source: trunk/src/SDMemTable.cc@ 515

Last change on this file since 515 was 504, checked in by kil064, 20 years ago

remiove pa offset from getStokesSpectrum
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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 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
398 const IPosition& shape = arr.shape();
399 IPosition start, end;
400 getCursorSlice(start, end, shape);
401
402// Get Q and U slices
403
404 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
405 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
406
407// Compute output
408
409 Array<Float> out;
410 if (polSel_==1) { // P
411 out = SDPolUtil::polarizedIntensity(Q,U);
412 } else if (polSel_==2) { // P.A.
413 out = SDPolUtil::positionAngle(Q,U);
414 }
415
416 // Copy to output
417
418 IPosition vecShape(1,shape(asap::ChanAxis));
419 Vector<Float> outV = out.reform(vecShape);
420 std::vector<float> stlout;
421 outV.tovector(stlout);
422 return stlout;
423
424 } else {
425
426 // Selects at the cursor location
427 return getFloatSpectrum(arr);
428 }
429}
430
431std::string SDMemTable::getPolarizationLabel (Bool linear, Bool stokes, Bool linPol, Int polIdx) const
432{
433 uInt idx = polSel_;
434 if (polIdx >=0) idx = polIdx;
435//
436 return SDPolUtil::polarizationLabel (idx, linear, stokes, linPol);
437}
438
439
440
441std::vector<float> SDMemTable::stokesToPolSpectrum (Int whichRow, Bool toLinear, uInt polIdx) const
442//
443// polIdx
444// 0:3 -> RR,LL,Real(RL),Imag(RL)
445// XX,YY,Real(XY),Image(XY)
446//
447// Gets only
448// RR = I + V
449// LL = I - V
450// at the moment
451//
452{
453 AlwaysAssert(asap::nAxes==4,AipsError);
454 if (nStokes()!=4) {
455 throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
456 }
457//
458 Array<Float> arr, out;
459 stokesCol_.get(whichRow, arr);
460
461// Set current cursor location
462
463 const IPosition& shape = arr.shape();
464 IPosition start, end;
465 getCursorSlice(start, end, shape);
466
467// Get the slice
468
469 if (toLinear) {
470 throw(AipsError("Conversion to linears not yet supported"));
471 } else {
472 Bool doRR = (polIdx==0);
473 if(polIdx>1) {
474 throw(AipsError("Only conversion to RR & LL is currently supported"));
475 }
476
477// Get I and V slices
478
479 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
480 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
481
482// Compute output
483
484 out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
485 }
486
487// Copy to output
488
489 IPosition vecShape(1,shape(asap::ChanAxis));
490 Vector<Float> outV = out.reform(vecShape);
491 std::vector<float> stlout;
492 outV.tovector(stlout);
493//
494 return stlout;
495}
496
497
498
499
500Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
501{
502
503// Get data
504
505 Array<Float> arr;
506 stokesCol_.get(whichRow, arr);
507
508// Set current cursor location and overwrite polarization axis
509
510 const IPosition& shape = arr.shape();
511 IPosition start(shape.nelements(),0);
512 IPosition end(shape-1);
513 if (iBeam!=-1) {
514 start(asap::BeamAxis) = iBeam;
515 end(asap::BeamAxis) = iBeam;
516 }
517 if (iIF!=-1) {
518 start(asap::IFAxis) = iIF;
519 end(asap::IFAxis) = iIF;
520 }
521
522// Get slice
523
524 return arr(start,end);
525}
526
527
528std::vector<string> SDMemTable::getCoordInfo() const
529{
530 String un;
531 Table t = table_.keywordSet().asTable("FREQUENCIES");
532 String sunit;
533 t.keywordSet().get("UNIT",sunit);
534 String dpl;
535 t.keywordSet().get("DOPPLER",dpl);
536 if (dpl == "") dpl = "RADIO";
537 String rfrm;
538 t.keywordSet().get("REFFRAME",rfrm);
539 std::vector<string> inf;
540 inf.push_back(sunit);
541 inf.push_back(rfrm);
542 inf.push_back(dpl);
543 t.keywordSet().get("BASEREFFRAME",rfrm);
544 inf.push_back(rfrm);
545 return inf;
546}
547
548void SDMemTable::setCoordInfo(std::vector<string> theinfo)
549{
