source: trunk/src/SDMemTable.cc @ 752

Last change on this file since 752 was 745, checked in by mar637, 19 years ago

removed setmask functionality
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 52.2 KB
Line 
1//#---------------------------------------------------------------------------
2//# SDMemTable.cc: A MemoryTable container for single dish integrations
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//#        Internet email: Malte.Marquarding@csiro.au
23//#        Postal address: Malte Marquarding,
24//#                        Australia Telescope National Facility,
25//#                        P.O. Box 76,
26//#                        Epping, NSW, 2121,
27//#                        AUSTRALIA
28//#
29//# $Id:
30//#---------------------------------------------------------------------------
31
32#include <map>
33
34#include <casa/aips.h>
35#include <casa/iostream.h>
36#include <casa/iomanip.h>
37#include <casa/Arrays/Array.h>
38#include <casa/Arrays/ArrayMath.h>
39#include <casa/Arrays/MaskArrMath.h>
40#include <casa/Arrays/ArrayLogical.h>
41#include <casa/Arrays/ArrayAccessor.h>
42#include <casa/Arrays/VectorSTLIterator.h>
43#include <casa/Arrays/Vector.h>
44#include <casa/BasicMath/Math.h>
45#include <casa/BasicSL/Constants.h>
46#include <casa/Quanta/MVAngle.h>
47
48#include <tables/Tables/TableParse.h>
49#include <tables/Tables/TableDesc.h>
50#include <tables/Tables/TableCopy.h>
51#include <tables/Tables/SetupNewTab.h>
52#include <tables/Tables/ScaColDesc.h>
53#include <tables/Tables/ArrColDesc.h>
54
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/TableRecord.h>
57#include <measures/Measures/MFrequency.h>
58#include <measures/Measures/MeasTable.h>
59#include <coordinates/Coordinates/CoordinateUtil.h>
60#include <casa/Quanta/MVTime.h>
61#include <casa/Quanta/MVAngle.h>
62
63#include "SDDefs.h"
64#include "SDContainer.h"
65#include "MathUtils.h"
66#include "SDPol.h"
67#include "SDAttr.h"
68
69#include "SDMemTable.h"
70
71using namespace casa;
72using namespace asap;
73
74SDMemTable::SDMemTable() :
75  IFSel_(0),
76  beamSel_(0),
77  polSel_(0)
78{
79  setup();
80  attach();
81}
82
83SDMemTable::SDMemTable(const std::string& name) :
84  IFSel_(0),
85  beamSel_(0),
86  polSel_(0)
87{
88  Table tab(name);
89  Int version;
90  tab.keywordSet().get("VERSION", version);
91  if (version != version_) {
92    throw(AipsError("Unsupported version of ASAP file."));
93  }
94  table_ = tab.copyToMemoryTable("dummy");
95  attach();
96}
97
98SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
99{
100  table_ = other.table_.copyToMemoryTable(String("dummy"));
101  // clear all rows()
102  if (clear) {
103    table_.removeRow(this->table_.rowNumbers());
104    IFSel_= 0;
105    beamSel_= 0;
106    polSel_= 0;
107  } else {
108    IFSel_= other.IFSel_;
109    beamSel_= other.beamSel_;
110    polSel_= other.polSel_;
111  }
112
113  attach();
114}
115
116SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
117  IFSel_(0),
118  beamSel_(0),
119  polSel_(0)
120{
121  Table t = tableCommand(exprs,tab);
122  if (t.nrow() == 0)
123      throw(AipsError("Query unsuccessful."));
124  table_ = t.copyToMemoryTable("dummy");
125  attach();
126  renumber();
127}
128
129SDMemTable::~SDMemTable()
130{
131  //cerr << "goodbye from SDMemTable @ " << this << endl;
132}
133
134SDMemTable SDMemTable::getScan(Int scanID) const
135{
136  String cond("SELECT * from $1 WHERE SCANID == ");
137  cond += String::toString(scanID);
138  return SDMemTable(table_, cond);
139}
140
141SDMemTable &SDMemTable::operator=(const SDMemTable& other)
142{
143  if (this != &other) {
144     IFSel_= other.IFSel_;
145     beamSel_= other.beamSel_;
146     polSel_= other.polSel_;
147     table_ = other.table_.copyToMemoryTable(String("dummy"));
148     attach();
149  }
150  return *this;
151}
152
153SDMemTable SDMemTable::getSource(const std::string& source) const
154{
155  String cond("SELECT * from $1 WHERE SRCNAME == ");
156  cond += source;
157  return SDMemTable(table_, cond);
158}
159
160void SDMemTable::setup()
161{
162  TableDesc td("", "1", TableDesc::Scratch);
163  td.comment() = "A SDMemTable";
164  td.rwKeywordSet().define("VERSION", Int(version_));
165
166  td.addColumn(ScalarColumnDesc<Double>("TIME"));
167  td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
168  td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
169  td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
170  td.addColumn(ArrayColumnDesc<Float>("TSYS"));
171  td.addColumn(ArrayColumnDesc<Float>("STOKES"));
172  td.addColumn(ScalarColumnDesc<Int>("SCANID"));
173  td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
174  td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
175  td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
176  td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
177  td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
178  td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
179  td.addColumn(ArrayColumnDesc<Float>("TCAL"));
180  td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
181  td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
182  td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
183  td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
184  td.addColumn(ArrayColumnDesc<Int>("FITID"));
185
186  // Now create Table SetUp from the description.
