source: trunk/src/SDMemTable.cc@ 458

Last change on this file since 458 was 457, checked in by kil064, 20 years ago

move SDMemTable::rotateXYPhase to SDMath
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 48.3 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/Quanta/MVAngle.h>
46
47#include <tables/Tables/TableParse.h>
48#include <tables/Tables/TableDesc.h>
49#include <tables/Tables/SetupNewTab.h>
50#include <tables/Tables/ScaColDesc.h>
51#include <tables/Tables/ArrColDesc.h>
52
53#include <tables/Tables/ExprNode.h>
54#include <tables/Tables/TableRecord.h>
55#include <measures/Measures/MFrequency.h>
56#include <measures/Measures/MeasTable.h>
57#include <coordinates/Coordinates/CoordinateUtil.h>
58#include <casa/Quanta/MVTime.h>
59#include <casa/Quanta/MVAngle.h>
60
61#include "SDDefs.h"
62#include "SDMemTable.h"
63#include "SDContainer.h"
64#include "MathUtils.h"
65#include "SDPol.h"
66
67
68
69using namespace casa;
70using namespace asap;
71
72SDMemTable::SDMemTable() :
73 IFSel_(0),
74 beamSel_(0),
75 polSel_(0)
76{
77 setup();
78 attach();
79}
80
81SDMemTable::SDMemTable(const std::string& name) :
82 IFSel_(0),
83 beamSel_(0),
84 polSel_(0)
85{
86 Table tab(name);
87 table_ = tab.copyToMemoryTable("dummy");
88 //cerr << "hello from C SDMemTable @ " << this << endl;
89 attach();
90}
91
92SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
93{
94 IFSel_= other.IFSel_;
95 beamSel_= other.beamSel_;
96 polSel_= other.polSel_;
97 chanMask_ = other.chanMask_;
98 table_ = other.table_.copyToMemoryTable(String("dummy"));
99 // clear all rows()
100 if (clear) {
101 table_.removeRow(this->table_.rowNumbers());
102 } else {
103 IFSel_ = other.IFSel_;
104 beamSel_ = other.beamSel_;
105 polSel_ = other.polSel_;
106 }
107//
108 attach();
109 //cerr << "hello from CC SDMemTable @ " << this << endl;
110}
111
112SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
113 IFSel_(0),
114 beamSel_(0),
115 polSel_(0)
116{
117 Table t = tableCommand(exprs,tab);
118 if (t.nrow() == 0)
119 throw(AipsError("Query unsuccessful."));
120 table_ = t.copyToMemoryTable("dummy");
121 attach();
122 renumber();
123}
124
125SDMemTable::~SDMemTable()
126{
127 //cerr << "goodbye from SDMemTable @ " << this << endl;
128}
129
130SDMemTable SDMemTable::getScan(Int scanID) const
131{
132 String cond("SELECT * from $1 WHERE SCANID == ");
133 cond += String::toString(scanID);
134 return SDMemTable(table_, cond);
135}
136
137SDMemTable &SDMemTable::operator=(const SDMemTable& other)
138{
139 if (this != &other) {
140 IFSel_= other.IFSel_;
141 beamSel_= other.beamSel_;
142 polSel_= other.polSel_;
143 chanMask_.resize(0);
144 chanMask_ = other.chanMask_;
145 table_ = other.table_.copyToMemoryTable(String("dummy"));
146 attach();
147 }
148 //cerr << "hello from ASS SDMemTable @ " << this << endl;
149 return *this;
150}
151
152SDMemTable SDMemTable::getSource(const std::string& source) const
153{
154 String cond("SELECT * from $1 WHERE SRCNAME == ");
155 cond += source;
156 return SDMemTable(table_, cond);
157}
158
159void SDMemTable::setup()
160{
161 TableDesc td("", "1", TableDesc::Scratch);
162 td.comment() = "A SDMemTable";
163
164 td.addColumn(ScalarColumnDesc<Double>("TIME"));
165 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
166 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
167 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
168 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
169 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
170 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
171 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
172 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
173 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
174 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
175 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
176 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
177 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
178 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
179 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
180 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
181 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
182 td.addColumn(ArrayColumnDesc<String>("HISTORY"));
183 td.addColumn(ArrayColumnDesc<Int>("FITID"));
184
185
186 // Now create Table SetUp from the description.
187
188 SetupNewTable aNewTab("dummy", td, Table::New);
189
190 // Bind the Stokes Virtual machine to the STOKES column Because we
191 // don't know how many polarizations will be in the data at this
192 // point, we must bind the Virtual Engine regardless. The STOKES
193 // column won't be accessed if not appropriate (nPol=4)
194
195 SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
196 aNewTab.bindColumn ("STOKES", stokesEngine);
197
198 // Create Table
199 table_ = Table(aNewTab, Table::Memory, 0);
200 // add subtable
201 TableDesc tdf("", "1", TableDesc::Scratch);
202 tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
203 tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
204 tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
205 tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
206 SetupNewTable fittab("fits", tdf, Table::New);
207 Table fitTable(fittab, Table::Memory);
208 table_.rwKeywordSet().defineTable("FITS", fitTable);
209
210
211}
212
213void SDMemTable::attach()
214{
215 timeCol_.attach(table_, "TIME");
216 srcnCol_.attach(table_, "SRCNAME");
217 specCol_.attach(table_, "SPECTRA");
218 flagsCol_.attach(table_, "FLAGTRA");
219 tsCol_.attach(table_, "TSYS");
220 stokesCol_.attach(table_, "STOKES");
221 scanCol_.attach(table_, "SCANID");
222 integrCol_.attach(table_, "INTERVAL");
223 freqidCol_.attach(table_, "FREQID");
224 restfreqidCol_.attach(table_, "RESTFREQID");
225 dirCol_.attach(table_, "DIRECTION");
226 fldnCol_.attach(table_, "FIELDNAME");
227 tcaltCol_.attach(table_, "TCALTIME");
228 tcalCol_.attach(table_, "TCAL");
229 azCol_.attach(table_, "AZIMUTH");
230 elCol_.attach(table_, "ELEVATION");
231 paraCol_.attach(table_, "PARANGLE");
232 rbeamCol_.attach(table_, "REFBEAM");
233 histCol_.attach(table_, "HISTORY");
