source: branches/Release12/src/SDMemTable.cc@ 798

Last change on this file since 798 was 787, checked in by phi196, 19 years ago

Added get_elevation, azimuth and parangle
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 53.5 KB
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1//#---------------------------------------------------------------------------
2//# SDMemTable.cc: A MemoryTable container for single dish integrations
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//# Internet email: Malte.Marquarding@csiro.au
23//# Postal address: Malte Marquarding,
24//# Australia Telescope National Facility,
25//# P.O. Box 76,
26//# Epping, NSW, 2121,
27//# AUSTRALIA
28//#
29//# $Id:
30//#---------------------------------------------------------------------------
31
32#include <map>
33
34#include <casa/aips.h>
35#include <casa/iostream.h>
36#include <casa/iomanip.h>
37#include <casa/Arrays/Array.h>
38#include <casa/Arrays/ArrayMath.h>
39#include <casa/Arrays/MaskArrMath.h>
40#include <casa/Arrays/ArrayLogical.h>
41#include <casa/Arrays/ArrayAccessor.h>
42#include <casa/Arrays/VectorSTLIterator.h>
43#include <casa/Arrays/Vector.h>
44#include <casa/BasicMath/Math.h>
45#include <casa/BasicSL/Constants.h>
46#include <casa/Quanta/MVAngle.h>
47
48#include <tables/Tables/TableParse.h>
49#include <tables/Tables/TableDesc.h>
50#include <tables/Tables/TableCopy.h>
51#include <tables/Tables/SetupNewTab.h>
52#include <tables/Tables/ScaColDesc.h>
53#include <tables/Tables/ArrColDesc.h>
54
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/TableRecord.h>
57#include <measures/Measures/MFrequency.h>
58#include <measures/Measures/MeasTable.h>
59#include <coordinates/Coordinates/CoordinateUtil.h>
60#include <casa/Quanta/MVTime.h>
61#include <casa/Quanta/MVAngle.h>
62
63#include "SDDefs.h"
64#include "SDContainer.h"
65#include "MathUtils.h"
66#include "SDPol.h"
67#include "SDAttr.h"
68
69#include "SDMemTable.h"
70
71using namespace casa;
72using namespace asap;
73
74SDMemTable::SDMemTable() :
75 IFSel_(0),
76 beamSel_(0),
77 polSel_(0)
78{
79 setup();
80 attach();
81}
82
83SDMemTable::SDMemTable(const std::string& name) :
84 IFSel_(0),
85 beamSel_(0),
86 polSel_(0)
87{
88 Table tab(name);
89 Int version;
90 tab.keywordSet().get("VERSION", version);
91 if (version != version_) {
92 throw(AipsError("Unsupported version of ASAP file."));
93 }
94 table_ = tab.copyToMemoryTable("dummy");
95 attach();
96}
97
98SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
99{
100 table_ = other.table_.copyToMemoryTable(String("dummy"));
101 // clear all rows()
102 if (clear) {
103 table_.removeRow(this->table_.rowNumbers());
104 IFSel_= 0;
105 beamSel_= 0;
106 polSel_= 0;
107 } else {
108 IFSel_= other.IFSel_;
109 beamSel_= other.beamSel_;
110 polSel_= other.polSel_;
111 }
112
113 attach();
114}
115
116SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
117 IFSel_(0),
118 beamSel_(0),
119 polSel_(0)
120{
121 Table t = tableCommand(exprs,tab);
122 if (t.nrow() == 0)
123 throw(AipsError("Query unsuccessful."));
124 table_ = t.copyToMemoryTable("dummy");
125 attach();
126 renumber();
127}
128
129SDMemTable::~SDMemTable()
130{
131 //cerr << "goodbye from SDMemTable @ " << this << endl;
132}
133
134SDMemTable SDMemTable::getScan(Int scanID) const
135{
136 String cond("SELECT * from $1 WHERE SCANID == ");
137 cond += String::toString(scanID);
138 return SDMemTable(table_, cond);
139}
140
141SDMemTable &SDMemTable::operator=(const SDMemTable& other)
142{
143 if (this != &other) {
144 IFSel_= other.IFSel_;
145 beamSel_= other.beamSel_;
146 polSel_= other.polSel_;
147 table_ = other.table_.copyToMemoryTable(String("dummy"));
148 attach();
149 }
150 return *this;
151}
152
153SDMemTable SDMemTable::getSource(const std::string& source) const
154{
155 String cond("SELECT * from $1 WHERE SRCNAME == ");
156 cond += source;
157 return SDMemTable(table_, cond);
158}
159
160void SDMemTable::setup()
161{
162 TableDesc td("", "1", TableDesc::Scratch);
163 td.comment() = "A SDMemTable";
164 td.rwKeywordSet().define("VERSION", Int(version_));
165
166 td.addColumn(ScalarColumnDesc<Double>("TIME"));
167 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
168 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
169 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
170 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
171 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
172 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
173 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
174 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
175 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
176 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
177 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
178 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
179 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
180 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
181 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
182 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
183 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
184 td.addColumn(ArrayColumnDesc<Int>("FITID"));
185
186 // Now create Table SetUp from the description.
187 SetupNewTable aNewTab("dummy", td, Table::New);
188
189 // Bind the Stokes Virtual machine to the STOKES column Because we
190 // don't know how many polarizations will be in the data at this
191 // point, we must bind the Virtual Engine regardless. The STOKES
192 // column won't be accessed if not appropriate (nPol=4)
193 SDStokesEngine::registerClass();
194 SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
195 aNewTab.bindColumn("STOKES", stokesEngine);
196
197 // Create Table
198 table_ = Table(aNewTab, Table::Memory, 0);
199 // add subtable
200 TableDesc tdf("", "1", TableDesc::Scratch);
201 tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
202 tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
203 tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
204 tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
205 tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
206 SetupNewTable fittab("fits", tdf, Table::New);
207 Table fitTable(fittab, Table::Memory);
208 table_.rwKeywordSet().defineTable("FITS", fitTable);
209
210 TableDesc tdh("", "1", TableDesc::Scratch);
211 tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
212 SetupNewTable histtab("hist", tdh, Table::New);
213 Table histTable(histtab, Table::Memory);
214 table_.rwKeywordSet().defineTable("HISTORY", histTable);
215}
216
217void SDMemTable::attach()
218{
219 timeCol_.attach(table_, "TIME");
220 srcnCol_.attach(table_, "SRCNAME");
221 specCol_.attach(table_, "SPECTRA");
222 flagsCol_.attach(table_, "FLAGTRA");
223 tsCol_.attach(table_, "TSYS");
224 stokesCol_.attach(table_, "STOKES");
225 scanCol_.attach(table_, "SCANID");
226 integrCol_.attach(table_, "INTERVAL");
227 freqidCol_.attach(table_, "FREQID");
228 restfreqidCol_.attach(table_, "RESTFREQID");
229 dirCol_.attach(table_, "DIRECTION");
