source: trunk/src/SDMemTable.cc@ 725

Last change on this file since 725 was 717, checked in by mar637, 19 years ago

implemented use of SDLog
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  • Property svn:keywords set to Author Date Id Revision
File size: 52.6 KB
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1//#---------------------------------------------------------------------------
2//# SDMemTable.cc: A MemoryTable container for single dish integrations
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//# Internet email: Malte.Marquarding@csiro.au
23//# Postal address: Malte Marquarding,
24//# Australia Telescope National Facility,
25//# P.O. Box 76,
26//# Epping, NSW, 2121,
27//# AUSTRALIA
28//#
29//# $Id:
30//#---------------------------------------------------------------------------
31
32#include <map>
33
34#include <casa/aips.h>
35#include <casa/iostream.h>
36#include <casa/iomanip.h>
37#include <casa/Arrays/Array.h>
38#include <casa/Arrays/ArrayMath.h>
39#include <casa/Arrays/MaskArrMath.h>
40#include <casa/Arrays/ArrayLogical.h>
41#include <casa/Arrays/ArrayAccessor.h>
42#include <casa/Arrays/VectorSTLIterator.h>
43#include <casa/Arrays/Vector.h>
44#include <casa/BasicMath/Math.h>
45#include <casa/BasicSL/Constants.h>
46#include <casa/Quanta/MVAngle.h>
47
48#include <tables/Tables/TableParse.h>
49#include <tables/Tables/TableDesc.h>
50#include <tables/Tables/TableCopy.h>
51#include <tables/Tables/SetupNewTab.h>
52#include <tables/Tables/ScaColDesc.h>
53#include <tables/Tables/ArrColDesc.h>
54
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/TableRecord.h>
57#include <measures/Measures/MFrequency.h>
58#include <measures/Measures/MeasTable.h>
59#include <coordinates/Coordinates/CoordinateUtil.h>
60#include <casa/Quanta/MVTime.h>
61#include <casa/Quanta/MVAngle.h>
62
63#include "SDDefs.h"
64#include "SDContainer.h"
65#include "MathUtils.h"
66#include "SDPol.h"
67#include "SDAttr.h"
68
69#include "SDMemTable.h"
70
71using namespace casa;
72using namespace asap;
73
74SDMemTable::SDMemTable() :
75 IFSel_(0),
76 beamSel_(0),
77 polSel_(0)
78{
79 setup();
80 attach();
81}
82
83SDMemTable::SDMemTable(const std::string& name) :
84 IFSel_(0),
85 beamSel_(0),
86 polSel_(0)
87{
88 Table tab(name);
89 Int version;
90 tab.keywordSet().get("VERSION", version);
91 if (version != version_) {
92 throw(AipsError("Unsupported version of ASAP file."));
93 }
94 table_ = tab.copyToMemoryTable("dummy");
95 attach();
96}
97
98SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
99{
100 table_ = other.table_.copyToMemoryTable(String("dummy"));
101 // clear all rows()
102 if (clear) {
103 table_.removeRow(this->table_.rowNumbers());
104 IFSel_= 0;
105 beamSel_= 0;
106 polSel_= 0;
107 chanMask_.resize(0);
108 } else {
109 IFSel_= other.IFSel_;
110 beamSel_= other.beamSel_;
111 polSel_= other.polSel_;
112 chanMask_.resize(0);
113 chanMask_ = other.chanMask_;
114 }
115
116 attach();
117}
118
119SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
120 IFSel_(0),
121 beamSel_(0),
122 polSel_(0)
123{
124 Table t = tableCommand(exprs,tab);
125 if (t.nrow() == 0)
126 throw(AipsError("Query unsuccessful."));
127 table_ = t.copyToMemoryTable("dummy");
128 attach();
129 renumber();
130}
131
132SDMemTable::~SDMemTable()
133{
134 //cerr << "goodbye from SDMemTable @ " << this << endl;
135}
136
137SDMemTable SDMemTable::getScan(Int scanID) const
138{
139 String cond("SELECT * from $1 WHERE SCANID == ");
140 cond += String::toString(scanID);
141 return SDMemTable(table_, cond);
142}
143
144SDMemTable &SDMemTable::operator=(const SDMemTable& other)
145{
146 if (this != &other) {
147 IFSel_= other.IFSel_;
148 beamSel_= other.beamSel_;
149 polSel_= other.polSel_;
150 chanMask_.resize(0);
151 chanMask_ = other.chanMask_;
152 table_ = other.table_.copyToMemoryTable(String("dummy"));
153 attach();
154 }
155 return *this;
156}
157
158SDMemTable SDMemTable::getSource(const std::string& source) const
159{
160 String cond("SELECT * from $1 WHERE SRCNAME == ");
161 cond += source;
162 return SDMemTable(table_, cond);
163}
164
165void SDMemTable::setup()
166{
167 TableDesc td("", "1", TableDesc::Scratch);
168 td.comment() = "A SDMemTable";
169 td.rwKeywordSet().define("VERSION", Int(version_));
170
171 td.addColumn(ScalarColumnDesc<Double>("TIME"));
172 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
173 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
174 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
175 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
176 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
177 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
178 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
179 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
180 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
181 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
182 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
183 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
184 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
185 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
186 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
187 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
188 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
189 td.addColumn(ArrayColumnDesc<Int>("FITID"));
190
191 // Now create Table SetUp from the description.