234 fitCol_.attach(table_,"FITID");
235}
236
237
238std::string SDMemTable::getSourceName(Int whichRow) const
239{
240 String name;
241 srcnCol_.get(whichRow, name);
242 return name;
243}
244
245std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
246{
247 Double tm;
248 if (whichRow > -1) {
249 timeCol_.get(whichRow, tm);
250 } else {
251 table_.keywordSet().get("UTC",tm);
252 }
253 MVTime mvt(tm);
254 if (showDate)
255 mvt.setFormat(MVTime::YMD);
256 else
257 mvt.setFormat(MVTime::TIME);
258 ostringstream oss;
259 oss << mvt;
260 return String(oss);
261}
262
263double SDMemTable::getInterval(Int whichRow) const
264{
265 Double intval;
266 integrCol_.get(whichRow, intval);
267 return intval;
268}
269
270bool SDMemTable::setIF(Int whichIF)
271{
272 if ( whichIF >= 0 && whichIF < nIF()) {
273 IFSel_ = whichIF;
274 return true;
275 }
276 return false;
277}
278
279bool SDMemTable::setBeam(Int whichBeam)
280{
281 if ( whichBeam >= 0 && whichBeam < nBeam()) {
282 beamSel_ = whichBeam;
283 return true;
284 }
285 return false;
286}
287
288bool SDMemTable::setPol(Int whichPol)
289{
290 if ( whichPol >= 0 && whichPol < nPol()) {
291 polSel_ = whichPol;
292 return true;
293 }
294 return false;
295}
296
297void SDMemTable::resetCursor()
298{
299 polSel_ = 0;
300 IFSel_ = 0;
301 beamSel_ = 0;
302}
303
304bool SDMemTable::setMask(std::vector<int> whichChans)
305{
306 std::vector<int>::iterator it;
307 uInt n = flagsCol_.shape(0)(3);
308 if (whichChans.empty()) {
309 chanMask_ = std::vector<bool>(n,true);
310 return true;
311 }
312 chanMask_.resize(n,true);
313 for (it = whichChans.begin(); it != whichChans.end(); ++it) {
314 if (*it < n) {
315 chanMask_[*it] = false;
316 }
317 }
318 return true;
319}
320
321std::vector<bool> SDMemTable::getMask(Int whichRow) const
322{
323
324 std::vector<bool> mask;
325
326 Array<uChar> arr;
327 flagsCol_.get(whichRow, arr);
328
329 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
330 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
331 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
332 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
333 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
334 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
335
336 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
337
338 std::vector<bool> tmp;
339 tmp = chanMask_; // WHY the fxxx do I have to make a copy here
340 std::vector<bool>::iterator miter;
341 miter = tmp.begin();
342
343 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
344 bool out =!static_cast<bool>(*i);
345 if (useUserMask) {
346 out = out && (*miter);
347 miter++;
348 }
349 mask.push_back(out);
350 }
351 return mask;
352}
353
354
355
356std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
357{
358
359 Array<Float> arr;
360 specCol_.get(whichRow, arr);
361 return getFloatSpectrum(arr);
362}
363
364std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow, Bool doPol,
365 Float paOffset) const
366 // Gets
367 // doPol=False : I,Q,U,V
368 // doPol=True : I,P,PA,V ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
369 //
370{
371 AlwaysAssert(asap::nAxes==4,AipsError);
372 if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
373 throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
374 }
375 Array<Float> arr;
376 stokesCol_.get(whichRow, arr);
377
378 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
379
380 // Set current cursor location
381 const IPosition& shape = arr.shape();
382 IPosition start, end;
383 setCursorSlice (start, end, shape);
384
385 // Get Q and U slices
386
387 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
388 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
389
390 // Compute output
391
392 Array<Float> out;
393 if (polSel_==1) { // P
394 out = SDPolUtil::polarizedIntensity(Q,U);
395 } else if (polSel_==2) { // P.A.
396 out = SDPolUtil::positionAngle(Q,U) + paOffset;
397 }
398
399 // Copy to output
400
401 IPosition vecShape(1,shape(asap::ChanAxis));
402 Vector<Float> outV = out.reform(vecShape);
403 std::vector<float> stlout;
404 outV.tovector(stlout);
405 return stlout;
406
407 } else {
408
409 // Selects at the cursor location
410 return getFloatSpectrum(arr);
411 }
412}
413
414std::vector<float> SDMemTable::getCircularSpectrum(Int whichRow,
415 Bool doRR) const
416 // Gets
417 // RR = I + V
418 // LL = I - V
419{
420 AlwaysAssert(asap::nAxes==4,AipsError);
421 if (nPol()!=4) {
422 throw (AipsError("You must have 4 polarizations to get RR or LL"));
423 }
424 Array<Float> arr;
425 stokesCol_.get(whichRow, arr);
426
427 // Set current cursor location
428
429 const IPosition& shape = arr.shape();
430 IPosition start, end;
431 setCursorSlice(start, end, shape);
432
433 // Get I and V slices
434
435 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
436 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
437
438 // Compute output
439
440 Array<Float> out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
441
442 // Copy to output
443
444 IPosition vecShape(1,shape(asap::ChanAxis));
445 Vector<Float> outV = out.reform(vecShape);
446 std::vector<float> stlout;
447 outV.tovector(stlout);
448
449 return stlout;
450}
451
452
453std::vector<string> SDMemTable::getCoordInfo() const
454{
455 String un;
456 Table t = table_.keywordSet().asTable("FREQUENCIES");
457 String sunit;
458 t.keywordSet().get("UNIT",sunit);
459 String dpl;
460 t.keywordSet().get("DOPPLER",dpl);
461 if (dpl == "") dpl = "RADIO";
462 String rfrm;
463 t.keywordSet().get("REFFRAME",rfrm);
464 std::vector<string> inf;
465 inf.push_back(sunit);
466 inf.push_back(rfrm);
467 inf.push_back(dpl);
468 t.keywordSet().get("BASEREFFRAME",rfrm);
469 inf.push_back(rfrm);
470 return inf;
471}
472
473void SDMemTable::setCoordInfo(std::vector<string> theinfo)
474{
475 std::vector<string>::iterator it;
476 String un,rfrm, brfrm,dpl;
477 un = theinfo[0]; // Abcissa unit
478 rfrm = theinfo[1]; // Active (or conversion) frame
479 dpl = theinfo[2]; // Doppler
480 brfrm = theinfo[3]; // Base frame
481
482 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
483
484 Vector<Double> rstf;
