.reference(arr);
1161    pos = 0;     
1162  } else {
1163    IPosition shp = fitarr.shape();
1164    IPosition start(4, beamSel_, IFSel_, polSel_,0);
1165    IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1166    // reform the output array slice to be of dim=1
1167    Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1168    const Vector<Int>& fits = tmp;
1169    VectorSTLIterator<Int> it(fits);
1170    Int i = 0;
1171    while (it != fits.end()) {
1172      if (*it == -1) {
1173        pos = i;
1174        break;
1175      }
1176      ++i;
1177      ++it;
1178    };
1179  }
1180  if (pos == -1) {
1181      mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1182      pos = fitarr.shape()[3];     // the new element position
1183  } else {
1184    if (fitarr.nelements() > 0)
1185      newarr = fitarr;
1186  }
1187  newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1188  fitCol_.put(whichRow, newarr);
1189
1190}
1191
1192SDFrequencyTable SDMemTable::getSDFreqTable() const
1193{
1194  const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1195  SDFrequencyTable sdft;
1196
1197  // Add refpix/refval/incr.  What are the units ? Hz I suppose
1198  // but it's nowhere described...
1199  Vector<Double> refPix, refVal, incr;
1200  ScalarColumn<Double> refPixCol(t, "REFPIX");
1201  ScalarColumn<Double> refValCol(t, "REFVAL");
1202  ScalarColumn<Double> incrCol(t, "INCREMENT");
1203  refPix = refPixCol.getColumn();
1204  refVal = refValCol.getColumn();
1205  incr = incrCol.getColumn();
1206
1207  uInt n = refPix.nelements();
1208  for (uInt i=0; i<n; i++) {
1209     sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1210  }
1211
1212  // Frequency reference frame.  I don't know if this
1213  // is the correct frame.  It might be 'REFFRAME'
1214  // rather than 'BASEREFFRAME' ?
1215  String baseFrame;
1216  t.keywordSet().get("BASEREFFRAME",baseFrame);
1217  sdft.setRefFrame(baseFrame);
1218
1219  // Equinox 
1220  Float equinox;
1221  t.keywordSet().get("EQUINOX", equinox);
1222  sdft.setEquinox(equinox);
1223
1224  // Rest Frequency
1225  Vector<Double> restFreqs;
1226  t.keywordSet().get("RESTFREQS", restFreqs);
1227  for (uInt i=0; i<restFreqs.nelements(); i++) {
1228     sdft.addRestFrequency(restFreqs[i]);
1229  }
1230  sdft.setRestFrequencyUnit(String("Hz"));
1231
1232  return sdft;
1233}
1234
1235bool SDMemTable::putSDContainer(const SDContainer& sdc)
1236{
1237  uInt rno = table_.nrow();
1238  table_.addRow();
1239
1240  timeCol_.put(rno, sdc.timestamp);
1241  srcnCol_.put(rno, sdc.sourcename);
1242  fldnCol_.put(rno, sdc.fieldname);
1243  specCol_.put(rno, sdc.getSpectrum());
1244  flagsCol_.put(rno, sdc.getFlags());
1245  tsCol_.put(rno, sdc.getTsys());
1246  scanCol_.put(rno, sdc.scanid);
1247  integrCol_.put(rno, sdc.interval);
1248  freqidCol_.put(rno, sdc.getFreqMap());
1249  restfreqidCol_.put(rno, sdc.getRestFreqMap());
1250  dirCol_.put(rno, sdc.getDirection());
1251  rbeamCol_.put(rno, sdc.refbeam);
1252  tcalCol_.put(rno, sdc.tcal);
1253  tcaltCol_.put(rno, sdc.tcaltime);
1254  azCol_.put(rno, sdc.azimuth);
1255  elCol_.put(rno, sdc.elevation);
1256  paraCol_.put(rno, sdc.parangle);
1257  fitCol_.put(rno, sdc.getFitMap());
1258  return true;
1259}
1260
1261SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1262{
1263  SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1264  timeCol_.get(whichRow, sdc.timestamp);
1265  srcnCol_.get(whichRow, sdc.sourcename);
1266  integrCol_.get(whichRow, sdc.interval);
1267  scanCol_.get(whichRow, sdc.scanid);
1268  fldnCol_.get(whichRow, sdc.fieldname);
1269  rbeamCol_.get(whichRow, sdc.refbeam);
1270  azCol_.get(whichRow, sdc.azimuth);
1271  elCol_.get(whichRow, sdc.elevation);
1272  paraCol_.get(whichRow, sdc.parangle);
1273  Vector<Float> tc;
1274  tcalCol_.get(whichRow, tc);
1275  sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1276  tcaltCol_.get(whichRow, sdc.tcaltime);
1277
1278  Array<Float> spectrum;
1279  Array<Float> tsys;
1280  Array<uChar> flagtrum;
1281  Vector<uInt> fmap;
1282  Array<Double> direction;
1283  Array<Int> fits;
1284 
1285  specCol_.get(whichRow, spectrum);
1286  sdc.putSpectrum(spectrum);
1287  flagsCol_.get(whichRow, flagtrum);
1288  sdc.putFlags(flagtrum);
1289  tsCol_.get(whichRow, tsys);
1290  sdc.putTsys(tsys);
1291  freqidCol_.get(whichRow, fmap);
1292  sdc.putFreqMap(fmap);