230 fldnCol_.attach(table_, "FIELDNAME");
231 tcaltCol_.attach(table_, "TCALTIME");
232 tcalCol_.attach(table_, "TCAL");
233 azCol_.attach(table_, "AZIMUTH");
234 elCol_.attach(table_, "ELEVATION");
235 paraCol_.attach(table_, "PARANGLE");
236 rbeamCol_.attach(table_, "REFBEAM");
237 fitCol_.attach(table_,"FITID");
238}
239
240
241std::string SDMemTable::getSourceName(Int whichRow) const
242{
243 String name;
244 srcnCol_.get(whichRow, name);
245 return name;
246}
247
248float SDMemTable::getElevation(Int whichRow) const
249{
250 float elevation;
251 elCol_.get(whichRow, elevation);
252 return elevation;
253}
254
255float SDMemTable::getAzimuth(Int whichRow) const
256{
257 float azimuth;
258 azCol_.get(whichRow, azimuth);
259 return azimuth;
260}
261
262float SDMemTable::getParAngle(Int whichRow) const
263{
264 float parangle;
265 paraCol_.get(whichRow, parangle);
266 return parangle;
267}
268
269std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
270{
271 Double tm;
272 if (whichRow > -1) {
273 timeCol_.get(whichRow, tm);
274 } else {
275 table_.keywordSet().get("UTC",tm);
276 }
277 MVTime mvt(tm);
278 if (showDate)
279 mvt.setFormat(MVTime::YMD);
280 else
281 mvt.setFormat(MVTime::TIME);
282 ostringstream oss;
283 oss << mvt;
284 return String(oss);
285}
286
287double SDMemTable::getInterval(Int whichRow) const
288{
289 Double intval;
290 integrCol_.get(whichRow, intval);
291 return intval;
292}
293
294bool SDMemTable::setIF(Int whichIF)
295{
296 if ( whichIF >= 0 && whichIF < nIF()) {
297 IFSel_ = whichIF;
298 return true;
299 }
300 return false;
301}
302
303bool SDMemTable::setBeam(Int whichBeam)
304{
305 if ( whichBeam >= 0 && whichBeam < nBeam()) {
306 beamSel_ = whichBeam;
307 return true;
308 }
309 return false;
310}
311
312bool SDMemTable::setPol(Int whichPol)
313{
314 if ( whichPol >= 0 && whichPol < nPol()) {
315 polSel_ = whichPol;
316 return true;
317 }
318 return false;
319}
320
321void SDMemTable::resetCursor()
322{
323 polSel_ = 0;
324 IFSel_ = 0;
325 beamSel_ = 0;
326}
327
328std::vector<bool> SDMemTable::getMask(Int whichRow) const
329{
330
331 std::vector<bool> mask;
332
333 Array<uChar> arr;
334 flagsCol_.get(whichRow, arr);
335
336 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
337 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
338 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
339 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
340 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
341 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
342
343 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
344 bool out =!static_cast<bool>(*i);
345 mask.push_back(out);
346 }
347 return mask;
348}
349
350
351
352std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
353{
354 Array<Float> arr;
355 specCol_.get(whichRow, arr);
356 return getFloatSpectrum(arr);
357}
358
359
360int SDMemTable::nStokes() const
361{
362 return stokesCol_.shape(0).nelements(); // All rows same shape
363}
364
365
366std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow,
367 Bool doPol) const
368 //
369 // Gets one STokes parameter depending on cursor polSel location
370 // doPol=False : I,Q,U,V
371 // doPol=True : I,P,PA,V ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
372 //
373{
374 AlwaysAssert(asap::nAxes==4,AipsError);
375 if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
376 throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
377 }
378
379 // For full conversion we are only supporting linears at the moment
380
381 if (nPol() > 2) {
382 String antName;
383 table_.keywordSet().get("AntennaName", antName);
384 Instrument inst = SDAttr::convertInstrument (antName, True);
385 SDAttr sdAtt;
386 if (sdAtt.feedPolType(inst) != LINEAR) {
387 throw(AipsError("Only linear polarizations are supported"));
388 }
389 }
390
391 Array<Float> arr;
392 stokesCol_.get(whichRow, arr);
393
394 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
395
396 // Set current cursor location
397
398 const IPosition& shape = arr.shape();
399 IPosition start, end;
400 getCursorSlice(start, end, shape);
401
402 // Get Q and U slices
403
404 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
405 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
406
407 // Compute output
408
409 Array<Float> out;
410 if (polSel_==1) { // P
411 out = SDPolUtil::polarizedIntensity(Q,U);
412 } else if (polSel_==2) { // P.A.
413 out = SDPolUtil::positionAngle(Q,U);
414 }
415
416 // Copy to output
417
418 IPosition vecShape(1,shape(asap::ChanAxis));
419 Vector<Float> outV = out.reform(vecShape);
420 std::vector<float> stlout;
421 outV.tovector(stlout);
422 return stlout;
423
424 } else {
425 // Selects at the cursor location
426 return getFloatSpectrum(arr);
427 }
428}
429
430std::string SDMemTable::getPolarizationLabel(Bool linear, Bool stokes,
431 Bool linPol, Int polIdx) const
432{
433 uInt idx = polSel_;
434 if (polIdx >=0) idx = polIdx;
435 return SDPolUtil::polarizationLabel(idx, linear, stokes, linPol);
436}
437
438
439
440std::vector<float> SDMemTable::stokesToPolSpectrum(Int whichRow,
441 Bool toLinear,
442 Int polIdx) const
443//
444// polIdx
445// 0:3 -> RR,LL,Real(RL),Imag(RL)
446// XX,YY,Real(XY),Image(XY)
447//
448// Gets only
449// RR = I + V
450// LL = I - V
451// at the moment
452//
453{
454 AlwaysAssert(asap::nAxes==4,AipsError);
455 if (nStokes()!=4) {
456 throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
457 }
458//
459 Array<Float> arr, out;
460 stokesCol_.get(whichRow, arr);
461
462// Set current cursor location
463
464 const IPosition& shape = arr.shape();
465 IPosition start, end;
466 getCursorSlice(start, end, shape);
467
468// Get the slice
469
470 if (toLinear) {
471 throw(AipsError("Conversion to linears not yet supported"));
472 } else {
473 uInt selection = polSel_;
474 if (polIdx > -1) selection = polIdx;
475 Bool doRR = (selection==0);
476 if (selection>1) {
477 throw(AipsError("Only conversion to RR & LL is currently supported"));
478 }
479
480 // Get I and V slices
481 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
482 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
483
484 // Compute output
485 out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
486 }
487
488 // Copy to output
489 IPosition vecShape(1,shape(asap::ChanAxis));
490 Vector<Float> outV = out.reform(vecShape);
491 std::vector<float> stlout;
492 outV.tovector(stlout);
493//
494 return stlout;
495}
496
497
498
499
500Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
501{
502
503// Get data
504
505 Array<Float> arr;
506 stokesCol_.get(whichRow, arr);
507
508// Set current cursor location and overwrite polarization axis
509
510 const IPosition& shape = arr.shape();
511 IPosition start(shape.nelements(),0);
512 IPosition end(shape-1);
513 if (iBeam!=-1) {
514 start(asap::BeamAxis) = iBeam;
515 end(asap::BeamAxis) = iBeam;
516 }
517 if (iIF!=-1) {
518 start(asap::IFAxis) = iIF;
519 end(asap::IFAxis) = iIF;
520 }
521
522// Get slice
523
524 return arr(start,end);
525}
526
527