192 SetupNewTable aNewTab("dummy", td, Table::New);
193
194 // Bind the Stokes Virtual machine to the STOKES column Because we
195 // don't know how many polarizations will be in the data at this
196 // point, we must bind the Virtual Engine regardless. The STOKES
197 // column won't be accessed if not appropriate (nPol=4)
198 SDStokesEngine::registerClass();
199 SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
200 aNewTab.bindColumn("STOKES", stokesEngine);
201
202 // Create Table
203 table_ = Table(aNewTab, Table::Memory, 0);
204 // add subtable
205 TableDesc tdf("", "1", TableDesc::Scratch);
206 tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
207 tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
208 tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
209 tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
210 tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
211 SetupNewTable fittab("fits", tdf, Table::New);
212 Table fitTable(fittab, Table::Memory);
213 table_.rwKeywordSet().defineTable("FITS", fitTable);
214
215 TableDesc tdh("", "1", TableDesc::Scratch);
216 tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
217 SetupNewTable histtab("hist", tdh, Table::New);
218 Table histTable(histtab, Table::Memory);
219 table_.rwKeywordSet().defineTable("HISTORY", histTable);
220}
221
222void SDMemTable::attach()
223{
224 timeCol_.attach(table_, "TIME");
225 srcnCol_.attach(table_, "SRCNAME");
226 specCol_.attach(table_, "SPECTRA");
227 flagsCol_.attach(table_, "FLAGTRA");
228 tsCol_.attach(table_, "TSYS");
229 stokesCol_.attach(table_, "STOKES");
230 scanCol_.attach(table_, "SCANID");
231 integrCol_.attach(table_, "INTERVAL");
232 freqidCol_.attach(table_, "FREQID");
233 restfreqidCol_.attach(table_, "RESTFREQID");
234 dirCol_.attach(table_, "DIRECTION");
235 fldnCol_.attach(table_, "FIELDNAME");
236 tcaltCol_.attach(table_, "TCALTIME");
237 tcalCol_.attach(table_, "TCAL");
238 azCol_.attach(table_, "AZIMUTH");
239 elCol_.attach(table_, "ELEVATION");
240 paraCol_.attach(table_, "PARANGLE");
241 rbeamCol_.attach(table_, "REFBEAM");
242 fitCol_.attach(table_,"FITID");
243}
244
245
246std::string SDMemTable::getSourceName(Int whichRow) const
247{
248 String name;
249 srcnCol_.get(whichRow, name);
250 return name;
251}
252
253std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
254{
255 Double tm;
256 if (whichRow > -1) {
257 timeCol_.get(whichRow, tm);
258 } else {
259 table_.keywordSet().get("UTC",tm);
260 }
261 MVTime mvt(tm);
262 if (showDate)
263 mvt.setFormat(MVTime::YMD);
264 else
265 mvt.setFormat(MVTime::TIME);
266 ostringstream oss;
267 oss << mvt;
268 return String(oss);
269}
270
271double SDMemTable::getInterval(Int whichRow) const
272{
273 Double intval;
274 integrCol_.get(whichRow, intval);
275 return intval;
276}
277
278bool SDMemTable::setIF(Int whichIF)
279{
280 if ( whichIF >= 0 && whichIF < nIF()) {
281 IFSel_ = whichIF;
282 return true;
283 }
284 return false;
285}
286
287bool SDMemTable::setBeam(Int whichBeam)
288{
289 if ( whichBeam >= 0 && whichBeam < nBeam()) {
290 beamSel_ = whichBeam;
291 return true;
292 }
293 return false;
294}
295
296bool SDMemTable::setPol(Int whichPol)
297{
298 if ( whichPol >= 0 && whichPol < nPol()) {
299 polSel_ = whichPol;
300 return true;
301 }
302 return false;
303}
304
305void SDMemTable::resetCursor()
306{
307 polSel_ = 0;
308 IFSel_ = 0;
309 beamSel_ = 0;
310}
311
312bool SDMemTable::setMask(std::vector<int> whichChans)
313{
314 std::vector<int>::iterator it;
315 uInt n = flagsCol_.shape(0)(3);
316 if (whichChans.empty()) {
317 chanMask_ = std::vector<bool>(n,true);
318 return true;
319 }
320 chanMask_.resize(n,true);
321 for (it = whichChans.begin(); it != whichChans.end(); ++it) {
322 if (*it < n) {
323 chanMask_[*it] = false;
324 }
325 }
326 return true;
327}
328
329std::vector<bool> SDMemTable::getMask(Int whichRow) const
330{
331
332 std::vector<bool> mask;
333
334 Array<uChar> arr;
335 flagsCol_.get(whichRow, arr);
336
337 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
338 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
339 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
340 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
341 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
342 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
343
344 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
345
346 std::vector<bool> tmp;
347 tmp = chanMask_; // WHY the fxxx do I have to make a copy here
348 std::vector<bool>::iterator miter;
349 miter = tmp.begin();
350
351 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
352 bool out =!static_cast<bool>(*i);
353 if (useUserMask) {
354 out = out && (*miter);
355 miter++;
356 }
357 mask.push_back(out);
358 }
359 return mask;
360}
361
362
363
364std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
365{
366 Array<Float> arr;
367 specCol_.get(whichRow, arr);
368 return getFloatSpectrum(arr);
369}
370
371
372int SDMemTable::nStokes() const
373{
374 return stokesCol_.shape(0).nelements(); // All rows same shape
375}
376
377
378std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow,
379 Bool doPol) const
380 //
381 // Gets one STokes parameter depending on cursor polSel location
382 // doPol=False : I,Q,U,V
383 // doPol=True : I,P,PA,V ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
384 //
385{
386 AlwaysAssert(asap::nAxes==4,AipsError);
387 if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
388 throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
389 }
390
391 // For full conversion we are only supporting linears at the moment
392
393 if (nPol() > 2) {
394 String antName;
395 table_.keywordSet().get("AntennaName", antName);
396 Instrument inst = SDAttr::convertInstrument (antName, True);
397 SDAttr sdAtt;
398 if (sdAtt.feedPolType(inst) != LINEAR) {
399 throw(AipsError("Only linear polarizations are supported"));
400 }
401 }
402
403 Array<Float> arr;
404 stokesCol_.get(whichRow, arr);
405
406 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
407
408 // Set current cursor location
409
410 const IPosition& shape = arr.shape();
411 IPosition start, end;
412 getCursorSlice(start, end, shape);
413
414 // Get Q and U slices
415
416 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
417 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
418
419 // Compute output
420
421 Array<Float> out;
422 if (polSel_==1) { // P
423 out = SDPolUtil::polarizedIntensity(Q,U);
424 } else if (polSel_==2) { // P.A.
425 out = SDPolUtil::positionAngle(Q,U);
426 }
427
428 // Copy to output
429
430 IPosition vecShape(1,shape(asap::ChanAxis));
431 Vector<Float> outV = out.reform(vecShape);
432 std::vector<float> stlout;
433 outV.tovector(stlout);
434 return stlout;
435
436 } else {
437 // Selects at the cursor location
438 return getFloatSpectrum(arr);
439 }
440}
441
442std::string SDMemTable::getPolarizationLabel(Bool linear, Bool stokes,
443 Bool linPol, Int polIdx) const
444{
445 uInt idx = polSel_;
446 if (polIdx >=0) idx = polIdx;
447 return SDPolUtil::polarizationLabel(idx, linear, stokes, linPol);
448}
449
450
451
452std::vector<float> SDMemTable::stokesToPolSpectrum(Int whichRow,
453 Bool toLinear,
454 Int polIdx) const
455//
456// polIdx
457// 0:3 -> RR,LL,Real(RL),Imag(RL)
458// XX,YY,Real(XY),Image(XY)
459//
460// Gets only
461// RR = I + V
462// LL = I - V
463// at the moment
464//
465{
466 AlwaysAssert(asap::nAxes==4,AipsError);
467 if (nStokes()!=4) {
468 throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
469 }
470//
471 Array<Float> arr, out;
472 stokesCol_.get(whichRow, arr);
473
474// Set current cursor location
475
476 const IPosition& shape = arr.shape();
477 IPosition start, end;
478 getCursorSlice(start, end, shape);
479
480// Get the slice
481
482 if (toLinear) {
483 throw(AipsError("Conversion to linears not yet supported"));
484 } else {
485 uInt selection = polSel_;
486 if (polIdx > -1) selection = polIdx;
487 Bool doRR = (selection==0);
488 if (selection>1) {
489 throw(AipsError("Only conversion to RR & LL is currently supported"));
490 }
491
492 // Get I and V slices