187  SetupNewTable aNewTab("dummy", td, Table::New);
188
189  // Bind the Stokes Virtual machine to the STOKES column Because we
190  // don't know how many polarizations will be in the data at this
191  // point, we must bind the Virtual Engine regardless.  The STOKES
192  // column won't be accessed if not appropriate (nPol=4)
193  SDStokesEngine::registerClass();
194  SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
195  aNewTab.bindColumn("STOKES", stokesEngine);
196
197  // Create Table
198  table_ = Table(aNewTab, Table::Memory, 0);
199  // add subtable
200  TableDesc tdf("", "1", TableDesc::Scratch);
201  tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
202  tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
203  tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
204  tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
205  tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
206  SetupNewTable fittab("fits", tdf, Table::New);
207  Table fitTable(fittab, Table::Memory);
208  table_.rwKeywordSet().defineTable("FITS", fitTable);
209
210  TableDesc tdh("", "1", TableDesc::Scratch);
211  tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
212  SetupNewTable histtab("hist", tdh, Table::New);
213  Table histTable(histtab, Table::Memory);
214  table_.rwKeywordSet().defineTable("HISTORY", histTable);
215}
216
217void SDMemTable::attach()
218{
219  timeCol_.attach(table_, "TIME");
220  srcnCol_.attach(table_, "SRCNAME");
221  specCol_.attach(table_, "SPECTRA");
222  flagsCol_.attach(table_, "FLAGTRA");
223  tsCol_.attach(table_, "TSYS");
224  stokesCol_.attach(table_, "STOKES");
225  scanCol_.attach(table_, "SCANID");
226  integrCol_.attach(table_, "INTERVAL");
227  freqidCol_.attach(table_, "FREQID");
228  restfreqidCol_.attach(table_, "RESTFREQID");
229  dirCol_.attach(table_, "DIRECTION");
230  fldnCol_.attach(table_, "FIELDNAME");
231  tcaltCol_.attach(table_, "TCALTIME");
232  tcalCol_.attach(table_, "TCAL");
233  azCol_.attach(table_, "AZIMUTH");
234  elCol_.attach(table_, "ELEVATION");
235  paraCol_.attach(table_, "PARANGLE");
236  rbeamCol_.attach(table_, "REFBEAM");
237  fitCol_.attach(table_,"FITID");
238}
239
240
241std::string SDMemTable::getSourceName(Int whichRow) const
242{
243  String name;
244  srcnCol_.get(whichRow, name);
245  return name;
246}
247
248std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
249{
250  Double tm;
251  if (whichRow > -1) {
252    timeCol_.get(whichRow, tm);
253  } else {
254    table_.keywordSet().get("UTC",tm);
255  }
256  MVTime mvt(tm);
257  if (showDate)
258    mvt.setFormat(MVTime::YMD);
259  else
260    mvt.setFormat(MVTime::TIME);
261  ostringstream oss;
262  oss << mvt;
263  return String(oss);
264}
265
266double SDMemTable::getInterval(Int whichRow) const
267{
268  Double intval;
269  integrCol_.get(whichRow, intval);
270  return intval;
271}
272
273bool SDMemTable::setIF(Int whichIF)
274{
275  if ( whichIF >= 0 && whichIF < nIF()) {
276    IFSel_ = whichIF;
277    return true;
278  }
279  return false;
280}
281
282bool SDMemTable::setBeam(Int whichBeam)
283{
284  if ( whichBeam >= 0 && whichBeam < nBeam()) {
285    beamSel_ = whichBeam;
286    return true;
287  }
288  return false;
289}
290
291bool SDMemTable::setPol(Int whichPol)
292{
293  if ( whichPol >= 0 && whichPol < nPol()) {
294    polSel_ = whichPol;
295    return true;
296  }
297  return false;
298}
299
300void SDMemTable::resetCursor()
301{
302   polSel_ = 0;
303   IFSel_ = 0;
304   beamSel_ = 0;
305}
306
307std::vector<bool> SDMemTable::getMask(Int whichRow) const
308{
309
310  std::vector<bool> mask;
311
312  Array<uChar> arr;
313  flagsCol_.get(whichRow, arr);
314
315  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
316  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
317  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
318  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
319  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
320  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
321
322  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
323    bool out =!static_cast<bool>(*i);
324    mask.push_back(out);
325  }
326  return mask;
327}
328
329
330
331std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
332{
333  Array<Float> arr;
334  specCol_.get(whichRow, arr);
335  return getFloatSpectrum(arr);
336}
337
338
339int SDMemTable::nStokes() const
340{
341   return stokesCol_.shape(0).nelements();        // All rows same shape
342}
343
344
345std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow,
346                                                 Bool doPol) const
347  //
348  // Gets one STokes parameter depending on cursor polSel location
349  //  doPol=False  : I,Q,U,V
350  //  doPol=True   : I,P,PA,V   ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
351  //
352{
353  AlwaysAssert(asap::nAxes==4,AipsError);
354  if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
355    throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
356  }
357
358  // For full conversion we are only supporting linears at the moment
359
360  if (nPol() > 2) {
361    String antName;
362    table_.keywordSet().get("AntennaName", antName);
363    Instrument inst = SDAttr::convertInstrument (antName, True);
364    SDAttr sdAtt;
365    if (sdAtt.feedPolType(inst) != LINEAR) {
366      throw(AipsError("Only linear polarizations are supported"));
367    }
368  }
369
370  Array<Float> arr;
371  stokesCol_.get(whichRow, arr);
372
373  if (doPol && (polSel_==1 || polSel_==2)) {       //   Q,U --> P, P.A.
374
375    // Set current cursor location
376
377    const IPosition& shape = arr.shape();
378    IPosition start, end;
379    getCursorSlice(start, end, shape);
380
381    // Get Q and U slices
382
383    Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
384    Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
385
386    // Compute output
387
388    Array<Float> out;
389    if (polSel_==1) {                                        // P
390      out = SDPolUtil::polarizedIntensity(Q,U);
391    } else if (polSel_==2) {                                 // P.A.
392      out = SDPolUtil::positionAngle(Q,U);
393    }
394
395    // Copy to output
396
397    IPosition vecShape(1,shape(asap::ChanAxis));
398    Vector<Float> outV = out.reform(vecShape);
399    std::vector<float> stlout;
400    outV.tovector(stlout);
401    return stlout;
402
403  } else {
404    // Selects at the cursor location
405    return getFloatSpectrum(arr);
406  }
407}
408
409std::string SDMemTable::getPolarizationLabel(Bool linear, Bool stokes,
410                                              Bool linPol, Int polIdx) const
411{
412   uInt idx = polSel_;
413   if (polIdx >=0) idx = polIdx;
414   return SDPolUtil::polarizationLabel(idx, linear, stokes, linPol);
415}
416
417
418
419std::vector<float> SDMemTable::stokesToPolSpectrum(Int whichRow,
420                                                   Bool toLinear,
421                                                   Int polIdx) const
422//
423// polIdx
424//   0:3 -> RR,LL,Real(RL),Imag(RL)
425//          XX,YY,Real(XY),Image(XY)
426//
427// Gets only
428//  RR = I + V
429//  LL = I - V
430// at the moment
431//
432{
433  AlwaysAssert(asap::nAxes==4,AipsError);
434  if (nStokes()!=4) {
435     throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
436  }
437//
438  Array<Float> arr, out;
439  stokesCol_.get(whichRow, arr);
440
441// Set current cursor location
442
443  const IPosition& shape = arr.shape();
444  IPosition start, end;
445  getCursorSlice(start, end, shape);
446
447// Get the slice
448
449  if (toLinear) {
450     throw(AipsError("Conversion to linears not yet supported"));
451  } else {
452    uInt selection = polSel_;
453    if (polIdx > -1) selection = polIdx;
454    Bool doRR = (selection==0);
455    if (selection>1) {
456      throw(AipsError("Only conversion to RR & LL is currently supported"));
457    }
458
459    // Get I and V slices
460    Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
461    Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
462
463    // Compute output
464    out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
465  }
466
467  // Copy to output
468   IPosition vecShape(1,shape(asap::ChanAxis));
