source: trunk/src/SDMemTable.cc@ 456

Last change on this file since 456 was 455, checked in by mar637, 20 years ago
  • added FITS subtable for fitting and relevant functions to set fits and put/get SDFitContainer
  • cleanup
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 49.3 KB
Line 
1//#---------------------------------------------------------------------------
2//# SDMemTable.cc: A MemoryTable container for single dish integrations
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//# Internet email: Malte.Marquarding@csiro.au
23//# Postal address: Malte Marquarding,
24//# Australia Telescope National Facility,
25//# P.O. Box 76,
26//# Epping, NSW, 2121,
27//# AUSTRALIA
28//#
29//# $Id:
30//#---------------------------------------------------------------------------
31
32#include <map>
33
34#include <casa/aips.h>
35#include <casa/iostream.h>
36#include <casa/iomanip.h>
37#include <casa/Arrays/Array.h>
38#include <casa/Arrays/ArrayMath.h>
39#include <casa/Arrays/MaskArrMath.h>
40#include <casa/Arrays/ArrayLogical.h>
41#include <casa/Arrays/ArrayAccessor.h>
42#include <casa/Arrays/VectorSTLIterator.h>
43#include <casa/Arrays/Vector.h>
44#include <casa/BasicMath/Math.h>
45#include <casa/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
68using namespace casa;
69using namespace asap;
70
71SDMemTable::SDMemTable() :
72 IFSel_(0),
73 beamSel_(0),
74 polSel_(0)
75{
76 setup();
77 attach();
78}
79
80SDMemTable::SDMemTable(const std::string& name) :
81 IFSel_(0),
82 beamSel_(0),
83 polSel_(0)
84{
85 Table tab(name);
86 table_ = tab.copyToMemoryTable("dummy");
87 //cerr << "hello from C SDMemTable @ " << this << endl;
88 attach();
89}
90
91SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
92{
93 IFSel_= other.IFSel_;
94 beamSel_= other.beamSel_;
95 polSel_= other.polSel_;
96 chanMask_ = other.chanMask_;
97 table_ = other.table_.copyToMemoryTable(String("dummy"));
98 // clear all rows()
99 if (clear) {
100 table_.removeRow(this->table_.rowNumbers());
101 } else {
102 IFSel_ = other.IFSel_;
103 beamSel_ = other.beamSel_;
104 polSel_ = other.polSel_;
105 }
106//
107 attach();
108 //cerr << "hello from CC SDMemTable @ " << this << endl;
109}
110
111SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
112 IFSel_(0),
113 beamSel_(0),
114 polSel_(0)
115{
116 Table t = tableCommand(exprs,tab);
117 if (t.nrow() == 0)
118 throw(AipsError("Query unsuccessful."));
119 table_ = t.copyToMemoryTable("dummy");
120 attach();
121 renumber();
122}
123
124SDMemTable::~SDMemTable()
125{
126 //cerr << "goodbye from SDMemTable @ " << this << endl;
127}
128
129SDMemTable SDMemTable::getScan(Int scanID) const
130{
131 String cond("SELECT * from $1 WHERE SCANID == ");
132 cond += String::toString(scanID);
133 return SDMemTable(table_, cond);
134}
135
136SDMemTable &SDMemTable::operator=(const SDMemTable& other)
137{
138 if (this != &other) {
139 IFSel_= other.IFSel_;
140 beamSel_= other.beamSel_;
141 polSel_= other.polSel_;
142 chanMask_.resize(0);
143 chanMask_ = other.chanMask_;
144 table_ = other.table_.copyToMemoryTable(String("dummy"));
145 attach();
146 }
147 //cerr << "hello from ASS SDMemTable @ " << this << endl;
148 return *this;
149}
150
151SDMemTable SDMemTable::getSource(const std::string& source) const
152{
153 String cond("SELECT * from $1 WHERE SRCNAME == ");
154 cond += source;
155 return SDMemTable(table_, cond);
156}
157
158void SDMemTable::setup()
159{
160 TableDesc td("", "1", TableDesc::Scratch);
161 td.comment() = "A SDMemTable";
162
163 td.addColumn(ScalarColumnDesc<Double>("TIME"));
164 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
165 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
166 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
167 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
168 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
169 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
170 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
171 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
172 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
173 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
174 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
175 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
176 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
177 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
178 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
179 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
180 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
181 td.addColumn(ArrayColumnDesc<String>("HISTORY"));
182 td.addColumn(ArrayColumnDesc<Int>("FITID"));
183
184
185 // Now create Table SetUp from the description.
186
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
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 SetupNewTable fittab("fits", tdf, Table::New);
206 Table fitTable(fittab, Table::Memory);
207 table_.rwKeywordSet().defineTable("FITS", fitTable);
208
209
210}
211
212void SDMemTable::attach()
213{
214 timeCol_.attach(table_, "TIME");
215 srcnCol_.attach(table_, "SRCNAME");
216 specCol_.attach(table_, "SPECTRA");
217 flagsCol_.attach(table_, "FLAGTRA");
218 tsCol_.attach(table_, "TSYS");
219 stokesCol_.attach(table_, "STOKES");
220 scanCol_.attach(table_, "SCANID");
221 integrCol_.attach(table_, "INTERVAL");
222 freqidCol_.attach(table_, "FREQID");
223 restfreqidCol_.attach(table_, "RESTFREQID");
224 dirCol_.attach(table_, "DIRECTION");
225 fldnCol_.attach(table_, "FIELDNAME");
226 tcaltCol_.attach(table_, "TCALTIME");
227 tcalCol_.attach(table_, "TCAL");
228 azCol_.attach(table_, "AZIMUTH");
229 elCol_.attach(table_, "ELEVATION");
230 paraCol_.attach(table_, "PARANGLE");
231 rbeamCol_.attach(table_, "REFBEAM");
232 histCol_.attach(table_, "HISTORY");
233 fitCol_.attach(table_,"FITID");
234}
235
236
237std::string SDMemTable::getSourceName(Int whichRow) const
238{
239 String name;
240 srcnCol_.get(whichRow, name);
241 return name;
242}
243
244std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