550 std::vector<string>::iterator it;
551 String un,rfrm, brfrm,dpl;
552 un = theinfo[0]; // Abcissa unit
553 rfrm = theinfo[1]; // Active (or conversion) frame
554 dpl = theinfo[2]; // Doppler
555 brfrm = theinfo[3]; // Base frame
556
557 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
558
559 Vector<Double> rstf;
560 t.keywordSet().get("RESTFREQS",rstf);
561
562 Bool canDo = True;
563 Unit u1("km/s");Unit u2("Hz");
564 if (Unit(un) == u1) {
565 Vector<Double> rstf;
566 t.keywordSet().get("RESTFREQS",rstf);
567 if (rstf.nelements() == 0) {
568 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
569 }
570 } else if (Unit(un) != u2 && un != "") {
571 throw(AipsError("Unit not conformant with Spectral Coordinates"));
572 }
573 t.rwKeywordSet().define("UNIT", un);
574
575 MFrequency::Types mdr;
576 if (!MFrequency::getType(mdr, rfrm)) {
577
578 Int a,b;const uInt* c;
579 const String* valid = MFrequency::allMyTypes(a, b, c);
580 String pfix = "Please specify a legal frame type. Types are\n";
581 throw(AipsError(pfix+(*valid)));
582 } else {
583 t.rwKeywordSet().define("REFFRAME",rfrm);
584 }
585
586 MDoppler::Types dtype;
587 dpl.upcase();
588 if (!MDoppler::getType(dtype, dpl)) {
589 throw(AipsError("Doppler type unknown"));
590 } else {
591 t.rwKeywordSet().define("DOPPLER",dpl);
592 }
593
594 if (!MFrequency::getType(mdr, brfrm)) {
595 Int a,b;const uInt* c;
596 const String* valid = MFrequency::allMyTypes(a, b, c);
597 String pfix = "Please specify a legal frame type. Types are\n";
598 throw(AipsError(pfix+(*valid)));
599 } else {
600 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
601 }
602}
603
604
605std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
606{
607 std::vector<double> abc(nChan());
608
609 // Get header units keyword
610 Table t = table_.keywordSet().asTable("FREQUENCIES");
611 String sunit;
612 t.keywordSet().get("UNIT",sunit);
613 if (sunit == "") sunit = "pixel";
614 Unit u(sunit);
615
616 // Easy if just wanting pixels
617 if (sunit==String("pixel")) {
618 // assume channels/pixels
619 std::vector<double>::iterator it;
620 uInt i=0;
621 for (it = abc.begin(); it != abc.end(); ++it) {
622 (*it) = Double(i++);
623 }
624 return abc;
625 }
626
627 // Continue with km/s or Hz. Get FreqIDs
628 Vector<uInt> freqIDs;
629 freqidCol_.get(whichRow, freqIDs);
630 uInt freqID = freqIDs(IFSel_);
631 restfreqidCol_.get(whichRow, freqIDs);
632 uInt restFreqID = freqIDs(IFSel_);
633
634 // Get SpectralCoordinate, set reference frame conversion,
635 // velocity conversion, and rest freq state
636
637 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
638 Vector<Double> pixel(nChan());
639 indgen(pixel);
640
641 if (u == Unit("km/s")) {
642 Vector<Double> world;
643 spc.pixelToVelocity(world,pixel);
644 std::vector<double>::iterator it;
645 uInt i = 0;
646 for (it = abc.begin(); it != abc.end(); ++it) {
647 (*it) = world[i];
648 i++;
649 }
650 } else if (u == Unit("Hz")) {
651
652 // Set world axis units
653 Vector<String> wau(1); wau = u.getName();
654 spc.setWorldAxisUnits(wau);
655
656 std::vector<double>::iterator it;
657 Double tmp;
658 uInt i = 0;
659 for (it = abc.begin(); it != abc.end(); ++it) {
660 spc.toWorld(tmp,pixel[i]);
661 (*it) = tmp;
662 i++;
663 }
664 }
665 return abc;
666}
667
668std::string SDMemTable::getAbcissaString(Int whichRow) const
669{
670 Table t = table_.keywordSet().asTable("FREQUENCIES");
671
672 String sunit;
673 t.keywordSet().get("UNIT",sunit);
674 if (sunit == "") sunit = "pixel";
675 Unit u(sunit);
676
677 Vector<uInt> freqIDs;
678 freqidCol_.get(whichRow, freqIDs);
679 uInt freqID = freqIDs(IFSel_);
680 restfreqidCol_.get(whichRow, freqIDs);
681 uInt restFreqID = freqIDs(IFSel_);
682
683 // Get SpectralCoordinate, with frame, velocity, rest freq state set
684 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
685
686 String s = "Channel";
687 if (u == Unit("km/s")) {