469   Vector<Float> outV = out.reform(vecShape);
470   std::vector<float> stlout;
471   outV.tovector(stlout);
472//
473   return stlout;
474}
475
476
477
478
479Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
480{
481
482// Get data
483
484  Array<Float> arr;
485  stokesCol_.get(whichRow, arr);
486
487// Set current cursor location and overwrite polarization axis
488
489  const IPosition& shape = arr.shape();
490  IPosition start(shape.nelements(),0);
491  IPosition end(shape-1);
492  if (iBeam!=-1) {
493     start(asap::BeamAxis) = iBeam;
494     end(asap::BeamAxis) = iBeam;
495  }
496  if (iIF!=-1) {
497     start(asap::IFAxis) = iIF;
498     end(asap::IFAxis) = iIF;
499  }
500
501// Get slice
502
503  return arr(start,end);
504}
505
506
507std::vector<string> SDMemTable::getCoordInfo() const
508{
509  String un;
510  Table t = table_.keywordSet().asTable("FREQUENCIES");
511  String sunit;
512  t.keywordSet().get("UNIT",sunit);
513  String dpl;
514  t.keywordSet().get("DOPPLER",dpl);
515  if (dpl == "") dpl = "RADIO";
516  String rfrm;
517  t.keywordSet().get("REFFRAME",rfrm);
518  std::vector<string> inf;
519  inf.push_back(sunit);
520  inf.push_back(rfrm);
521  inf.push_back(dpl);
522  t.keywordSet().get("BASEREFFRAME",rfrm);
523  inf.push_back(rfrm);
524  return inf;
525}
526
527void SDMemTable::setCoordInfo(std::vector<string> theinfo)
528{
529  std::vector<string>::iterator it;
530  String un,rfrm, brfrm,dpl;
531  un = theinfo[0];              // Abcissa unit
532  rfrm = theinfo[1];            // Active (or conversion) frame
533  dpl = theinfo[2];             // Doppler
534  brfrm = theinfo[3];           // Base frame
535
536  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
537
538  Vector<Double> rstf;
539  t.keywordSet().get("RESTFREQS",rstf);
540
541  Bool canDo = True;
542  Unit u1("km/s");Unit u2("Hz");
543  if (Unit(un) == u1) {
544    Vector<Double> rstf;
545    t.keywordSet().get("RESTFREQS",rstf);
546    if (rstf.nelements() == 0) {
547        throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
548    }
549  } else if (Unit(un) != u2 && un != "") {
550        throw(AipsError("Unit not conformant with Spectral Coordinates"));
551  }
552  t.rwKeywordSet().define("UNIT", un);
553
554  MFrequency::Types mdr;
555  if (!MFrequency::getType(mdr, rfrm)) {
556
557    Int a,b;const uInt* c;
558    const String* valid = MFrequency::allMyTypes(a, b, c);
559    String pfix = "Please specify a legal frame type. Types are\n";
560    throw(AipsError(pfix+(*valid)));
561  } else {
562    t.rwKeywordSet().define("REFFRAME",rfrm);
563  }
564
565  MDoppler::Types dtype;
566  dpl.upcase();
567  if (!MDoppler::getType(dtype, dpl)) {
568    throw(AipsError("Doppler type unknown"));
569  } else {
570    t.rwKeywordSet().define("DOPPLER",dpl);
571  }
572
573  if (!MFrequency::getType(mdr, brfrm)) {
574     Int a,b;const uInt* c;
575     const String* valid = MFrequency::allMyTypes(a, b, c);
576     String pfix = "Please specify a legal frame type. Types are\n";
577     throw(AipsError(pfix+(*valid)));
578   } else {
579    t.rwKeywordSet().define("BASEREFFRAME",brfrm);
580   }
581}
582
583
584std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
585{
586  std::vector<double> abc(nChan());
587
588  // Get header units keyword
589  Table t = table_.keywordSet().asTable("FREQUENCIES");
590  String sunit;
591  t.keywordSet().get("UNIT",sunit);
592  if (sunit == "") sunit = "pixel";
593  Unit u(sunit);
594
595  // Easy if just wanting pixels
596  if (sunit==String("pixel")) {
597    // assume channels/pixels
598    std::vector<double>::iterator it;
599    uInt i=0;
600    for (it = abc.begin(); it != abc.end(); ++it) {
601      (*it) = Double(i++);
602    }
603    return abc;
604  }
605
606  // Continue with km/s or Hz.  Get FreqIDs
607  Vector<uInt> freqIDs;
608  freqidCol_.get(whichRow, freqIDs);
609  uInt freqID = freqIDs(IFSel_);
610  restfreqidCol_.get(whichRow, freqIDs);
611  uInt restFreqID = freqIDs(IFSel_);
612
613  // Get SpectralCoordinate, set reference frame conversion,
614  // velocity conversion, and rest freq state
615
616  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
617  Vector<Double> pixel(nChan());
618  indgen(pixel);
619
620  if (u == Unit("km/s")) {
621     Vector<Double> world;
622     spc.pixelToVelocity(world,pixel);
623     std::vector<double>::iterator it;
624     uInt i = 0;
625     for (it = abc.begin(); it != abc.end(); ++it) {
626       (*it) = world[i];
627       i++;
628     }
629  } else if (u == Unit("Hz")) {
630
631    // Set world axis units
632    Vector<String> wau(1); wau = u.getName();
633    spc.setWorldAxisUnits(wau);
634
635    std::vector<double>::iterator it;
636    Double tmp;
637    uInt i = 0;
638    for (it = abc.begin(); it != abc.end(); ++it) {
639      spc.toWorld(tmp,pixel[i]);
640      (*it) = tmp;
641      i++;
642    }
643  }
644  return abc;
645}
646
647std::string SDMemTable::getAbcissaString(Int whichRow) const
648{
649  Table t = table_.keywordSet().asTable("FREQUENCIES");
650
651  String sunit;
652  t.keywordSet().get("UNIT",sunit);
653  if (sunit == "") sunit = "pixel";
654  Unit u(sunit);
655
656  Vector<uInt> freqIDs;
657  freqidCol_.get(whichRow, freqIDs);
658  uInt freqID = freqIDs(IFSel_);
659  restfreqidCol_.get(whichRow, freqIDs);
660  uInt restFreqID = freqIDs(IFSel_);
661
662  // Get SpectralCoordinate, with frame, velocity, rest freq state set
663  SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
664
665  String s = "Channel";
666  if (u == Unit("km/s")) {
667    s = CoordinateUtil::axisLabel(spc,0,True,True,True);
668  } else if (u == Unit("Hz")) {
669    Vector<String> wau(1);wau = u.getName();
670    spc.setWorldAxisUnits(wau);
671
672    s = CoordinateUtil::axisLabel(spc,0,True,True,False);
673  }
674  return s;
675}
676
677void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
678{
679  Array<Float> arr;
680  specCol_.get(whichRow, arr);
681  if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
682    throw(AipsError("Attempting to set spectrum with incorrect length."));
683  }
684
685  // Setup accessors
686  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
687  aa0.reset(aa0.begin(uInt(beamSel_)));                   // Beam selection
688  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
689  aa1.reset(aa1.begin(uInt(IFSel_)));                     // IF selection
690  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
691  aa2.reset(aa2.begin(uInt(polSel_)));                    // Pol selection
692
693  // Iterate
694  std::vector<float>::iterator it = spectrum.begin();
695  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
696    (*i) = Float(*it);
697    it++;
698  }
699  specCol_.put(whichRow, arr);
700}
701
702void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
703{
704  Array<Float> arr;
705  specCol_.get(whichRow, arr);
706
707  // Iterate and extract
708  spectrum.resize(arr.shape()(3));
709  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
710  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
711  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
712  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
713  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
714  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
715
716  ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
717  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
718    (*va) = (*i);
719    va++;
720  }
721}
722
723
724/*
725void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
726  Array<uChar> arr;
727  flagsCol_.get(whichRow, arr);
728  mask.resize(arr.shape()(3));
729
730  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
731  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
732  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
733  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
734  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
735  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
736
737  Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
738
739  ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
740  std::vector<bool> tmp;
741  tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
742                   // iterator should work on chanMask_??