493 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
494 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
495
496 // Compute output
497 out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
498 }
499
500 // Copy to output
501 IPosition vecShape(1,shape(asap::ChanAxis));
502 Vector<Float> outV = out.reform(vecShape);
503 std::vector<float> stlout;
504 outV.tovector(stlout);
505//
506 return stlout;
507}
508
509
510
511
512Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
513{
514
515// Get data
516
517 Array<Float> arr;
518 stokesCol_.get(whichRow, arr);
519
520// Set current cursor location and overwrite polarization axis
521
522 const IPosition& shape = arr.shape();
523 IPosition start(shape.nelements(),0);
524 IPosition end(shape-1);
525 if (iBeam!=-1) {
526 start(asap::BeamAxis) = iBeam;
527 end(asap::BeamAxis) = iBeam;
528 }
529 if (iIF!=-1) {
530 start(asap::IFAxis) = iIF;
531 end(asap::IFAxis) = iIF;
532 }
533
534// Get slice
535
536 return arr(start,end);
537}
538
539
540std::vector<string> SDMemTable::getCoordInfo() const
541{
542 String un;
543 Table t = table_.keywordSet().asTable("FREQUENCIES");
544 String sunit;
545 t.keywordSet().get("UNIT",sunit);
546 String dpl;
547 t.keywordSet().get("DOPPLER",dpl);
548 if (dpl == "") dpl = "RADIO";
549 String rfrm;
550 t.keywordSet().get("REFFRAME",rfrm);
551 std::vector<string> inf;
552 inf.push_back(sunit);
553 inf.push_back(rfrm);
554 inf.push_back(dpl);
555 t.keywordSet().get("BASEREFFRAME",rfrm);
556 inf.push_back(rfrm);
557 return inf;
558}
559
560void SDMemTable::setCoordInfo(std::vector<string> theinfo)
561{
562 std::vector<string>::iterator it;
563 String un,rfrm, brfrm,dpl;
564 un = theinfo[0]; // Abcissa unit
565 rfrm = theinfo[1]; // Active (or conversion) frame
566 dpl = theinfo[2]; // Doppler
567 brfrm = theinfo[3]; // Base frame
568
569 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
570
571 Vector<Double> rstf;
572 t.keywordSet().get("RESTFREQS",rstf);
573
574 Bool canDo = True;
575 Unit u1("km/s");Unit u2("Hz");
576 if (Unit(un) == u1) {
577 Vector<Double> rstf;
578 t.keywordSet().get("RESTFREQS",rstf);
579 if (rstf.nelements() == 0) {
580 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
581 }
582 } else if (Unit(un) != u2 && un != "") {
583 throw(AipsError("Unit not conformant with Spectral Coordinates"));
584 }
585 t.rwKeywordSet().define("UNIT", un);
586
587 MFrequency::Types mdr;
588 if (!MFrequency::getType(mdr, rfrm)) {
589
590 Int a,b;const uInt* c;
591 const String* valid = MFrequency::allMyTypes(a, b, c);
592 String pfix = "Please specify a legal frame type. Types are\n";
593 throw(AipsError(pfix+(*valid)));
594 } else {
595 t.rwKeywordSet().define("REFFRAME",rfrm);
596 }
597
598 MDoppler::Types dtype;
599 dpl.upcase();
600 if (!MDoppler::getType(dtype, dpl)) {
601 throw(AipsError("Doppler type unknown"));
602 } else {
603 t.rwKeywordSet().define("DOPPLER",dpl);
604 }
605
606 if (!MFrequency::getType(mdr, brfrm)) {
607 Int a,b;const uInt* c;
608 const String* valid = MFrequency::allMyTypes(a, b, c);
609 String pfix = "Please specify a legal frame type. Types are\n";
610 throw(AipsError(pfix+(*valid)));
611 } else {
612 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
613 }
614}
615
616
617std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
618{
619 std::vector<double> abc(nChan());
620
621 // Get header units keyword
622 Table t = table_.keywordSet().asTable("FREQUENCIES");
623 String sunit;
624 t.keywordSet().get("UNIT",sunit);
625 if (sunit == "") sunit = "pixel";
626 Unit u(sunit);
627
628 // Easy if just wanting pixels
629 if (sunit==String("pixel")) {
630 // assume channels/pixels
631 std::vector<double>::iterator it;
632 uInt i=0;
633 for (it = abc.begin(); it != abc.end(); ++it) {
634 (*it) = Double(i++);
635 }
636 return abc;
637 }
638
639 // Continue with km/s or Hz. Get FreqIDs
640 Vector<uInt> freqIDs;
641 freqidCol_.get(whichRow, freqIDs);
642 uInt freqID = freqIDs(IFSel_);
643 restfreqidCol_.get(whichRow, freqIDs);
644 uInt restFreqID = freqIDs(IFSel_);
645
646 // Get SpectralCoordinate, set reference frame conversion,
647 // velocity conversion, and rest freq state
648
649 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
650 Vector<Double> pixel(nChan());
651 indgen(pixel);
652
653 if (u == Unit("km/s")) {
654 Vector<Double> world;
655 spc.pixelToVelocity(world,pixel);
656 std::vector<double>::iterator it;
657 uInt i = 0;
658 for (it = abc.begin(); it != abc.end(); ++it) {
659 (*it) = world[i];
660 i++;
661 }
662 } else if (u == Unit("Hz")) {
663
664 // Set world axis units
665 Vector<String> wau(1); wau = u.getName();
666 spc.setWorldAxisUnits(wau);
667
668 std::vector<double>::iterator it;
669 Double tmp;
670 uInt i = 0;
671 for (it = abc.begin(); it != abc.end(); ++it) {
672 spc.toWorld(tmp,pixel[i]);
673 (*it) = tmp;
674 i++;
675 }
676 }
677 return abc;
678}
679
680std::string SDMemTable::getAbcissaString(Int whichRow) const
681{
682 Table t = table_.keywordSet().asTable("FREQUENCIES");
683
684 String sunit;
685 t.keywordSet().get("UNIT",sunit);
686 if (sunit == "") sunit = "pixel";
687 Unit u(sunit);
688
689 Vector<uInt> freqIDs;
690 freqidCol_.get(whichRow, freqIDs);
691 uInt freqID = freqIDs(IFSel_);
692 restfreqidCol_.get(whichRow, freqIDs);
693 uInt restFreqID = freqIDs(IFSel_);
694
695 // Get SpectralCoordinate, with frame, velocity, rest freq state set
696 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
697
698 String s = "Channel";
699 if (u == Unit("km/s")) {
700 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
701 } else if (u == Unit("Hz")) {
702 Vector<String> wau(1);wau = u.getName();
703 spc.setWorldAxisUnits(wau);
704
705 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
706 }
707 return s;
708}
709
710void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
711{
712 Array<Float> arr;
713 specCol_.get(whichRow, arr);
714 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
715 throw(AipsError("Attempting to set spectrum with incorrect length."));
716 }
717
718 // Setup accessors
719 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
720 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
721 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
722 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
723 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
724 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
725
726 // Iterate
727 std::vector<float>::iterator it = spectrum.begin();
728 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
729 (*i) = Float(*it);
730 it++;
731 }
732 specCol_.put(whichRow, arr);
733}
734
735void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
736{
737 Array<Float> arr;
738 specCol_.get(whichRow, arr);
739
740 // Iterate and extract
741 spectrum.resize(arr.shape()(3));
742 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
743 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
744 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
745 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
746 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
747 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
748
749 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
750 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
751 (*va) = (*i);
752 va++;
753 }
754}
755
756
757/*
758void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
759 Array<uChar> arr;
760 flagsCol_.get(whichRow, arr);
761 mask.resize(arr.shape()(3));
762
763 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
764 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
765 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
766 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
767 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
768 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
769
770 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
771
772 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
773 std::vector<bool> tmp;
774 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
775 // iterator should work on chanMask_??