528std::vector<string> SDMemTable::getCoordInfo() const
529{
530 String un;
531 Table t = table_.keywordSet().asTable("FREQUENCIES");
532 String sunit;
533 t.keywordSet().get("UNIT",sunit);
534 String dpl;
535 t.keywordSet().get("DOPPLER",dpl);
536 if (dpl == "") dpl = "RADIO";
537 String rfrm;
538 t.keywordSet().get("REFFRAME",rfrm);
539 std::vector<string> inf;
540 inf.push_back(sunit);
541 inf.push_back(rfrm);
542 inf.push_back(dpl);
543 t.keywordSet().get("BASEREFFRAME",rfrm);
544 inf.push_back(rfrm);
545 return inf;
546}
547
548void SDMemTable::setCoordInfo(std::vector<string> theinfo)
549{
550 std::vector<string>::iterator it;
551 String un,rfrm, brfrm,dpl;
552 un = theinfo[0]; // Abcissa unit
553 rfrm = theinfo[1]; // Active (or conversion) frame
554 dpl = theinfo[2]; // Doppler
555 brfrm = theinfo[3]; // Base frame
556 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
557
558 Vector<Double> rstf;
559 t.keywordSet().get("RESTFREQS",rstf);
560
561 Bool canDo = True;
562 Unit u1("km/s");Unit u2("Hz");
563 if (Unit(un) == u1) {
564 Vector<Double> rstf;
565 t.keywordSet().get("RESTFREQS",rstf);
566 if (rstf.nelements() == 0) {
567 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
568 }
569 } else if (Unit(un) != u2 && un != "") {
570 throw(AipsError("Unit not conformant with Spectral Coordinates"));
571 }
572 t.rwKeywordSet().define("UNIT", un);
573
574 MFrequency::Types mdr;
575 if (!MFrequency::getType(mdr, rfrm)) {
576
577 Int a,b;const uInt* c;
578 const String* valid = MFrequency::allMyTypes(a, b, c);
579 String pfix = "Please specify a legal frame type. Types are\n";
580 throw(AipsError(pfix+(*valid)));
581 } else {
582 t.rwKeywordSet().define("REFFRAME",rfrm);
583 }
584
585 MDoppler::Types dtype;
586 dpl.upcase();
587 if (!MDoppler::getType(dtype, dpl)) {
588 throw(AipsError("Doppler type unknown"));
589 } else {
590 t.rwKeywordSet().define("DOPPLER",dpl);
591 }
592
593 if (!MFrequency::getType(mdr, brfrm)) {
594 Int a,b;const uInt* c;
595 const String* valid = MFrequency::allMyTypes(a, b, c);
596 String pfix = "Please specify a legal frame type. Types are\n";
597 throw(AipsError(pfix+(*valid)));
598 } else {
599 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
600 }
601}
602
603
604std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
605{
606 std::vector<double> abc(nChan());
607
608 // Get header units keyword
609 Table t = table_.keywordSet().asTable("FREQUENCIES");
610 String sunit;
611 t.keywordSet().get("UNIT",sunit);
612 if (sunit == "") sunit = "pixel";
613 Unit u(sunit);
614
615 // Easy if just wanting pixels
616 if (sunit==String("pixel")) {
617 // assume channels/pixels
618 std::vector<double>::iterator it;
619 uInt i=0;
620 for (it = abc.begin(); it != abc.end(); ++it) {
621 (*it) = Double(i++);
622 }
623 return abc;
624 }
625
626 // Continue with km/s or Hz. Get FreqIDs
627 Vector<uInt> freqIDs;
628 freqidCol_.get(whichRow, freqIDs);
629 uInt freqID = freqIDs(IFSel_);
630 restfreqidCol_.get(whichRow, freqIDs);
631 uInt restFreqID = freqIDs(IFSel_);
632
633 // Get SpectralCoordinate, set reference frame conversion,
634 // velocity conversion, and rest freq state
635
636 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
637 Vector<Double> pixel(nChan());
638 indgen(pixel);
639
640 if (u == Unit("km/s")) {
641 Vector<Double> world;
642 spc.pixelToVelocity(world,pixel);
643 std::vector<double>::iterator it;
644 uInt i = 0;
645 for (it = abc.begin(); it != abc.end(); ++it) {
646 (*it) = world[i];
647 i++;
648 }
649 } else if (u == Unit("Hz")) {
650
651 // Set world axis units
652 Vector<String> wau(1); wau = u.getName();
653 spc.setWorldAxisUnits(wau);
654
655 std::vector<double>::iterator it;
656 Double tmp;
657 uInt i = 0;
658 for (it = abc.begin(); it != abc.end(); ++it) {
659 spc.toWorld(tmp,pixel[i]);
660 (*it) = tmp;
661 i++;
662 }
663 }
664 return abc;
665}
666
667std::string SDMemTable::getAbcissaString(Int whichRow) const
668{
669 Table t = table_.keywordSet().asTable("FREQUENCIES");
670
671 String sunit;
672 t.keywordSet().get("UNIT",sunit);
673 if (sunit == "") sunit = "pixel";
674 Unit u(sunit);
675
676 Vector<uInt> freqIDs;
677 freqidCol_.get(whichRow, freqIDs);
678 uInt freqID = freqIDs(IFSel_);
679 restfreqidCol_.get(whichRow, freqIDs);
680 uInt restFreqID = freqIDs(IFSel_);
681
682 // Get SpectralCoordinate, with frame, velocity, rest freq state set
683 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
684
685 String s = "Channel";
686 if (u == Unit("km/s")) {
687 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
688 } else if (u == Unit("Hz")) {
689 Vector<String> wau(1);wau = u.getName();
690 spc.setWorldAxisUnits(wau);
691
692 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
693 }
694 return s;
695}
696
697void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
698{
699 Array<Float> arr;
700 specCol_.get(whichRow, arr);
701 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
702 throw(AipsError("Attempting to set spectrum with incorrect length."));
703 }
704
705 // Setup accessors
706 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
707 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
708 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
709 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
710 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
711 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
712
713 // Iterate
714 std::vector<float>::iterator it = spectrum.begin();
715 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
716 (*i) = Float(*it);
717 it++;
718 }
719 specCol_.put(whichRow, arr);
720}
721
722void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
723{
724 Array<Float> arr;
725 specCol_.get(whichRow, arr);
726
727 // Iterate and extract
728 spectrum.resize(arr.shape()(3));
729 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
730 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
731 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
732 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
733 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
734 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
735
736 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
737 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
738 (*va) = (*i);
739 va++;
740 }
741}
742
743
744/*
745void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
746 Array<uChar> arr;
747 flagsCol_.get(whichRow, arr);
748 mask.resize(arr.shape()(3));
749
750 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
751 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
752 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
753 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
754 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
755 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
756
757 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
758
759 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
760 std::vector<bool> tmp;
761 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
762 // iterator should work on chanMask_??