245{
246 Double tm;
247 if (whichRow > -1) {
248 timeCol_.get(whichRow, tm);
249 } else {
250 table_.keywordSet().get("UTC",tm);
251 }
252 MVTime mvt(tm);
253 if (showDate)
254 mvt.setFormat(MVTime::YMD);
255 else
256 mvt.setFormat(MVTime::TIME);
257 ostringstream oss;
258 oss << mvt;
259 return String(oss);
260}
261
262double SDMemTable::getInterval(Int whichRow) const
263{
264 Double intval;
265 integrCol_.get(whichRow, intval);
266 return intval;
267}
268
269bool SDMemTable::setIF(Int whichIF)
270{
271 if ( whichIF >= 0 && whichIF < nIF()) {
272 IFSel_ = whichIF;
273 return true;
274 }
275 return false;
276}
277
278bool SDMemTable::setBeam(Int whichBeam)
279{
280 if ( whichBeam >= 0 && whichBeam < nBeam()) {
281 beamSel_ = whichBeam;
282 return true;
283 }
284 return false;
285}
286
287bool SDMemTable::setPol(Int whichPol)
288{
289 if ( whichPol >= 0 && whichPol < nPol()) {
290 polSel_ = whichPol;
291 return true;
292 }
293 return false;
294}
295
296void SDMemTable::resetCursor()
297{
298 polSel_ = 0;
299 IFSel_ = 0;
300 beamSel_ = 0;
301}
302
303bool SDMemTable::setMask(std::vector<int> whichChans)
304{
305 std::vector<int>::iterator it;
306 uInt n = flagsCol_.shape(0)(3);
307 if (whichChans.empty()) {
308 chanMask_ = std::vector<bool>(n,true);
309 return true;
310 }
311 chanMask_.resize(n,true);
312 for (it = whichChans.begin(); it != whichChans.end(); ++it) {
313 if (*it < n) {
314 chanMask_[*it] = false;
315 }
316 }
317 return true;
318}
319
320std::vector<bool> SDMemTable::getMask(Int whichRow) const
321{
322
323 std::vector<bool> mask;
324
325 Array<uChar> arr;
326 flagsCol_.get(whichRow, arr);
327
328 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
329 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
330 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
331 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
332 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
333 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
334
335 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
336
337 std::vector<bool> tmp;
338 tmp = chanMask_; // WHY the fxxx do I have to make a copy here
339 std::vector<bool>::iterator miter;
340 miter = tmp.begin();
341
342 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
343 bool out =!static_cast<bool>(*i);
344 if (useUserMask) {
345 out = out && (*miter);
346 miter++;
347 }
348 mask.push_back(out);
349 }
350 return mask;
351}
352
353
354
355std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
356{
357
358 Array<Float> arr;
359 specCol_.get(whichRow, arr);
360 return getFloatSpectrum(arr);
361}
362
363std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow, Bool doPol,
364 Float paOffset) const
365 // Gets
366 // doPol=False : I,Q,U,V
367 // doPol=True : I,P,PA,V ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
368 //
369{
370 AlwaysAssert(asap::nAxes==4,AipsError);
371 if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
372 throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
373 }
374 Array<Float> arr;
375 stokesCol_.get(whichRow, arr);
376
377 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
378
379 // Set current cursor location
380 const IPosition& shape = arr.shape();
381 IPosition start, end;
382 setCursorSlice (start, end, shape);
383
384 // Get Q and U slices
385
386 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
387 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
388
389 // Compute output
390
391 Array<Float> out;
392 if (polSel_==1) { // P
393 out = SDPolUtil::polarizedIntensity(Q,U);
394 } else if (polSel_==2) { // P.A.
395 out = SDPolUtil::positionAngle(Q,U) + paOffset;
396 }
397
398 // Copy to output
399
400 IPosition vecShape(1,shape(asap::ChanAxis));
401 Vector<Float> outV = out.reform(vecShape);
402 std::vector<float> stlout;
403 outV.tovector(stlout);
404 return stlout;
405
406 } else {
407
408 // Selects at the cursor location
409 return getFloatSpectrum(arr);
410 }
411}
412
413std::vector<float> SDMemTable::getCircularSpectrum(Int whichRow,
414 Bool doRR) const
415 // Gets
416 // RR = I + V
417 // LL = I - V
418{
419 AlwaysAssert(asap::nAxes==4,AipsError);
420 if (nPol()!=4) {
421 throw (AipsError("You must have 4 polarizations to get RR or LL"));
422 }
423 Array<Float> arr;
424 stokesCol_.get(whichRow, arr);
425
426 // Set current cursor location
427
428 const IPosition& shape = arr.shape();
429 IPosition start, end;
430 setCursorSlice(start, end, shape);
431
432 // Get I and V slices
433
434 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
435 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
436
437 // Compute output
438
439 Array<Float> out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
440
441 // Copy to output
442
443 IPosition vecShape(1,shape(asap::ChanAxis));
444 Vector<Float> outV = out.reform(vecShape);
445 std::vector<float> stlout;
446 outV.tovector(stlout);
447
448 return stlout;
449}
450
451
452std::vector<string> SDMemTable::getCoordInfo() const
453{
454 String un;
455 Table t = table_.keywordSet().asTable("FREQUENCIES");
456 String sunit;
457 t.keywordSet().get("UNIT",sunit);
458 String dpl;
459 t.keywordSet().get("DOPPLER",dpl);
460 if (dpl == "") dpl = "RADIO";
461 String rfrm;
462 t.keywordSet().get("REFFRAME",rfrm);
463 std::vector<string> inf;
464 inf.push_back(sunit);
465 inf.push_back(rfrm);
466 inf.push_back(dpl);
467 t.keywordSet().get("BASEREFFRAME",rfrm);
468 inf.push_back(rfrm);
469 return inf;
470}
471
472void SDMemTable::setCoordInfo(std::vector<string> theinfo)
473{
474 std::vector<string>::iterator it;
475 String un,rfrm, brfrm,dpl;
476 un = theinfo[0]; // Abcissa unit
477 rfrm = theinfo[1]; // Active (or conversion) frame
478 dpl = theinfo[2]; // Doppler
479 brfrm = theinfo[3]; // Base frame
480
481 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
482
483 Vector<Double> rstf;
484 t.keywordSet().get("RESTFREQS",rstf);
485
486 Bool canDo = True;
487 Unit u1("km/s");Unit u2("Hz");
488 if (Unit(un) == u1) {