743  std::vector<bool>::iterator miter;
744  miter = tmp.begin();
745
746  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
747    bool out =!static_cast<bool>(*i);
748    if (useUserMask) {
749      out = out && (*miter);
750      miter++;
751    }
752    (*va) = out;
753    va++;
754  }
755}
756*/
757
758MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
759                                                Bool toStokes) const
760{
761  // Get flags
762  Array<uChar> farr;
763  flagsCol_.get(whichRow, farr);
764
765  // Get data and convert mask to Bool
766  Array<Float> arr;
767  Array<Bool> mask;
768  if (toStokes) {
769     stokesCol_.get(whichRow, arr);
770
771     Array<Bool> tMask(farr.shape());
772     convertArray(tMask, farr);
773     mask = SDPolUtil::stokesData (tMask, True);
774  } else {
775     specCol_.get(whichRow, arr);
776     mask.resize(farr.shape());
777     convertArray(mask, farr);
778  }
779
780  return MaskedArray<Float>(arr,!mask);
781}
782
783Float SDMemTable::getTsys(Int whichRow) const
784{
785  Array<Float> arr;
786  tsCol_.get(whichRow, arr);
787  Float out;
788
789  IPosition ip(arr.shape());
790  ip(asap::BeamAxis) = beamSel_;
791  ip(asap::IFAxis) = IFSel_;
792  ip(asap::PolAxis) = polSel_;
793  ip(asap::ChanAxis)=0;               // First channel only
794
795  out = arr(ip);
796  return out;
797}
798
799MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
800{
801  MDirection::Types mdr = getDirectionReference();
802  Array<Double> posit;
803  dirCol_.get(whichRow,posit);
804  Vector<Double> wpos(2);
805  Int rb;
806  rbeamCol_.get(whichRow,rb);
807  wpos[0] = posit(IPosition(2,beamSel_,0));
808  wpos[1] = posit(IPosition(2,beamSel_,1));
809  if (refBeam && rb > -1) {  // use refBeam instead if it exists
810    wpos[0] = posit(IPosition(2,rb,0));
811    wpos[1] = posit(IPosition(2,rb,1));
812  }
813
814  Quantum<Double> lon(wpos[0],Unit(String("rad")));
815  Quantum<Double> lat(wpos[1],Unit(String("rad")));
816  return MDirection(lon, lat, mdr);
817}
818
819MEpoch SDMemTable::getEpoch(Int whichRow) const
820{
821  MEpoch::Types met = getTimeReference();
822
823  Double obstime;
824  timeCol_.get(whichRow,obstime);
825  MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
826  return MEpoch(tm2, met);
827}
828
829MPosition SDMemTable::getAntennaPosition () const
830{
831  Vector<Double> antpos;
832  table_.keywordSet().get("AntennaPosition", antpos);
833  MVPosition mvpos(antpos(0),antpos(1),antpos(2));
834  return MPosition(mvpos);
835}
836
837
838SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
839{
840
841  Table t = table_.keywordSet().asTable("FREQUENCIES");
842  if (freqID> t.nrow() ) {
843    throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
844  }
845
846  Double rp,rv,inc;
847  String rf;
848  ROScalarColumn<Double> rpc(t, "REFPIX");
849  ROScalarColumn<Double> rvc(t, "REFVAL");
850  ROScalarColumn<Double> incc(t, "INCREMENT");
851  t.keywordSet().get("BASEREFFRAME",rf);
852
853  // Create SpectralCoordinate (units Hz)
854  MFrequency::Types mft;
855  if (!MFrequency::getType(mft, rf)) {
856    ostringstream oss;
857    pushLog("WARNING: Frequency type unknown assuming TOPO");
858    mft = MFrequency::TOPO;
859  }
860  rpc.get(freqID, rp);
861  rvc.get(freqID, rv);
862  incc.get(freqID, inc);
863
864  SpectralCoordinate spec(mft,rv,inc,rp);
865  return spec;
866}
867
868
869SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
870                                                     uInt restFreqID,
871                                                     uInt whichRow) const
872{
873
874  // Create basic SC
875  SpectralCoordinate spec = getSpectralCoordinate (freqID);
876
877  Table t = table_.keywordSet().asTable("FREQUENCIES");
878
879  // Set rest frequency
880  Vector<Double> restFreqIDs;
881  t.keywordSet().get("RESTFREQS",restFreqIDs);
882  if (restFreqID < restFreqIDs.nelements()) {    // Should always be true
883    spec.setRestFrequency(restFreqIDs(restFreqID),True);
884  }
885
886  // Set up frame conversion layer
887  String frm;
888  t.keywordSet().get("REFFRAME",frm);
889  if (frm == "") frm = "TOPO";
890  MFrequency::Types mtype;
891  if (!MFrequency::getType(mtype, frm)) {
892    // Should never happen
893    pushLog("WARNING: Frequency type unknown assuming TOPO");
894    mtype = MFrequency::TOPO;
895  }
896
897  // Set reference frame conversion  (requires row)
898  MDirection dir = getDirection(whichRow);
899  MEpoch epoch = getEpoch(whichRow);
900  MPosition pos = getAntennaPosition();
901
902  if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
903    throw(AipsError("Couldn't convert frequency frame."));
904  }
905
906  // Now velocity conversion if appropriate
907  String unitStr;
908  t.keywordSet().get("UNIT",unitStr);
909
910  String dpl;
911  t.keywordSet().get("DOPPLER",dpl);
912  MDoppler::Types dtype;
913  MDoppler::getType(dtype, dpl);
914
915  // Only set velocity unit if non-blank and non-Hz
916  if (!unitStr.empty()) {
917     Unit unitU(unitStr);
918     if (unitU==Unit("Hz")) {
919     } else {
920        spec.setVelocity(unitStr, dtype);
921     }
922  }
923
924  return spec;
925}
926
927
928Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
929                               uInt freqID) {
930  Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
931  if (freqID > t.nrow() ) {
932    throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
933  }
934  ScalarColumn<Double> rpc(t, "REFPIX");
935  ScalarColumn<Double> rvc(t, "REFVAL");
936  ScalarColumn<Double> incc(t, "INCREMENT");
937
938  rpc.put(freqID, speccord.referencePixel()[0]);
939  rvc.put(freqID, speccord.referenceValue()[0]);
940  incc.put(freqID, speccord.increment()[0]);
941
942  return True;
943}
944
945Int SDMemTable::nCoordinates() const
946{
947  return table_.keywordSet().asTable("FREQUENCIES").nrow();
948}
949
950
951std::vector<double> SDMemTable::getRestFreqs() const
952{
953  Table t = table_.keywordSet().asTable("FREQUENCIES");
954  Vector<Double> tvec;
955  t.keywordSet().get("RESTFREQS",tvec);
956  std::vector<double> stlout;
957  tvec.tovector(stlout);
958  return stlout;
959}
960
961bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
962{
963  TableDesc td("", "1", TableDesc::Scratch);
964  td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
965  td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
966  td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
967  SetupNewTable aNewTab("freqs", td, Table::New);
968  Table aTable (aNewTab, Table::Memory, sdft.length());
969  ScalarColumn<Double> sc0(aTable, "REFPIX");
970  ScalarColumn<Double> sc1(aTable, "REFVAL");
971  ScalarColumn<Double> sc2(aTable, "INCREMENT");
972  for (uInt i=0; i < sdft.length(); ++i) {
973    sc0.put(i,sdft.referencePixel(i));
974    sc1.put(i,sdft.referenceValue(i));
975    sc2.put(i,sdft.increment(i));
976  }
977  String rf = sdft.refFrame();
978  if (rf.contains("TOPO")) rf = "TOPO";
979
980  aTable.rwKeywordSet().define("BASEREFFRAME", rf);
981  aTable.rwKeywordSet().define("REFFRAME", rf);
982  aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
983  aTable.rwKeywordSet().define("UNIT", String(""));
984  aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
