source: trunk/src/SDMemTable.cc@ 525

Last change on this file since 525 was 521, checked in by kil064, 20 years ago

add restFreqIDs to summary listing
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  • Property svn:keywords set to Author Date Id Revision
File size: 52.4 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 //cerr << "hello from C SDMemTable @ " << this << endl;
96 attach();
97}
98
99SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
100{
101 table_ = other.table_.copyToMemoryTable(String("dummy"));
102 // clear all rows()
103 if (clear) {
104 table_.removeRow(this->table_.rowNumbers());
105 IFSel_= 0;
106 beamSel_= 0;
107 polSel_= 0;
108 chanMask_.resize(0);
109 } else {
110 IFSel_= other.IFSel_;
111 beamSel_= other.beamSel_;
112 polSel_= other.polSel_;
113 chanMask_.resize(0);
114 chanMask_ = other.chanMask_;
115 }
116
117 attach();
118 //cerr << "hello from CC SDMemTable @ " << this << endl;
119}
120
121SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
122 IFSel_(0),
123 beamSel_(0),
124 polSel_(0)
125{
126 Table t = tableCommand(exprs,tab);
127 if (t.nrow() == 0)
128 throw(AipsError("Query unsuccessful."));
129 table_ = t.copyToMemoryTable("dummy");
130 attach();
131 renumber();
132}
133
134SDMemTable::~SDMemTable()
135{
136 //cerr << "goodbye from SDMemTable @ " << this << endl;
137}
138
139SDMemTable SDMemTable::getScan(Int scanID) const
140{
141 String cond("SELECT * from $1 WHERE SCANID == ");
142 cond += String::toString(scanID);
143 return SDMemTable(table_, cond);
144}
145
146SDMemTable &SDMemTable::operator=(const SDMemTable& other)
147{
148 if (this != &other) {
149 IFSel_= other.IFSel_;
150 beamSel_= other.beamSel_;
151 polSel_= other.polSel_;
152 chanMask_.resize(0);
153 chanMask_ = other.chanMask_;
154 table_ = other.table_.copyToMemoryTable(String("dummy"));
155 attach();
156 }
157 return *this;
158}
159
160SDMemTable SDMemTable::getSource(const std::string& source) const
161{
162 String cond("SELECT * from $1 WHERE SRCNAME == ");
163 cond += source;
164 return SDMemTable(table_, cond);
165}
166
167void SDMemTable::setup()
168{
169 TableDesc td("", "1", TableDesc::Scratch);
170 td.comment() = "A SDMemTable";
171 td.rwKeywordSet().define("VERSION", Int(version_));
172
173 td.addColumn(ScalarColumnDesc<Double>("TIME"));
174 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
175 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
176 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
177 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
178 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
179 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
180 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
181 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
182 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
183 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
184 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
185 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
186 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
187 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
188 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
189 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
190 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
191 td.addColumn(ArrayColumnDesc<Int>("FITID"));
192
193 // Now create Table SetUp from the description.