489 Vector<Double> rstf;
490 t.keywordSet().get("RESTFREQS",rstf);
491 if (rstf.nelements() == 0) {
492 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
493 }
494 } else if (Unit(un) != u2 && un != "") {
495 throw(AipsError("Unit not conformant with Spectral Coordinates"));
496 }
497 t.rwKeywordSet().define("UNIT", un);
498
499 MFrequency::Types mdr;
500 if (!MFrequency::getType(mdr, rfrm)) {
501
502 Int a,b;const uInt* c;
503 const String* valid = MFrequency::allMyTypes(a, b, c);
504 String pfix = "Please specify a legal frame type. Types are\n";
505 throw(AipsError(pfix+(*valid)));
506 } else {
507 t.rwKeywordSet().define("REFFRAME",rfrm);
508 }
509
510 MDoppler::Types dtype;
511 dpl.upcase();
512 if (!MDoppler::getType(dtype, dpl)) {
513 throw(AipsError("Doppler type unknown"));
514 } else {
515 t.rwKeywordSet().define("DOPPLER",dpl);
516 }
517
518 if (!MFrequency::getType(mdr, brfrm)) {
519 Int a,b;const uInt* c;
520 const String* valid = MFrequency::allMyTypes(a, b, c);
521 String pfix = "Please specify a legal frame type. Types are\n";
522 throw(AipsError(pfix+(*valid)));
523 } else {
524 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
525 }
526}
527
528
529std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
530{
531 std::vector<double> abc(nChan());
532
533 // Get header units keyword
534 Table t = table_.keywordSet().asTable("FREQUENCIES");
535 String sunit;
536 t.keywordSet().get("UNIT",sunit);
537 if (sunit == "") sunit = "pixel";
538 Unit u(sunit);
539
540 // Easy if just wanting pixels
541 if (sunit==String("pixel")) {
542 // assume channels/pixels
543 std::vector<double>::iterator it;
544 uInt i=0;
545 for (it = abc.begin(); it != abc.end(); ++it) {
546 (*it) = Double(i++);
547 }
548 return abc;
549 }
550
551 // Continue with km/s or Hz. Get FreqIDs
552 Vector<uInt> freqIDs;
553 freqidCol_.get(whichRow, freqIDs);
554 uInt freqID = freqIDs(IFSel_);
555 restfreqidCol_.get(whichRow, freqIDs);
556 uInt restFreqID = freqIDs(IFSel_);
557
558 // Get SpectralCoordinate, set reference frame conversion,
559 // velocity conversion, and rest freq state
560
561 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
562 Vector<Double> pixel(nChan());
563 indgen(pixel);
564
565 if (u == Unit("km/s")) {
566 Vector<Double> world;
567 spc.pixelToVelocity(world,pixel);
568 std::vector<double>::iterator it;
569 uInt i = 0;
570 for (it = abc.begin(); it != abc.end(); ++it) {
571 (*it) = world[i];
572 i++;
573 }
574 } else if (u == Unit("Hz")) {
575
576 // Set world axis units
577 Vector<String> wau(1); wau = u.getName();
578 spc.setWorldAxisUnits(wau);
579
580 std::vector<double>::iterator it;
581 Double tmp;
582 uInt i = 0;
583 for (it = abc.begin(); it != abc.end(); ++it) {
584 spc.toWorld(tmp,pixel[i]);
585 (*it) = tmp;
586 i++;
587 }
588 }
589 return abc;
590}
591
592std::string SDMemTable::getAbcissaString(Int whichRow) const
593{
594 Table t = table_.keywordSet().asTable("FREQUENCIES");
595
596 String sunit;
597 t.keywordSet().get("UNIT",sunit);
598 if (sunit == "") sunit = "pixel";
599 Unit u(sunit);
600
601 Vector<uInt> freqIDs;
602 freqidCol_.get(whichRow, freqIDs);
603 uInt freqID = freqIDs(IFSel_);
604 restfreqidCol_.get(whichRow, freqIDs);
605 uInt restFreqID = freqIDs(IFSel_);
606
607 // Get SpectralCoordinate, with frame, velocity, rest freq state set
608 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
609
610 String s = "Channel";
611 if (u == Unit("km/s")) {
612 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
613 } else if (u == Unit("Hz")) {
614 Vector<String> wau(1);wau = u.getName();
615 spc.setWorldAxisUnits(wau);
616
617 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
618 }
619 return s;
620}
621
622void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
623{
624 Array<Float> arr;
625 specCol_.get(whichRow, arr);
626 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
627 throw(AipsError("Attempting to set spectrum with incorrect length."));
628 }
629
630 // Setup accessors
631 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
632 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
633 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
634 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
635 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
636 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
637
638 // Iterate
639 std::vector<float>::iterator it = spectrum.begin();
640 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
641 (*i) = Float(*it);
642 it++;
643 }
644 specCol_.put(whichRow, arr);
645}
646
647void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
648{
649 Array<Float> arr;
650 specCol_.get(whichRow, arr);
651
652 // Iterate and extract
653 spectrum.resize(arr.shape()(3));
654 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
655 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
656 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
657 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
658 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
659 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
660
661 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
662 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
663 (*va) = (*i);
664 va++;
665 }
666}
667
668
669/*
670void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
671 Array<uChar> arr;
672 flagsCol_.get(whichRow, arr);
673 mask.resize(arr.shape()(3));
674
675 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
676 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
677 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
678 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
679 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
680 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
681
682 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
683
684 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
685 std::vector<bool> tmp;
686 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
687 // iterator should work on chanMask_??