763 std::vector<bool>::iterator miter;
764 miter = tmp.begin();
765
766 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
767 bool out =!static_cast<bool>(*i);
768 if (useUserMask) {
769 out = out && (*miter);
770 miter++;
771 }
772 (*va) = out;
773 va++;
774 }
775}
776*/
777
778MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
779 Bool toStokes) const
780{
781 // Get flags
782 Array<uChar> farr;
783 flagsCol_.get(whichRow, farr);
784
785 // Get data and convert mask to Bool
786 Array<Float> arr;
787 Array<Bool> mask;
788 if (toStokes) {
789 stokesCol_.get(whichRow, arr);
790
791 Array<Bool> tMask(farr.shape());
792 convertArray(tMask, farr);
793 mask = SDPolUtil::stokesData (tMask, True);
794 } else {
795 specCol_.get(whichRow, arr);
796 mask.resize(farr.shape());
797 convertArray(mask, farr);
798 }
799
800 return MaskedArray<Float>(arr,!mask);
801}
802
803Float SDMemTable::getTsys(Int whichRow) const
804{
805 Array<Float> arr;
806 tsCol_.get(whichRow, arr);
807 Float out;
808
809 IPosition ip(arr.shape());
810 ip(asap::BeamAxis) = beamSel_;
811 ip(asap::IFAxis) = IFSel_;
812 ip(asap::PolAxis) = polSel_;
813 ip(asap::ChanAxis)=0; // First channel only
814
815 out = arr(ip);
816 return out;
817}
818
819MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
820{
821 MDirection::Types mdr = getDirectionReference();
822 Array<Double> posit;
823 dirCol_.get(whichRow,posit);
824 Vector<Double> wpos(2);
825 Int rb;
826 rbeamCol_.get(whichRow,rb);
827 wpos[0] = posit(IPosition(2,beamSel_,0));
828 wpos[1] = posit(IPosition(2,beamSel_,1));
829 if (refBeam && rb > -1) { // use refBeam instead if it exists
830 wpos[0] = posit(IPosition(2,rb,0));
831 wpos[1] = posit(IPosition(2,rb,1));
832 }
833
834 Quantum<Double> lon(wpos[0],Unit(String("rad")));
835 Quantum<Double> lat(wpos[1],Unit(String("rad")));
836 return MDirection(lon, lat, mdr);
837}
838
839MEpoch SDMemTable::getEpoch(Int whichRow) const
840{
841 MEpoch::Types met = getTimeReference();
842
843 Double obstime;
844 timeCol_.get(whichRow,obstime);
845 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
846 return MEpoch(tm2, met);
847}
848
849MPosition SDMemTable::getAntennaPosition () const
850{
851 Vector<Double> antpos;
852 table_.keywordSet().get("AntennaPosition", antpos);
853 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
854 return MPosition(mvpos);
855}
856
857
858SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
859{
860
861 Table t = table_.keywordSet().asTable("FREQUENCIES");
862 if (freqID> t.nrow() ) {
863 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
864 }
865
866 Double rp,rv,inc;
867 String rf;
868 ROScalarColumn<Double> rpc(t, "REFPIX");
869 ROScalarColumn<Double> rvc(t, "REFVAL");
870 ROScalarColumn<Double> incc(t, "INCREMENT");
871 t.keywordSet().get("BASEREFFRAME",rf);
872
873 // Create SpectralCoordinate (units Hz)
874 MFrequency::Types mft;
875 if (!MFrequency::getType(mft, rf)) {
876 ostringstream oss;
877 pushLog("WARNING: Frequency type unknown assuming TOPO");
878 mft = MFrequency::TOPO;
879 }
880 rpc.get(freqID, rp);
881 rvc.get(freqID, rv);
882 incc.get(freqID, inc);
883
884 SpectralCoordinate spec(mft,rv,inc,rp);
885 return spec;
886}
887
888
889SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
890 uInt restFreqID,
891 uInt whichRow) const
892{
893
894 // Create basic SC
895 SpectralCoordinate spec = getSpectralCoordinate (freqID);
896
897 Table t = table_.keywordSet().asTable("FREQUENCIES");
898
899 // Set rest frequency
900 Vector<Double> restFreqIDs;
901 t.keywordSet().get("RESTFREQS",restFreqIDs);
902 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
903 spec.setRestFrequency(restFreqIDs(restFreqID),True);
904 }
905
906 // Set up frame conversion layer
907 String frm;
908 t.keywordSet().get("REFFRAME",frm);
909 if (frm == "") frm = "TOPO";
910 MFrequency::Types mtype;
911 if (!MFrequency::getType(mtype, frm)) {
912 // Should never happen
913 pushLog("WARNING: Frequency type unknown assuming TOPO");
914 mtype = MFrequency::TOPO;
915 }
916
917 // Set reference frame conversion (requires row)
918 MDirection dir = getDirection(whichRow);
919 MEpoch epoch = getEpoch(whichRow);
920 MPosition pos = getAntennaPosition();
921
922 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
923 throw(AipsError("Couldn't convert frequency frame."));
924 }
925
926 // Now velocity conversion if appropriate
927 String unitStr;
928 t.keywordSet().get("UNIT",unitStr);
929
930 String dpl;
931 t.keywordSet().get("DOPPLER",dpl);
932 MDoppler::Types dtype;
933 MDoppler::getType(dtype, dpl);
934
935 // Only set velocity unit if non-blank and non-Hz
936 if (!unitStr.empty()) {
937 Unit unitU(unitStr);
938 if (unitU==Unit("Hz")) {
939 } else {
940 spec.setVelocity(unitStr, dtype);
941 }
942 }
943
944 return spec;
945}
946
947
948Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
949 uInt freqID) {
950 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
951 if (freqID > t.nrow() ) {
952 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
953 }
954 ScalarColumn<Double> rpc(t, "REFPIX");
955 ScalarColumn<Double> rvc(t, "REFVAL");
956 ScalarColumn<Double> incc(t, "INCREMENT");
957
958 rpc.put(freqID, speccord.referencePixel()[0]);
959 rvc.put(freqID, speccord.referenceValue()[0]);
960 incc.put(freqID, speccord.increment()[0]);
961
962 return True;
963}
964
965Int SDMemTable::nCoordinates() const
966{
967 return table_.keywordSet().asTable("FREQUENCIES").nrow();
968}
969
970
971std::vector<double> SDMemTable::getRestFreqs() const
972{
973 Table t = table_.keywordSet().asTable("FREQUENCIES");
974 Vector<Double> tvec;
975 t.keywordSet().get("RESTFREQS",tvec);
976 std::vector<double> stlout;
977 tvec.tovector(stlout);
978 return stlout;
979}
980
981bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
982{
983 TableDesc td("", "1", TableDesc::Scratch);
984 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
985 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
986 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
987 SetupNewTable aNewTab("freqs", td, Table::New);
988 Table aTable (aNewTab, Table::Memory, sdft.length());
989 ScalarColumn<Double> sc0(aTable, "REFPIX");
990 ScalarColumn<Double> sc1(aTable, "REFVAL");
991 ScalarColumn<Double> sc2(aTable, "INCREMENT");
992 for (uInt i=0; i < sdft.length(); ++i) {
993 sc0.put(i,sdft.referencePixel(i));
994 sc1.put(i,sdft.referenceValue(i));
995 sc2.put(i,sdft.increment(i));
996 }
997 String rf = sdft.refFrame();
998 if (rf.contains("TOPO")) rf = "TOPO";
999 String brf = sdft.baseRefFrame();
1000 if (brf.contains("TOPO")) brf = "TOPO";
1001
1002 aTable.rwKeywordSet().define("BASEREFFRAME", brf);
1003 aTable.rwKeywordSet().define("REFFRAME", rf);
1004 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
1005 aTable.rwKeywordSet().define("UNIT", sdft.unit());
1006 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