776 std::vector<bool>::iterator miter;
777 miter = tmp.begin();
778
779 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
780 bool out =!static_cast<bool>(*i);
781 if (useUserMask) {
782 out = out && (*miter);
783 miter++;
784 }
785 (*va) = out;
786 va++;
787 }
788}
789*/
790
791MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
792 Bool toStokes) const
793{
794 // Get flags
795 Array<uChar> farr;
796 flagsCol_.get(whichRow, farr);
797
798 // Get data and convert mask to Bool
799 Array<Float> arr;
800 Array<Bool> mask;
801 if (toStokes) {
802 stokesCol_.get(whichRow, arr);
803
804 Array<Bool> tMask(farr.shape());
805 convertArray(tMask, farr);
806 mask = SDPolUtil::stokesData (tMask, True);
807 } else {
808 specCol_.get(whichRow, arr);
809 mask.resize(farr.shape());
810 convertArray(mask, farr);
811 }
812
813 return MaskedArray<Float>(arr,!mask);
814}
815
816Float SDMemTable::getTsys(Int whichRow) const
817{
818 Array<Float> arr;
819 tsCol_.get(whichRow, arr);
820 Float out;
821
822 IPosition ip(arr.shape());
823 ip(asap::BeamAxis) = beamSel_;
824 ip(asap::IFAxis) = IFSel_;
825 ip(asap::PolAxis) = polSel_;
826 ip(asap::ChanAxis)=0; // First channel only
827
828 out = arr(ip);
829 return out;
830}
831
832MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
833{
834 MDirection::Types mdr = getDirectionReference();
835 Array<Double> posit;
836 dirCol_.get(whichRow,posit);
837 Vector<Double> wpos(2);
838 Int rb;
839 rbeamCol_.get(whichRow,rb);
840 wpos[0] = posit(IPosition(2,beamSel_,0));
841 wpos[1] = posit(IPosition(2,beamSel_,1));
842 if (refBeam && rb > -1) { // use refBeam instead if it exists
843 wpos[0] = posit(IPosition(2,rb,0));
844 wpos[1] = posit(IPosition(2,rb,1));
845 }
846
847 Quantum<Double> lon(wpos[0],Unit(String("rad")));
848 Quantum<Double> lat(wpos[1],Unit(String("rad")));
849 return MDirection(lon, lat, mdr);
850}
851
852MEpoch SDMemTable::getEpoch(Int whichRow) const
853{
854 MEpoch::Types met = getTimeReference();
855
856 Double obstime;
857 timeCol_.get(whichRow,obstime);
858 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
859 return MEpoch(tm2, met);
860}
861
862MPosition SDMemTable::getAntennaPosition () const
863{
864 Vector<Double> antpos;
865 table_.keywordSet().get("AntennaPosition", antpos);
866 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
867 return MPosition(mvpos);
868}
869
870
871SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
872{
873
874 Table t = table_.keywordSet().asTable("FREQUENCIES");
875 if (freqID> t.nrow() ) {
876 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
877 }
878
879 Double rp,rv,inc;
880 String rf;
881 ROScalarColumn<Double> rpc(t, "REFPIX");
882 ROScalarColumn<Double> rvc(t, "REFVAL");
883 ROScalarColumn<Double> incc(t, "INCREMENT");
884 t.keywordSet().get("BASEREFFRAME",rf);
885
886 // Create SpectralCoordinate (units Hz)
887 MFrequency::Types mft;
888 if (!MFrequency::getType(mft, rf)) {
889 ostringstream oss;
890 pushLog("WARNING: Frequency type unknown assuming TOPO");
891 mft = MFrequency::TOPO;
892 }
893 rpc.get(freqID, rp);
894 rvc.get(freqID, rv);
895 incc.get(freqID, inc);
896
897 SpectralCoordinate spec(mft,rv,inc,rp);
898 return spec;
899}
900
901
902SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
903 uInt restFreqID,
904 uInt whichRow) const
905{
906
907 // Create basic SC
908 SpectralCoordinate spec = getSpectralCoordinate (freqID);
909
910 Table t = table_.keywordSet().asTable("FREQUENCIES");
911
912 // Set rest frequency
913 Vector<Double> restFreqIDs;
914 t.keywordSet().get("RESTFREQS",restFreqIDs);
915 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
916 spec.setRestFrequency(restFreqIDs(restFreqID),True);
917 }
918
919 // Set up frame conversion layer
920 String frm;
921 t.keywordSet().get("REFFRAME",frm);
922 if (frm == "") frm = "TOPO";
923 MFrequency::Types mtype;
924 if (!MFrequency::getType(mtype, frm)) {
925 // Should never happen
926 pushLog("WARNING: Frequency type unknown assuming TOPO");
927 mtype = MFrequency::TOPO;
928 }
929
930 // Set reference frame conversion (requires row)
931 MDirection dir = getDirection(whichRow);
932 MEpoch epoch = getEpoch(whichRow);
933 MPosition pos = getAntennaPosition();
934
935 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
936 throw(AipsError("Couldn't convert frequency frame."));
937 }
938
939 // Now velocity conversion if appropriate
940 String unitStr;
941 t.keywordSet().get("UNIT",unitStr);
942
943 String dpl;
944 t.keywordSet().get("DOPPLER",dpl);
945 MDoppler::Types dtype;
946 MDoppler::getType(dtype, dpl);
947
948 // Only set velocity unit if non-blank and non-Hz
949 if (!unitStr.empty()) {
950 Unit unitU(unitStr);
951 if (unitU==Unit("Hz")) {
952 } else {
953 spec.setVelocity(unitStr, dtype);
954 }
955 }
956
957 return spec;
958}
959
960
961Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
962 uInt freqID) {
963 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
964 if (freqID > t.nrow() ) {
965 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
966 }
967 ScalarColumn<Double> rpc(t, "REFPIX");
968 ScalarColumn<Double> rvc(t, "REFVAL");
969 ScalarColumn<Double> incc(t, "INCREMENT");
970
971 rpc.put(freqID, speccord.referencePixel()[0]);
972 rvc.put(freqID, speccord.referenceValue()[0]);
973 incc.put(freqID, speccord.increment()[0]);
974
975 return True;
976}
977
978Int SDMemTable::nCoordinates() const
979{
980 return table_.keywordSet().asTable("FREQUENCIES").nrow();
981}
982
983
984std::vector<double> SDMemTable::getRestFreqs() const
985{
986 Table t = table_.keywordSet().asTable("FREQUENCIES");
987 Vector<Double> tvec;
988 t.keywordSet().get("RESTFREQS",tvec);
989 std::vector<double> stlout;
990 tvec.tovector(stlout);
991 return stlout;
992}
993
994bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
995{
996 TableDesc td("", "1", TableDesc::Scratch);
997 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
998 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
999 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
1000 SetupNewTable aNewTab("freqs", td, Table::New);
1001 Table aTable (aNewTab, Table::Memory, sdft.length());
1002 ScalarColumn<Double> sc0(aTable, "REFPIX");
1003 ScalarColumn<Double> sc1(aTable, "REFVAL");
1004 ScalarColumn<Double> sc2(aTable, "INCREMENT");
1005 for (uInt i=0; i < sdft.length(); ++i) {
1006 sc0.put(i,sdft.referencePixel(i));
1007 sc1.put(i,sdft.referenceValue(i));
1008 sc2.put(i,sdft.increment(i));
1009 }
1010 String rf = sdft.refFrame();
1011 if (rf.contains("TOPO")) rf = "TOPO";
1012
1013 aTable.rwKeywordSet().define("BASEREFFRAME", rf);
1014 aTable.rwKeywordSet().define("REFFRAME", rf);
1015 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
1016 aTable.rwKeywordSet().define("UNIT", String(""));
1017 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
1018 Vector<Double> rfvec;