1293  restfreqidCol_.get(whichRow, fmap);
1294  sdc.putRestFreqMap(fmap);
1295  dirCol_.get(whichRow, direction);
1296  sdc.putDirection(direction);
1297  fitCol_.get(whichRow, fits);
1298  sdc.putFitMap(fits);
1299  return sdc;
1300}
1301
1302bool SDMemTable::putSDHeader(const SDHeader& sdh)
1303{
1304  table_.rwKeywordSet().define("nIF", sdh.nif);
1305  table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1306  table_.rwKeywordSet().define("nPol", sdh.npol);
1307  table_.rwKeywordSet().define("nChan", sdh.nchan);
1308  table_.rwKeywordSet().define("Observer", sdh.observer);
1309  table_.rwKeywordSet().define("Project", sdh.project);
1310  table_.rwKeywordSet().define("Obstype", sdh.obstype);
1311  table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1312  table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1313  table_.rwKeywordSet().define("Equinox", sdh.equinox);
1314  table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1315  table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1316  table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1317  table_.rwKeywordSet().define("UTC", sdh.utc);
1318  table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1319  table_.rwKeywordSet().define("Epoch", sdh.epoch);
1320  return true;
1321}
1322
1323SDHeader SDMemTable::getSDHeader() const
1324{
1325  SDHeader sdh;
1326  table_.keywordSet().get("nBeam",sdh.nbeam);
1327  table_.keywordSet().get("nIF",sdh.nif);
1328  table_.keywordSet().get("nPol",sdh.npol);
1329  table_.keywordSet().get("nChan",sdh.nchan);
1330  table_.keywordSet().get("Observer", sdh.observer);
1331  table_.keywordSet().get("Project", sdh.project);
1332  table_.keywordSet().get("Obstype", sdh.obstype);
1333  table_.keywordSet().get("AntennaName", sdh.antennaname);
1334  table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1335  table_.keywordSet().get("Equinox", sdh.equinox);
1336  table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1337  table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1338  table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1339  table_.keywordSet().get("UTC", sdh.utc);
1340  table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1341  table_.keywordSet().get("Epoch", sdh.epoch);
1342  return sdh;
1343}
1344void SDMemTable::makePersistent(const std::string& filename)
1345{ 
1346  table_.deepCopy(filename,Table::New);
1347
1348}
1349
1350Int SDMemTable::nScan() const {
1351  Int n = 0;
1352  Int previous = -1;Int current=0;
1353  for (uInt i=0; i< scanCol_.nrow();i++) {
1354    scanCol_.getScalar(i,current);
1355    if (previous != current) {
1356      previous = current;
1357      n++;
1358    }
1359  }
1360  return n;
1361}
1362
1363String SDMemTable::formatSec(Double x) const
1364{
1365  Double xcop = x;
1366  MVTime mvt(xcop/24./3600.);  // make days
1367
1368  if (x < 59.95)
1369    return  String("      ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1370  else if (x < 3599.95)
1371    return String("   ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1372  else {
1373    ostringstream oss;
1374    oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1375    oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1376    return String(oss);
1377  }   
1378};
1379
1380String SDMemTable::formatDirection(const MDirection& md) const
1381{
1382  Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1383  Int prec = 7;
1384
1385  MVAngle mvLon(t[0]);
1386  String sLon = mvLon.string(MVAngle::TIME,prec);
1387  MVAngle mvLat(t[1]);
1388  String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1389  return sLon + String(" ") + sLat;
1390}
1391
1392
1393std::string SDMemTable::getFluxUnit() const
1394{
1395  String tmp;
1396  table_.keywordSet().get("FluxUnit", tmp);
1397  return tmp;
1398}
1399
1400void SDMemTable::setFluxUnit(const std::string& unit)
1401{
1402  String tmp(unit);
1403  Unit tU(tmp);
1404  if (tU==Unit("K") || tU==Unit("Jy")) {
1405     table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1406  } else {
1407     throw AipsError("Illegal unit - must be compatible with Jy or K");
1408  }
1409}
1410
1411
1412void SDMemTable::setInstrument(const std::string& name)
1413{
1414  Bool throwIt = True;
1415  Instrument ins = SDAttr::convertInstrument(name, throwIt);
1416  String nameU(name);
1417  nameU.upcase();
1418  table_.rwKeywordSet().define(String("AntennaName"), nameU);