688 std::vector<bool>::iterator miter;
689 miter = tmp.begin();
690
691 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
692 bool out =!static_cast<bool>(*i);
693 if (useUserMask) {
694 out = out && (*miter);
695 miter++;
696 }
697 (*va) = out;
698 va++;
699 }
700}
701*/
702
703MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
704 Bool toStokes) const
705{
706 // Get flags
707 Array<uChar> farr;
708 flagsCol_.get(whichRow, farr);
709
710 // Get data and convert mask to Bool
711 Array<Float> arr;
712 Array<Bool> mask;
713 if (toStokes) {
714 stokesCol_.get(whichRow, arr);
715
716 Array<Bool> tMask(farr.shape());
717 convertArray(tMask, farr);
718 mask = SDPolUtil::stokesMask (tMask, True);
719 } else {
720 specCol_.get(whichRow, arr);
721 mask.resize(farr.shape());
722 convertArray(mask, farr);
723 }
724
725 return MaskedArray<Float>(arr,!mask);
726}
727
728Float SDMemTable::getTsys(Int whichRow) const
729{
730 Array<Float> arr;
731 tsCol_.get(whichRow, arr);
732 Float out;
733
734 IPosition ip(arr.shape());
735 ip(asap::BeamAxis) = beamSel_;
736 ip(asap::IFAxis) = IFSel_;
737 ip(asap::PolAxis) = polSel_;
738 ip(asap::ChanAxis)=0; // First channel only
739
740 out = arr(ip);
741 return out;
742}
743
744MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
745{
746 MDirection::Types mdr = getDirectionReference();
747 Array<Double> posit;
748 dirCol_.get(whichRow,posit);
749 Vector<Double> wpos(2);
750 Int rb;
751 rbeamCol_.get(whichRow,rb);
752 wpos[0] = posit(IPosition(2,beamSel_,0));
753 wpos[1] = posit(IPosition(2,beamSel_,1));
754 if (refBeam && rb > -1) { // use refBeam instead if it exists
755 wpos[0] = posit(IPosition(2,rb,0));
756 wpos[1] = posit(IPosition(2,rb,1));
757 }
758
759 Quantum<Double> lon(wpos[0],Unit(String("rad")));
760 Quantum<Double> lat(wpos[1],Unit(String("rad")));
761 return MDirection(lon, lat, mdr);
762}
763
764MEpoch SDMemTable::getEpoch(Int whichRow) const
765{
766 MEpoch::Types met = getTimeReference();
767
768 Double obstime;
769 timeCol_.get(whichRow,obstime);
770 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
771 return MEpoch(tm2, met);
772}
773
774MPosition SDMemTable::getAntennaPosition () const
775{
776 Vector<Double> antpos;
777 table_.keywordSet().get("AntennaPosition", antpos);
778 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
779 return MPosition(mvpos);
780}
781
782
783SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
784{
785
786 Table t = table_.keywordSet().asTable("FREQUENCIES");
787 if (freqID> t.nrow() ) {
788 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
789 }
790
791 Double rp,rv,inc;
792 String rf;
793 ROScalarColumn<Double> rpc(t, "REFPIX");
794 ROScalarColumn<Double> rvc(t, "REFVAL");
795 ROScalarColumn<Double> incc(t, "INCREMENT");
796 t.keywordSet().get("BASEREFFRAME",rf);
797
798 // Create SpectralCoordinate (units Hz)
799 MFrequency::Types mft;
800 if (!MFrequency::getType(mft, rf)) {
801 cerr << "Frequency type unknown assuming TOPO" << endl;
802 mft = MFrequency::TOPO;
803 }
804 rpc.get(freqID, rp);
805 rvc.get(freqID, rv);
806 incc.get(freqID, inc);
807
808 SpectralCoordinate spec(mft,rv,inc,rp);
809 return spec;
810}
811
812
813SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
814 uInt restFreqID,
815 uInt whichRow) const
816{
817
818 // Create basic SC
819 SpectralCoordinate spec = getSpectralCoordinate (freqID);
820
821 Table t = table_.keywordSet().asTable("FREQUENCIES");
822
823 // Set rest frequency
824 Vector<Double> restFreqIDs;
825 t.keywordSet().get("RESTFREQS",restFreqIDs);
826 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
827 spec.setRestFrequency(restFreqIDs(restFreqID),True);
828 }
829
830 // Set up frame conversion layer
831 String frm;
832 t.keywordSet().get("REFFRAME",frm);
833 if (frm == "") frm = "TOPO";
834 MFrequency::Types mtype;
835 if (!MFrequency::getType(mtype, frm)) {
836 // Should never happen
837 cerr << "Frequency type unknown assuming TOPO" << endl;
838 mtype = MFrequency::TOPO;
839 }
840
841 // Set reference frame conversion (requires row)
842 MDirection dir = getDirection(whichRow);
843 MEpoch epoch = getEpoch(whichRow);
844 MPosition pos = getAntennaPosition();
845
846 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
847 throw(AipsError("Couldn't convert frequency frame."));
848 }
849
850 // Now velocity conversion if appropriate
851 String unitStr;
852 t.keywordSet().get("UNIT",unitStr);
853
854 String dpl;
855 t.keywordSet().get("DOPPLER",dpl);
856 MDoppler::Types dtype;
857 MDoppler::getType(dtype, dpl);
858
859 // Only set velocity unit if non-blank and non-Hz
860 if (!unitStr.empty()) {
861 Unit unitU(unitStr);
862 if (unitU==Unit("Hz")) {
863 } else {
864 spec.setVelocity(unitStr, dtype);
865 }
866 }
867
868 return spec;
869}
870
871
872Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
873 uInt freqID) {
874 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
875 if (freqID > t.nrow() ) {
876 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
877 }
878 ScalarColumn<Double> rpc(t, "REFPIX");
879 ScalarColumn<Double> rvc(t, "REFVAL");
880 ScalarColumn<Double> incc(t, "INCREMENT");
881
882 rpc.put(freqID, speccord.referencePixel()[0]);
883 rvc.put(freqID, speccord.referenceValue()[0]);
884 incc.put(freqID, speccord.increment()[0]);
885
886 return True;
887}
888
889Int SDMemTable::nCoordinates() const
890{
891 return table_.keywordSet().asTable("FREQUENCIES").nrow();
892}
893
894
895std::vector<double> SDMemTable::getRestFreqs() const
896{
897 Table t = table_.keywordSet().asTable("FREQUENCIES");
898 Vector<Double> tvec;
899 t.keywordSet().get("RESTFREQS",tvec);
900 std::vector<double> stlout;
901 tvec.tovector(stlout);
902 return stlout;
903}
904
905bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
906{
907 TableDesc td("", "1", TableDesc::Scratch);
908 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
909 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
910 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
911 SetupNewTable aNewTab("freqs", td, Table::New);
912 Table aTable (aNewTab, Table::Memory, sdft.length());
913 ScalarColumn<Double> sc0(aTable, "REFPIX");
914 ScalarColumn<Double> sc1(aTable, "REFVAL");
915 ScalarColumn<Double> sc2(aTable, "INCREMENT");
916 for (uInt i=0; i < sdft.length(); ++i) {
917 sc0.put(i,sdft.referencePixel(i));
918 sc1.put(i,sdft.referenceValue(i));
919 sc2.put(i,sdft.increment(i));
920 }
921 String rf = sdft.refFrame();
922 if (rf.contains("TOPO")) rf = "TOPO";
923