985  Vector<Double> rfvec;
986  String rfunit;
987  sdft.restFrequencies(rfvec,rfunit);
988  Quantum<Vector<Double> > q(rfvec, rfunit);
989  rfvec.resize();
990  rfvec = q.getValue("Hz");
991  aTable.rwKeywordSet().define("RESTFREQS", rfvec);
992  table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
993  return true;
994}
995
996bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
997{
998  TableDesc td("", "1", TableDesc::Scratch);
999  td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1000  td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1001  td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1002  td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1003  td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1004  SetupNewTable aNewTab("fits", td, Table::New);
1005  Table aTable(aNewTab, Table::Memory);
1006  ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1007  ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1008  ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1009  ArrayColumn<Bool> sc3(aTable, "PARMASK");
1010  ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1011  for (uInt i; i<sdft.length(); ++i) {
1012    const Vector<Double>& parms = sdft.getParameters(i);
1013    const Vector<Bool>& parmask = sdft.getParameterMask(i);
1014    const Vector<String>& funcs = sdft.getFunctions(i);
1015    const Vector<Int>& comps = sdft.getComponents(i);
1016    const Vector<String>& finfo = sdft.getFrameInfo(i);
1017    sc0.put(i,funcs);
1018    sc1.put(i,comps);
1019    sc3.put(i,parmask);
1020    sc2.put(i,parms);
1021    sc4.put(i,finfo);
1022  }
1023  table_.rwKeywordSet().defineTable("FITS", aTable);
1024  return true;
1025}
1026
1027SDFitTable SDMemTable::getSDFitTable() const
1028{
1029  const Table& t = table_.keywordSet().asTable("FITS");
1030  Vector<Double> parms;
1031  Vector<Bool> parmask;
1032  Vector<String> funcs;
1033  Vector<String> finfo;
1034  Vector<Int> comps;
1035  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1036  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1037  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1038  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1039  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1040  uInt n = t.nrow();
1041  SDFitTable sdft;
1042  for (uInt i=0; i<n; ++i) {
1043    parmaskCol.get(i, parmask);
1044    parmsCol.get(i, parms);
1045    funcsCol.get(i, funcs);
1046    compsCol.get(i, comps);
1047    finfoCol.get(i, finfo);
1048    sdft.addFit(parms, parmask, funcs, comps, finfo);
1049  }
1050  return sdft;
1051}
1052
1053SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1054  const Table& t = table_.keywordSet().asTable("FITS");
1055  if (t.nrow() == 0 || whichRow >= t.nrow()) return SDFitTable();
1056  Array<Int> fitid;
1057  fitCol_.get(whichRow, fitid);
1058  if (fitid.nelements() == 0) return SDFitTable();
1059
1060  IPosition shp = fitid.shape();
1061  IPosition start(4, beamSel_, IFSel_, polSel_,0);
1062  IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1063
1064  // reform the output array slice to be of dim=1
1065  Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1066
1067  Vector<Double> parms;
1068  Vector<Bool> parmask;
1069  Vector<String> funcs;
1070  Vector<String> finfo;
1071  Vector<Int> comps;
1072  ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1073  ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1074  ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1075  ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1076  ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1077  SDFitTable sdft;
1078  Int k=-1;
1079  for (uInt i=0; i< tmp.nelements(); ++i) {
1080    k = tmp[i];
1081    if ( k > -1 && k < t.nrow() ) {
1082      parms.resize();
1083      parmsCol.get(k, parms);
1084      parmask.resize();
1085      parmaskCol.get(k, parmask);
1086      funcs.resize();
1087      funcsCol.get(k, funcs);
1088      comps.resize();
1089      compsCol.get(k, comps);
1090      finfo.resize();
1091      finfoCol.get(k, finfo);
1092      sdft.addFit(parms, parmask, funcs, comps, finfo);
1093    }
1094  }
1095  return sdft;
1096}
1097
1098void SDMemTable::addFit(uInt whichRow,
1099                        const Vector<Double>& p, const Vector<Bool>& m,
1100                        const Vector<String>& f, const Vector<Int>& c)
1101{
1102  if (whichRow >= nRow()) {
1103    throw(AipsError("Specified row out of range"));
1104  }
1105  Table t = table_.keywordSet().asTable("FITS");
1106  uInt nrow = t.nrow();
1107  t.addRow();
1108  ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1109  ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1110  ArrayColumn<Int> compsCol(t, "COMPONENTS");
1111  ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1112  ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1113  parmsCol.put(nrow, p);
1114  parmaskCol.put(nrow, m);
1115  compsCol.put(nrow, c);
1116  funcsCol.put(nrow, f);
1117  Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1118  finfoCol.put(nrow, fi);
1119
1120  Array<Int> fitarr;
1121  fitCol_.get(whichRow, fitarr);
1122
1123  Array<Int> newarr;               // The new Array containing the fitid
1124  Int pos =-1;                     // The fitid position in the array
1125  if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1126    Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1127    arr = -1;
1128    newarr.reference(arr);
1129    pos = 0;
1130  } else {
1131    IPosition shp = fitarr.shape();
1132    IPosition start(4, beamSel_, IFSel_, polSel_,0);
1133    IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1134    // reform the output array slice to be of dim=1
1135    Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1136    const Vector<Int>& fits = tmp;
1137    VectorSTLIterator<Int> it(fits);
1138    Int i = 0;
1139    while (it != fits.end()) {
1140      if (*it == -1) {
1141        pos = i;
1142        break;
1143      }
1144      ++i;
1145      ++it;
1146    };
1147  }
1148  if (pos == -1) {
1149      mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1150      pos = fitarr.shape()[3];     // the new element position
1151  } else {
1152    if (fitarr.nelements() > 0)
1153      newarr = fitarr;
1154  }
1155  newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1156  fitCol_.put(whichRow, newarr);
1157
1158}
1159
1160SDFrequencyTable SDMemTable::getSDFreqTable() const
1161{
1162  const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1163  SDFrequencyTable sdft;
1164
1165  // Add refpix/refval/incr.  What are the units ? Hz I suppose
1166  // but it's nowhere described...
1167  Vector<Double> refPix, refVal, incr;
1168  ScalarColumn<Double> refPixCol(t, "REFPIX");
1169  ScalarColumn<Double> refValCol(t, "REFVAL");
1170  ScalarColumn<Double> incrCol(t, "INCREMENT");
1171  refPix = refPixCol.getColumn();
1172  refVal = refValCol.getColumn();
1173  incr = incrCol.getColumn();
1174
1175  uInt n = refPix.nelements();
1176  for (uInt i=0; i<n; i++) {
1177     sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1178  }
1179
1180  // Frequency reference frame.  I don't know if this
1181  // is the correct frame.  It might be 'REFFRAME'
1182  // rather than 'BASEREFFRAME' ?