485 t.keywordSet().get("RESTFREQS",rstf);
486
487 Bool canDo = True;
488 Unit u1("km/s");Unit u2("Hz");
489 if (Unit(un) == u1) {
490 Vector<Double> rstf;
491 t.keywordSet().get("RESTFREQS",rstf);
492 if (rstf.nelements() == 0) {
493 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
494 }
495 } else if (Unit(un) != u2 && un != "") {
496 throw(AipsError("Unit not conformant with Spectral Coordinates"));
497 }
498 t.rwKeywordSet().define("UNIT", un);
499
500 MFrequency::Types mdr;
501 if (!MFrequency::getType(mdr, rfrm)) {
502
503 Int a,b;const uInt* c;
504 const String* valid = MFrequency::allMyTypes(a, b, c);
505 String pfix = "Please specify a legal frame type. Types are\n";
506 throw(AipsError(pfix+(*valid)));
507 } else {
508 t.rwKeywordSet().define("REFFRAME",rfrm);
509 }
510
511 MDoppler::Types dtype;
512 dpl.upcase();
513 if (!MDoppler::getType(dtype, dpl)) {
514 throw(AipsError("Doppler type unknown"));
515 } else {
516 t.rwKeywordSet().define("DOPPLER",dpl);
517 }
518
519 if (!MFrequency::getType(mdr, brfrm)) {
520 Int a,b;const uInt* c;
521 const String* valid = MFrequency::allMyTypes(a, b, c);
522 String pfix = "Please specify a legal frame type. Types are\n";
523 throw(AipsError(pfix+(*valid)));
524 } else {
525 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
526 }
527}
528
529
530std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
531{
532 std::vector<double> abc(nChan());
533
534 // Get header units keyword
535 Table t = table_.keywordSet().asTable("FREQUENCIES");
536 String sunit;
537 t.keywordSet().get("UNIT",sunit);
538 if (sunit == "") sunit = "pixel";
539 Unit u(sunit);
540
541 // Easy if just wanting pixels
542 if (sunit==String("pixel")) {
543 // assume channels/pixels
544 std::vector<double>::iterator it;
545 uInt i=0;
546 for (it = abc.begin(); it != abc.end(); ++it) {
547 (*it) = Double(i++);
548 }
549 return abc;
550 }
551
552 // Continue with km/s or Hz. Get FreqIDs
553 Vector<uInt> freqIDs;
554 freqidCol_.get(whichRow, freqIDs);
555 uInt freqID = freqIDs(IFSel_);
556 restfreqidCol_.get(whichRow, freqIDs);
557 uInt restFreqID = freqIDs(IFSel_);
558
559 // Get SpectralCoordinate, set reference frame conversion,
560 // velocity conversion, and rest freq state
561
562 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
563 Vector<Double> pixel(nChan());
564 indgen(pixel);
565
566 if (u == Unit("km/s")) {
567 Vector<Double> world;
568 spc.pixelToVelocity(world,pixel);
569 std::vector<double>::iterator it;
570 uInt i = 0;
571 for (it = abc.begin(); it != abc.end(); ++it) {
572 (*it) = world[i];
573 i++;
574 }
575 } else if (u == Unit("Hz")) {
576
577 // Set world axis units
578 Vector<String> wau(1); wau = u.getName();
579 spc.setWorldAxisUnits(wau);
580
581 std::vector<double>::iterator it;
582 Double tmp;
583 uInt i = 0;
584 for (it = abc.begin(); it != abc.end(); ++it) {
585 spc.toWorld(tmp,pixel[i]);
586 (*it) = tmp;
587 i++;
588 }
589 }
590 return abc;
591}
592
593std::string SDMemTable::getAbcissaString(Int whichRow) const
594{
595 Table t = table_.keywordSet().asTable("FREQUENCIES");
596
597 String sunit;
598 t.keywordSet().get("UNIT",sunit);
599 if (sunit == "") sunit = "pixel";
600 Unit u(sunit);
601
602 Vector<uInt> freqIDs;
603 freqidCol_.get(whichRow, freqIDs);
604 uInt freqID = freqIDs(IFSel_);
605 restfreqidCol_.get(whichRow, freqIDs);
606 uInt restFreqID = freqIDs(IFSel_);
607
608 // Get SpectralCoordinate, with frame, velocity, rest freq state set
609 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
610
611 String s = "Channel";
612 if (u == Unit("km/s")) {
613 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
614 } else if (u == Unit("Hz")) {
615 Vector<String> wau(1);wau = u.getName();
616 spc.setWorldAxisUnits(wau);
617
618 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
619 }
620 return s;
621}
622
623void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
624{
625 Array<Float> arr;
626 specCol_.get(whichRow, arr);
627 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
628 throw(AipsError("Attempting to set spectrum with incorrect length."));
629 }
630
631 // Setup accessors
632 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
633 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
634 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
635 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
636 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
637 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
638
639 // Iterate
640 std::vector<float>::iterator it = spectrum.begin();
641 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
642 (*i) = Float(*it);
643 it++;
644 }
645 specCol_.put(whichRow, arr);
646}
647
648void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
649{
650 Array<Float> arr;
651 specCol_.get(whichRow, arr);
652
653 // Iterate and extract
654 spectrum.resize(arr.shape()(3));
655 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
656 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
657 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
658 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
659 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
660 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
661
662 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
663 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
664 (*va) = (*i);
665 va++;
666 }
667}
668
669
670/*
671void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
672 Array<uChar> arr;
673 flagsCol_.get(whichRow, arr);
674 mask.resize(arr.shape()(3));
675
676 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
677 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
678 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
679 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
680 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
681 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
682
683 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
684
685 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
686 std::vector<bool> tmp;
687 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
688 // iterator should work on chanMask_??