194 SetupNewTable aNewTab("dummy", td, Table::New);
195
196 // Bind the Stokes Virtual machine to the STOKES column Because we
197 // don't know how many polarizations will be in the data at this
198 // point, we must bind the Virtual Engine regardless. The STOKES
199 // column won't be accessed if not appropriate (nPol=4)
200 SDStokesEngine::registerClass();
201 SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
202 aNewTab.bindColumn("STOKES", stokesEngine);
203
204 // Create Table
205 table_ = Table(aNewTab, Table::Memory, 0);
206 // add subtable
207 TableDesc tdf("", "1", TableDesc::Scratch);
208 tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
209 tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
210 tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
211 tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
212 tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
213 SetupNewTable fittab("fits", tdf, Table::New);
214 Table fitTable(fittab, Table::Memory);
215 table_.rwKeywordSet().defineTable("FITS", fitTable);
216
217 TableDesc tdh("", "1", TableDesc::Scratch);
218 tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
219 SetupNewTable histtab("hist", tdh, Table::New);
220 Table histTable(histtab, Table::Memory);
221 table_.rwKeywordSet().defineTable("HISTORY", histTable);
222}
223
224void SDMemTable::attach()
225{
226 timeCol_.attach(table_, "TIME");
227 srcnCol_.attach(table_, "SRCNAME");
228 specCol_.attach(table_, "SPECTRA");
229 flagsCol_.attach(table_, "FLAGTRA");
230 tsCol_.attach(table_, "TSYS");
231 stokesCol_.attach(table_, "STOKES");
232 scanCol_.attach(table_, "SCANID");
233 integrCol_.attach(table_, "INTERVAL");
234 freqidCol_.attach(table_, "FREQID");
235 restfreqidCol_.attach(table_, "RESTFREQID");
236 dirCol_.attach(table_, "DIRECTION");
237 fldnCol_.attach(table_, "FIELDNAME");
238 tcaltCol_.attach(table_, "TCALTIME");
239 tcalCol_.attach(table_, "TCAL");
240 azCol_.attach(table_, "AZIMUTH");
241 elCol_.attach(table_, "ELEVATION");
242 paraCol_.attach(table_, "PARANGLE");
243 rbeamCol_.attach(table_, "REFBEAM");
244 fitCol_.attach(table_,"FITID");
245}
246
247
248std::string SDMemTable::getSourceName(Int whichRow) const
249{
250 String name;
251 srcnCol_.get(whichRow, name);
252 return name;
253}
254
255std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
256{
257 Double tm;
258 if (whichRow > -1) {
259 timeCol_.get(whichRow, tm);
260 } else {
261 table_.keywordSet().get("UTC",tm);
262 }
263 MVTime mvt(tm);
264 if (showDate)
265 mvt.setFormat(MVTime::YMD);
266 else
267 mvt.setFormat(MVTime::TIME);
268 ostringstream oss;
269 oss << mvt;
270 return String(oss);
271}
272
273double SDMemTable::getInterval(Int whichRow) const
274{
275 Double intval;
276 integrCol_.get(whichRow, intval);
277 return intval;
278}
279
280bool SDMemTable::setIF(Int whichIF)
281{
282 if ( whichIF >= 0 && whichIF < nIF()) {
283 IFSel_ = whichIF;
284 return true;
285 }
286 return false;
287}
288
289bool SDMemTable::setBeam(Int whichBeam)
290{
291 if ( whichBeam >= 0 && whichBeam < nBeam()) {
292 beamSel_ = whichBeam;
293 return true;
294 }
295 return false;
296}
297
298bool SDMemTable::setPol(Int whichPol)
299{
300 if ( whichPol >= 0 && whichPol < nPol()) {
301 polSel_ = whichPol;
302 return true;
303 }
304 return false;
305}
306
307void SDMemTable::resetCursor()
308{
309 polSel_ = 0;
310 IFSel_ = 0;
311 beamSel_ = 0;
312}
313
314bool SDMemTable::setMask(std::vector<int> whichChans)
315{
316 std::vector<int>::iterator it;
317 uInt n = flagsCol_.shape(0)(3);
318 if (whichChans.empty()) {
319 chanMask_ = std::vector<bool>(n,true);
320 return true;
321 }
322 chanMask_.resize(n,true);
323 for (it = whichChans.begin(); it != whichChans.end(); ++it) {
324 if (*it < n) {
325 chanMask_[*it] = false;
326 }
327 }
328 return true;
329}
330
331std::vector<bool> SDMemTable::getMask(Int whichRow) const
332{
333
334 std::vector<bool> mask;
335
336 Array<uChar> arr;
337 flagsCol_.get(whichRow, arr);
338
339 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
340 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
341 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
342 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
343 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
344 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
345
346 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
347
348 std::vector<bool> tmp;
349 tmp = chanMask_; // WHY the fxxx do I have to make a copy here
350 std::vector<bool>::iterator miter;
351 miter = tmp.begin();
352
353 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
354 bool out =!static_cast<bool>(*i);
355 if (useUserMask) {
356 out = out && (*miter);
357 miter++;
358 }
359 mask.push_back(out);
360 }
361 return mask;
362}
363
364
365
366std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
367{
368 Array<Float> arr;
369 specCol_.get(whichRow, arr);
370 return getFloatSpectrum(arr);
371}
372
373
374int SDMemTable::nStokes() const
375{
376 return stokesCol_.shape(0).nelements(); // All rows same shape
377}
378
379
380std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow, Bool doPol) 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
392// For full conversion we are only supporting linears at the moment
393
394 if (nPol() > 2) {
395 String antName;
396 table_.keywordSet().get("AntennaName", antName);
397 Instrument inst = SDAttr::convertInstrument (antName, True);
398 SDAttr sdAtt;
399 if (sdAtt.feedPolType(inst) != LINEAR) {
400 throw(AipsError("Only linear polarizations are supported"));
401 }
402 }
403//
404 Array<Float> arr;
405 stokesCol_.get(whichRow, arr);
406//
407 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
408
409// Set current cursor location
410
411 const IPosition& shape = arr.shape();
412 IPosition start, end;
413 getCursorSlice(start, end, shape);
414
415// Get Q and U slices
416
417 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
418 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
419
420// Compute output
421
422 Array<Float> out;
423 if (polSel_==1) { // P
424 out = SDPolUtil::polarizedIntensity(Q,U);
425 } else if (polSel_==2) { // P.A.