1183  String baseFrame;
1184  t.keywordSet().get("BASEREFFRAME",baseFrame);
1185  sdft.setRefFrame(baseFrame);
1186
1187  // Equinox
1188  Float equinox;
1189  t.keywordSet().get("EQUINOX", equinox);
1190  sdft.setEquinox(equinox);
1191
1192  // Rest Frequency
1193  Vector<Double> restFreqs;
1194  t.keywordSet().get("RESTFREQS", restFreqs);
1195  for (uInt i=0; i<restFreqs.nelements(); i++) {
1196     sdft.addRestFrequency(restFreqs[i]);
1197  }
1198  sdft.setRestFrequencyUnit(String("Hz"));
1199
1200  return sdft;
1201}
1202
1203bool SDMemTable::putSDContainer(const SDContainer& sdc)
1204{
1205  uInt rno = table_.nrow();
1206  table_.addRow();
1207
1208  timeCol_.put(rno, sdc.timestamp);
1209  srcnCol_.put(rno, sdc.sourcename);
1210  fldnCol_.put(rno, sdc.fieldname);
1211  specCol_.put(rno, sdc.getSpectrum());
1212  flagsCol_.put(rno, sdc.getFlags());
1213  tsCol_.put(rno, sdc.getTsys());
1214  scanCol_.put(rno, sdc.scanid);
1215  integrCol_.put(rno, sdc.interval);
1216  freqidCol_.put(rno, sdc.getFreqMap());
1217  restfreqidCol_.put(rno, sdc.getRestFreqMap());
1218  dirCol_.put(rno, sdc.getDirection());
1219  rbeamCol_.put(rno, sdc.refbeam);
1220  tcalCol_.put(rno, sdc.tcal);
1221  tcaltCol_.put(rno, sdc.tcaltime);
1222  azCol_.put(rno, sdc.azimuth);
1223  elCol_.put(rno, sdc.elevation);
1224  paraCol_.put(rno, sdc.parangle);
1225  fitCol_.put(rno, sdc.getFitMap());
1226  return true;
1227}
1228
1229SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1230{
1231  SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1232  timeCol_.get(whichRow, sdc.timestamp);
1233  srcnCol_.get(whichRow, sdc.sourcename);
1234  integrCol_.get(whichRow, sdc.interval);
1235  scanCol_.get(whichRow, sdc.scanid);
1236  fldnCol_.get(whichRow, sdc.fieldname);
1237  rbeamCol_.get(whichRow, sdc.refbeam);
1238  azCol_.get(whichRow, sdc.azimuth);
1239  elCol_.get(whichRow, sdc.elevation);
1240  paraCol_.get(whichRow, sdc.parangle);
1241  Vector<Float> tc;
1242  tcalCol_.get(whichRow, tc);
1243  sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1244  tcaltCol_.get(whichRow, sdc.tcaltime);
1245
1246  Array<Float> spectrum;
1247  Array<Float> tsys;
1248  Array<uChar> flagtrum;
1249  Vector<uInt> fmap;
1250  Array<Double> direction;
1251  Array<Int> fits;
1252
1253  specCol_.get(whichRow, spectrum);
1254  sdc.putSpectrum(spectrum);
1255  flagsCol_.get(whichRow, flagtrum);
1256  sdc.putFlags(flagtrum);
1257  tsCol_.get(whichRow, tsys);
1258  sdc.putTsys(tsys);
1259  freqidCol_.get(whichRow, fmap);
1260  sdc.putFreqMap(fmap);
1261  restfreqidCol_.get(whichRow, fmap);
1262  sdc.putRestFreqMap(fmap);
1263  dirCol_.get(whichRow, direction);
1264  sdc.putDirection(direction);
1265  fitCol_.get(whichRow, fits);
1266  sdc.putFitMap(fits);
1267  return sdc;
1268}
1269
1270bool SDMemTable::putSDHeader(const SDHeader& sdh)
1271{
1272  table_.rwKeywordSet().define("nIF", sdh.nif);
1273  table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1274  table_.rwKeywordSet().define("nPol", sdh.npol);
1275  table_.rwKeywordSet().define("nChan", sdh.nchan);
1276  table_.rwKeywordSet().define("Observer", sdh.observer);
1277  table_.rwKeywordSet().define("Project", sdh.project);
1278  table_.rwKeywordSet().define("Obstype", sdh.obstype);
1279  table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1280  table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1281  table_.rwKeywordSet().define("Equinox", sdh.equinox);
1282  table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1283  table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1284  table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1285  table_.rwKeywordSet().define("UTC", sdh.utc);
1286  table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1287  table_.rwKeywordSet().define("Epoch", sdh.epoch);
1288  return true;
1289}
1290
1291SDHeader SDMemTable::getSDHeader() const
1292{
1293  SDHeader sdh;
1294  table_.keywordSet().get("nBeam",sdh.nbeam);
1295  table_.keywordSet().get("nIF",sdh.nif);
1296  table_.keywordSet().get("nPol",sdh.npol);
1297  table_.keywordSet().get("nChan",sdh.nchan);
1298  table_.keywordSet().get("Observer", sdh.observer);
1299  table_.keywordSet().get("Project", sdh.project);
1300  table_.keywordSet().get("Obstype", sdh.obstype);
1301  table_.keywordSet().get("AntennaName", sdh.antennaname);
1302  table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1303  table_.keywordSet().get("Equinox", sdh.equinox);
1304  table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1305  table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1306  table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1307  table_.keywordSet().get("UTC", sdh.utc);
1308  table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1309  table_.keywordSet().get("Epoch", sdh.epoch);
1310  return sdh;
1311}
1312void SDMemTable::makePersistent(const std::string& filename)
1313{
1314  table_.deepCopy(filename,Table::New);
1315
1316}
1317
1318Int SDMemTable::nScan() const {
1319  Int n = 0;
1320  Int previous = -1;Int current=0;
1321  for (uInt i=0; i< scanCol_.nrow();i++) {
1322    scanCol_.getScalar(i,current);
1323    if (previous != current) {
1324      previous = current;
1325      n++;
1326    }
1327  }
1328  return n;
1329}
1330
1331String SDMemTable::formatSec(Double x) const
1332{
1333  Double xcop = x;
1334  MVTime mvt(xcop/24./3600.);  // make days
1335
1336  if (x < 59.95)
1337    return  String("      ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1338  else if (x < 3599.95)
1339    return String("   ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1340  else {
1341    ostringstream oss;
1342    oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1343    oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1344    return String(oss);
1345  }
1346};
1347
1348String SDMemTable::formatDirection(const MDirection& md) const
1349{
1350  Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1351  Int prec = 7;
1352
1353  MVAngle mvLon(t[0]);
1354  String sLon = mvLon.string(MVAngle::TIME,prec);
1355  MVAngle mvLat(t[1]);
1356  String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1357  return sLon + String(" ") + sLat;
1358}
1359
1360
1361std::string SDMemTable::getFluxUnit() const
1362{
1363  String tmp;
1364  table_.keywordSet().get("FluxUnit", tmp);
1365  return tmp;
1366}
1367
1368void SDMemTable::setFluxUnit(const std::string& unit)
1369{
1370  String tmp(unit);
1371  Unit tU(tmp);
1372  if (tU==Unit("K") || tU==Unit("Jy")) {
1373     table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1374  } else {
1375     throw AipsError("Illegal unit - must be compatible with Jy or K");
1376  }
1377}
1378
1379
1380void SDMemTable::setInstrument(const std::string& name)
1381{
1382  Bool throwIt = True;
1383  Instrument ins = SDAttr::convertInstrument(name, throwIt);
1384  String nameU(name);
1385  nameU.upcase();
1386  table_.rwKeywordSet().define(String("AntennaName"), nameU);
1387}
1388
1389std::string SDMemTable::summary(bool verbose) const  {
1390
1391  // Format header info
1392  ostringstream oss;
1393  oss << endl;
1394  oss << "--------------------------------------------------------------------------------" << endl;
1395  oss << " Scan Table Summary" << endl;
1396  oss << "--------------------------------------------------------------------------------" << endl;