1007 Vector<Double> rfvec;
1008 String rfunit;
1009 sdft.restFrequencies(rfvec,rfunit);
1010 Quantum<Vector<Double> > q(rfvec, rfunit);
1011 rfvec.resize();
1012 rfvec = q.getValue("Hz");
1013 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
1014 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
1015 return true;
1016}
1017
1018bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
1019{
1020 TableDesc td("", "1", TableDesc::Scratch);
1021 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1022 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1023 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1024 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1025 td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1026 SetupNewTable aNewTab("fits", td, Table::New);
1027 Table aTable(aNewTab, Table::Memory);
1028 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1029 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1030 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1031 ArrayColumn<Bool> sc3(aTable, "PARMASK");
1032 ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1033 for (uInt i; i<sdft.length(); ++i) {
1034 const Vector<Double>& parms = sdft.getParameters(i);
1035 const Vector<Bool>& parmask = sdft.getParameterMask(i);
1036 const Vector<String>& funcs = sdft.getFunctions(i);
1037 const Vector<Int>& comps = sdft.getComponents(i);
1038 const Vector<String>& finfo = sdft.getFrameInfo(i);
1039 sc0.put(i,funcs);
1040 sc1.put(i,comps);
1041 sc3.put(i,parmask);
1042 sc2.put(i,parms);
1043 sc4.put(i,finfo);
1044 }
1045 table_.rwKeywordSet().defineTable("FITS", aTable);
1046 return true;
1047}
1048
1049SDFitTable SDMemTable::getSDFitTable() const
1050{
1051 const Table& t = table_.keywordSet().asTable("FITS");
1052 Vector<Double> parms;
1053 Vector<Bool> parmask;
1054 Vector<String> funcs;
1055 Vector<String> finfo;
1056 Vector<Int> comps;
1057 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1058 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1059 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1060 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1061 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1062 uInt n = t.nrow();
1063 SDFitTable sdft;
1064 for (uInt i=0; i<n; ++i) {
1065 parmaskCol.get(i, parmask);
1066 parmsCol.get(i, parms);
1067 funcsCol.get(i, funcs);
1068 compsCol.get(i, comps);
1069 finfoCol.get(i, finfo);
1070 sdft.addFit(parms, parmask, funcs, comps, finfo);
1071 }
1072 return sdft;
1073}
1074
1075SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1076 const Table& t = table_.keywordSet().asTable("FITS");
1077 if (t.nrow() == 0 || whichRow >= t.nrow()) return SDFitTable();
1078 Array<Int> fitid;
1079 fitCol_.get(whichRow, fitid);
1080 if (fitid.nelements() == 0) return SDFitTable();
1081
1082 IPosition shp = fitid.shape();
1083 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1084 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1085
1086 // reform the output array slice to be of dim=1
1087 Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1088
1089 Vector<Double> parms;
1090 Vector<Bool> parmask;
1091 Vector<String> funcs;
1092 Vector<String> finfo;
1093 Vector<Int> comps;
1094 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1095 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1096 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1097 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1098 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1099 SDFitTable sdft;
1100 Int k=-1;
1101 for (uInt i=0; i< tmp.nelements(); ++i) {
1102 k = tmp[i];
1103 if ( k > -1 && k < t.nrow() ) {
1104 parms.resize();
1105 parmsCol.get(k, parms);
1106 parmask.resize();
1107 parmaskCol.get(k, parmask);
1108 funcs.resize();
1109 funcsCol.get(k, funcs);
1110 comps.resize();
1111 compsCol.get(k, comps);
1112 finfo.resize();
1113 finfoCol.get(k, finfo);
1114 sdft.addFit(parms, parmask, funcs, comps, finfo);
1115 }
1116 }
1117 return sdft;
1118}
1119
1120void SDMemTable::addFit(uInt whichRow,
1121 const Vector<Double>& p, const Vector<Bool>& m,
1122 const Vector<String>& f, const Vector<Int>& c)
1123{
1124 if (whichRow >= nRow()) {
1125 throw(AipsError("Specified row out of range"));
1126 }
1127 Table t = table_.keywordSet().asTable("FITS");
1128 uInt nrow = t.nrow();
1129 t.addRow();
1130 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1131 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1132 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1133 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1134 ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1135 parmsCol.put(nrow, p);
1136 parmaskCol.put(nrow, m);
1137 compsCol.put(nrow, c);
1138 funcsCol.put(nrow, f);
1139 Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1140 finfoCol.put(nrow, fi);
1141
1142 Array<Int> fitarr;
1143 fitCol_.get(whichRow, fitarr);
1144
1145 Array<Int> newarr; // The new Array containing the fitid
1146 Int pos =-1; // The fitid position in the array
1147 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1148 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1149 arr = -1;
1150 newarr.reference(arr);
1151 pos = 0;
1152 } else {
1153 IPosition shp = fitarr.shape();
1154 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1155 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1156 // reform the output array slice to be of dim=1
1157 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1158 const Vector<Int>& fits = tmp;
1159 VectorSTLIterator<Int> it(fits);
1160 Int i = 0;
1161 while (it != fits.end()) {
1162 if (*it == -1) {
1163 pos = i;
1164 break;
1165 }
1166 ++i;
1167 ++it;
1168 };
1169 }
1170 if (pos == -1) {
1171 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1172 pos = fitarr.shape()[3]; // the new element position
1173 } else {
1174 if (fitarr.nelements() > 0)
1175 newarr = fitarr;
1176 }
1177 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1178 fitCol_.put(whichRow, newarr);
1179
1180}
1181
1182SDFrequencyTable SDMemTable::getSDFreqTable() const
1183{
1184 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1185 SDFrequencyTable sdft;
1186
1187 // Add refpix/refval/incr. What are the units ? Hz I suppose
1188 // but it's nowhere described...
1189 Vector<Double> refPix, refVal, incr;
1190 ScalarColumn<Double> refPixCol(t, "REFPIX");
1191 ScalarColumn<Double> refValCol(t, "REFVAL");
1192 ScalarColumn<Double> incrCol(t, "INCREMENT");
1193 refPix = refPixCol.getColumn();
1194 refVal = refValCol.getColumn();
1195 incr = incrCol.getColumn();
1196
1197 uInt n = refPix.nelements();
1198 for (uInt i=0; i<n; i++) {
1199 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1200 }
1201
1202 // Frequency reference frame. I don't know if this
1203 // is the correct frame. It might be 'REFFRAME'
1204 // rather than 'BASEREFFRAME' ?