426 out = SDPolUtil::positionAngle(Q,U);
427 }
428
429 // Copy to output
430
431 IPosition vecShape(1,shape(asap::ChanAxis));
432 Vector<Float> outV = out.reform(vecShape);
433 std::vector<float> stlout;
434 outV.tovector(stlout);
435 return stlout;
436
437 } else {
438
439 // Selects at the cursor location
440 return getFloatSpectrum(arr);
441 }
442}
443
444std::string SDMemTable::getPolarizationLabel (Bool linear, Bool stokes, Bool linPol, Int polIdx) const
445{
446 uInt idx = polSel_;
447 if (polIdx >=0) idx = polIdx;
448//
449 return SDPolUtil::polarizationLabel (idx, linear, stokes, linPol);
450}
451
452
453
454std::vector<float> SDMemTable::stokesToPolSpectrum (Int whichRow, Bool toLinear, uInt 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 Bool doRR = (polIdx==0);
486 if(polIdx>1) {
487 throw(AipsError("Only conversion to RR & LL is currently supported"));
488 }
489
490// Get I and V slices
491
492 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
493 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
494
495// Compute output
496
497 out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
498 }
499
500// Copy to output
501
502 IPosition vecShape(1,shape(asap::ChanAxis));
503 Vector<Float> outV = out.reform(vecShape);
504 std::vector<float> stlout;
505 outV.tovector(stlout);
506//
507 return stlout;
508}
509
510
511
512
513Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
514{
515
516// Get data
517
518 Array<Float> arr;
519 stokesCol_.get(whichRow, arr);
520
521// Set current cursor location and overwrite polarization axis
522
523 const IPosition& shape = arr.shape();
524 IPosition start(shape.nelements(),0);
525 IPosition end(shape-1);
526 if (iBeam!=-1) {
527 start(asap::BeamAxis) = iBeam;
528 end(asap::BeamAxis) = iBeam;
529 }
530 if (iIF!=-1) {
531 start(asap::IFAxis) = iIF;
532 end(asap::IFAxis) = iIF;
533 }
534
535// Get slice
536
537 return arr(start,end);
538}
539
540
541std::vector<string> SDMemTable::getCoordInfo() const
542{
543 String un;
544 Table t = table_.keywordSet().asTable("FREQUENCIES");
545 String sunit;
546 t.keywordSet().get("UNIT",sunit);
547 String dpl;
548 t.keywordSet().get("DOPPLER",dpl);
549 if (dpl == "") dpl = "RADIO";
550 String rfrm;
551 t.keywordSet().get("REFFRAME",rfrm);
552 std::vector<string> inf;
553 inf.push_back(sunit);
554 inf.push_back(rfrm);
555 inf.push_back(dpl);
556 t.keywordSet().get("BASEREFFRAME",rfrm);
557 inf.push_back(rfrm);
558 return inf;
559}
560
561void SDMemTable::setCoordInfo(std::vector<string> theinfo)
562{
563 std::vector<string>::iterator it;
564 String un,rfrm, brfrm,dpl;
565 un = theinfo[0]; // Abcissa unit
566 rfrm = theinfo[1]; // Active (or conversion) frame
567 dpl = theinfo[2]; // Doppler
568 brfrm = theinfo[3]; // Base frame
569
570 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
571
572 Vector<Double> rstf;
573 t.keywordSet().get("RESTFREQS",rstf);
574
575 Bool canDo = True;
576 Unit u1("km/s");Unit u2("Hz");
577 if (Unit(un) == u1) {
578 Vector<Double> rstf;
579 t.keywordSet().get("RESTFREQS",rstf);
580 if (rstf.nelements() == 0) {
581 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
582 }
583 } else if (Unit(un) != u2 && un != "") {
584 throw(AipsError("Unit not conformant with Spectral Coordinates"));
585 }
586 t.rwKeywordSet().define("UNIT", un);
587
588 MFrequency::Types mdr;
589 if (!MFrequency::getType(mdr, rfrm)) {
590
591 Int a,b;const uInt* c;
592 const String* valid = MFrequency::allMyTypes(a, b, c);
593 String pfix = "Please specify a legal frame type. Types are\n";
594 throw(AipsError(pfix+(*valid)));
595 } else {
596 t.rwKeywordSet().define("REFFRAME",rfrm);
597 }
598
599 MDoppler::Types dtype;
600 dpl.upcase();
601 if (!MDoppler::getType(dtype, dpl)) {
602 throw(AipsError("Doppler type unknown"));
