source: trunk/src/SDMemTable.cc@ 503

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