1205 String frame;
1206 t.keywordSet().get("REFFRAME",frame);
1207 sdft.setRefFrame(frame);
1208 t.keywordSet().get("BASEREFFRAME",frame);
1209 sdft.setBaseRefFrame(frame);
1210
1211 // Equinox
1212 Float equinox;
1213 t.keywordSet().get("EQUINOX", equinox);
1214 sdft.setEquinox(equinox);
1215
1216 String unit;
1217 t.keywordSet().get("UNIT", unit);
1218 sdft.setUnit(unit);
1219
1220 // Rest Frequency
1221 Vector<Double> restFreqs;
1222 t.keywordSet().get("RESTFREQS", restFreqs);
1223 for (uInt i=0; i<restFreqs.nelements(); i++) {
1224 sdft.addRestFrequency(restFreqs[i]);
1225 }
1226 sdft.setRestFrequencyUnit(String("Hz"));
1227
1228 return sdft;
1229}
1230
1231bool SDMemTable::putSDContainer(const SDContainer& sdc)
1232{
1233 uInt rno = table_.nrow();
1234 table_.addRow();
1235
1236 timeCol_.put(rno, sdc.timestamp);
1237 srcnCol_.put(rno, sdc.sourcename);
1238 fldnCol_.put(rno, sdc.fieldname);
1239 specCol_.put(rno, sdc.getSpectrum());
1240 flagsCol_.put(rno, sdc.getFlags());
1241 tsCol_.put(rno, sdc.getTsys());
1242 scanCol_.put(rno, sdc.scanid);
1243 integrCol_.put(rno, sdc.interval);
1244 freqidCol_.put(rno, sdc.getFreqMap());
1245 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1246 dirCol_.put(rno, sdc.getDirection());
1247 rbeamCol_.put(rno, sdc.refbeam);
1248 tcalCol_.put(rno, sdc.tcal);
1249 tcaltCol_.put(rno, sdc.tcaltime);
1250 azCol_.put(rno, sdc.azimuth);
1251 elCol_.put(rno, sdc.elevation);
1252 paraCol_.put(rno, sdc.parangle);
1253 fitCol_.put(rno, sdc.getFitMap());
1254 return true;
1255}
1256
1257SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1258{
1259 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1260 timeCol_.get(whichRow, sdc.timestamp);
1261 srcnCol_.get(whichRow, sdc.sourcename);
1262 integrCol_.get(whichRow, sdc.interval);
1263 scanCol_.get(whichRow, sdc.scanid);
1264 fldnCol_.get(whichRow, sdc.fieldname);
1265 rbeamCol_.get(whichRow, sdc.refbeam);
1266 azCol_.get(whichRow, sdc.azimuth);
1267 elCol_.get(whichRow, sdc.elevation);
1268 paraCol_.get(whichRow, sdc.parangle);
1269 Vector<Float> tc;
1270 tcalCol_.get(whichRow, tc);
1271 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1272 tcaltCol_.get(whichRow, sdc.tcaltime);
1273
1274 Array<Float> spectrum;
1275 Array<Float> tsys;
1276 Array<uChar> flagtrum;
1277 Vector<uInt> fmap;
1278 Array<Double> direction;
1279 Array<Int> fits;
1280
1281 specCol_.get(whichRow, spectrum);
1282 sdc.putSpectrum(spectrum);
1283 flagsCol_.get(whichRow, flagtrum);
1284 sdc.putFlags(flagtrum);
1285 tsCol_.get(whichRow, tsys);
1286 sdc.putTsys(tsys);
1287 freqidCol_.get(whichRow, fmap);
1288 sdc.putFreqMap(fmap);
1289 restfreqidCol_.get(whichRow, fmap);
1290 sdc.putRestFreqMap(fmap);
1291 dirCol_.get(whichRow, direction);
1292 sdc.putDirection(direction);
1293 fitCol_.get(whichRow, fits);
1294 sdc.putFitMap(fits);
1295 return sdc;
1296}
1297
1298bool SDMemTable::putSDHeader(const SDHeader& sdh)
1299{
1300 table_.rwKeywordSet().define("nIF", sdh.nif);
1301 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1302 table_.rwKeywordSet().define("nPol", sdh.npol);
1303 table_.rwKeywordSet().define("nChan", sdh.nchan);
1304 table_.rwKeywordSet().define("Observer", sdh.observer);
1305 table_.rwKeywordSet().define("Project", sdh.project);
1306 table_.rwKeywordSet().define("Obstype", sdh.obstype);
1307 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1308 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1309 table_.rwKeywordSet().define("Equinox", sdh.equinox);
1310 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1311 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1312 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1313 table_.rwKeywordSet().define("UTC", sdh.utc);
1314 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1315 table_.rwKeywordSet().define("Epoch", sdh.epoch);
1316 return true;
1317}
1318
1319SDHeader SDMemTable::getSDHeader() const
1320{
1321 SDHeader sdh;
1322 table_.keywordSet().get("nBeam",sdh.nbeam);
1323 table_.keywordSet().get("nIF",sdh.nif);
1324 table_.keywordSet().get("nPol",sdh.npol);
1325 table_.keywordSet().get("nChan",sdh.nchan);
1326 table_.keywordSet().get("Observer", sdh.observer);
1327 table_.keywordSet().get("Project", sdh.project);
1328 table_.keywordSet().get("Obstype", sdh.obstype);
1329 table_.keywordSet().get("AntennaName", sdh.antennaname);
1330 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1331 table_.keywordSet().get("Equinox", sdh.equinox);
1332 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1333 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1334 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1335 table_.keywordSet().get("UTC", sdh.utc);
1336 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1337 table_.keywordSet().get("Epoch", sdh.epoch);
1338 return sdh;
1339}
1340void SDMemTable::makePersistent(const std::string& filename)
1341{
1342 table_.deepCopy(filename,Table::New);
1343
1344}
1345
1346Int SDMemTable::nScan() const {
1347 Int n = 0;
1348 Int previous = -1;Int current=0;
1349 for (uInt i=0; i< scanCol_.nrow();i++) {
1350 scanCol_.getScalar(i,current);
1351 if (previous != current) {
1352 previous = current;
1353 n++;
1354 }
1355 }
1356 return n;
1357}
1358
1359String SDMemTable::formatSec(Double x) const
1360{
1361 Double xcop = x;
1362 MVTime mvt(xcop/24./3600.); // make days
1363
1364 if (x < 59.95)
1365 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1366 else if (x < 3599.95)
1367 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1368 else {
1369 ostringstream oss;
1370 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1371 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1372 return String(oss);
1373 }
1374};
1375
1376String SDMemTable::formatDirection(const MDirection& md) const
1377{
1378 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1379 Int prec = 7;
1380
1381 MVAngle mvLon(t[0]);
1382 String sLon = mvLon.string(MVAngle::TIME,prec);
1383 MVAngle mvLat(t[1]);
1384 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1385 return sLon + String(" ") + sLat;
1386}
1387
1388
1389std::string SDMemTable::getFluxUnit() const
1390{
1391 String tmp;
1392 table_.keywordSet().get("FluxUnit", tmp);
1393 return tmp;
1394}
1395
1396void SDMemTable::setFluxUnit(const std::string& unit)
1397{
1398 String tmp(unit);
1399 Unit tU(tmp);
1400 if (tU==Unit("K") || tU==Unit("Jy")) {
1401 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1402 } else {
1403 throw AipsError("Illegal unit - must be compatible with Jy or K");
1404 }
1405}
1406
1407
1408void SDMemTable::setInstrument(const std::string& name)
1409{
1410 Bool throwIt = True;
1411 Instrument ins = SDAttr::convertInstrument(name, throwIt);
1412 String nameU(name);
1413 nameU.upcase();
1414 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1415}
1416
1417std::string SDMemTable::summary(bool verbose) const {
1418
1419 // Format header info
1420 ostringstream oss;
1421 oss << endl;
1422 oss << "--------------------------------------------------------------------------------" << endl;