603 } else {
604 t.rwKeywordSet().define("DOPPLER",dpl);
605 }
606
607 if (!MFrequency::getType(mdr, brfrm)) {
608 Int a,b;const uInt* c;
609 const String* valid = MFrequency::allMyTypes(a, b, c);
610 String pfix = "Please specify a legal frame type. Types are\n";
611 throw(AipsError(pfix+(*valid)));
612 } else {
613 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
614 }
615}
616
617
618std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
619{
620 std::vector<double> abc(nChan());
621
622 // Get header units keyword
623 Table t = table_.keywordSet().asTable("FREQUENCIES");
624 String sunit;
625 t.keywordSet().get("UNIT",sunit);
626 if (sunit == "") sunit = "pixel";
627 Unit u(sunit);
628
629 // Easy if just wanting pixels
630 if (sunit==String("pixel")) {
631 // assume channels/pixels
632 std::vector<double>::iterator it;
633 uInt i=0;
634 for (it = abc.begin(); it != abc.end(); ++it) {
635 (*it) = Double(i++);
636 }
637 return abc;
638 }
639
640 // Continue with km/s or Hz. Get FreqIDs
641 Vector<uInt> freqIDs;
642 freqidCol_.get(whichRow, freqIDs);
643 uInt freqID = freqIDs(IFSel_);
644 restfreqidCol_.get(whichRow, freqIDs);
645 uInt restFreqID = freqIDs(IFSel_);
646
647 // Get SpectralCoordinate, set reference frame conversion,
648 // velocity conversion, and rest freq state
649
650 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
651 Vector<Double> pixel(nChan());
652 indgen(pixel);
653
654 if (u == Unit("km/s")) {
655 Vector<Double> world;
656 spc.pixelToVelocity(world,pixel);
657 std::vector<double>::iterator it;
658 uInt i = 0;
659 for (it = abc.begin(); it != abc.end(); ++it) {
660 (*it) = world[i];
661 i++;
662 }
663 } else if (u == Unit("Hz")) {
664
665 // Set world axis units
666 Vector<String> wau(1); wau = u.getName();
667 spc.setWorldAxisUnits(wau);
668
669 std::vector<double>::iterator it;
670 Double tmp;
671 uInt i = 0;
672 for (it = abc.begin(); it != abc.end(); ++it) {
673 spc.toWorld(tmp,pixel[i]);
674 (*it) = tmp;
675 i++;
676 }
677 }
678 return abc;
679}
680
681std::string SDMemTable::getAbcissaString(Int whichRow) const
682{
683 Table t = table_.keywordSet().asTable("FREQUENCIES");
684
685 String sunit;
686 t.keywordSet().get("UNIT",sunit);
687 if (sunit == "") sunit = "pixel";
688 Unit u(sunit);
689
690 Vector<uInt> freqIDs;
691 freqidCol_.get(whichRow, freqIDs);
692 uInt freqID = freqIDs(IFSel_);
693 restfreqidCol_.get(whichRow, freqIDs);
694 uInt restFreqID = freqIDs(IFSel_);
695
696 // Get SpectralCoordinate, with frame, velocity, rest freq state set
697 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
698
699 String s = "Channel";
700 if (u == Unit("km/s")) {
701 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
702 } else if (u == Unit("Hz")) {
703 Vector<String> wau(1);wau = u.getName();
704 spc.setWorldAxisUnits(wau);
705
706 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
707 }
708 return s;
709}
710
711void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
712{
713 Array<Float> arr;
714 specCol_.get(whichRow, arr);
715 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
716 throw(AipsError("Attempting to set spectrum with incorrect length."));
717 }
718
719 // Setup accessors
720 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
721 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
722 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
723 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
724 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
725 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
726
727 // Iterate
728 std::vector<float>::iterator it = spectrum.begin();
729 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
730 (*i) = Float(*it);
731 it++;
732 }
733 specCol_.put(whichRow, arr);
734}