924 aTable.rwKeywordSet().define("BASEREFFRAME", rf);
925 aTable.rwKeywordSet().define("REFFRAME", rf);
926 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
927 aTable.rwKeywordSet().define("UNIT", String(""));
928 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
929 Vector<Double> rfvec;
930 String rfunit;
931 sdft.restFrequencies(rfvec,rfunit);
932 Quantum<Vector<Double> > q(rfvec, rfunit);
933 rfvec.resize();
934 rfvec = q.getValue("Hz");
935 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
936 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
937 return true;
938}
939
940bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
941{
942 TableDesc td("", "1", TableDesc::Scratch);
943 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
944 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
945 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
946 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
947 SetupNewTable aNewTab("fits", td, Table::New);
948 Table aTable(aNewTab, Table::Memory);
949 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
950 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
951 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
952 ArrayColumn<Bool> sc3(aTable, "PARMASK");
953 for (uInt i; i<sdft.length(); ++i) {
954 const Vector<Double>& parms = sdft.getFitParameters(i);
955 const Vector<Bool>& parmask = sdft.getFitParameterMask(i);
956 const Vector<String>& funcs = sdft.getFitFunctions(i);
957 const Vector<Int>& comps = sdft.getFitComponents(i);
958 sc0.put(i,funcs);
959 sc1.put(i,comps);
960 sc3.put(i,parmask);
961 sc2.put(i,parms);
962 }
963 table_.rwKeywordSet().defineTable("FITS", aTable);
964 return true;
965}
966
967SDFitTable SDMemTable::getSDFitTable() const
968{
969 const Table& t = table_.keywordSet().asTable("FITS");
970 Vector<Double> parms;
971 Vector<Bool> parmask;
972 Vector<String> funcs;
973 Vector<Int> comps;
974 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
975 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
976 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
977 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
978 uInt n = t.nrow();
979 SDFitTable sdft(n);
980 for (uInt i=0; i<n; ++i) {
981 parmaskCol.get(i, parmask);
982 sdft.putFitParameterMask(i, parmask);
983 parmsCol.get(i, parms);
984 sdft.putFitParameters(i, parms);
985 funcsCol.get(i, funcs);
986 sdft.putFitFunctions(i, funcs);
987 compsCol.get(i, comps);
988 sdft.putFitComponents(i, comps);
989 }
990 return sdft;
991}
992
993
994void SDMemTable::addFit(uInt whichRow,
995 const Vector<Double>& p, const Vector<Bool>& m,
996 const Vector<String>& f, const Vector<Int>& c)
997{
998 if (whichRow >= nRow()) {
999 throw(AipsError("Specified row out of range"));
1000 }
1001 Table t = table_.keywordSet().asTable("FITS");
1002 uInt nrow = t.nrow();
1003 t.addRow();
1004 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1005 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1006 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1007 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1008 parmsCol.put(nrow, p);
1009 parmaskCol.put(nrow, m);
1010 compsCol.put(nrow, c);
1011 funcsCol.put(nrow, f);
1012
1013 Array<Int> fitarr;
1014 fitCol_.get(whichRow, fitarr);
1015
1016 Array<Int> newarr; // The new Array containing the fitid
1017 Int pos =-1; // The fitid position in the array
1018 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1019 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1020 arr = -1;
1021 newarr.reference(arr);
1022 pos = 0;
1023 } else {
1024 IPosition shp = fitarr.shape();
1025 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1026 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1027 // reform the output array slice to be of dim=1
1028 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1029 const Vector<Int>& fits = tmp;
1030 VectorSTLIterator<Int> it(fits);
1031 Int i = 0;
1032 while (it != fits.end()) {
1033 if (*it == -1) {
1034 pos = i;
1035 break;
1036 }
1037 ++i;
1038 ++it;
1039 };
1040 }
1041 if (pos == -1) {
1042 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1043 pos = fitarr.shape()[3]; // the new element position
1044 } else {
1045 if (fitarr.nelements() > 0)
1046 newarr = fitarr;
1047 }
1048 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1049 fitCol_.put(whichRow, newarr);
1050
1051}
1052
1053SDFrequencyTable SDMemTable::getSDFreqTable() const
1054{
1055 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1056 SDFrequencyTable sdft;
1057
1058 // Add refpix/refval/incr. What are the units ? Hz I suppose
1059 // but it's nowhere described...
1060 Vector<Double> refPix, refVal, incr;
1061 ScalarColumn<Double> refPixCol(t, "REFPIX");
1062 ScalarColumn<Double> refValCol(t, "REFVAL");
1063 ScalarColumn<Double> incrCol(t, "INCREMENT");
1064 refPix = refPixCol.getColumn();
1065 refVal = refValCol.getColumn();
1066 incr = incrCol.getColumn();
1067
1068 uInt n = refPix.nelements();
1069 for (uInt i=0; i<n; i++) {
1070 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1071 }
1072
1073 // Frequency reference frame. I don't know if this
1074 // is the correct frame. It might be 'REFFRAME'
1075 // rather than 'BASEREFFRAME' ?
1076 String baseFrame;
1077 t.keywordSet().get("BASEREFFRAME",baseFrame);
1078 sdft.setRefFrame(baseFrame);
1079
1080 // Equinox
1081 Float equinox;
1082 t.keywordSet().get("EQUINOX", equinox);
1083 sdft.setEquinox(equinox);
1084
1085 // Rest Frequency
1086 Vector<Double> restFreqs;
1087 t.keywordSet().get("RESTFREQS", restFreqs);
1088 for (uInt i=0; i<restFreqs.nelements(); i++) {
1089 sdft.addRestFrequency(restFreqs[i]);
1090 }
1091 sdft.setRestFrequencyUnit(String("Hz"));
1092
1093 return sdft;
1094}
1095
1096bool SDMemTable::putSDContainer(const SDContainer& sdc)
1097{
1098 uInt rno = table_.nrow();
1099 table_.addRow();
1100
1101 timeCol_.put(rno, sdc.timestamp);
1102 srcnCol_.put(rno, sdc.sourcename);
1103 fldnCol_.put(rno, sdc.fieldname);
1104 specCol_.put(rno, sdc.getSpectrum());
1105 flagsCol_.put(rno, sdc.getFlags());
1106 tsCol_.put(rno, sdc.getTsys());
1107 scanCol_.put(rno, sdc.scanid);
1108 integrCol_.put(rno, sdc.interval);
1109 freqidCol_.put(rno, sdc.getFreqMap());
1110 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1111 dirCol_.put(rno, sdc.getDirection());
1112 rbeamCol_.put(rno, sdc.refbeam);
1113 tcalCol_.put(rno, sdc.tcal);
1114 tcaltCol_.put(rno, sdc.tcaltime);
1115 azCol_.put(rno, sdc.azimuth);
1116 elCol_.put(rno, sdc.elevation);
1117 paraCol_.put(rno, sdc.parangle);