689 std::vector<bool>::iterator miter;
690 miter = tmp.begin();
691
692 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
693 bool out =!static_cast<bool>(*i);
694 if (useUserMask) {
695 out = out && (*miter);
696 miter++;
697 }
698 (*va) = out;
699 va++;
700 }
701}
702*/
703
704MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
705 Bool toStokes) const
706{
707 // Get flags
708 Array<uChar> farr;
709 flagsCol_.get(whichRow, farr);
710
711 // Get data and convert mask to Bool
712 Array<Float> arr;
713 Array<Bool> mask;
714 if (toStokes) {
715 stokesCol_.get(whichRow, arr);
716
717 Array<Bool> tMask(farr.shape());
718 convertArray(tMask, farr);
719 mask = SDPolUtil::stokesMask (tMask, True);
720 } else {
721 specCol_.get(whichRow, arr);
722 mask.resize(farr.shape());
723 convertArray(mask, farr);
724 }
725
726 return MaskedArray<Float>(arr,!mask);
727}
728
729Float SDMemTable::getTsys(Int whichRow) const
730{
731 Array<Float> arr;
732 tsCol_.get(whichRow, arr);
733 Float out;
734
735 IPosition ip(arr.shape());
736 ip(asap::BeamAxis) = beamSel_;
737 ip(asap::IFAxis) = IFSel_;
738 ip(asap::PolAxis) = polSel_;
739 ip(asap::ChanAxis)=0; // First channel only
740
741 out = arr(ip);
742 return out;
743}
744
745MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
746{
747 MDirection::Types mdr = getDirectionReference();
748 Array<Double> posit;
749 dirCol_.get(whichRow,posit);
750 Vector<Double> wpos(2);
751 Int rb;
752 rbeamCol_.get(whichRow,rb);
753 wpos[0] = posit(IPosition(2,beamSel_,0));
754 wpos[1] = posit(IPosition(2,beamSel_,1));
755 if (refBeam && rb > -1) { // use refBeam instead if it exists
756 wpos[0] = posit(IPosition(2,rb,0));
757 wpos[1] = posit(IPosition(2,rb,1));
758 }
759
760 Quantum<Double> lon(wpos[0],Unit(String("rad")));
761 Quantum<Double> lat(wpos[1],Unit(String("rad")));
762 return MDirection(lon, lat, mdr);
763}
764
765MEpoch SDMemTable::getEpoch(Int whichRow) const
766{
767 MEpoch::Types met = getTimeReference();
768
769 Double obstime;
770 timeCol_.get(whichRow,obstime);
771 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
772 return MEpoch(tm2, met);
773}
774
775MPosition SDMemTable::getAntennaPosition () const
776{
777 Vector<Double> antpos;
778 table_.keywordSet().get("AntennaPosition", antpos);
779 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
780 return MPosition(mvpos);
781}
782
783
784SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
785{
786
787 Table t = table_.keywordSet().asTable("FREQUENCIES");
788 if (freqID> t.nrow() ) {
789 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
790 }
791
792 Double rp,rv,inc;
793 String rf;
794 ROScalarColumn<Double> rpc(t, "REFPIX");
795 ROScalarColumn<Double> rvc(t, "REFVAL");
796 ROScalarColumn<Double> incc(t, "INCREMENT");
797 t.keywordSet().get("BASEREFFRAME",rf);
798
799 // Create SpectralCoordinate (units Hz)
800 MFrequency::Types mft;
801 if (!MFrequency::getType(mft, rf)) {
802 cerr << "Frequency type unknown assuming TOPO" << endl;
803 mft = MFrequency::TOPO;
804 }
805 rpc.get(freqID, rp);
806 rvc.get(freqID, rv);
807 incc.get(freqID, inc);
808
809 SpectralCoordinate spec(mft,rv,inc,rp);
810 return spec;
811}
812
813
814SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
815 uInt restFreqID,
816 uInt whichRow) const
817{
818
819 // Create basic SC
820 SpectralCoordinate spec = getSpectralCoordinate (freqID);
821
822 Table t = table_.keywordSet().asTable("FREQUENCIES");
823
824 // Set rest frequency
825 Vector<Double> restFreqIDs;
826 t.keywordSet().get("RESTFREQS",restFreqIDs);
827 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
828 spec.setRestFrequency(restFreqIDs(restFreqID),True);
829 }
830
831 // Set up frame conversion layer
832 String frm;
833 t.keywordSet().get("REFFRAME",frm);
834 if (frm == "") frm = "TOPO";
835 MFrequency::Types mtype;
836 if (!MFrequency::getType(mtype, frm)) {
837 // Should never happen
838 cerr << "Frequency type unknown assuming TOPO" << endl;
839 mtype = MFrequency::TOPO;
840 }
841
842 // Set reference frame conversion (requires row)
843 MDirection dir = getDirection(whichRow);
844 MEpoch epoch = getEpoch(whichRow);
845 MPosition pos = getAntennaPosition();
846
847 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
848 throw(AipsError("Couldn't convert frequency frame."));
849 }
850
851 // Now velocity conversion if appropriate
852 String unitStr;
853 t.keywordSet().get("UNIT",unitStr);
854
855 String dpl;
856 t.keywordSet().get("DOPPLER",dpl);
857 MDoppler::Types dtype;
858 MDoppler::getType(dtype, dpl);
859
860 // Only set velocity unit if non-blank and non-Hz
861 if (!unitStr.empty()) {
862 Unit unitU(unitStr);
863 if (unitU==Unit("Hz")) {
864 } else {
865 spec.setVelocity(unitStr, dtype);
866 }
867 }
868
869 return spec;
870}
871
872
873Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
874 uInt freqID) {
875 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
876 if (freqID > t.nrow() ) {
877 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
878 }
879 ScalarColumn<Double> rpc(t, "REFPIX");
880 ScalarColumn<Double> rvc(t, "REFVAL");
881 ScalarColumn<Double> incc(t, "INCREMENT");
882
883 rpc.put(freqID, speccord.referencePixel()[0]);
884 rvc.put(freqID, speccord.referenceValue()[0]);
885 incc.put(freqID, speccord.increment()[0]);
886
887 return True;
888}
889
890Int SDMemTable::nCoordinates() const
891{
892 return table_.keywordSet().asTable("FREQUENCIES").nrow();
893}
894
895
896std::vector<double> SDMemTable::getRestFreqs() const
897{
898 Table t = table_.keywordSet().asTable("FREQUENCIES");
899 Vector<Double> tvec;
900 t.keywordSet().get("RESTFREQS",tvec);
901 std::vector<double> stlout;
902 tvec.tovector(stlout);
903 return stlout;
904}
905
906bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
907{
908 TableDesc td("", "1", TableDesc::Scratch);
909 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