735
736void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
737{
738 Array<Float> arr;
739 specCol_.get(whichRow, arr);
740
741 // Iterate and extract
742 spectrum.resize(arr.shape()(3));
743 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
744 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
745 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
746 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
747 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
748 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
749
750 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
751 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
752 (*va) = (*i);
753 va++;
754 }
755}
756
757
758/*
759void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
760 Array<uChar> arr;
761 flagsCol_.get(whichRow, arr);
762 mask.resize(arr.shape()(3));
763
764 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
765 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
766 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
767 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
768 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
769 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
770
771 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
772
773 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
774 std::vector<bool> tmp;
775 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
776 // iterator should work on chanMask_??
777 std::vector<bool>::iterator miter;
778 miter = tmp.begin();
779
780 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
781 bool out =!static_cast<bool>(*i);
782 if (useUserMask) {
783 out = out && (*miter);
784 miter++;
785 }
786 (*va) = out;
787 va++;
788 }
789}
790*/
791
792MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
793 Bool toStokes) const
794{
795 // Get flags
796 Array<uChar> farr;
797 flagsCol_.get(whichRow, farr);
798
799 // Get data and convert mask to Bool
800 Array<Float> arr;
801 Array<Bool> mask;
802 if (toStokes) {
803 stokesCol_.get(whichRow, arr);
804
805 Array<Bool> tMask(farr.shape());
806 convertArray(tMask, farr);
807 mask = SDPolUtil::stokesData (tMask, True);
808 } else {
809 specCol_.get(whichRow, arr);
810 mask.resize(farr.shape());
811 convertArray(mask, farr);
812 }
813
814 return MaskedArray<Float>(arr,!mask);
815}
816
817Float SDMemTable::getTsys(Int whichRow) const
818{
819 Array<Float> arr;
820 tsCol_.get(whichRow, arr);
821 Float out;
822
823 IPosition ip(arr.shape());
824 ip(asap::BeamAxis) = beamSel_;
825 ip(asap::IFAxis) = IFSel_;
826 ip(asap::PolAxis) = polSel_;
827 ip(asap::ChanAxis)=0; // First channel only
828
829 out = arr(ip);
830 return out;
831}
832
833MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
834{
835 MDirection::Types mdr = getDirectionReference();
836 Array<Double> posit;
837 dirCol_.get(whichRow,posit);
838 Vector<Double> wpos(2);
839 Int rb;
840 rbeamCol_.get(whichRow,rb);
841 wpos[0] = posit(IPosition(2,beamSel_,0));
842 wpos[1] = posit(IPosition(2,beamSel_,1));
843 if (refBeam && rb > -1) { // use refBeam instead if it exists
844 wpos[0] = posit(IPosition(2,rb,0));
845 wpos[1] = posit(IPosition(2,rb,1));
846 }
847
848 Quantum<Double> lon(wpos[0],Unit(String("rad")));
849 Quantum<Double> lat(wpos[1],Unit(String("rad")));
850 return MDirection(lon, lat, mdr);
851}
852
853MEpoch SDMemTable::getEpoch(Int whichRow) const
854{
855 MEpoch::Types met = getTimeReference();
856
857 Double obstime;
858 timeCol_.get(whichRow,obstime);
859 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
860 return MEpoch(tm2, met);
861}
862
863MPosition SDMemTable::getAntennaPosition () const
864{
865 Vector<Double> antpos;
866 table_.keywordSet().get("AntennaPosition", antpos);
867 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