1118 histCol_.put(rno, sdc.getHistory());
1119 fitCol_.put(rno, sdc.getFitMap());
1120
1121 return true;
1122}
1123
1124SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1125{
1126 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1127 timeCol_.get(whichRow, sdc.timestamp);
1128 srcnCol_.get(whichRow, sdc.sourcename);
1129 integrCol_.get(whichRow, sdc.interval);
1130 scanCol_.get(whichRow, sdc.scanid);
1131 fldnCol_.get(whichRow, sdc.fieldname);
1132 rbeamCol_.get(whichRow, sdc.refbeam);
1133 azCol_.get(whichRow, sdc.azimuth);
1134 elCol_.get(whichRow, sdc.elevation);
1135 paraCol_.get(whichRow, sdc.parangle);
1136 Vector<Float> tc;
1137 tcalCol_.get(whichRow, tc);
1138 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1139 tcaltCol_.get(whichRow, sdc.tcaltime);
1140
1141 Array<Float> spectrum;
1142 Array<Float> tsys;
1143 Array<uChar> flagtrum;
1144 Vector<uInt> fmap;
1145 Array<Double> direction;
1146 Vector<String> histo;
1147 Array<Int> fits;
1148
1149 specCol_.get(whichRow, spectrum);
1150 sdc.putSpectrum(spectrum);
1151 flagsCol_.get(whichRow, flagtrum);
1152 sdc.putFlags(flagtrum);
1153 tsCol_.get(whichRow, tsys);
1154 sdc.putTsys(tsys);
1155 freqidCol_.get(whichRow, fmap);
1156 sdc.putFreqMap(fmap);
1157 restfreqidCol_.get(whichRow, fmap);
1158 sdc.putRestFreqMap(fmap);
1159 dirCol_.get(whichRow, direction);
1160 sdc.putDirection(direction);
1161 histCol_.get(whichRow, histo);
1162 sdc.putHistory(histo);
1163 fitCol_.get(whichRow, fits);
1164 sdc.putFitMap(fits);
1165 return sdc;
1166}
1167
1168bool SDMemTable::putSDHeader(const SDHeader& sdh)
1169{
1170 table_.rwKeywordSet().define("nIF", sdh.nif);
1171 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1172 table_.rwKeywordSet().define("nPol", sdh.npol);
1173 table_.rwKeywordSet().define("nChan", sdh.nchan);
1174 table_.rwKeywordSet().define("Observer", sdh.observer);
1175 table_.rwKeywordSet().define("Project", sdh.project);
1176 table_.rwKeywordSet().define("Obstype", sdh.obstype);
1177 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1178 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1179 table_.rwKeywordSet().define("Equinox", sdh.equinox);
1180 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1181 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1182 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1183 table_.rwKeywordSet().define("UTC", sdh.utc);
1184 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1185 table_.rwKeywordSet().define("Epoch", sdh.epoch);
1186 return true;
1187}
1188
1189SDHeader SDMemTable::getSDHeader() const
1190{
1191 SDHeader sdh;
1192 table_.keywordSet().get("nBeam",sdh.nbeam);
1193 table_.keywordSet().get("nIF",sdh.nif);
1194 table_.keywordSet().get("nPol",sdh.npol);
1195 table_.keywordSet().get("nChan",sdh.nchan);
1196 table_.keywordSet().get("Observer", sdh.observer);
1197 table_.keywordSet().get("Project", sdh.project);
1198 table_.keywordSet().get("Obstype", sdh.obstype);
1199 table_.keywordSet().get("AntennaName", sdh.antennaname);
1200 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1201 table_.keywordSet().get("Equinox", sdh.equinox);
1202 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1203 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1204 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1205 table_.keywordSet().get("UTC", sdh.utc);
1206 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1207 table_.keywordSet().get("Epoch", sdh.epoch);
1208 return sdh;
1209}
1210void SDMemTable::makePersistent(const std::string& filename)
1211{
1212 table_.deepCopy(filename,Table::New);
1213}
1214
1215Int SDMemTable::nScan() const {
1216 Int n = 0;
1217 Int previous = -1;Int current=0;
1218 for (uInt i=0; i< scanCol_.nrow();i++) {
1219 scanCol_.getScalar(i,current);
1220 if (previous != current) {
1221 previous = current;
1222 n++;
1223 }
1224 }
1225 return n;
1226}
1227
1228String SDMemTable::formatSec(Double x) const
1229{
1230 Double xcop = x;
1231 MVTime mvt(xcop/24./3600.); // make days
1232
1233 if (x < 59.95)
1234 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1235 else if (x < 3599.95)
1236 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1237 else {
1238 ostringstream oss;
1239 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1240 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1241 return String(oss);
1242 }
1243};
1244
1245String SDMemTable::formatDirection(const MDirection& md) const
1246{
1247 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1248 Int prec = 7;
1249
1250 MVAngle mvLon(t[0]);
1251 String sLon = mvLon.string(MVAngle::TIME,prec);
1252 MVAngle mvLat(t[1]);
1253 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1254 return sLon + String(" ") + sLat;
1255}
1256
1257
1258std::string SDMemTable::getFluxUnit() const
1259{
1260 String tmp;
1261 table_.keywordSet().get("FluxUnit", tmp);
1262 return tmp;
1263}
1264
1265void SDMemTable::setFluxUnit(const std::string& unit)
1266{
1267 String tmp(unit);
1268 Unit tU(tmp);
1269 if (tU==Unit("K") || tU==Unit("Jy")) {
1270 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1271 } else {
1272 throw AipsError("Illegal unit - must be compatible with Jy or K");
1273 }
1274}
1275
1276
1277void SDMemTable::setInstrument(const std::string& name)
1278{
1279 Bool throwIt = True;
1280 Instrument ins = convertInstrument(name, throwIt);
1281 String nameU(name);
1282 nameU.upcase();
1283 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1284}
1285
1286std::string SDMemTable::summary(bool verbose) const {
1287
1288 // Format header info
1289 ostringstream oss;
1290 oss << endl;
1291 oss << "--------------------------------------------------------------------------------" << endl;
1292 oss << " Scan Table Summary" << endl;
1293 oss << "--------------------------------------------------------------------------------" << endl;
1294 oss.flags(std::ios_base::left);
1295 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1296 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1297 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1298 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1299 oss << endl;
1300 String tmp;
1301 table_.keywordSet().get("Observer", tmp);
1302 oss << setw(15) << "Observer:" << tmp << endl;
1303 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1304 table_.keywordSet().get("Project", tmp);
1305 oss << setw(15) << "Project:" << tmp << endl;
1306 table_.keywordSet().get("Obstype", tmp);
1307 oss << setw(15) << "Obs. Type:" << tmp << endl;