688 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
689 } else if (u == Unit("Hz")) {
690 Vector<String> wau(1);wau = u.getName();
691 spc.setWorldAxisUnits(wau);
692
693 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
694 }
695 return s;
696}
697
698void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
699{
700 Array<Float> arr;
701 specCol_.get(whichRow, arr);
702 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
703 throw(AipsError("Attempting to set spectrum with incorrect length."));
704 }
705
706 // Setup accessors
707 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
708 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
709 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
710 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
711 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
712 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
713
714 // Iterate
715 std::vector<float>::iterator it = spectrum.begin();
716 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
717 (*i) = Float(*it);
718 it++;
719 }
720 specCol_.put(whichRow, arr);
721}
722
723void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
724{
725 Array<Float> arr;
726 specCol_.get(whichRow, arr);
727
728 // Iterate and extract
729 spectrum.resize(arr.shape()(3));
730 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
731 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
732 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
733 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
734 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
735 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
736
737 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
738 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
739 (*va) = (*i);
740 va++;
741 }
742}
743
744
745/*
746void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
747 Array<uChar> arr;
748 flagsCol_.get(whichRow, arr);
749 mask.resize(arr.shape()(3));
750
751 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
752 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
753 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
754 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
755 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
756 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
757
758 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
759
760 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
761 std::vector<bool> tmp;
762 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
763 // iterator should work on chanMask_??
764 std::vector<bool>::iterator miter;
765 miter = tmp.begin();
766
767 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
768 bool out =!static_cast<bool>(*i);
769 if (useUserMask) {
770 out = out && (*miter);
771 miter++;
772 }
773 (*va) = out;
774 va++;
775 }
776}
777*/
778
779MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
780 Bool toStokes) const
781{
782 // Get flags
783 Array<uChar> farr;
784 flagsCol_.get(whichRow, farr);
785
786 // Get data and convert mask to Bool
787 Array<Float> arr;
788 Array<Bool> mask;
789 if (toStokes) {
790 stokesCol_.get(whichRow, arr);
791
792 Array<Bool> tMask(farr.shape());
793 convertArray(tMask, farr);
794 mask = SDPolUtil::stokesData (tMask, True);
795 } else {
796 specCol_.get(whichRow, arr);
797 mask.resize(farr.shape());
798 convertArray(mask, farr);
799 }
800
801 return MaskedArray<Float>(arr,!mask);
802}
803
804Float SDMemTable::getTsys(Int whichRow) const
805{
806 Array<Float> arr;
807 tsCol_.get(whichRow, arr);
808 Float out;
809
810 IPosition ip(arr.shape());
811 ip(asap::BeamAxis) = beamSel_;
812 ip(asap::IFAxis) = IFSel_;
813 ip(asap::PolAxis) = polSel_;
814 ip(asap::ChanAxis)=0; // First channel only
815
816 out = arr(ip);
817 return out;
818}
819
820MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
821{
822 MDirection::Types mdr = getDirectionReference();