868 return MPosition(mvpos);
869}
870
871
872SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
873{
874
875 Table t = table_.keywordSet().asTable("FREQUENCIES");
876 if (freqID> t.nrow() ) {
877 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
878 }
879
880 Double rp,rv,inc;
881 String rf;
882 ROScalarColumn<Double> rpc(t, "REFPIX");
883 ROScalarColumn<Double> rvc(t, "REFVAL");
884 ROScalarColumn<Double> incc(t, "INCREMENT");
885 t.keywordSet().get("BASEREFFRAME",rf);
886
887 // Create SpectralCoordinate (units Hz)
888 MFrequency::Types mft;
889 if (!MFrequency::getType(mft, rf)) {
890 cerr << "Frequency type unknown assuming TOPO" << endl;
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 cerr << "Frequency type unknown assuming TOPO" << endl;
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 Array<Int> fitid;
1088 fitCol_.get(whichRow, fitid);
1089 if (fitid.nelements() == 0) return SDFitTable();
1090
1091 IPosition shp = fitid.shape();
1092 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1093 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1094
1095 // reform the output array slice to be of dim=1
1096 Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1097
1098 const Table& t = table_.keywordSet().asTable("FITS");
1099 Vector<Double> parms;
1100 Vector<Bool> parmask;
1101 Vector<String> funcs;
1102 Vector<String> finfo;
1103 Vector<Int> comps;
1104 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1105 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1106 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1107 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1108 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1109 if (t.nrow() == 0) return SDFitTable();
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(0) << 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 cerr << "Unknown equinox using J2000" << endl;
1659 }
1660
1661 return mdr;
1662}
1663
1664MEpoch::Types SDMemTable::getTimeReference() const
1665{
1666 MEpoch::Types met;
1667 String ep;
1668 table_.keywordSet().get("Epoch",ep);
1669 if (!MEpoch::getType(met, ep)) {
1670 cerr << "Epoch type unknown - using UTC" << endl;
1671 met = MEpoch::UTC;
1672 }
1673
1674 return met;
1675}
1676
1677
1678Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1679 const String& sUnit,
1680 const vector<string>& lines,
1681 const String& source,
1682 Int whichIF)
1683{
1684 const Int nIFs = nIF();
1685 if (whichIF>=nIFs) {
1686 throw(AipsError("Illegal IF index"));
1687 }
1688
1689 // Find vector of restfrequencies
1690 // Double takes precedence over String
1691 Unit unit;
1692 Vector<Double> restFreqs;
1693 if (restFreqsIn.nelements()>0) {
1694 restFreqs.resize(restFreqsIn.nelements());
1695 restFreqs = restFreqsIn;
1696 unit = Unit(sUnit);
1697 } else if (lines.size()>0) {
1698 const uInt nLines = lines.size();
1699 unit = Unit("Hz");
1700 restFreqs.resize(nLines);
1701 MFrequency lineFreq;
1702 for (uInt i=0; i<nLines; i++) {
1703 String tS(lines[i]);
1704 tS.upcase();
1705 if (MeasTable::Line(lineFreq, tS)) {
1706 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1707 } else {
1708 String s = String(lines[i]) +
1709 String(" is an unrecognized spectral line");
1710 throw(AipsError(s));
1711 }
1712 }
1713 } else {
1714 throw(AipsError("You have not specified any rest frequencies or lines"));
1715 }
1716
1717 // If multiple restfreqs, must be length nIF. In this
1718 // case we will just replace the rest frequencies
1719 // We can't disinguish scalar and vector of length 1
1720 const uInt nRestFreqs = restFreqs.nelements();
1721 Int idx = -1;
1722 SDFrequencyTable sdft = getSDFreqTable();
1723
1724 if (nRestFreqs>1) {
1725 // Replace restFreqs, one per IF
1726 if (nRestFreqs != nIFs) {