1397  oss.flags(std::ios_base::left);
1398  oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1399      << setw(15) << "IFs:" << setw(4) << nIF() << endl
1400      << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1401      << setw(15) << "Channels:"  << setw(4) << nChan() << endl;
1402  oss << endl;
1403  String tmp;
1404  table_.keywordSet().get("Observer", tmp);
1405  oss << setw(15) << "Observer:" << tmp << endl;
1406  oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1407  table_.keywordSet().get("Project", tmp);
1408  oss << setw(15) << "Project:" << tmp << endl;
1409  table_.keywordSet().get("Obstype", tmp);
1410  oss << setw(15) << "Obs. Type:" << tmp << endl;
1411  table_.keywordSet().get("AntennaName", tmp);
1412  oss << setw(15) << "Antenna Name:" << tmp << endl;
1413  table_.keywordSet().get("FluxUnit", tmp);
1414  oss << setw(15) << "Flux Unit:" << tmp << endl;
1415  Table t = table_.keywordSet().asTable("FREQUENCIES");
1416  Vector<Double> vec;
1417  t.keywordSet().get("RESTFREQS",vec);
1418  oss << setw(15) << "Rest Freqs:";
1419  if (vec.nelements() > 0) {
1420      oss << setprecision(10) << vec << " [Hz]" << endl;
1421  } else {
1422      oss << "None set" << endl;
1423  }
1424  oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1425  oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1426      << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1427  oss << endl;
1428
1429  String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1430  oss << setw(5) << "Scan"
1431      << setw(15) << "Source"
1432      << setw(24) << dirtype
1433      << setw(10) << "Time"
1434      << setw(18) << "Integration"
1435      << setw(7) << "FreqIDs" << endl;
1436  oss << "--------------------------------------------------------------------------------" << endl;
1437
1438  // Generate list of scan start and end integrations
1439  Vector<Int> scanIDs = scanCol_.getColumn();
1440  Vector<uInt> startInt, endInt;
1441  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1442
1443  const uInt nScans = startInt.nelements();
1444  String name;
1445  Vector<uInt> freqIDs, listFQ;
1446  Vector<uInt> restFreqIDs, listRestFQ;
1447  uInt nInt;
1448
1449  for (uInt i=0; i<nScans; i++) {
1450    // Get things from first integration of scan
1451    String time = getTime(startInt(i),False);
1452    String tInt = formatSec(Double(getInterval(startInt(i))));
1453    String posit = formatDirection(getDirection(startInt(i),True));
1454    srcnCol_.getScalar(startInt(i),name);
1455
1456    // Find all the FreqIDs in this scan
1457    listFQ.resize(0);
1458    listRestFQ.resize(0);
1459    for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1460      freqidCol_.get(j, freqIDs);
1461      for (uInt k=0; k<freqIDs.nelements(); k++) {
1462        mathutil::addEntry(listFQ, freqIDs(k));
1463      }
1464//
1465      restfreqidCol_.get(j, restFreqIDs);
1466      for (uInt k=0; k<restFreqIDs.nelements(); k++) {
1467        mathutil::addEntry(listRestFQ, restFreqIDs(k));
1468      }
1469    }
1470
1471    nInt = endInt(i) - startInt(i) + 1;
1472    oss << setw(3) << std::right << i << std::left << setw(2) << "  "
1473        << setw(15) << name
1474        << setw(24) << posit
1475        << setw(10) << time
1476        << setw(3) << std::right << nInt  << setw(3) << " x " << std::left
1477        << setw(6) <<  tInt
1478        << " " << listFQ << " " << listRestFQ << endl;
1479  }
1480  oss << endl;
1481  oss << "Table contains " << table_.nrow() << " integration(s) in "
1482      << nScans << " scan(s)." << endl;
1483
1484  // Frequency Table
1485  if (verbose) {
1486    std::vector<string> info = getCoordInfo();
1487    SDFrequencyTable sdft = getSDFreqTable();
1488    oss << endl << endl;
1489    oss << "FreqID  Frame   RefFreq(Hz)     RefPix   Increment(Hz)" << endl;
1490    oss << "--------------------------------------------------------------------------------" << endl;
1491    for (uInt i=0; i<sdft.length(); i++) {
1492      oss << setw(8) << i << setw(8)
1493          << info[3] << setw(16) << setprecision(8)
1494          << sdft.referenceValue(i) << setw(10)
1495          << sdft.referencePixel(i) << setw(12)
1496          << sdft.increment(i) << endl;
1497    }
1498    oss << "--------------------------------------------------------------------------------" << endl;
1499  }
1500  return String(oss);
1501}
1502/*
1503std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1504  ostringstream oss;
1505  Vector<Int> scanIDs = scanCol_.getColumn();
1506  Vector<uInt> startInt, endInt;
1507  mathutil::scanBoundaries(startInt, endInt, scanIDs);
1508  const uInt nScans = startInt.nelements();
1509  std::vector<int>::const_iterator it(whichScans);
1510  return String(oss);
1511}
1512*/
1513Int SDMemTable::nBeam() const
1514{
1515  Int n;
1516  table_.keywordSet().get("nBeam",n);
1517  return n;
1518}
1519
1520Int SDMemTable::nIF() const {
1521  Int n;
1522  table_.keywordSet().get("nIF",n);
1523  return n;
1524}
1525
1526Int SDMemTable::nPol() const {
1527  Int n;
1528  table_.keywordSet().get("nPol",n);
1529  return n;
1530}
1531
1532Int SDMemTable::nChan() const {
1533  Int n;
1534  table_.keywordSet().get("nChan",n);
1535  return n;
1536}
1537
1538Table SDMemTable::getHistoryTable() const
1539{
1540  return table_.keywordSet().asTable("HISTORY");
1541}
1542
1543void SDMemTable::appendToHistoryTable(const Table& otherHist)
1544{
1545  Table t = table_.rwKeywordSet().asTable("HISTORY");
1546  const String sep = "--------------------------------------------------------------------------------";
1547  addHistory(sep);
1548  TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1549  addHistory(sep);
1550}
1551
1552void SDMemTable::addHistory(const std::string& hist)
1553{
1554  Table t = table_.rwKeywordSet().asTable("HISTORY");
1555  uInt nrow = t.nrow();
1556  t.addRow();
1557  ScalarColumn<String> itemCol(t, "ITEM");
1558  itemCol.put(nrow, hist);
1559}
1560
1561std::vector<std::string> SDMemTable::getHistory() const
1562{
1563  Vector<String> history;
1564  const Table& t = table_.keywordSet().asTable("HISTORY");
1565  uInt nrow = t.nrow();
1566  ROScalarColumn<String> itemCol(t, "ITEM");
1567  std::vector<std::string> stlout;
1568  String hist;
1569  for (uInt i=0; i<nrow; ++i) {
1570    itemCol.get(i, hist);
1571    stlout.push_back(hist);
1572  }
1573  return stlout;
1574}
1575
1576
1577/*
1578  void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1579
1580  std::vector<int>::iterator it;
1581  ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1582  for (it = whichChans.begin(); it != whichChans.end(); it++) {
1583    j.reset(j.begin(uInt(*it)));
1584    for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1585      for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1586        for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1587             iii != iii.end(); ++iii) {
1588          (*iii) =
1589        }
1590      }
1591    }
1592  }
1593
1594}
1595*/
1596void SDMemTable::flag(int whichRow)
1597  {
1598  Array<uChar> arr;
1599  flagsCol_.get(whichRow, arr);
1600
1601  ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1602  aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1603  ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1604  aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1605  ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1606  aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1607