1423 oss << " Scan Table Summary" << endl;
1424 oss << "--------------------------------------------------------------------------------" << endl;
1425 oss.flags(std::ios_base::left);
1426 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1427 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1428 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1429 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1430 oss << endl;
1431 String tmp;
1432 table_.keywordSet().get("Observer", tmp);
1433 oss << setw(15) << "Observer:" << tmp << endl;
1434 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1435 table_.keywordSet().get("Project", tmp);
1436 oss << setw(15) << "Project:" << tmp << endl;
1437 table_.keywordSet().get("Obstype", tmp);
1438 oss << setw(15) << "Obs. Type:" << tmp << endl;
1439 table_.keywordSet().get("AntennaName", tmp);
1440 oss << setw(15) << "Antenna Name:" << tmp << endl;
1441 table_.keywordSet().get("FluxUnit", tmp);
1442 oss << setw(15) << "Flux Unit:" << tmp << endl;
1443 Table t = table_.keywordSet().asTable("FREQUENCIES");
1444 Vector<Double> vec;
1445 t.keywordSet().get("RESTFREQS",vec);
1446 oss << setw(15) << "Rest Freqs:";
1447 if (vec.nelements() > 0) {
1448 oss << setprecision(10) << vec << " [Hz]" << endl;
1449 } else {
1450 oss << "None set" << endl;
1451 }
1452 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1453 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1454 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1455 oss << endl;
1456
1457 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1458 oss << setw(5) << "Scan"
1459 << setw(15) << "Source"
1460 << setw(24) << dirtype
1461 << setw(10) << "Time"
1462 << setw(18) << "Integration"
1463 << setw(7) << "FreqIDs" << endl;
1464 oss << "--------------------------------------------------------------------------------" << endl;
1465
1466 // Generate list of scan start and end integrations
1467 Vector<Int> scanIDs = scanCol_.getColumn();
1468 Vector<uInt> startInt, endInt;
1469 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1470
1471 const uInt nScans = startInt.nelements();
1472 String name;
1473 Vector<uInt> freqIDs, listFQ;
1474 Vector<uInt> restFreqIDs, listRestFQ;
1475 uInt nInt;
1476
1477 for (uInt i=0; i<nScans; i++) {
1478 // Get things from first integration of scan
1479 String time = getTime(startInt(i),False);
1480 String tInt = formatSec(Double(getInterval(startInt(i))));
1481 String posit = formatDirection(getDirection(startInt(i),True));
1482 srcnCol_.getScalar(startInt(i),name);
1483
1484 // Find all the FreqIDs in this scan
1485 listFQ.resize(0);
1486 listRestFQ.resize(0);
1487 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1488 freqidCol_.get(j, freqIDs);
1489 for (uInt k=0; k<freqIDs.nelements(); k++) {
1490 mathutil::addEntry(listFQ, freqIDs(k));
1491 }
1492//
1493 restfreqidCol_.get(j, restFreqIDs);
1494 for (uInt k=0; k<restFreqIDs.nelements(); k++) {
1495 mathutil::addEntry(listRestFQ, restFreqIDs(k));
1496 }
1497 }
1498
1499 nInt = endInt(i) - startInt(i) + 1;
1500 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1501 << setw(15) << name
1502 << setw(24) << posit
1503 << setw(10) << time
1504 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1505 << setw(6) << tInt
1506 << " " << listFQ << " " << listRestFQ << endl;
1507 }
1508 oss << endl;
1509 oss << "Table contains " << table_.nrow() << " integration(s) in "
1510 << nScans << " scan(s)." << endl;
1511
1512 // Frequency Table
1513 if (verbose) {
1514 std::vector<string> info = getCoordInfo();
1515 SDFrequencyTable sdft = getSDFreqTable();
1516 oss << endl << endl;
1517 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1518 oss << "--------------------------------------------------------------------------------" << endl;
1519 for (uInt i=0; i<sdft.length(); i++) {
1520 oss << setw(8) << i << setw(8)
1521 << info[3] << setw(16) << setprecision(8)
1522 << sdft.referenceValue(i) << setw(10)
1523 << sdft.referencePixel(i) << setw(12)
1524 << sdft.increment(i) << endl;
1525 }
1526 oss << "--------------------------------------------------------------------------------" << endl;
1527 }
1528 return String(oss);
1529}
1530/*
1531std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1532 ostringstream oss;
1533 Vector<Int> scanIDs = scanCol_.getColumn();
1534 Vector<uInt> startInt, endInt;
1535 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1536 const uInt nScans = startInt.nelements();
1537 std::vector<int>::const_iterator it(whichScans);
1538 return String(oss);
1539}
1540*/
1541Int SDMemTable::nBeam() const
1542{
1543 Int n;
1544 table_.keywordSet().get("nBeam",n);
1545 return n;
1546}
1547
1548Int SDMemTable::nIF() const {
1549 Int n;
1550 table_.keywordSet().get("nIF",n);
1551 return n;
1552}
1553
1554Int SDMemTable::nPol() const {
1555 Int n;
1556 table_.keywordSet().get("nPol",n);
1557 return n;
1558}
1559
1560Int SDMemTable::nChan() const {
1561 Int n;
1562 table_.keywordSet().get("nChan",n);
1563 return n;
1564}
1565
1566Table SDMemTable::getHistoryTable() const
1567{
1568 return table_.keywordSet().asTable("HISTORY");
1569}
1570
1571void SDMemTable::appendToHistoryTable(const Table& otherHist)
1572{
1573 Table t = table_.rwKeywordSet().asTable("HISTORY");
1574 const String sep = "--------------------------------------------------------------------------------";
1575 addHistory(sep);
1576 TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1577 addHistory(sep);
1578}
1579
1580void SDMemTable::addHistory(const std::string& hist)
1581{
1582 Table t = table_.rwKeywordSet().asTable("HISTORY");
1583 uInt nrow = t.nrow();
1584 t.addRow();
1585 ScalarColumn<String> itemCol(t, "ITEM");
1586 itemCol.put(nrow, hist);
1587}
1588
1589std::vector<std::string> SDMemTable::getHistory() const
1590{
1591 Vector<String> history;
1592 const Table& t = table_.keywordSet().asTable("HISTORY");
1593 uInt nrow = t.nrow();
1594 ROScalarColumn<String> itemCol(t, "ITEM");
1595 std::vector<std::string> stlout;
1596 String hist;
1597 for (uInt i=0; i<nrow; ++i) {
1598 itemCol.get(i, hist);
1599 stlout.push_back(hist);
1600 }
1601 return stlout;
1602}
1603
1604
1605/*
1606 void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1607
1608 std::vector<int>::iterator it;
1609 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1610 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1611 j.reset(j.begin(uInt(*it)));
1612 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1613 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1614 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1615 iii != iii.end(); ++iii) {
1616 (*iii) =
1617 }
1618 }
1619 }
1620 }
1621
1622}
1623*/
1624void SDMemTable::flag(int whichRow)
1625 {
1626 Array<uChar> arr;
1627 flagsCol_.get(whichRow, arr);
1628
1629 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1630 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1631 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1632 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1633 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1634 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1635