1308 table_.keywordSet().get("AntennaName", tmp);
1309 oss << setw(15) << "Antenna Name:" << tmp << endl;
1310 table_.keywordSet().get("FluxUnit", tmp);
1311 oss << setw(15) << "Flux Unit:" << tmp << endl;
1312 Table t = table_.keywordSet().asTable("FREQUENCIES");
1313 Vector<Double> vec;
1314 t.keywordSet().get("RESTFREQS",vec);
1315 oss << setw(15) << "Rest Freqs:";
1316 if (vec.nelements() > 0) {
1317 oss << setprecision(0) << vec << " [Hz]" << endl;
1318 } else {
1319 oss << "None set" << endl;
1320 }
1321 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1322 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1323 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1324 oss << endl;
1325
1326 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1327 oss << setw(5) << "Scan"
1328 << setw(15) << "Source"
1329 << setw(24) << dirtype
1330 << setw(10) << "Time"
1331 << setw(18) << "Integration"
1332 << setw(7) << "FreqIDs" << endl;
1333 oss << "--------------------------------------------------------------------------------" << endl;
1334
1335 // Generate list of scan start and end integrations
1336 Vector<Int> scanIDs = scanCol_.getColumn();
1337 Vector<uInt> startInt, endInt;
1338 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1339
1340 const uInt nScans = startInt.nelements();
1341 String name;
1342 Vector<uInt> freqIDs, listFQ;
1343 uInt nInt;
1344
1345 for (uInt i=0; i<nScans; i++) {
1346 // Get things from first integration of scan
1347 String time = getTime(startInt(i),False);
1348 String tInt = formatSec(Double(getInterval(startInt(i))));
1349 String posit = formatDirection(getDirection(startInt(i),True));
1350 srcnCol_.getScalar(startInt(i),name);
1351
1352 // Find all the FreqIDs in this scan
1353 listFQ.resize(0);
1354 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1355 freqidCol_.get(j, freqIDs);
1356 for (uInt k=0; k<freqIDs.nelements(); k++) {
1357 mathutil::addEntry(listFQ, freqIDs(k));
1358 }
1359 }
1360
1361 nInt = endInt(i) - startInt(i) + 1;
1362 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1363 << setw(15) << name
1364 << setw(24) << posit
1365 << setw(10) << time
1366 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1367 << setw(6) << tInt
1368 << " " << listFQ << endl;
1369 }
1370 oss << endl;
1371 oss << "Table contains " << table_.nrow() << " integration(s) in "
1372 << nScans << " scan(s)." << endl;
1373
1374 // Frequency Table
1375 if (verbose) {
1376 std::vector<string> info = getCoordInfo();
1377 SDFrequencyTable sdft = getSDFreqTable();
1378 oss << endl << endl;
1379 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1380 oss << "--------------------------------------------------------------------------------" << endl;
1381 for (uInt i=0; i<sdft.length(); i++) {
1382 oss << setw(8) << i << setw(8)
1383 << info[3] << setw(16) << setprecision(8)
1384 << sdft.referenceValue(i) << setw(10)
1385 << sdft.referencePixel(i) << setw(12)
1386 << sdft.increment(i) << endl;
1387 }
1388 oss << "--------------------------------------------------------------------------------" << endl;
1389 }
1390 return String(oss);
1391}
1392
1393Int SDMemTable::nBeam() const
1394{
1395 Int n;
1396 table_.keywordSet().get("nBeam",n);
1397 return n;
1398}
1399
1400Int SDMemTable::nIF() const {
1401 Int n;
1402 table_.keywordSet().get("nIF",n);
1403 return n;
1404}
1405
1406Int SDMemTable::nPol() const {
1407 Int n;
1408 table_.keywordSet().get("nPol",n);
1409 return n;
1410}
1411
1412Int SDMemTable::nChan() const {
1413 Int n;
1414 table_.keywordSet().get("nChan",n);
1415 return n;
1416}
1417
1418bool SDMemTable::appendHistory(const std::string& hist, int whichRow)
1419{
1420 Vector<String> history;
1421 histCol_.get(whichRow, history);
1422 history.resize(history.nelements()+1,True);
1423 history[history.nelements()-1] = hist;
1424 histCol_.put(whichRow, history);
1425}
1426
1427std::vector<std::string> SDMemTable::history(int whichRow) const
1428{
1429 Vector<String> history;
1430 histCol_.get(whichRow, history);
1431 std::vector<std::string> stlout;
1432 // there is no Array<String>.tovector(std::vector<std::string>), so
1433 // do it by hand
1434 for (uInt i=0; i<history.nelements(); ++i) {
1435 stlout.push_back(history[i]);
1436 }
1437 return stlout;
1438}
1439/*
1440void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1441
1442 std::vector<int>::iterator it;
1443 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1444 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1445 j.reset(j.begin(uInt(*it)));
1446 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1447 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1448 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1449 iii != iii.end(); ++iii) {
1450 (*iii) =
1451 }
1452 }
1453 }
1454 }
1455
1456}
1457*/
1458void SDMemTable::flag(int whichRow)
1459{
1460 Array<uChar> arr;
1461 flagsCol_.get(whichRow, arr);
1462
1463 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1464 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1465 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1466 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1467 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1468 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1469
1470 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1471 (*i) = uChar(True);
1472 }
1473
1474 flagsCol_.put(whichRow, arr);
1475}
1476
1477MDirection::Types SDMemTable::getDirectionReference() const
1478{
1479 Float eq;
1480 table_.keywordSet().get("Equinox",eq);
1481 std::map<float,string> mp;
1482 mp[2000.0] = "J2000";
1483 mp[1950.0] = "B1950";
1484 MDirection::Types mdr;
1485 if (!MDirection::getType(mdr, mp[eq])) {
1486 mdr = MDirection::J2000;
1487 cerr << "Unknown equinox using J2000" << endl;
1488 }
1489
1490 return mdr;
1491}
1492
1493MEpoch::Types SDMemTable::getTimeReference() const
1494{
1495 MEpoch::Types met;
1496 String ep;
1497 table_.keywordSet().get("Epoch",ep);
1498 if (!MEpoch::getType(met, ep)) {
1499 cerr << "Epoch type unknown - using UTC" << endl;
1500 met = MEpoch::UTC;
1501 }
1502
1503 return met;
1504}
1505
1506
1507Instrument SDMemTable::convertInstrument(const String& instrument,
1508 Bool throwIt)
1509{
1510 String t(instrument);
1511 t.upcase();
1512
1513 // The strings are what SDReader returns, after cunning interrogation
1514 // of station names... :-(
1515 Instrument inst = asap::UNKNOWN;
1516 if (t==String("DSS-43")) {
1517 inst = TIDBINBILLA;
1518 } else if (t==String("ATPKSMB")) {