823 Array<Double> posit;
824 dirCol_.get(whichRow,posit);
825 Vector<Double> wpos(2);
826 Int rb;
827 rbeamCol_.get(whichRow,rb);
828 wpos[0] = posit(IPosition(2,beamSel_,0));
829 wpos[1] = posit(IPosition(2,beamSel_,1));
830 if (refBeam && rb > -1) { // use refBeam instead if it exists
831 wpos[0] = posit(IPosition(2,rb,0));
832 wpos[1] = posit(IPosition(2,rb,1));
833 }
834
835 Quantum<Double> lon(wpos[0],Unit(String("rad")));
836 Quantum<Double> lat(wpos[1],Unit(String("rad")));
837 return MDirection(lon, lat, mdr);
838}
839
840MEpoch SDMemTable::getEpoch(Int whichRow) const
841{
842 MEpoch::Types met = getTimeReference();
843
844 Double obstime;
845 timeCol_.get(whichRow,obstime);
846 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
847 return MEpoch(tm2, met);
848}
849
850MPosition SDMemTable::getAntennaPosition () const
851{
852 Vector<Double> antpos;
853 table_.keywordSet().get("AntennaPosition", antpos);
854 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
855 return MPosition(mvpos);
856}
857
858
859SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
860{
861
862 Table t = table_.keywordSet().asTable("FREQUENCIES");
863 if (freqID> t.nrow() ) {
864 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
865 }
866
867 Double rp,rv,inc;
868 String rf;
869 ROScalarColumn<Double> rpc(t, "REFPIX");
870 ROScalarColumn<Double> rvc(t, "REFVAL");
871 ROScalarColumn<Double> incc(t, "INCREMENT");
872 t.keywordSet().get("BASEREFFRAME",rf);
873
874 // Create SpectralCoordinate (units Hz)
875 MFrequency::Types mft;
876 if (!MFrequency::getType(mft, rf)) {
877 cerr << "Frequency type unknown assuming TOPO" << endl;
878 mft = MFrequency::TOPO;
879 }
880 rpc.get(freqID, rp);
881 rvc.get(freqID, rv);
882 incc.get(freqID, inc);
883
884 SpectralCoordinate spec(mft,rv,inc,rp);
885 return spec;
886}
887
888
889SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
890 uInt restFreqID,
891 uInt whichRow) const
892{
893
894 // Create basic SC
895 SpectralCoordinate spec = getSpectralCoordinate (freqID);
896
897 Table t = table_.keywordSet().asTable("FREQUENCIES");
898
899 // Set rest frequency
900 Vector<Double> restFreqIDs;
901 t.keywordSet().get("RESTFREQS",restFreqIDs);
902 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
903 spec.setRestFrequency(restFreqIDs(restFreqID),True);
904 }
905
906 // Set up frame conversion layer
907 String frm;
908 t.keywordSet().get("REFFRAME",frm);
909 if (frm == "") frm = "TOPO";
910 MFrequency::Types mtype;
911 if (!MFrequency::getType(mtype, frm)) {
912 // Should never happen
913 cerr << "Frequency type unknown assuming TOPO" << endl;
914 mtype = MFrequency::TOPO;
915 }
916
917 // Set reference frame conversion (requires row)
918 MDirection dir = getDirection(whichRow);
919 MEpoch epoch = getEpoch(whichRow);
920 MPosition pos = getAntennaPosition();
921
922 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
923 throw(AipsError("Couldn't convert frequency frame."));
924 }
925
926 // Now velocity conversion if appropriate
927 String unitStr;
928 t.keywordSet().get("UNIT",unitStr);
929
930 String dpl;
931 t.keywordSet().get("DOPPLER",dpl);
932 MDoppler::Types dtype;
933 MDoppler::getType(dtype, dpl);
934
935 // Only set velocity unit if non-blank and non-Hz
936 if (!unitStr.empty()) {
937 Unit unitU(unitStr);
938 if (unitU==Unit("Hz")) {
939 } else {
940 spec.setVelocity(unitStr, dtype);
941 }
942 }
943
944 return spec;
945}
946
947
948Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
949 uInt freqID) {
950 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
951 if (freqID > t.nrow() ) {
952 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
953 }
954 ScalarColumn<Double> rpc(t, "REFPIX");
955 ScalarColumn<Double> rvc(t, "REFVAL");
956 ScalarColumn<Double> incc(t, "INCREMENT");
957
958 rpc.put(freqID, speccord.referencePixel()[0]);
959 rvc.put(freqID, speccord.referenceValue()[0]);