1636 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1637 (*i) = uChar(True);
1638 }
1639
1640 flagsCol_.put(whichRow, arr);
1641}
1642
1643MDirection::Types SDMemTable::getDirectionReference() const
1644{
1645 Float eq;
1646 table_.keywordSet().get("Equinox",eq);
1647 std::map<float,string> mp;
1648 mp[2000.0] = "J2000";
1649 mp[1950.0] = "B1950";
1650 MDirection::Types mdr;
1651 if (!MDirection::getType(mdr, mp[eq])) {
1652 mdr = MDirection::J2000;
1653 pushLog("WARNING: Unknown equinox using J2000");
1654 }
1655
1656 return mdr;
1657}
1658
1659MEpoch::Types SDMemTable::getTimeReference() const
1660{
1661 MEpoch::Types met;
1662 String ep;
1663 table_.keywordSet().get("Epoch",ep);
1664 if (!MEpoch::getType(met, ep)) {
1665 pushLog("WARNING: Epoch type unknown - using UTC");
1666 met = MEpoch::UTC;
1667 }
1668
1669 return met;
1670}
1671
1672
1673Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1674 const String& sUnit,
1675 const vector<string>& lines,
1676 const String& source,
1677 Int whichIF)
1678{
1679 const Int nIFs = nIF();
1680 if (whichIF>=nIFs) {
1681 throw(AipsError("Illegal IF index"));
1682 }
1683
1684 // Find vector of restfrequencies
1685 // Double takes precedence over String
1686 Unit unit;
1687 Vector<Double> restFreqs;
1688 if (restFreqsIn.nelements()>0) {
1689 restFreqs.resize(restFreqsIn.nelements());
1690 restFreqs = restFreqsIn;
1691 unit = Unit(sUnit);
1692 } else if (lines.size()>0) {
1693 const uInt nLines = lines.size();
1694 unit = Unit("Hz");
1695 restFreqs.resize(nLines);
1696 MFrequency lineFreq;
1697 for (uInt i=0; i<nLines; i++) {
1698 String tS(lines[i]);
1699 tS.upcase();
1700 if (MeasTable::Line(lineFreq, tS)) {
1701 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1702 } else {
1703 String s = String(lines[i]) +
1704 String(" is an unrecognized spectral line");
1705 throw(AipsError(s));
1706 }
1707 }
1708 } else {
1709 throw(AipsError("You have not specified any rest frequencies or lines"));
1710 }
1711
1712 // If multiple restfreqs, must be length nIF. In this
1713 // case we will just replace the rest frequencies
1714 // We can't disinguish scalar and vector of length 1
1715 const uInt nRestFreqs = restFreqs.nelements();
1716 Int idx = -1;
1717 SDFrequencyTable sdft = getSDFreqTable();
1718
1719 ostringstream oss;
1720 if (nRestFreqs>1) {
1721 // Replace restFreqs, one per IF
1722 if (nRestFreqs != nIFs) {
1723 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1724 }
1725 ostringstream oss;
1726 oss << "Replaced rest frequencies, one per IF, with given list : " << restFreqs;
1727 sdft.deleteRestFrequencies();
1728 for (uInt i=0; i<nRestFreqs; i++) {
1729 Quantum<Double> rf(restFreqs[i], unit);
1730 sdft.addRestFrequency(rf.getValue("Hz"));
1731 }
1732 } else {
1733
1734 // Add new rest freq
1735 Quantum<Double> rf(restFreqs[0], unit);
1736 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1737 if (whichIF>=0) {
1738 oss << "Selected given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1739 } else {
1740 oss << "Selected given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1741 }
1742 }
1743 pushLog(String(oss));
1744 // Replace
1745 Bool empty = source.empty();
1746 Bool ok = False;
1747 if (putSDFreqTable(sdft)) {
1748 const uInt nRow = table_.nrow();
1749 String srcName;
1750 Vector<uInt> restFreqIDs;
1751 for (uInt i=0; i<nRow; i++) {
1752 srcnCol_.get(i, srcName);
1753 restfreqidCol_.get(i,restFreqIDs);
1754 if (idx==-1) {
1755 // Replace vector of restFreqs; one per IF.
1756 // No selection possible
1757 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1758 } else {
1759 // Set RestFreqID for selected data
1760 if (empty || source==srcName) {
1761 if (whichIF<0) {
1762 restFreqIDs = idx;
1763 } else {
1764 restFreqIDs[whichIF] = idx;
1765 }
1766 }
1767 }
1768 restfreqidCol_.put(i,restFreqIDs);
1769 }
1770 ok = True;
1771 } else {
1772 ok = False;
1773 }
1774
1775 return ok;
1776}
1777
1778std::string SDMemTable::spectralLines() const
1779{
1780 Vector<String> lines = MeasTable::Lines();
1781 MFrequency lineFreq;
1782 Double freq;
1783 ostringstream oss;
1784
1785 oss.flags(std::ios_base::left);
1786 oss << "Line Frequency (Hz)" << endl;
1787 oss << "-----------------------" << endl;
1788 for (uInt i=0; i<lines.nelements(); i++) {
1789 MeasTable::Line(lineFreq, lines[i]);
1790 freq = lineFreq.getValue().getValue(); // Hz
1791 oss << setw(11) << lines[i] << setprecision(10) << freq << endl;
1792 }
1793 return String(oss);
1794}
1795
1796void SDMemTable::renumber()
1797{
1798 uInt nRow = scanCol_.nrow();
1799 Int newscanid = 0;
1800 Int cIdx;// the current scanid
1801 // get the first scanid
1802 scanCol_.getScalar(0,cIdx);
1803 Int pIdx = cIdx;// the scanid of the previous row
1804 for (uInt i=0; i<nRow;++i) {
1805 scanCol_.getScalar(i,cIdx);
1806 if (pIdx == cIdx) {
1807 // renumber
1808 scanCol_.put(i,newscanid);
1809 } else {
1810 ++newscanid;
1811 pIdx = cIdx; // store scanid
1812 --i; // don't increment next loop
1813 }
1814 }
1815}
1816
1817
1818void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1819 const IPosition& shape) const
1820{
1821 const uInt nDim = shape.nelements();
1822 start.resize(nDim);
1823 end.resize(nDim);
1824
1825 start(asap::BeamAxis) = beamSel_;
1826 end(asap::BeamAxis) = beamSel_;
1827 start(asap::IFAxis) = IFSel_;
1828 end(asap::IFAxis) = IFSel_;
1829
1830 start(asap::PolAxis) = polSel_;
1831 end(asap::PolAxis) = polSel_;
1832
1833 start(asap::ChanAxis) = 0;
1834 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1835}
1836
1837
1838std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1839 // Get spectrum at cursor location
1840{
1841
1842 // Setup accessors
1843 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1844 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1845
1846 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1847 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1848
1849 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1850 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1851
1852 std::vector<float> spectrum;
1853 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1854 spectrum.push_back(*i);
1855 }
1856 return spectrum;
1857}
1858
1859void SDMemTable::calculateAZEL()
1860{
1861 MPosition mp = getAntennaPosition();
1862 ostringstream oss;
1863 oss << "Computed azimuth/elevation using " << endl
1864 << mp << endl;
1865 for (uInt i=0; i<nRow();++i) {
1866 MEpoch me = getEpoch(i);
1867 MDirection md = getDirection(i,False);
1868 oss << " Time: " << getTime(i,False) << " Direction: " << formatDirection(md)
1869 << endl << " => ";
1870 MeasFrame frame(mp, me);
1871 Vector<Double> azel =
1872 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
1873 frame)
1874 )().getAngle("rad").getValue();
1875 azCol_.put(i,azel[0]);
1876 elCol_.put(i,azel[1]);
1877 oss << "azel: " << azel[0]/C::pi*180.0 << " "
1878 << azel[1]/C::pi*180.0 << " (deg)" << endl;
1879 }
1880 pushLog(String(oss));
1881}
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