910 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
911 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
912 SetupNewTable aNewTab("freqs", td, Table::New);
913 Table aTable (aNewTab, Table::Memory, sdft.length());
914 ScalarColumn<Double> sc0(aTable, "REFPIX");
915 ScalarColumn<Double> sc1(aTable, "REFVAL");
916 ScalarColumn<Double> sc2(aTable, "INCREMENT");
917 for (uInt i=0; i < sdft.length(); ++i) {
918 sc0.put(i,sdft.referencePixel(i));
919 sc1.put(i,sdft.referenceValue(i));
920 sc2.put(i,sdft.increment(i));
921 }
922 String rf = sdft.refFrame();
923 if (rf.contains("TOPO")) rf = "TOPO";
924
925 aTable.rwKeywordSet().define("BASEREFFRAME", rf);
926 aTable.rwKeywordSet().define("REFFRAME", rf);
927 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
928 aTable.rwKeywordSet().define("UNIT", String(""));
929 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
930 Vector<Double> rfvec;
931 String rfunit;
932 sdft.restFrequencies(rfvec,rfunit);
933 Quantum<Vector<Double> > q(rfvec, rfunit);
934 rfvec.resize();
935 rfvec = q.getValue("Hz");
936 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
937 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
938 return true;
939}
940
941bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
942{
943 TableDesc td("", "1", TableDesc::Scratch);
944 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
945 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
946 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
947 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
948 SetupNewTable aNewTab("fits", td, Table::New);
949 Table aTable(aNewTab, Table::Memory);
950 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
951 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
952 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
953 ArrayColumn<Bool> sc3(aTable, "PARMASK");
954 for (uInt i; i<sdft.length(); ++i) {
955 const Vector<Double>& parms = sdft.getFitParameters(i);
956 const Vector<Bool>& parmask = sdft.getFitParameterMask(i);
957 const Vector<String>& funcs = sdft.getFitFunctions(i);
958 const Vector<Int>& comps = sdft.getFitComponents(i);
959 sc0.put(i,funcs);
960 sc1.put(i,comps);
961 sc3.put(i,parmask);
962 sc2.put(i,parms);
963 }
964 table_.rwKeywordSet().defineTable("FITS", aTable);
965 return true;
966}
967
968SDFitTable SDMemTable::getSDFitTable() const
969{
970 const Table& t = table_.keywordSet().asTable("FITS");
971 Vector<Double> parms;
972 Vector<Bool> parmask;
973 Vector<String> funcs;
974 Vector<Int> comps;
975 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
976 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
977 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
978 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
979 uInt n = t.nrow();
980 SDFitTable sdft(n);
981 for (uInt i=0; i<n; ++i) {
982 parmaskCol.get(i, parmask);
983 sdft.putFitParameterMask(i, parmask);
984 parmsCol.get(i, parms);
985 sdft.putFitParameters(i, parms);
986 funcsCol.get(i, funcs);
987 sdft.putFitFunctions(i, funcs);
988 compsCol.get(i, comps);
989 sdft.putFitComponents(i, comps);
990 }
991 return sdft;
992}
993
994
995void SDMemTable::addFit(uInt whichRow,
996 const Vector<Double>& p, const Vector<Bool>& m,
997 const Vector<String>& f, const Vector<Int>& c)
998{
999 if (whichRow >= nRow()) {
1000 throw(AipsError("Specified row out of range"));
1001 }
1002 Table t = table_.keywordSet().asTable("FITS");
1003 uInt nrow = t.nrow();
1004 t.addRow();
1005 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1006 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1007 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1008 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1009 parmsCol.put(nrow, p);
1010 parmaskCol.put(nrow, m);
1011 compsCol.put(nrow, c);
1012 funcsCol.put(nrow, f);
1013
1014 Array<Int> fitarr;
1015 fitCol_.get(whichRow, fitarr);
1016
1017 Array<Int> newarr; // The new Array containing the fitid
1018 Int pos =-1; // The fitid position in the array
1019 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1020 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1021 arr = -1;
1022 newarr.reference(arr);
1023 pos = 0;
1024 } else {
1025 IPosition shp = fitarr.shape();
1026 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1027 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1028 // reform the output array slice to be of dim=1
1029 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1030 const Vector<Int>& fits = tmp;
1031 VectorSTLIterator<Int> it(fits);
1032 Int i = 0;
1033 while (it != fits.end()) {
1034 if (*it == -1) {
1035 pos = i;
1036 break;
1037 }
1038 ++i;
1039 ++it;
1040 };
1041 }
1042 if (pos == -1) {
1043 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1044 pos = fitarr.shape()[3]; // the new element position
1045 } else {
1046 if (fitarr.nelements() > 0)
1047 newarr = fitarr;
1048 }
1049 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1050 fitCol_.put(whichRow, newarr);
1051
1052}
1053
1054SDFrequencyTable SDMemTable::getSDFreqTable() const
1055{
1056 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1057 SDFrequencyTable sdft;
1058
1059 // Add refpix/refval/incr. What are the units ? Hz I suppose
1060 // but it's nowhere described...
1061 Vector<Double> refPix, refVal, incr;
1062 ScalarColumn<Double> refPixCol(t, "REFPIX");
1063 ScalarColumn<Double> refValCol(t, "REFVAL");
1064 ScalarColumn<Double> incrCol(t, "INCREMENT");
1065 refPix = refPixCol.getColumn();
1066 refVal = refValCol.getColumn();
1067 incr = incrCol.getColumn();
1068
1069 uInt n = refPix.nelements();
1070 for (uInt i=0; i<n; i++) {
1071 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1072 }
1073
1074 // Frequency reference frame. I don't know if this
1075 // is the correct frame. It might be 'REFFRAME'
1076 // rather than 'BASEREFFRAME' ?