960 incc.put(freqID, speccord.increment()[0]);
961
962 return True;
963}
964
965Int SDMemTable::nCoordinates() const
966{
967 return table_.keywordSet().asTable("FREQUENCIES").nrow();
968}
969
970
971std::vector<double> SDMemTable::getRestFreqs() const
972{
973 Table t = table_.keywordSet().asTable("FREQUENCIES");
974 Vector<Double> tvec;
975 t.keywordSet().get("RESTFREQS",tvec);
976 std::vector<double> stlout;
977 tvec.tovector(stlout);
978 return stlout;
979}
980
981bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
982{
983 TableDesc td("", "1", TableDesc::Scratch);
984 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
985 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
986 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
987 SetupNewTable aNewTab("freqs", td, Table::New);
988 Table aTable (aNewTab, Table::Memory, sdft.length());
989 ScalarColumn<Double> sc0(aTable, "REFPIX");
990 ScalarColumn<Double> sc1(aTable, "REFVAL");
991 ScalarColumn<Double> sc2(aTable, "INCREMENT");
992 for (uInt i=0; i < sdft.length(); ++i) {
993 sc0.put(i,sdft.referencePixel(i));
994 sc1.put(i,sdft.referenceValue(i));
995 sc2.put(i,sdft.increment(i));
996 }
997 String rf = sdft.refFrame();
998 if (rf.contains("TOPO")) rf = "TOPO";
999
1000 aTable.rwKeywordSet().define("BASEREFFRAME", rf);
1001 aTable.rwKeywordSet().define("REFFRAME", rf);
1002 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
1003 aTable.rwKeywordSet().define("UNIT", String(""));
1004 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
1005 Vector<Double> rfvec;
1006 String rfunit;
1007 sdft.restFrequencies(rfvec,rfunit);
1008 Quantum<Vector<Double> > q(rfvec, rfunit);
1009 rfvec.resize();
1010 rfvec = q.getValue("Hz");
1011 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
1012 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
1013 return true;
1014}
1015
1016bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
1017{
1018 TableDesc td("", "1", TableDesc::Scratch);
1019 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
1020 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
1021 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
1022 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
1023 td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
1024 SetupNewTable aNewTab("fits", td, Table::New);
1025 Table aTable(aNewTab, Table::Memory);
1026 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
1027 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
1028 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
1029 ArrayColumn<Bool> sc3(aTable, "PARMASK");
1030 ArrayColumn<String> sc4(aTable, "FRAMEINFO");
1031 for (uInt i; i<sdft.length(); ++i) {
1032 const Vector<Double>& parms = sdft.getParameters(i);
1033 const Vector<Bool>& parmask = sdft.getParameterMask(i);
1034 const Vector<String>& funcs = sdft.getFunctions(i);
1035 const Vector<Int>& comps = sdft.getComponents(i);
1036 const Vector<String>& finfo = sdft.getFrameInfo(i);
1037 sc0.put(i,funcs);
1038 sc1.put(i,comps);
1039 sc3.put(i,parmask);
1040 sc2.put(i,parms);
1041 sc4.put(i,finfo);
1042 }
1043 table_.rwKeywordSet().defineTable("FITS", aTable);
1044 return true;
1045}
1046
1047SDFitTable SDMemTable::getSDFitTable() const
1048{
1049 const Table& t = table_.keywordSet().asTable("FITS");
1050 Vector<Double> parms;
1051 Vector<Bool> parmask;
1052 Vector<String> funcs;
1053 Vector<String> finfo;
1054 Vector<Int> comps;
1055 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1056 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1057 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1058 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1059 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1060 uInt n = t.nrow();
1061 SDFitTable sdft;
1062 for (uInt i=0; i<n; ++i) {
1063 parmaskCol.get(i, parmask);
1064 parmsCol.get(i, parms);