1019 String rfunit;
1020 sdft.restFrequencies(rfvec,rfunit);
1021 Quantum<Vector<Double> > q(rfvec, rfunit);
1022 rfvec.resize();
1023 rfvec = q.getValue("Hz");
1024 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
1025 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
1026 return true;
1027}
1028
1029bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
1030{
1031 TableDesc td("", "1", TableDesc::Scratch);
1032 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1033 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1034 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1035 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1036 td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1037 SetupNewTable aNewTab("fits", td, Table::New);
1038 Table aTable(aNewTab, Table::Memory);
1039 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1040 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1041 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1042 ArrayColumn<Bool> sc3(aTable, "PARMASK");
1043 ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1044 for (uInt i; i<sdft.length(); ++i) {
1045 const Vector<Double>& parms = sdft.getParameters(i);
1046 const Vector<Bool>& parmask = sdft.getParameterMask(i);
1047 const Vector<String>& funcs = sdft.getFunctions(i);
1048 const Vector<Int>& comps = sdft.getComponents(i);
1049 const Vector<String>& finfo = sdft.getFrameInfo(i);
1050 sc0.put(i,funcs);
1051 sc1.put(i,comps);
1052 sc3.put(i,parmask);
1053 sc2.put(i,parms);
1054 sc4.put(i,finfo);
1055 }
1056 table_.rwKeywordSet().defineTable("FITS", aTable);
1057 return true;
1058}
1059
1060SDFitTable SDMemTable::getSDFitTable() const
1061{
1062 const Table& t = table_.keywordSet().asTable("FITS");
1063 Vector<Double> parms;
1064 Vector<Bool> parmask;
1065 Vector<String> funcs;
1066 Vector<String> finfo;
1067 Vector<Int> comps;
1068 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1069 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1070 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1071 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1072 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1073 uInt n = t.nrow();
1074 SDFitTable sdft;
1075 for (uInt i=0; i<n; ++i) {
1076 parmaskCol.get(i, parmask);
1077 parmsCol.get(i, parms);
1078 funcsCol.get(i, funcs);
1079 compsCol.get(i, comps);
1080 finfoCol.get(i, finfo);
1081 sdft.addFit(parms, parmask, funcs, comps, finfo);
1082 }
1083 return sdft;
1084}
1085
1086SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1087 const Table& t = table_.keywordSet().asTable("FITS");
1088 if (t.nrow() == 0 || whichRow >= t.nrow()) return SDFitTable();
1089 Array<Int> fitid;
1090 fitCol_.get(whichRow, fitid);
1091 if (fitid.nelements() == 0) return SDFitTable();
1092
1093 IPosition shp = fitid.shape();
1094 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1095 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1096
1097 // reform the output array slice to be of dim=1
1098 Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1099
1100 Vector<Double> parms;
1101 Vector<Bool> parmask;
1102 Vector<String> funcs;
1103 Vector<String> finfo;
1104 Vector<Int> comps;
1105 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1106 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1107 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1108 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1109 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1110 SDFitTable sdft;
1111 Int k=-1;
1112 for (uInt i=0; i< tmp.nelements(); ++i) {
1113 k = tmp[i];
1114 if ( k > -1 && k < t.nrow() ) {
1115 parms.resize();
1116 parmsCol.get(k, parms);
1117 parmask.resize();
1118 parmaskCol.get(k, parmask);
1119 funcs.resize();
1120 funcsCol.get(k, funcs);
1121 comps.resize();
1122 compsCol.get(k, comps);
1123 finfo.resize();
1124 finfoCol.get(k, finfo);
1125 sdft.addFit(parms, parmask, funcs, comps, finfo);
1126 }
1127 }
1128 return sdft;
1129}
1130
1131void SDMemTable::addFit(uInt whichRow,
1132 const Vector<Double>& p, const Vector<Bool>& m,
1133 const Vector<String>& f, const Vector<Int>& c)
1134{
1135 if (whichRow >= nRow()) {
1136 throw(AipsError("Specified row out of range"));
1137 }
1138 Table t = table_.keywordSet().asTable("FITS");
1139 uInt nrow = t.nrow();
1140 t.addRow();
1141 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1142 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1143 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1144 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1145 ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1146 parmsCol.put(nrow, p);
1147 parmaskCol.put(nrow, m);
1148 compsCol.put(nrow, c);
1149 funcsCol.put(nrow, f);
1150 Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1151 finfoCol.put(nrow, fi);
1152
1153 Array<Int> fitarr;
1154 fitCol_.get(whichRow, fitarr);
1155
1156 Array<Int> newarr; // The new Array containing the fitid
1157 Int pos =-1; // The fitid position in the array
1158 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1159 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1160 arr = -1;
1161 newarr.reference(arr);
1162 pos = 0;
1163 } else {
1164 IPosition shp = fitarr.shape();
1165 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1166 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1167 // reform the output array slice to be of dim=1
1168 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1169 const Vector<Int>& fits = tmp;
1170 VectorSTLIterator<Int> it(fits);
1171 Int i = 0;
1172 while (it != fits.end()) {
1173 if (*it == -1) {
1174 pos = i;
1175 break;
1176 }
1177 ++i;
1178 ++it;
1179 };
1180 }
1181 if (pos == -1) {
1182 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1183 pos = fitarr.shape()[3]; // the new element position
1184 } else {
1185 if (fitarr.nelements() > 0)
1186 newarr = fitarr;
1187 }
1188 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1189 fitCol_.put(whichRow, newarr);
1190
1191}
1192
1193SDFrequencyTable SDMemTable::getSDFreqTable() const
1194{
1195 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1196 SDFrequencyTable sdft;
1197
1198 // Add refpix/refval/incr. What are the units ? Hz I suppose
1199 // but it's nowhere described...
1200 Vector<Double> refPix, refVal, incr;
1201 ScalarColumn<Double> refPixCol(t, "REFPIX");
1202 ScalarColumn<Double> refValCol(t, "REFVAL");
1203 ScalarColumn<Double> incrCol(t, "INCREMENT");
1204 refPix = refPixCol.getColumn();
1205 refVal = refValCol.getColumn();
1206 incr = incrCol.getColumn();
1207
1208 uInt n = refPix.nelements();
1209 for (uInt i=0; i<n; i++) {
1210 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1211 }
1212
1213 // Frequency reference frame. I don't know if this
1214 // is the correct frame. It might be 'REFFRAME'
1215 // rather than 'BASEREFFRAME' ?