1077 String baseFrame;
1078 t.keywordSet().get("BASEREFFRAME",baseFrame);
1079 sdft.setRefFrame(baseFrame);
1080
1081 // Equinox
1082 Float equinox;
1083 t.keywordSet().get("EQUINOX", equinox);
1084 sdft.setEquinox(equinox);
1085
1086 // Rest Frequency
1087 Vector<Double> restFreqs;
1088 t.keywordSet().get("RESTFREQS", restFreqs);
1089 for (uInt i=0; i<restFreqs.nelements(); i++) {
1090 sdft.addRestFrequency(restFreqs[i]);
1091 }
1092 sdft.setRestFrequencyUnit(String("Hz"));
1093
1094 return sdft;
1095}
1096
1097bool SDMemTable::putSDContainer(const SDContainer& sdc)
1098{
1099 uInt rno = table_.nrow();
1100 table_.addRow();
1101
1102 timeCol_.put(rno, sdc.timestamp);
1103 srcnCol_.put(rno, sdc.sourcename);
1104 fldnCol_.put(rno, sdc.fieldname);
1105 specCol_.put(rno, sdc.getSpectrum());
1106 flagsCol_.put(rno, sdc.getFlags());
1107 tsCol_.put(rno, sdc.getTsys());
1108 scanCol_.put(rno, sdc.scanid);
1109 integrCol_.put(rno, sdc.interval);
1110 freqidCol_.put(rno, sdc.getFreqMap());
1111 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1112 dirCol_.put(rno, sdc.getDirection());
1113 rbeamCol_.put(rno, sdc.refbeam);
1114 tcalCol_.put(rno, sdc.tcal);
1115 tcaltCol_.put(rno, sdc.tcaltime);
1116 azCol_.put(rno, sdc.azimuth);
1117 elCol_.put(rno, sdc.elevation);
1118 paraCol_.put(rno, sdc.parangle);
1119 histCol_.put(rno, sdc.getHistory());
1120 fitCol_.put(rno, sdc.getFitMap());
1121
1122 return true;
1123}
1124
1125SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1126{
1127 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1128 timeCol_.get(whichRow, sdc.timestamp);
1129 srcnCol_.get(whichRow, sdc.sourcename);
1130 integrCol_.get(whichRow, sdc.interval);
1131 scanCol_.get(whichRow, sdc.scanid);
1132 fldnCol_.get(whichRow, sdc.fieldname);
1133 rbeamCol_.get(whichRow, sdc.refbeam);
1134 azCol_.get(whichRow, sdc.azimuth);
1135 elCol_.get(whichRow, sdc.elevation);
1136 paraCol_.get(whichRow, sdc.parangle);
1137 Vector<Float> tc;
1138 tcalCol_.get(whichRow, tc);
1139 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1140 tcaltCol_.get(whichRow, sdc.tcaltime);
1141
1142 Array<Float> spectrum;
1143 Array<Float> tsys;
1144 Array<uChar> flagtrum;
1145 Vector<uInt> fmap;
1146 Array<Double> direction;
1147 Vector<String> histo;
1148 Array<Int> fits;
1149
1150 specCol_.get(whichRow, spectrum);
1151 sdc.putSpectrum(spectrum);
1152 flagsCol_.get(whichRow, flagtrum);
1153 sdc.putFlags(flagtrum);
1154 tsCol_.get(whichRow, tsys);
1155 sdc.putTsys(tsys);
1156 freqidCol_.get(whichRow, fmap);
1157 sdc.putFreqMap(fmap);
1158 restfreqidCol_.get(whichRow, fmap);
1159 sdc.putRestFreqMap(fmap);
1160 dirCol_.get(whichRow, direction);
1161 sdc.putDirection(direction);
1162 histCol_.get(whichRow, histo);
1163 sdc.putHistory(histo);
1164 fitCol_.get(whichRow, fits);
1165 sdc.putFitMap(fits);
1166 return sdc;
1167}
1168
1169bool SDMemTable::putSDHeader(const SDHeader& sdh)
1170{
1171 table_.rwKeywordSet().define("nIF", sdh.nif);
1172 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1173 table_.rwKeywordSet().define("nPol", sdh.npol);
1174 table_.rwKeywordSet().define("nChan", sdh.nchan);
1175 table_.rwKeywordSet().define("Observer", sdh.observer);
1176 table_.rwKeywordSet().define("Project", sdh.project);
1177 table_.rwKeywordSet().define("Obstype", sdh.obstype);
1178 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1179 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1180 table_.rwKeywordSet().define("Equinox", sdh.equinox);
1181 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1182 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1183 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1184 table_.rwKeywordSet().define("UTC", sdh.utc);
1185 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1186 table_.rwKeywordSet().define("Epoch", sdh.epoch);
1187 return true;
1188}
1189
1190SDHeader SDMemTable::getSDHeader() const
1191{
1192 SDHeader sdh;
1193 table_.keywordSet().get("nBeam",sdh.nbeam);
1194 table_.keywordSet().get("nIF",sdh.nif);
1195 table_.keywordSet().get("nPol",sdh.npol);
1196 table_.keywordSet().get("nChan",sdh.nchan);
1197 table_.keywordSet().get("Observer", sdh.observer);
1198 table_.keywordSet().get("Project", sdh.project);
1199 table_.keywordSet().get("Obstype", sdh.obstype);
1200 table_.keywordSet().get("AntennaName", sdh.antennaname);
1201 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1202 table_.keywordSet().get("Equinox", sdh.equinox);
1203 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1204 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1205 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1206 table_.keywordSet().get("UTC", sdh.utc);
1207 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1208 table_.keywordSet().get("Epoch", sdh.epoch);
1209 return sdh;
1210}
1211void SDMemTable::makePersistent(const std::string& filename)
1212{
1213 table_.deepCopy(filename,Table::New);
1214}
1215
1216Int SDMemTable::nScan() const {
1217 Int n = 0;
1218 Int previous = -1;Int current=0;
1219 for (uInt i=0; i< scanCol_.nrow();i++) {
1220 scanCol_.getScalar(i,current);
1221 if (previous != current) {
1222 previous = current;
1223 n++;
1224 }
1225 }
1226 return n;
1227}
1228
1229String SDMemTable::formatSec(Double x) const
1230{
1231 Double xcop = x;
1232 MVTime mvt(xcop/24./3600.); // make days
1233
1234 if (x < 59.95)
1235 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1236 else if (x < 3599.95)
1237 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1238 else {
1239 ostringstream oss;
1240 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1241 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1242 return String(oss);
1243 }
1244};
1245
1246String SDMemTable::formatDirection(const MDirection& md) const
1247{
1248 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1249 Int prec = 7;
1250
1251 MVAngle mvLon(t[0]);
1252 String sLon = mvLon.string(MVAngle::TIME,prec);
1253 MVAngle mvLat(t[1]);
1254 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1255 return sLon + String(" ") + sLat;
1256}
1257
1258
1259std::string SDMemTable::getFluxUnit() const
1260{
1261 String tmp;
1262 table_.keywordSet().get("FluxUnit", tmp);
1263 return tmp;
1264}
1265
1266void SDMemTable::setFluxUnit(const std::string& unit)
1267{
1268 String tmp(unit);
1269 Unit tU(tmp);
1270 if (tU==Unit("K") || tU==Unit("Jy")) {
1271 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1272 } else {
1273 throw AipsError("Illegal unit - must be compatible with Jy or K");
1274 }
1275}
1276
1277
1278void SDMemTable::setInstrument(const std::string& name)
1279{
1280 Bool throwIt = True;