1065 funcsCol.get(i, funcs);
1066 compsCol.get(i, comps);
1067 finfoCol.get(i, finfo);
1068 sdft.addFit(parms, parmask, funcs, comps, finfo);
1069 }
1070 return sdft;
1071}
1072
1073SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1074 Array<Int> fitid;
1075 fitCol_.get(whichRow, fitid);
1076 if (fitid.nelements() == 0) return SDFitTable();
1077
1078 IPosition shp = fitid.shape();
1079 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1080 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1081
1082 // reform the output array slice to be of dim=1
1083 Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1084
1085 const Table& t = table_.keywordSet().asTable("FITS");
1086 Vector<Double> parms;
1087 Vector<Bool> parmask;
1088 Vector<String> funcs;
1089 Vector<String> finfo;
1090 Vector<Int> comps;
1091 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1092 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1093 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1094 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1095 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1096 if (t.nrow() == 0) return SDFitTable();
1097 SDFitTable sdft;
1098 Int k=-1;
1099 for (uInt i=0; i< tmp.nelements(); ++i) {
1100 k = tmp[i];
1101 if ( k > -1 && k < t.nrow() ) {
1102 parms.resize();
1103 parmsCol.get(k, parms);
1104 parmask.resize();
1105 parmaskCol.get(k, parmask);
1106 funcs.resize();
1107 funcsCol.get(k, funcs);
1108 comps.resize();
1109 compsCol.get(k, comps);
1110 finfo.resize();
1111 finfoCol.get(k, finfo);
1112 sdft.addFit(parms, parmask, funcs, comps, finfo);
1113 }
1114 }
1115 return sdft;
1116}
1117
1118void SDMemTable::addFit(uInt whichRow,
1119 const Vector<Double>& p, const Vector<Bool>& m,
1120 const Vector<String>& f, const Vector<Int>& c)
1121{
1122 if (whichRow >= nRow()) {
1123 throw(AipsError("Specified row out of range"));
1124 }
1125 Table t = table_.keywordSet().asTable("FITS");
1126 uInt nrow = t.nrow();
1127 t.addRow();
1128 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1129 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1130 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1131 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1132 ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1133 parmsCol.put(nrow, p);
1134 parmaskCol.put(nrow, m);
1135 compsCol.put(nrow, c);
1136 funcsCol.put(nrow, f);
1137 Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1138 finfoCol.put(nrow, fi);
1139
1140 Array<Int> fitarr;
1141 fitCol_.get(whichRow, fitarr);
1142
1143 Array<Int> newarr; // The new Array containing the fitid
1144 Int pos =-1; // The fitid position in the array
1145 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1146 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1147 arr = -1;
1148 newarr.reference(arr);
1149 pos = 0;
1150 } else {
1151 IPosition shp = fitarr.shape();
1152 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1153 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1154 // reform the output array slice to be of dim=1
1155 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1156 const Vector<Int>& fits = tmp;
1157 VectorSTLIterator<Int> it(fits);
1158 Int i = 0;
1159 while (it != fits.end()) {
1160 if (*it == -1) {
1161 pos = i;
1162 break;
1163 }
1164 ++i;
1165 ++it;
1166 };
1167 }
1168 if (pos == -1) {
1169 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1170 pos = fitarr.shape()[3]; // the new element position
1171 } else {
1172 if (fitarr.nelements() > 0)
1173 newarr = fitarr;
1174 }
1175 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1176 fitCol_.put(whichRow, newarr);
1177
1178}
1179
1180SDFrequencyTable SDMemTable::getSDFreqTable() const
1181{
1182 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1183 SDFrequencyTable sdft;
1184
1185 // Add refpix/refval/incr. What are the units ? Hz I suppose
1186 // but it's nowhere described...