1419}
1420
1421std::string SDMemTable::summary(bool verbose) const  {
1422
1423  // Format header info
1424  ostringstream oss;
1425  oss << endl;
1426  oss << "--------------------------------------------------------------------------------" << endl;
1427  oss << " Scan Table Summary" << endl;
1428  oss << "--------------------------------------------------------------------------------" << endl;
1429  oss.flags(std::ios_base::left);
1430  oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1431      << setw(15) << "IFs:" << setw(4) << nIF() << endl
1432      << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1433      << setw(15) << "Channels:"  << setw(4) << nChan() << endl;
1434  oss << endl;
1435  String tmp;
1436  table_.keywordSet().get("Observer", tmp);
1437  oss << setw(15) << "Observer:" << tmp << endl;
1438  oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1439  table_.keywordSet().get("Project", tmp);
1440  oss << setw(15) << "Project:" << tmp << endl;
1441  table_.keywordSet().get("Obstype", tmp);
1442  oss << setw(15) << "Obs. Type:" << tmp << endl;
1443  table_.keywordSet().get("AntennaName", tmp);
1444  oss << setw(15) << "Antenna Name:" << tmp << endl;
1445  table_.keywordSet().get("FluxUnit", tmp);
1446  oss << setw(15) << "Flux Unit:" << tmp << endl;
1447  Table t = table_.keywordSet().asTable("FREQUENCIES");
1448  Vector<Double> vec;
1449  t.keywordSet().get("RESTFREQS",vec);
1450  oss << setw(15) << "Rest Freqs:";
1451  if (vec.nelements() > 0) {
1452      oss << setprecision(10) << vec << " [Hz]" << endl;
1453  } else {
1454      oss << "None set" << endl;
1455  }
1456  oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1457  oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1458      << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1459  oss << endl;
1460
1461  String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1462  oss << setw(5) << "Scan"
1463      << setw(15) << "Source"
1464      << setw(24) << dirtype
1465      << setw(10) << "Time"
1466      << setw(18) << "Integration"
1467      << setw(7) << "FreqIDs" << endl;
1468  oss << "--------------------------------------------------------------------------------" << endl;
1469 
1470  // Generate list of scan start and end integrations
1471  Vector<Int> scanIDs = scanCol_.getColumn();
1472  Vector<uInt> startInt, endInt;
1473  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1474
1475  const uInt nScans = startInt.nelements();
1476  String name;
1477  Vector<uInt> freqIDs, listFQ;
1478  Vector<uInt> restFreqIDs, listRestFQ;
1479  uInt nInt;
1480
1481  for (uInt i=0; i<nScans; i++) {
1482    // Get things from first integration of scan
1483    String time = getTime(startInt(i),False);
1484    String tInt = formatSec(Double(getInterval(startInt(i))));
1485    String posit = formatDirection(getDirection(startInt(i),True));
1486    srcnCol_.getScalar(startInt(i),name);
1487
1488    // Find all the FreqIDs in this scan
1489    listFQ.resize(0);     
1490    listRestFQ.resize(0);     
1491    for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1492      freqidCol_.get(j, freqIDs);
1493      for (uInt k=0; k<freqIDs.nelements(); k++) {
1494        mathutil::addEntry(listFQ, freqIDs(k));
1495      }
1496//
1497      restfreqidCol_.get(j, restFreqIDs);
1498      for (uInt k=0; k<restFreqIDs.nelements(); k++) {
1499        mathutil::addEntry(listRestFQ, restFreqIDs(k));
1500      }
1501    }
1502
1503    nInt = endInt(i) - startInt(i) + 1;
1504    oss << setw(3) << std::right << i << std::left << setw(2) << "  "
1505        << setw(15) << name
1506        << setw(24) << posit
1507        << setw(10) << time
1508        << setw(3) << std::right << nInt  << setw(3) << " x " << std::left
1509        << setw(6) <<  tInt
1510        << " " << listFQ << " " << listRestFQ << endl;
1511  }
1512  oss << endl;
1513  oss << "Table contains " << table_.nrow() << " integration(s) in "
1514      << nScans << " scan(s)." << endl;
1515
1516  // Frequency Table
1517  if (verbose) {
1518    std::vector<string> info = getCoordInfo();
1519    SDFrequencyTable sdft = getSDFreqTable();
1520    oss << endl << endl;
1521    oss << "FreqID  Frame   RefFreq(Hz)     RefPix   Increment(Hz)" << endl;
1522    oss << "--------------------------------------------------------------------------------" << endl;