1727 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1728 }
1729 cout << "Replacing rest frequencies, one per IF, with given list : " << restFreqs << endl;
1730 sdft.deleteRestFrequencies();
1731 for (uInt i=0; i<nRestFreqs; i++) {
1732 Quantum<Double> rf(restFreqs[i], unit);
1733 sdft.addRestFrequency(rf.getValue("Hz"));
1734 }
1735 } else {
1736
1737 // Add new rest freq
1738 Quantum<Double> rf(restFreqs[0], unit);
1739 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1740 if (whichIF>=0) {
1741 cout << "Selecting given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
1742 } else {
1743 cout << "Selecting given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
1744 }
1745 }
1746
1747 // Replace
1748 Bool empty = source.empty();
1749 Bool ok = False;
1750 if (putSDFreqTable(sdft)) {
1751 const uInt nRow = table_.nrow();
1752 String srcName;
1753 Vector<uInt> restFreqIDs;
1754 for (uInt i=0; i<nRow; i++) {
1755 srcnCol_.get(i, srcName);
1756 restfreqidCol_.get(i,restFreqIDs);
1757 if (idx==-1) {
1758 // Replace vector of restFreqs; one per IF.
1759 // No selection possible
1760 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1761 } else {
1762 // Set RestFreqID for selected data
1763 if (empty || source==srcName) {
1764 if (whichIF<0) {
1765 restFreqIDs = idx;
1766 } else {
1767 restFreqIDs[whichIF] = idx;
1768 }
1769 }
1770 }
1771 restfreqidCol_.put(i,restFreqIDs);
1772 }
1773 ok = True;
1774 } else {
1775 ok = False;
1776 }
1777
1778 return ok;
1779}
1780
1781void SDMemTable::spectralLines() const
1782{
1783 Vector<String> lines = MeasTable::Lines();
1784 MFrequency lineFreq;
1785 Double freq;
1786
1787 cout.flags(std::ios_base::left);
1788 cout << "Line Frequency (Hz)" << endl;
1789 cout << "-----------------------" << endl;
1790 for (uInt i=0; i<lines.nelements(); i++) {
1791 MeasTable::Line(lineFreq, lines[i]);
1792 freq = lineFreq.getValue().getValue(); // Hz
1793 cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1794 }
1795}
1796
1797void SDMemTable::renumber()
1798{
1799 uInt nRow = scanCol_.nrow();
1800 Int newscanid = 0;
1801 Int cIdx;// the current scanid
1802 // get the first scanid
1803 scanCol_.getScalar(0,cIdx);
1804 Int pIdx = cIdx;// the scanid of the previous row
1805 for (uInt i=0; i<nRow;++i) {
1806 scanCol_.getScalar(i,cIdx);
1807 if (pIdx == cIdx) {
1808 // renumber
1809 scanCol_.put(i,newscanid);
1810 } else {
1811 ++newscanid;
1812 pIdx = cIdx; // store scanid
1813 --i; // don't increment next loop
1814 }
1815 }
1816}
1817
1818
1819void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1820 const IPosition& shape) const
1821{
1822 const uInt nDim = shape.nelements();
1823 start.resize(nDim);
1824 end.resize(nDim);
1825
1826 start(asap::BeamAxis) = beamSel_;
1827 end(asap::BeamAxis) = beamSel_;
1828 start(asap::IFAxis) = IFSel_;
1829 end(asap::IFAxis) = IFSel_;
1830
1831 start(asap::PolAxis) = polSel_;
1832 end(asap::PolAxis) = polSel_;
1833
1834 start(asap::ChanAxis) = 0;
1835 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1836}
1837
1838
1839std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1840 // Get spectrum at cursor location
1841{
1842
1843 // Setup accessors
1844 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1845 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1846
1847 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1848 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1849
1850 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1851 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1852
1853 std::vector<float> spectrum;
1854 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1855 spectrum.push_back(*i);
1856 }
1857 return spectrum;
1858}
1859
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