1187 Vector<Double> refPix, refVal, incr;
1188 ScalarColumn<Double> refPixCol(t, "REFPIX");
1189 ScalarColumn<Double> refValCol(t, "REFVAL");
1190 ScalarColumn<Double> incrCol(t, "INCREMENT");
1191 refPix = refPixCol.getColumn();
1192 refVal = refValCol.getColumn();
1193 incr = incrCol.getColumn();
1194
1195 uInt n = refPix.nelements();
1196 for (uInt i=0; i<n; i++) {
1197 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1198 }
1199
1200 // Frequency reference frame. I don't know if this
1201 // is the correct frame. It might be 'REFFRAME'
1202 // rather than 'BASEREFFRAME' ?
1203 String baseFrame;
1204 t.keywordSet().get("BASEREFFRAME",baseFrame);
1205 sdft.setRefFrame(baseFrame);
1206
1207 // Equinox
1208 Float equinox;
1209 t.keywordSet().get("EQUINOX", equinox);
1210 sdft.setEquinox(equinox);
1211
1212 // Rest Frequency
1213 Vector<Double> restFreqs;
1214 t.keywordSet().get("RESTFREQS", restFreqs);
1215 for (uInt i=0; i<restFreqs.nelements(); i++) {
1216 sdft.addRestFrequency(restFreqs[i]);
1217 }
1218 sdft.setRestFrequencyUnit(String("Hz"));
1219
1220 return sdft;
1221}
1222
1223bool SDMemTable::putSDContainer(const SDContainer& sdc)
1224{
1225 uInt rno = table_.nrow();
1226 table_.addRow();
1227
1228 timeCol_.put(rno, sdc.timestamp);
1229 srcnCol_.put(rno, sdc.sourcename);
1230 fldnCol_.put(rno, sdc.fieldname);
1231 specCol_.put(rno, sdc.getSpectrum());
1232 flagsCol_.put(rno, sdc.getFlags());
1233 tsCol_.put(rno, sdc.getTsys());
1234 scanCol_.put(rno, sdc.scanid);
1235 integrCol_.put(rno, sdc.interval);
1236 freqidCol_.put(rno, sdc.getFreqMap());
1237 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1238 dirCol_.put(rno, sdc.getDirection());
1239 rbeamCol_.put(rno, sdc.refbeam);
1240 tcalCol_.put(rno, sdc.tcal);
1241 tcaltCol_.put(rno, sdc.tcaltime);
1242 azCol_.put(rno, sdc.azimuth);
1243 elCol_.put(rno, sdc.elevation);
1244 paraCol_.put(rno, sdc.parangle);
1245 fitCol_.put(rno, sdc.getFitMap());
1246 return true;
1247}
1248
1249SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1250{
1251 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1252 timeCol_.get(whichRow, sdc.timestamp);
1253 srcnCol_.get(whichRow, sdc.sourcename);
1254 integrCol_.get(whichRow, sdc.interval);
1255 scanCol_.get(whichRow, sdc.scanid);
1256 fldnCol_.get(whichRow, sdc.fieldname);
1257 rbeamCol_.get(whichRow, sdc.refbeam);
1258 azCol_.get(whichRow, sdc.azimuth);
1259 elCol_.get(whichRow, sdc.elevation);
1260 paraCol_.get(whichRow, sdc.parangle);
1261 Vector<Float> tc;
1262 tcalCol_.get(whichRow, tc);
1263 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1264 tcaltCol_.get(whichRow, sdc.tcaltime);
1265
1266 Array<Float> spectrum;
1267 Array<Float> tsys;
1268 Array<uChar> flagtrum;
1269 Vector<uInt> fmap;
1270 Array<Double> direction;
1271 Array<Int> fits;
1272
1273 specCol_.get(whichRow, spectrum);
1274 sdc.putSpectrum(spectrum);
1275 flagsCol_.get(whichRow, flagtrum);
1276 sdc.putFlags(flagtrum);
1277 tsCol_.get(whichRow, tsys);
1278 sdc.putTsys(tsys);