1608  for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1609    (*i) = uChar(True);
1610  }
1611
1612  flagsCol_.put(whichRow, arr);
1613}
1614
1615MDirection::Types SDMemTable::getDirectionReference() const
1616{
1617  Float eq;
1618  table_.keywordSet().get("Equinox",eq);
1619  std::map<float,string> mp;
1620  mp[2000.0] = "J2000";
1621  mp[1950.0] = "B1950";
1622  MDirection::Types mdr;
1623  if (!MDirection::getType(mdr, mp[eq])) {
1624    mdr = MDirection::J2000;
1625    pushLog("WARNING: Unknown equinox using J2000");
1626
1627  }
1628
1629  return mdr;
1630}
1631
1632MEpoch::Types SDMemTable::getTimeReference() const
1633{
1634  MEpoch::Types met;
1635  String ep;
1636  table_.keywordSet().get("Epoch",ep);
1637  if (!MEpoch::getType(met, ep)) {
1638     pushLog("WARNING: Epoch type unknown - using UTC");
1639    met = MEpoch::UTC;
1640  }
1641
1642  return met;
1643}
1644
1645
1646Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1647                              const String& sUnit,
1648                              const vector<string>& lines,
1649                              const String& source,
1650                              Int whichIF)
1651{
1652   const Int nIFs = nIF();
1653   if (whichIF>=nIFs) {
1654      throw(AipsError("Illegal IF index"));
1655   }
1656
1657   // Find vector of restfrequencies
1658   // Double takes precedence over String
1659   Unit unit;
1660   Vector<Double> restFreqs;
1661   if (restFreqsIn.nelements()>0) {
1662      restFreqs.resize(restFreqsIn.nelements());
1663      restFreqs = restFreqsIn;
1664      unit = Unit(sUnit);
1665   } else if (lines.size()>0) {
1666      const uInt nLines = lines.size();
1667      unit = Unit("Hz");
1668      restFreqs.resize(nLines);
1669      MFrequency lineFreq;
1670      for (uInt i=0; i<nLines; i++) {
1671         String tS(lines[i]);
1672         tS.upcase();
1673         if (MeasTable::Line(lineFreq, tS)) {
1674            restFreqs[i] = lineFreq.getValue().getValue();          // Hz
1675         } else {
1676            String s = String(lines[i]) +
1677              String(" is an unrecognized spectral line");
1678            throw(AipsError(s));
1679         }
1680      }
1681   } else {
1682      throw(AipsError("You have not specified any rest frequencies or lines"));
1683   }
1684
1685   // If multiple restfreqs, must be length nIF. In this
1686   // case we will just replace the rest frequencies
1687   // We can't disinguish scalar and vector of length 1
1688   const uInt nRestFreqs = restFreqs.nelements();
1689   Int idx = -1;
1690   SDFrequencyTable sdft = getSDFreqTable();
1691
1692   ostringstream oss;
1693   if (nRestFreqs>1) {
1694     // Replace restFreqs, one per IF
1695     if (nRestFreqs != nIFs) {
1696       throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1697     }
1698     ostringstream oss;
1699     oss << "Replacing rest frequencies, one per IF, with given list : " << restFreqs;
1700     sdft.deleteRestFrequencies();
1701     for (uInt i=0; i<nRestFreqs; i++) {
1702       Quantum<Double> rf(restFreqs[i], unit);
1703       sdft.addRestFrequency(rf.getValue("Hz"));
1704     }
1705   } else {
1706
1707     // Add new rest freq
1708      Quantum<Double> rf(restFreqs[0], unit);
1709      idx = sdft.addRestFrequency(rf.getValue("Hz"));
1710      if (whichIF>=0) {
1711         oss << "Selecting given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1712      } else {
1713         oss << "Selecting given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1714      }
1715   }
1716   pushLog(String(oss));
1717   // Replace
1718   Bool empty = source.empty();
1719   Bool ok = False;
1720   if (putSDFreqTable(sdft)) {
1721      const uInt nRow = table_.nrow();
1722      String srcName;
1723      Vector<uInt> restFreqIDs;
1724      for (uInt i=0; i<nRow; i++) {
1725         srcnCol_.get(i, srcName);
1726         restfreqidCol_.get(i,restFreqIDs);
1727         if (idx==-1) {
1728           // Replace vector of restFreqs; one per IF.
1729           // No selection possible
1730            for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1731         } else {
1732           // Set RestFreqID for selected data
1733            if (empty || source==srcName) {
1734               if (whichIF<0) {
1735                  restFreqIDs = idx;
1736               } else {
1737                  restFreqIDs[whichIF] = idx;
1738               }
1739            }
1740         }
1741         restfreqidCol_.put(i,restFreqIDs);
1742      }
1743      ok = True;
1744   } else {
1745     ok = False;
1746   }
1747
1748   return ok;
1749}
1750
1751std::string SDMemTable::spectralLines() const
1752{
1753   Vector<String> lines = MeasTable::Lines();
1754   MFrequency lineFreq;
1755   Double freq;
1756   ostringstream oss;
1757
1758   oss.flags(std::ios_base::left);
1759   oss << "Line      Frequency (Hz)" << endl;
1760   oss << "-----------------------" << endl;
1761   for (uInt i=0; i<lines.nelements(); i++) {
1762     MeasTable::Line(lineFreq, lines[i]);
1763     freq = lineFreq.getValue().getValue();          // Hz
1764     oss << setw(11) << lines[i] << setprecision(10) << freq << endl;
1765   }
1766   return String(oss);
1767}
1768
1769void SDMemTable::renumber()
1770{
1771  uInt nRow = scanCol_.nrow();
1772  Int newscanid = 0;
1773  Int cIdx;// the current scanid
1774  // get the first scanid
1775  scanCol_.getScalar(0,cIdx);
1776  Int pIdx = cIdx;// the scanid of the previous row
1777  for (uInt i=0; i<nRow;++i) {
1778    scanCol_.getScalar(i,cIdx);
1779    if (pIdx == cIdx) {
1780      // renumber
1781      scanCol_.put(i,newscanid);
1782    } else {
1783      ++newscanid;
1784      pIdx = cIdx;   // store scanid
1785      --i;           // don't increment next loop
1786    }
1787  }
1788}
1789
1790
1791void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1792                                const IPosition& shape) const
1793{
1794  const uInt nDim = shape.nelements();
1795  start.resize(nDim);
1796  end.resize(nDim);
1797
1798  start(asap::BeamAxis) = beamSel_;
1799  end(asap::BeamAxis) = beamSel_;
1800  start(asap::IFAxis) = IFSel_;
1801  end(asap::IFAxis) = IFSel_;
1802
1803  start(asap::PolAxis) = polSel_;
1804  end(asap::PolAxis) = polSel_;
1805
1806  start(asap::ChanAxis) = 0;
1807  end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1808}
1809
1810
1811std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1812  // Get spectrum at cursor location
1813{
1814
1815  // Setup accessors
1816  ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1817  aa0.reset(aa0.begin(uInt(beamSel_)));                    // Beam selection
1818
1819  ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1820  aa1.reset(aa1.begin(uInt(IFSel_)));                      // IF selection
1821
1822  ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1823  aa2.reset(aa2.begin(uInt(polSel_)));                     // Pol selection
1824
1825  std::vector<float> spectrum;
1826  for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1827    spectrum.push_back(*i);
1828  }
1829  return spectrum;
1830}
1831
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