1216 String baseFrame;
1217 t.keywordSet().get("BASEREFFRAME",baseFrame);
1218 sdft.setRefFrame(baseFrame);
1219
1220 // Equinox
1221 Float equinox;
1222 t.keywordSet().get("EQUINOX", equinox);
1223 sdft.setEquinox(equinox);
1224
1225 // Rest Frequency
1226 Vector<Double> restFreqs;
1227 t.keywordSet().get("RESTFREQS", restFreqs);
1228 for (uInt i=0; i<restFreqs.nelements(); i++) {
1229 sdft.addRestFrequency(restFreqs[i]);
1230 }
1231 sdft.setRestFrequencyUnit(String("Hz"));
1232
1233 return sdft;
1234}
1235
1236bool SDMemTable::putSDContainer(const SDContainer& sdc)
1237{
1238 uInt rno = table_.nrow();
1239 table_.addRow();
1240
1241 timeCol_.put(rno, sdc.timestamp);
1242 srcnCol_.put(rno, sdc.sourcename);
1243 fldnCol_.put(rno, sdc.fieldname);
1244 specCol_.put(rno, sdc.getSpectrum());
1245 flagsCol_.put(rno, sdc.getFlags());
1246 tsCol_.put(rno, sdc.getTsys());
1247 scanCol_.put(rno, sdc.scanid);
1248 integrCol_.put(rno, sdc.interval);
1249 freqidCol_.put(rno, sdc.getFreqMap());
1250 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1251 dirCol_.put(rno, sdc.getDirection());
1252 rbeamCol_.put(rno, sdc.refbeam);
1253 tcalCol_.put(rno, sdc.tcal);
1254 tcaltCol_.put(rno, sdc.tcaltime);
1255 azCol_.put(rno, sdc.azimuth);
1256 elCol_.put(rno, sdc.elevation);
1257 paraCol_.put(rno, sdc.parangle);
1258 fitCol_.put(rno, sdc.getFitMap());
1259 return true;
1260}
1261
1262SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1263{
1264 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1265 timeCol_.get(whichRow, sdc.timestamp);
1266 srcnCol_.get(whichRow, sdc.sourcename);
1267 integrCol_.get(whichRow, sdc.interval);
1268 scanCol_.get(whichRow, sdc.scanid);
1269 fldnCol_.get(whichRow, sdc.fieldname);
1270 rbeamCol_.get(whichRow, sdc.refbeam);
1271 azCol_.get(whichRow, sdc.azimuth);
1272 elCol_.get(whichRow, sdc.elevation);
1273 paraCol_.get(whichRow, sdc.parangle);
1274 Vector<Float> tc;
1275 tcalCol_.get(whichRow, tc);
1276 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1277 tcaltCol_.get(whichRow, sdc.tcaltime);
1278
1279 Array<Float> spectrum;
1280 Array<Float> tsys;
1281 Array<uChar> flagtrum;
1282 Vector<uInt> fmap;
1283 Array<Double> direction;
1284 Array<Int> fits;
1285
1286 specCol_.get(whichRow, spectrum);
1287 sdc.putSpectrum(spectrum);
1288 flagsCol_.get(whichRow, flagtrum);
1289 sdc.putFlags(flagtrum);
1290 tsCol_.get(whichRow, tsys);
1291 sdc.putTsys(tsys);
1292 freqidCol_.get(whichRow, fmap);
1293 sdc.putFreqMap(fmap);
1294 restfreqidCol_.get(whichRow, fmap);
1295 sdc.putRestFreqMap(fmap);
1296 dirCol_.get(whichRow, direction);
1297 sdc.putDirection(direction);
1298 fitCol_.get(whichRow, fits);
1299 sdc.putFitMap(fits);
1300 return sdc;
1301}
1302
1303bool SDMemTable::putSDHeader(const SDHeader& sdh)
1304{
1305 table_.rwKeywordSet().define("nIF", sdh.nif);
1306 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1307 table_.rwKeywordSet().define("nPol", sdh.npol);
1308 table_.rwKeywordSet().define("nChan", sdh.nchan);
1309 table_.rwKeywordSet().define("Observer", sdh.observer);
1310 table_.rwKeywordSet().define("Project", sdh.project);
1311 table_.rwKeywordSet().define("Obstype", sdh.obstype);
1312 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1313 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1314 table_.rwKeywordSet().define("Equinox", sdh.equinox);
1315 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1316 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1317 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1318 table_.rwKeywordSet().define("UTC", sdh.utc);
1319 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1320 table_.rwKeywordSet().define("Epoch", sdh.epoch);
1321 return true;
1322}
1323
1324SDHeader SDMemTable::getSDHeader() const
1325{
1326 SDHeader sdh;
1327 table_.keywordSet().get("nBeam",sdh.nbeam);
1328 table_.keywordSet().get("nIF",sdh.nif);
1329 table_.keywordSet().get("nPol",sdh.npol);
1330 table_.keywordSet().get("nChan",sdh.nchan);
1331 table_.keywordSet().get("Observer", sdh.observer);
1332 table_.keywordSet().get("Project", sdh.project);
1333 table_.keywordSet().get("Obstype", sdh.obstype);
1334 table_.keywordSet().get("AntennaName", sdh.antennaname);
1335 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1336 table_.keywordSet().get("Equinox", sdh.equinox);
1337 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1338 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1339 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1340 table_.keywordSet().get("UTC", sdh.utc);
1341 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1342 table_.keywordSet().get("Epoch", sdh.epoch);
1343 return sdh;
1344}
1345void SDMemTable::makePersistent(const std::string& filename)
1346{
1347 table_.deepCopy(filename,Table::New);
1348
1349}
1350
1351Int SDMemTable::nScan() const {
1352 Int n = 0;
1353 Int previous = -1;Int current=0;
1354 for (uInt i=0; i< scanCol_.nrow();i++) {
1355 scanCol_.getScalar(i,current);
1356 if (previous != current) {
1357 previous = current;
1358 n++;
1359 }
1360 }
1361 return n;
1362}
1363
1364String SDMemTable::formatSec(Double x) const
1365{
1366 Double xcop = x;
1367 MVTime mvt(xcop/24./3600.); // make days
1368
1369 if (x < 59.95)
1370 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1371 else if (x < 3599.95)
1372 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1373 else {
1374 ostringstream oss;
1375 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1376 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1377 return String(oss);
1378 }
1379};
1380
1381String SDMemTable::formatDirection(const MDirection& md) const
1382{
1383 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1384 Int prec = 7;
1385
1386 MVAngle mvLon(t[0]);
1387 String sLon = mvLon.string(MVAngle::TIME,prec);
1388 MVAngle mvLat(t[1]);
1389 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1390 return sLon + String(" ") + sLat;
1391}
1392
1393
1394std::string SDMemTable::getFluxUnit() const
1395{
1396 String tmp;
1397 table_.keywordSet().get("FluxUnit", tmp);
1398 return tmp;
1399}
1400
1401void SDMemTable::setFluxUnit(const std::string& unit)
1402{
1403 String tmp(unit);
1404 Unit tU(tmp);
1405 if (tU==Unit("K") || tU==Unit("Jy")) {
1406 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1407 } else {
1408 throw AipsError("Illegal unit - must be compatible with Jy or K");
1409 }
1410}
1411
1412
1413void SDMemTable::setInstrument(const std::string& name)
1414{
1415 Bool throwIt = True;
1416 Instrument ins = SDAttr::convertInstrument(name, throwIt);
1417 String nameU(name);
1418 nameU.upcase();
1419 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1420}
1421
1422std::string SDMemTable::summary(bool verbose) const {
1423
1424 // Format header info
1425 ostringstream oss;