1281 Instrument ins = convertInstrument(name, throwIt);
1282 String nameU(name);
1283 nameU.upcase();
1284 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1285}
1286
1287std::string SDMemTable::summary(bool verbose) const {
1288
1289 // Format header info
1290 ostringstream oss;
1291 oss << endl;
1292 oss << "--------------------------------------------------------------------------------" << endl;
1293 oss << " Scan Table Summary" << endl;
1294 oss << "--------------------------------------------------------------------------------" << endl;
1295 oss.flags(std::ios_base::left);
1296 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1297 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1298 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1299 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1300 oss << endl;
1301 String tmp;
1302 table_.keywordSet().get("Observer", tmp);
1303 oss << setw(15) << "Observer:" << tmp << endl;
1304 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1305 table_.keywordSet().get("Project", tmp);
1306 oss << setw(15) << "Project:" << tmp << endl;
1307 table_.keywordSet().get("Obstype", tmp);
1308 oss << setw(15) << "Obs. Type:" << tmp << endl;
1309 table_.keywordSet().get("AntennaName", tmp);
1310 oss << setw(15) << "Antenna Name:" << tmp << endl;
1311 table_.keywordSet().get("FluxUnit", tmp);
1312 oss << setw(15) << "Flux Unit:" << tmp << endl;
1313 Table t = table_.keywordSet().asTable("FREQUENCIES");
1314 Vector<Double> vec;
1315 t.keywordSet().get("RESTFREQS",vec);
1316 oss << setw(15) << "Rest Freqs:";
1317 if (vec.nelements() > 0) {
1318 oss << setprecision(0) << vec << " [Hz]" << endl;
1319 } else {
1320 oss << "None set" << endl;
1321 }
1322 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1323 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1324 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1325 oss << endl;
1326
1327 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1328 oss << setw(5) << "Scan"
1329 << setw(15) << "Source"
1330 << setw(24) << dirtype
1331 << setw(10) << "Time"
1332 << setw(18) << "Integration"
1333 << setw(7) << "FreqIDs" << endl;
1334 oss << "--------------------------------------------------------------------------------" << endl;
1335
1336 // Generate list of scan start and end integrations
1337 Vector<Int> scanIDs = scanCol_.getColumn();
1338 Vector<uInt> startInt, endInt;
1339 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1340
1341 const uInt nScans = startInt.nelements();
1342 String name;
1343 Vector<uInt> freqIDs, listFQ;
1344 uInt nInt;
1345
1346 for (uInt i=0; i<nScans; i++) {
1347 // Get things from first integration of scan
1348 String time = getTime(startInt(i),False);
1349 String tInt = formatSec(Double(getInterval(startInt(i))));
1350 String posit = formatDirection(getDirection(startInt(i),True));
1351 srcnCol_.getScalar(startInt(i),name);
1352
1353 // Find all the FreqIDs in this scan
1354 listFQ.resize(0);
1355 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1356 freqidCol_.get(j, freqIDs);
1357 for (uInt k=0; k<freqIDs.nelements(); k++) {
1358 mathutil::addEntry(listFQ, freqIDs(k));
1359 }
1360 }
1361
1362 nInt = endInt(i) - startInt(i) + 1;
1363 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1364 << setw(15) << name
1365 << setw(24) << posit
1366 << setw(10) << time
1367 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1368 << setw(6) << tInt
1369 << " " << listFQ << endl;
1370 }
1371 oss << endl;
1372 oss << "Table contains " << table_.nrow() << " integration(s) in "
1373 << nScans << " scan(s)." << endl;
1374
1375 // Frequency Table
1376 if (verbose) {
1377 std::vector<string> info = getCoordInfo();
1378 SDFrequencyTable sdft = getSDFreqTable();
1379 oss << endl << endl;
1380 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1381 oss << "--------------------------------------------------------------------------------" << endl;
1382 for (uInt i=0; i<sdft.length(); i++) {
1383 oss << setw(8) << i << setw(8)
1384 << info[3] << setw(16) << setprecision(8)
1385 << sdft.referenceValue(i) << setw(10)
1386 << sdft.referencePixel(i) << setw(12)
1387 << sdft.increment(i) << endl;
1388 }
1389 oss << "--------------------------------------------------------------------------------" << endl;
1390 }
1391 return String(oss);
1392}
1393
1394Int SDMemTable::nBeam() const
1395{
1396 Int n;
1397 table_.keywordSet().get("nBeam",n);
1398 return n;
1399}
1400
1401Int SDMemTable::nIF() const {
1402 Int n;
1403 table_.keywordSet().get("nIF",n);
1404 return n;
1405}
1406
1407Int SDMemTable::nPol() const {
1408 Int n;
1409 table_.keywordSet().get("nPol",n);
1410 return n;
1411}
1412
1413Int SDMemTable::nChan() const {
1414 Int n;
1415 table_.keywordSet().get("nChan",n);
1416 return n;
1417}
1418
1419bool SDMemTable::appendHistory(const std::string& hist, int whichRow)
1420{
1421 Vector<String> history;
1422 histCol_.get(whichRow, history);
1423 history.resize(history.nelements()+1,True);
1424 history[history.nelements()-1] = hist;
1425 histCol_.put(whichRow, history);
1426}
1427
1428std::vector<std::string> SDMemTable::history(int whichRow) const
1429{
1430 Vector<String> history;
1431 histCol_.get(whichRow, history);
1432 std::vector<std::string> stlout;
1433 // there is no Array<String>.tovector(std::vector<std::string>), so
1434 // do it by hand
1435 for (uInt i=0; i<history.nelements(); ++i) {
1436 stlout.push_back(history[i]);
1437 }
1438 return stlout;
1439}
1440/*
1441void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1442
1443 std::vector<int>::iterator it;
1444 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1445 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1446 j.reset(j.begin(uInt(*it)));
1447 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1448 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1449 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1450 iii != iii.end(); ++iii) {
1451 (*iii) =
1452 }
1453 }
1454 }
1455 }
1456
1457}
1458*/
1459void SDMemTable::flag(int whichRow)
1460{
1461 Array<uChar> arr;
1462 flagsCol_.get(whichRow, arr);
1463
1464 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1465 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1466 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1467 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1468 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1469 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1470
1471 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1472 (*i) = uChar(True);
1473 }
1474
1475 flagsCol_.put(whichRow, arr);