1523    for (uInt i=0; i<sdft.length(); i++) {
1524      oss << setw(8) << i << setw(8)
1525          << info[3] << setw(16) << setprecision(8)
1526          << sdft.referenceValue(i) << setw(10)
1527          << sdft.referencePixel(i) << setw(12)
1528          << sdft.increment(i) << endl;
1529    }
1530    oss << "--------------------------------------------------------------------------------" << endl;
1531  }
1532  return String(oss);
1533}
1534/*
1535std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1536  ostringstream oss;
1537  Vector<Int> scanIDs = scanCol_.getColumn();
1538  Vector<uInt> startInt, endInt;
1539  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1540  const uInt nScans = startInt.nelements();
1541  std::vector<int>::const_iterator it(whichScans);
1542  return String(oss);
1543}
1544*/
1545Int SDMemTable::nBeam() const
1546{
1547  Int n;
1548  table_.keywordSet().get("nBeam",n);
1549  return n;
1550}
1551
1552Int SDMemTable::nIF() const {
1553  Int n;
1554  table_.keywordSet().get("nIF",n);
1555  return n;
1556}
1557
1558Int SDMemTable::nPol() const {
1559  Int n;
1560  table_.keywordSet().get("nPol",n);
1561  return n;
1562}
1563
1564Int SDMemTable::nChan() const {
1565  Int n;
1566  table_.keywordSet().get("nChan",n);
1567  return n;
1568}
1569
1570Table SDMemTable::getHistoryTable() const
1571{
1572  return table_.keywordSet().asTable("HISTORY");
1573}
1574
1575void SDMemTable::appendToHistoryTable(const Table& otherHist)
1576{
1577  Table t = table_.rwKeywordSet().asTable("HISTORY");
1578  const String sep = "--------------------------------------------------------------------------------";
1579  addHistory(sep);
1580  TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1581  addHistory(sep);
1582}
1583
1584void SDMemTable::addHistory(const std::string& hist)
1585{
1586  Table t = table_.rwKeywordSet().asTable("HISTORY");
1587  uInt nrow = t.nrow(); 
1588  t.addRow();
1589  ScalarColumn<String> itemCol(t, "ITEM");
1590  itemCol.put(nrow, hist);
1591}
1592
1593std::vector<std::string> SDMemTable::getHistory() const
1594{
1595  Vector<String> history;
1596  const Table& t = table_.keywordSet().asTable("HISTORY");
1597  uInt nrow = t.nrow(); 
1598  ROScalarColumn<String> itemCol(t, "ITEM");
1599  std::vector<std::string> stlout;
1600  String hist;
1601  for (uInt i=0; i<nrow; ++i) {
1602    itemCol.get(i, hist);
1603    stlout.push_back(hist);
1604  }
1605  return stlout;
1606}
1607
1608
1609/*
1610  void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1611
1612  std::vector<int>::iterator it;
1613  ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1614  for (it = whichChans.begin(); it != whichChans.end(); it++) {
1615    j.reset(j.begin(uInt(*it)));
1616    for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1617      for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1618        for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1619             iii != iii.end(); ++iii) {
1620          (*iii) =
1621        }
1622      }
1623    }
1624  }
1625
1626}
1627*/
1628void SDMemTable::flag(int whichRow)
1629  {
1630  Array<uChar> arr;
1631  flagsCol_.get(whichRow, arr);
1632
1633  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1634  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1635  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1636  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1637  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1638  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1639
1640  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1641    (*i) = uChar(True);
1642  }
1643
1644  flagsCol_.put(whichRow, arr);
1645}
1646
1647MDirection::Types SDMemTable::getDirectionReference() const
1648{ 
1649  Float eq;
1650  table_.keywordSet().get("Equinox",eq);
1651  std::map<float,string> mp;
1652  mp[2000.0] = "J2000";
1653  mp[1950.0] = "B1950";
1654  MDirection::Types mdr;
1655  if (!MDirection::getType(mdr, mp[eq])) {   
1656    mdr = MDirection::J2000;
1657    cerr  << "Unknown equinox using J2000" << endl;
1658  }
1659
1660  return mdr;
1661}
1662
1663MEpoch::Types SDMemTable::getTimeReference() const
1664{
1665  MEpoch::Types met;
1666  String ep;
1667  table_.keywordSet().get("Epoch",ep);
1668  if (!MEpoch::getType(met, ep)) {
1669    cerr << "Epoch type unknown - using UTC" << endl;
1670    met = MEpoch::UTC;