1426 oss << endl;
1427 oss << "--------------------------------------------------------------------------------" << endl;
1428 oss << " Scan Table Summary" << endl;
1429 oss << "--------------------------------------------------------------------------------" << endl;
1430 oss.flags(std::ios_base::left);
1431 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1432 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1433 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1434 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1435 oss << endl;
1436 String tmp;
1437 table_.keywordSet().get("Observer", tmp);
1438 oss << setw(15) << "Observer:" << tmp << endl;
1439 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1440 table_.keywordSet().get("Project", tmp);
1441 oss << setw(15) << "Project:" << tmp << endl;
1442 table_.keywordSet().get("Obstype", tmp);
1443 oss << setw(15) << "Obs. Type:" << tmp << endl;
1444 table_.keywordSet().get("AntennaName", tmp);
1445 oss << setw(15) << "Antenna Name:" << tmp << endl;
1446 table_.keywordSet().get("FluxUnit", tmp);
1447 oss << setw(15) << "Flux Unit:" << tmp << endl;
1448 Table t = table_.keywordSet().asTable("FREQUENCIES");
1449 Vector<Double> vec;
1450 t.keywordSet().get("RESTFREQS",vec);
1451 oss << setw(15) << "Rest Freqs:";
1452 if (vec.nelements() > 0) {
1453 oss << setprecision(10) << vec << " [Hz]" << endl;
1454 } else {
1455 oss << "None set" << endl;
1456 }
1457 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1458 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1459 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1460 oss << endl;
1461
1462 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1463 oss << setw(5) << "Scan"
1464 << setw(15) << "Source"
1465 << setw(24) << dirtype
1466 << setw(10) << "Time"
1467 << setw(18) << "Integration"
1468 << setw(7) << "FreqIDs" << endl;
1469 oss << "--------------------------------------------------------------------------------" << endl;
1470
1471 // Generate list of scan start and end integrations
1472 Vector<Int> scanIDs = scanCol_.getColumn();
1473 Vector<uInt> startInt, endInt;
1474 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1475
1476 const uInt nScans = startInt.nelements();
1477 String name;
1478 Vector<uInt> freqIDs, listFQ;
1479 Vector<uInt> restFreqIDs, listRestFQ;
1480 uInt nInt;
1481
1482 for (uInt i=0; i<nScans; i++) {
1483 // Get things from first integration of scan
1484 String time = getTime(startInt(i),False);
1485 String tInt = formatSec(Double(getInterval(startInt(i))));
1486 String posit = formatDirection(getDirection(startInt(i),True));
1487 srcnCol_.getScalar(startInt(i),name);
1488
1489 // Find all the FreqIDs in this scan
1490 listFQ.resize(0);
1491 listRestFQ.resize(0);
1492 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1493 freqidCol_.get(j, freqIDs);
1494 for (uInt k=0; k<freqIDs.nelements(); k++) {
1495 mathutil::addEntry(listFQ, freqIDs(k));
1496 }
1497//
1498 restfreqidCol_.get(j, restFreqIDs);
1499 for (uInt k=0; k<restFreqIDs.nelements(); k++) {
1500 mathutil::addEntry(listRestFQ, restFreqIDs(k));
1501 }
1502 }
1503
1504 nInt = endInt(i) - startInt(i) + 1;
1505 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1506 << setw(15) << name
1507 << setw(24) << posit
1508 << setw(10) << time
1509 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1510 << setw(6) << tInt
1511 << " " << listFQ << " " << listRestFQ << endl;
1512 }
1513 oss << endl;
1514 oss << "Table contains " << table_.nrow() << " integration(s) in "
1515 << nScans << " scan(s)." << endl;
1516
1517 // Frequency Table
1518 if (verbose) {
1519 std::vector<string> info = getCoordInfo();
1520 SDFrequencyTable sdft = getSDFreqTable();
1521 oss << endl << endl;
1522 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1523 oss << "--------------------------------------------------------------------------------" << endl;
1524 for (uInt i=0; i<sdft.length(); i++) {
1525 oss << setw(8) << i << setw(8)
1526 << info[3] << setw(16) << setprecision(8)
1527 << sdft.referenceValue(i) << setw(10)
1528 << sdft.referencePixel(i) << setw(12)
1529 << sdft.increment(i) << endl;
1530 }
1531 oss << "--------------------------------------------------------------------------------" << endl;
1532 }
1533 return String(oss);
1534}
1535/*
1536std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1537 ostringstream oss;
1538 Vector<Int> scanIDs = scanCol_.getColumn();
1539 Vector<uInt> startInt, endInt;
1540 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1541 const uInt nScans = startInt.nelements();
1542 std::vector<int>::const_iterator it(whichScans);
1543 return String(oss);
1544}
1545*/
1546Int SDMemTable::nBeam() const
1547{
1548 Int n;
1549 table_.keywordSet().get("nBeam",n);
1550 return n;
1551}
1552
1553Int SDMemTable::nIF() const {
1554 Int n;
1555 table_.keywordSet().get("nIF",n);
1556 return n;
1557}
1558
1559Int SDMemTable::nPol() const {
1560 Int n;
1561 table_.keywordSet().get("nPol",n);
1562 return n;
1563}
1564
1565Int SDMemTable::nChan() const {
1566 Int n;
1567 table_.keywordSet().get("nChan",n);
1568 return n;
1569}
1570
1571Table SDMemTable::getHistoryTable() const
1572{
1573 return table_.keywordSet().asTable("HISTORY");
1574}
1575
1576void SDMemTable::appendToHistoryTable(const Table& otherHist)
1577{
1578 Table t = table_.rwKeywordSet().asTable("HISTORY");
1579 const String sep = "--------------------------------------------------------------------------------";
1580 addHistory(sep);
1581 TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1582 addHistory(sep);
1583}
1584
1585void SDMemTable::addHistory(const std::string& hist)
1586{
1587 Table t = table_.rwKeywordSet().asTable("HISTORY");
1588 uInt nrow = t.nrow();
1589 t.addRow();
1590 ScalarColumn<String> itemCol(t, "ITEM");
1591 itemCol.put(nrow, hist);
1592}
1593
1594std::vector<std::string> SDMemTable::getHistory() const
1595{
1596 Vector<String> history;
1597 const Table& t = table_.keywordSet().asTable("HISTORY");
1598 uInt nrow = t.nrow();
1599 ROScalarColumn<String> itemCol(t, "ITEM");
1600 std::vector<std::string> stlout;
1601 String hist;
1602 for (uInt i=0; i<nrow; ++i) {
1603 itemCol.get(i, hist);
1604 stlout.push_back(hist);
1605 }
1606 return stlout;
1607}
1608
1609
1610/*
1611 void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1612
1613 std::vector<int>::iterator it;
1614 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1615 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1616 j.reset(j.begin(uInt(*it)));
1617 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1618 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1619 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1620 iii != iii.end(); ++iii) {
1621 (*iii) =
1622 }