1519 inst = ATPKSMB;
1520 } else if (t==String("ATPKSHOH")) {
1521 inst = ATPKSHOH;
1522 } else if (t==String("ATMOPRA")) {
1523 inst = ATMOPRA;
1524 } else if (t==String("CEDUNA")) {
1525 inst = CEDUNA;
1526 } else if (t==String("HOBART")) {
1527 inst = HOBART;
1528 } else {
1529 if (throwIt) {
1530 throw AipsError("Unrecognized instrument - use function scan.set_instrument to set");
1531 }
1532 }
1533 return inst;
1534}
1535
1536Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1537 const String& sUnit,
1538 const vector<string>& lines,
1539 const String& source,
1540 Int whichIF)
1541{
1542 const Int nIFs = nIF();
1543 if (whichIF>=nIFs) {
1544 throw(AipsError("Illegal IF index"));
1545 }
1546
1547 // Find vector of restfrequencies
1548 // Double takes precedence over String
1549 Unit unit;
1550 Vector<Double> restFreqs;
1551 if (restFreqsIn.nelements()>0) {
1552 restFreqs.resize(restFreqsIn.nelements());
1553 restFreqs = restFreqsIn;
1554 unit = Unit(sUnit);
1555 } else if (lines.size()>0) {
1556 const uInt nLines = lines.size();
1557 unit = Unit("Hz");
1558 restFreqs.resize(nLines);
1559 MFrequency lineFreq;
1560 for (uInt i=0; i<nLines; i++) {
1561 String tS(lines[i]);
1562 tS.upcase();
1563 if (MeasTable::Line(lineFreq, tS)) {
1564 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1565 } else {
1566 String s = String(lines[i]) +
1567 String(" is an unrecognized spectral line");
1568 throw(AipsError(s));
1569 }
1570 }
1571 } else {
1572 throw(AipsError("You have not specified any rest frequencies or lines"));
1573 }
1574
1575 // If multiple restfreqs, must be length nIF. In this
1576 // case we will just replace the rest frequencies
1577 const uInt nRestFreqs = restFreqs.nelements();
1578 Int idx = -1;
1579 SDFrequencyTable sdft = getSDFreqTable();
1580
1581 if (nRestFreqs>1) {
1582 // Replace restFreqs, one per IF
1583 if (nRestFreqs != nIFs) {
1584 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1585 }
1586 cout << "Replacing rest frequencies with given list, one per IF" << endl;
1587 sdft.deleteRestFrequencies();
1588 for (uInt i=0; i<nRestFreqs; i++) {
1589 Quantum<Double> rf(restFreqs[i], unit);
1590 sdft.addRestFrequency(rf.getValue("Hz"));
1591 }
1592 } else {
1593
1594 // Add new rest freq
1595 Quantum<Double> rf(restFreqs[0], unit);
1596 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1597 cout << "Selecting given rest frequency" << endl;
1598 }
1599
1600 // Replace
1601 Bool empty = source.empty();
1602 Bool ok = False;
1603 if (putSDFreqTable(sdft)) {
1604 const uInt nRow = table_.nrow();
1605 String srcName;
1606 Vector<uInt> restFreqIDs;
1607 for (uInt i=0; i<nRow; i++) {
1608 srcnCol_.get(i, srcName);
1609 restfreqidCol_.get(i,restFreqIDs);
1610
1611 if (idx==-1) {
1612 // Replace vector of restFreqs; one per IF.
1613 // No selection possible
1614 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1615 } else {
1616 // Set RestFreqID for selected data
1617 if (empty || source==srcName) {
1618 if (whichIF<0) {
1619 restFreqIDs = idx;
1620 } else {
1621 restFreqIDs[whichIF] = idx;
1622 }
1623 }
1624 }
1625 restfreqidCol_.put(i,restFreqIDs);
1626 }
1627 ok = True;
1628 } else {
1629 ok = False;
1630 }
1631
1632 return ok;
1633}
1634
1635void SDMemTable::spectralLines() const
1636{
1637 Vector<String> lines = MeasTable::Lines();
1638 MFrequency lineFreq;
1639 Double freq;
1640
1641 cout.flags(std::ios_base::left);
1642 cout << "Line Frequency (Hz)" << endl;
1643 cout << "-----------------------" << endl;
1644 for (uInt i=0; i<lines.nelements(); i++) {
1645 MeasTable::Line(lineFreq, lines[i]);
1646 freq = lineFreq.getValue().getValue(); // Hz
1647 cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1648 }
1649}
1650
1651void SDMemTable::renumber()
1652{
1653 uInt nRow = scanCol_.nrow();
1654 Int newscanid = 0;
1655 Int cIdx;// the current scanid
1656 // get the first scanid
1657 scanCol_.getScalar(0,cIdx);
1658 Int pIdx = cIdx;// the scanid of the previous row
1659 for (uInt i=0; i<nRow;++i) {
1660 scanCol_.getScalar(i,cIdx);
1661 if (pIdx == cIdx) {
1662 // renumber
1663 scanCol_.put(i,newscanid);
1664 } else {
1665 ++newscanid;
1666 pIdx = cIdx; // store scanid
1667 --i; // don't increment next loop
1668 }
1669 }
1670}
1671
1672
1673void SDMemTable::rotateXYPhase (Float value, Bool doAll)
1674 // phase in degrees
1675 // Applies to all Beams and IFs
1676 // Might want to optionally select on Beam/IF
1677{
1678 if (nPol() != 4) {
1679 throw(AipsError("You must have 4 polarizations to run this function"));
1680 }
1681
1682 IPosition start(asap::nAxes,0);
1683 IPosition end(asap::nAxes);
1684
1685 uInt nRow = specCol_.nrow();
1686 Array<Float> data;
1687 for (uInt i=0; i<nRow;++i) {
1688 specCol_.get(i,data);
1689 IPosition shape = data.shape();
1690
1691 // Set slice
1692 if (!doAll) {
1693 setCursorSlice (start, end, shape);
1694 } else {
1695 end = shape-1;
1696 }
1697
1698 // Get polarization slice references
1699 start(asap::PolAxis) = 2;
1700 end(asap::PolAxis) = 2;
1701 Array<Float> C3 = data(start,end);
1702
1703 start(asap::PolAxis) = 3;
1704 end(asap::PolAxis) = 3;
1705 Array<Float> C4 = data(start,end);
1706
1707 // Rotate
1708 SDPolUtil::rotateXYPhase(C3, C4, value);
1709
1710 // Put
1711 specCol_.put(i,data);
1712 }
1713}
1714
1715void SDMemTable::setCursorSlice(IPosition& start, IPosition& end,
1716 const IPosition& shape) const
1717{
1718 const uInt nDim = shape.nelements();
1719 start.resize(nDim);
1720 end.resize(nDim);
1721
1722 start(asap::BeamAxis) = beamSel_;
1723 end(asap::BeamAxis) = beamSel_;
1724 start(asap::IFAxis) = IFSel_;
1725 end(asap::IFAxis) = IFSel_;
1726
1727 start(asap::PolAxis) = polSel_;
1728 end(asap::PolAxis) = polSel_;
1729
1730 start(asap::ChanAxis) = 0;
1731 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1732}
1733
1734
1735std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1736 // Get spectrum at cursor location
1737{
1738
1739 // Setup accessors
1740 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1741 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1742
1743 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1744 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1745
1746 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1747 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1748
1749 std::vector<float> spectrum;
1750 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1751 spectrum.push_back(*i);
1752 }
1753 return spectrum;
1754}
1755
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