1476}
1477
1478MDirection::Types SDMemTable::getDirectionReference() const
1479{
1480 Float eq;
1481 table_.keywordSet().get("Equinox",eq);
1482 std::map<float,string> mp;
1483 mp[2000.0] = "J2000";
1484 mp[1950.0] = "B1950";
1485 MDirection::Types mdr;
1486 if (!MDirection::getType(mdr, mp[eq])) {
1487 mdr = MDirection::J2000;
1488 cerr << "Unknown equinox using J2000" << endl;
1489 }
1490
1491 return mdr;
1492}
1493
1494MEpoch::Types SDMemTable::getTimeReference() const
1495{
1496 MEpoch::Types met;
1497 String ep;
1498 table_.keywordSet().get("Epoch",ep);
1499 if (!MEpoch::getType(met, ep)) {
1500 cerr << "Epoch type unknown - using UTC" << endl;
1501 met = MEpoch::UTC;
1502 }
1503
1504 return met;
1505}
1506
1507
1508Instrument SDMemTable::convertInstrument(const String& instrument,
1509 Bool throwIt)
1510{
1511 String t(instrument);
1512 t.upcase();
1513
1514 // The strings are what SDReader returns, after cunning interrogation
1515 // of station names... :-(
1516 Instrument inst = asap::UNKNOWN;
1517 if (t==String("DSS-43")) {
1518 inst = TIDBINBILLA;
1519 } else if (t==String("ATPKSMB")) {
1520 inst = ATPKSMB;
1521 } else if (t==String("ATPKSHOH")) {
1522 inst = ATPKSHOH;
1523 } else if (t==String("ATMOPRA")) {
1524 inst = ATMOPRA;
1525 } else if (t==String("CEDUNA")) {
1526 inst = CEDUNA;
1527 } else if (t==String("HOBART")) {
1528 inst = HOBART;
1529 } else {
1530 if (throwIt) {
1531 throw AipsError("Unrecognized instrument - use function scan.set_instrument to set");
1532 }
1533 }
1534 return inst;
1535}
1536
1537Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1538 const String& sUnit,
1539 const vector<string>& lines,
1540 const String& source,
1541 Int whichIF)
1542{
1543 const Int nIFs = nIF();
1544 if (whichIF>=nIFs) {
1545 throw(AipsError("Illegal IF index"));
1546 }
1547
1548 // Find vector of restfrequencies
1549 // Double takes precedence over String
1550 Unit unit;
1551 Vector<Double> restFreqs;
1552 if (restFreqsIn.nelements()>0) {
1553 restFreqs.resize(restFreqsIn.nelements());
1554 restFreqs = restFreqsIn;
1555 unit = Unit(sUnit);
1556 } else if (lines.size()>0) {
1557 const uInt nLines = lines.size();
1558 unit = Unit("Hz");
1559 restFreqs.resize(nLines);
1560 MFrequency lineFreq;
1561 for (uInt i=0; i<nLines; i++) {
1562 String tS(lines[i]);
1563 tS.upcase();
1564 if (MeasTable::Line(lineFreq, tS)) {
1565 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1566 } else {
1567 String s = String(lines[i]) +
1568 String(" is an unrecognized spectral line");
1569 throw(AipsError(s));
1570 }
1571 }
1572 } else {
1573 throw(AipsError("You have not specified any rest frequencies or lines"));
1574 }
1575
1576 // If multiple restfreqs, must be length nIF. In this
1577 // case we will just replace the rest frequencies
1578 const uInt nRestFreqs = restFreqs.nelements();
1579 Int idx = -1;
1580 SDFrequencyTable sdft = getSDFreqTable();
1581
1582 if (nRestFreqs>1) {
1583 // Replace restFreqs, one per IF
1584 if (nRestFreqs != nIFs) {
1585 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1586 }
1587 cout << "Replacing rest frequencies with given list, one per IF" << endl;
1588 sdft.deleteRestFrequencies();
1589 for (uInt i=0; i<nRestFreqs; i++) {
1590 Quantum<Double> rf(restFreqs[i], unit);
1591 sdft.addRestFrequency(rf.getValue("Hz"));
1592 }
1593 } else {
1594
1595 // Add new rest freq
1596 Quantum<Double> rf(restFreqs[0], unit);
1597 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1598 cout << "Selecting given rest frequency" << endl;
1599 }
1600
1601 // Replace
1602 Bool empty = source.empty();
1603 Bool ok = False;
1604 if (putSDFreqTable(sdft)) {
1605 const uInt nRow = table_.nrow();
1606 String srcName;
1607 Vector<uInt> restFreqIDs;
1608 for (uInt i=0; i<nRow; i++) {
1609 srcnCol_.get(i, srcName);
1610 restfreqidCol_.get(i,restFreqIDs);
1611
1612 if (idx==-1) {
1613 // Replace vector of restFreqs; one per IF.
1614 // No selection possible
1615 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1616 } else {
1617 // Set RestFreqID for selected data
1618 if (empty || source==srcName) {
1619 if (whichIF<0) {
1620 restFreqIDs = idx;
1621 } else {
1622 restFreqIDs[whichIF] = idx;
1623 }
1624 }
1625 }
1626 restfreqidCol_.put(i,restFreqIDs);
1627 }
1628 ok = True;
1629 } else {
1630 ok = False;
1631 }
1632
1633 return ok;
1634}
1635
1636void SDMemTable::spectralLines() const
1637{
1638 Vector<String> lines = MeasTable::Lines();
1639 MFrequency lineFreq;
1640 Double freq;
1641
1642 cout.flags(std::ios_base::left);
1643 cout << "Line Frequency (Hz)" << endl;
1644 cout << "-----------------------" << endl;
1645 for (uInt i=0; i<lines.nelements(); i++) {
1646 MeasTable::Line(lineFreq, lines[i]);
1647 freq = lineFreq.getValue().getValue(); // Hz
1648 cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1649 }
1650}
1651
1652void SDMemTable::renumber()
1653{
1654 uInt nRow = scanCol_.nrow();
1655 Int newscanid = 0;
1656 Int cIdx;// the current scanid
1657 // get the first scanid
1658 scanCol_.getScalar(0,cIdx);
1659 Int pIdx = cIdx;// the scanid of the previous row
1660 for (uInt i=0; i<nRow;++i) {
1661 scanCol_.getScalar(i,cIdx);
1662 if (pIdx == cIdx) {
1663 // renumber
1664 scanCol_.put(i,newscanid);
1665 } else {
1666 ++newscanid;
1667 pIdx = cIdx; // store scanid
1668 --i; // don't increment next loop
1669 }
1670 }
1671}
1672
1673
1674void SDMemTable::setCursorSlice(IPosition& start, IPosition& end,
1675 const IPosition& shape) const
1676{
1677 const uInt nDim = shape.nelements();
1678 start.resize(nDim);
1679 end.resize(nDim);
1680
1681 start(asap::BeamAxis) = beamSel_;
1682 end(asap::BeamAxis) = beamSel_;
1683 start(asap::IFAxis) = IFSel_;
1684 end(asap::IFAxis) = IFSel_;
1685
1686 start(asap::PolAxis) = polSel_;
1687 end(asap::PolAxis) = polSel_;
1688
1689 start(asap::ChanAxis) = 0;
1690 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1691}
1692
1693
1694std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1695 // Get spectrum at cursor location
1696{
1697
1698 // Setup accessors
1699 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1700 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1701
1702 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1703 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1704
1705 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1706 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1707
1708 std::vector<float> spectrum;
1709 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1710 spectrum.push_back(*i);
1711 }
1712 return spectrum;
1713}
1714
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