1623 }
1624 }
1625 }
1626
1627}
1628*/
1629void SDMemTable::flag(int whichRow)
1630 {
1631 Array<uChar> arr;
1632 flagsCol_.get(whichRow, arr);
1633
1634 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1635 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1636 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1637 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1638 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1639 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1640
1641 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1642 (*i) = uChar(True);
1643 }
1644
1645 flagsCol_.put(whichRow, arr);
1646}
1647
1648MDirection::Types SDMemTable::getDirectionReference() const
1649{
1650 Float eq;
1651 table_.keywordSet().get("Equinox",eq);
1652 std::map<float,string> mp;
1653 mp[2000.0] = "J2000";
1654 mp[1950.0] = "B1950";
1655 MDirection::Types mdr;
1656 if (!MDirection::getType(mdr, mp[eq])) {
1657 mdr = MDirection::J2000;
1658 pushLog("WARNING: Unknown equinox using J2000");
1659
1660 }
1661
1662 return mdr;
1663}
1664
1665MEpoch::Types SDMemTable::getTimeReference() const
1666{
1667 MEpoch::Types met;
1668 String ep;
1669 table_.keywordSet().get("Epoch",ep);
1670 if (!MEpoch::getType(met, ep)) {
1671 pushLog("WARNING: Epoch type unknown - using UTC");
1672 met = MEpoch::UTC;
1673 }
1674
1675 return met;
1676}
1677
1678
1679Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1680 const String& sUnit,
1681 const vector<string>& lines,
1682 const String& source,
1683 Int whichIF)
1684{
1685 const Int nIFs = nIF();
1686 if (whichIF>=nIFs) {
1687 throw(AipsError("Illegal IF index"));
1688 }
1689
1690 // Find vector of restfrequencies
1691 // Double takes precedence over String
1692 Unit unit;
1693 Vector<Double> restFreqs;
1694 if (restFreqsIn.nelements()>0) {
1695 restFreqs.resize(restFreqsIn.nelements());
1696 restFreqs = restFreqsIn;
1697 unit = Unit(sUnit);
1698 } else if (lines.size()>0) {
1699 const uInt nLines = lines.size();
1700 unit = Unit("Hz");
1701 restFreqs.resize(nLines);
1702 MFrequency lineFreq;
1703 for (uInt i=0; i<nLines; i++) {
1704 String tS(lines[i]);
1705 tS.upcase();
1706 if (MeasTable::Line(lineFreq, tS)) {
1707 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1708 } else {
1709 String s = String(lines[i]) +
1710 String(" is an unrecognized spectral line");
1711 throw(AipsError(s));
1712 }
1713 }
1714 } else {
1715 throw(AipsError("You have not specified any rest frequencies or lines"));
1716 }
1717
1718 // If multiple restfreqs, must be length nIF. In this
1719 // case we will just replace the rest frequencies
1720 // We can't disinguish scalar and vector of length 1
1721 const uInt nRestFreqs = restFreqs.nelements();
1722 Int idx = -1;
1723 SDFrequencyTable sdft = getSDFreqTable();
1724
1725 ostringstream oss;
1726 if (nRestFreqs>1) {
1727 // Replace restFreqs, one per IF
1728 if (nRestFreqs != nIFs) {
1729 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1730 }
1731 ostringstream oss;
1732 oss << "Replacing rest frequencies, one per IF, with given list : " << restFreqs;
1733 sdft.deleteRestFrequencies();
1734 for (uInt i=0; i<nRestFreqs; i++) {
1735 Quantum<Double> rf(restFreqs[i], unit);
1736 sdft.addRestFrequency(rf.getValue("Hz"));
1737 }
1738 } else {
1739
1740 // Add new rest freq
1741 Quantum<Double> rf(restFreqs[0], unit);
1742 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1743 if (whichIF>=0) {
1744 oss << "Selecting given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1745 } else {
1746 oss << "Selecting given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1747 }
1748 }
1749 pushLog(String(oss));
1750 // Replace
1751 Bool empty = source.empty();
1752 Bool ok = False;
1753 if (putSDFreqTable(sdft)) {
1754 const uInt nRow = table_.nrow();
1755 String srcName;
1756 Vector<uInt> restFreqIDs;
1757 for (uInt i=0; i<nRow; i++) {
1758 srcnCol_.get(i, srcName);
1759 restfreqidCol_.get(i,restFreqIDs);
1760 if (idx==-1) {
1761 // Replace vector of restFreqs; one per IF.
1762 // No selection possible
1763 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1764 } else {
1765 // Set RestFreqID for selected data
1766 if (empty || source==srcName) {
1767 if (whichIF<0) {
1768 restFreqIDs = idx;
1769 } else {
1770 restFreqIDs[whichIF] = idx;
1771 }
1772 }
1773 }
1774 restfreqidCol_.put(i,restFreqIDs);
1775 }
1776 ok = True;
1777 } else {
1778 ok = False;
1779 }
1780
1781 return ok;
1782}
1783
1784std::string SDMemTable::spectralLines() const
1785{
1786 Vector<String> lines = MeasTable::Lines();
1787 MFrequency lineFreq;
1788 Double freq;
1789 ostringstream oss;
1790
1791 oss.flags(std::ios_base::left);
1792 oss << "Line Frequency (Hz)" << endl;
1793 oss << "-----------------------" << endl;
1794 for (uInt i=0; i<lines.nelements(); i++) {
1795 MeasTable::Line(lineFreq, lines[i]);
1796 freq = lineFreq.getValue().getValue(); // Hz
1797 oss << setw(11) << lines[i] << setprecision(10) << freq << endl;
1798 }
1799 return String(oss);
1800}
1801
1802void SDMemTable::renumber()
1803{
1804 uInt nRow = scanCol_.nrow();
1805 Int newscanid = 0;
1806 Int cIdx;// the current scanid
1807 // get the first scanid
1808 scanCol_.getScalar(0,cIdx);
1809 Int pIdx = cIdx;// the scanid of the previous row
1810 for (uInt i=0; i<nRow;++i) {
1811 scanCol_.getScalar(i,cIdx);
1812 if (pIdx == cIdx) {
1813 // renumber
1814 scanCol_.put(i,newscanid);
1815 } else {
1816 ++newscanid;
1817 pIdx = cIdx; // store scanid
1818 --i; // don't increment next loop
1819 }
1820 }
1821}
1822
1823
1824void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1825 const IPosition& shape) const
1826{
1827 const uInt nDim = shape.nelements();
1828 start.resize(nDim);
1829 end.resize(nDim);
1830
1831 start(asap::BeamAxis) = beamSel_;
1832 end(asap::BeamAxis) = beamSel_;
1833 start(asap::IFAxis) = IFSel_;
1834 end(asap::IFAxis) = IFSel_;
1835
1836 start(asap::PolAxis) = polSel_;
1837 end(asap::PolAxis) = polSel_;
1838
1839 start(asap::ChanAxis) = 0;
1840 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1841}
1842
1843
1844std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1845 // Get spectrum at cursor location
1846{
1847
1848 // Setup accessors
1849 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1850 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1851
1852 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1853 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1854
1855 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1856 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1857
1858 std::vector<float> spectrum;
1859 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1860 spectrum.push_back(*i);
1861 }
1862 return spectrum;
1863}
1864
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