1671  }
1672
1673  return met;
1674}
1675
1676
1677Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1678                              const String& sUnit,
1679                              const vector<string>& lines,
1680                              const String& source,
1681                              Int whichIF)
1682{
1683   const Int nIFs = nIF();
1684   if (whichIF>=nIFs) {
1685      throw(AipsError("Illegal IF index"));
1686   }
1687
1688   // Find vector of restfrequencies
1689   // Double takes precedence over String
1690   Unit unit;
1691   Vector<Double> restFreqs;
1692   if (restFreqsIn.nelements()>0) {
1693      restFreqs.resize(restFreqsIn.nelements());
1694      restFreqs = restFreqsIn;
1695      unit = Unit(sUnit);
1696   } else if (lines.size()>0) {
1697      const uInt nLines = lines.size();
1698      unit = Unit("Hz");
1699      restFreqs.resize(nLines);
1700      MFrequency lineFreq;
1701      for (uInt i=0; i<nLines; i++) {
1702         String tS(lines[i]);
1703         tS.upcase();
1704         if (MeasTable::Line(lineFreq, tS)) {
1705            restFreqs[i] = lineFreq.getValue().getValue();          // Hz
1706         } else {
1707            String s = String(lines[i]) +
1708              String(" is an unrecognized spectral line");
1709            throw(AipsError(s));
1710         }
1711      }
1712   } else {
1713      throw(AipsError("You have not specified any rest frequencies or lines"));
1714   }
1715
1716   // If multiple restfreqs, must be length nIF. In this
1717   // case we will just replace the rest frequencies
1718   // We can't disinguish scalar and vector of length 1
1719   const uInt nRestFreqs = restFreqs.nelements();
1720   Int idx = -1;
1721   SDFrequencyTable sdft = getSDFreqTable();
1722
1723   if (nRestFreqs>1) {
1724     // Replace restFreqs, one per IF
1725      if (nRestFreqs != nIFs) {
1726         throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1727      }
1728      cout << "Replacing rest frequencies, one per IF, with given list : " << restFreqs << endl;
1729      sdft.deleteRestFrequencies();
1730      for (uInt i=0; i<nRestFreqs; i++) {
1731         Quantum<Double> rf(restFreqs[i], unit);
1732         sdft.addRestFrequency(rf.getValue("Hz"));
1733      }
1734   } else {
1735
1736     // Add new rest freq
1737      Quantum<Double> rf(restFreqs[0], unit);
1738      idx = sdft.addRestFrequency(rf.getValue("Hz"));
1739      if (whichIF>=0) {
1740         cout << "Selecting given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1741      } else {
1742         cout << "Selecting given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1743      }
1744   }
1745   
1746   // Replace
1747   Bool empty = source.empty();
1748   Bool ok = False;
1749   if (putSDFreqTable(sdft)) {
1750      const uInt nRow = table_.nrow();
1751      String srcName;
1752      Vector<uInt> restFreqIDs;
1753      for (uInt i=0; i<nRow; i++) {
1754         srcnCol_.get(i, srcName);
1755         restfreqidCol_.get(i,restFreqIDs);       
1756         if (idx==-1) {
1757           // Replace vector of restFreqs; one per IF.
1758           // No selection possible
1759            for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1760         } else {
1761           // Set RestFreqID for selected data
1762            if (empty || source==srcName) {
1763               if (whichIF<0) {
1764                  restFreqIDs = idx;
1765               } else {             
1766                  restFreqIDs[whichIF] = idx;
1767               }
1768            }
1769         }
1770         restfreqidCol_.put(i,restFreqIDs);       
1771      }
1772      ok = True;
1773   } else {
1774     ok = False;
1775   }
1776
1777   return ok;
1778}
1779
1780void SDMemTable::spectralLines() const
1781{
1782   Vector<String> lines = MeasTable::Lines();
1783   MFrequency lineFreq;
1784   Double freq;
1785
1786   cout.flags(std::ios_base::left);
1787   cout << "Line      Frequency (Hz)" << endl;
1788   cout << "-----------------------" << endl;
1789   for (uInt i=0; i<lines.nelements(); i++) {
1790     MeasTable::Line(lineFreq, lines[i]);
1791     freq = lineFreq.getValue().getValue();          // Hz
1792     cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1793   }
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
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