1279 freqidCol_.get(whichRow, fmap);
1280 sdc.putFreqMap(fmap);
1281 restfreqidCol_.get(whichRow, fmap);
1282 sdc.putRestFreqMap(fmap);
1283 dirCol_.get(whichRow, direction);
1284 sdc.putDirection(direction);
1285 fitCol_.get(whichRow, fits);
1286 sdc.putFitMap(fits);
1287 return sdc;
1288}
1289
1290bool SDMemTable::putSDHeader(const SDHeader& sdh)
1291{
1292 table_.rwKeywordSet().define("nIF", sdh.nif);
1293 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1294 table_.rwKeywordSet().define("nPol", sdh.npol);
1295 table_.rwKeywordSet().define("nChan", sdh.nchan);
1296 table_.rwKeywordSet().define("Observer", sdh.observer);
1297 table_.rwKeywordSet().define("Project", sdh.project);
1298 table_.rwKeywordSet().define("Obstype", sdh.obstype);
1299 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1300 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1301 table_.rwKeywordSet().define("Equinox", sdh.equinox);
1302 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1303 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1304 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1305 table_.rwKeywordSet().define("UTC", sdh.utc);
1306 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1307 table_.rwKeywordSet().define("Epoch", sdh.epoch);
1308 return true;
1309}
1310
1311SDHeader SDMemTable::getSDHeader() const
1312{
1313 SDHeader sdh;
1314 table_.keywordSet().get("nBeam",sdh.nbeam);
1315 table_.keywordSet().get("nIF",sdh.nif);
1316 table_.keywordSet().get("nPol",sdh.npol);
1317 table_.keywordSet().get("nChan",sdh.nchan);
1318 table_.keywordSet().get("Observer", sdh.observer);
1319 table_.keywordSet().get("Project", sdh.project);
1320 table_.keywordSet().get("Obstype", sdh.obstype);
1321 table_.keywordSet().get("AntennaName", sdh.antennaname);
1322 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1323 table_.keywordSet().get("Equinox", sdh.equinox);
1324 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1325 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1326 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1327 table_.keywordSet().get("UTC", sdh.utc);
1328 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1329 table_.keywordSet().get("Epoch", sdh.epoch);
1330 return sdh;
1331}
1332void SDMemTable::makePersistent(const std::string& filename)
1333{
1334 table_.deepCopy(filename,Table::New);
1335
1336}
1337
1338Int SDMemTable::nScan() const {
1339 Int n = 0;
1340 Int previous = -1;Int current=0;
1341 for (uInt i=0; i< scanCol_.nrow();i++) {
1342 scanCol_.getScalar(i,current);
1343 if (previous != current) {
1344 previous = current;
1345 n++;
1346 }
1347 }
1348 return n;
1349}
1350
1351String SDMemTable::formatSec(Double x) const
1352{
1353 Double xcop = x;
1354 MVTime mvt(xcop/24./3600.); // make days
1355
1356 if (x < 59.95)
1357 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1358 else if (x < 3599.95)
1359 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1360 else {
1361 ostringstream oss;
1362 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1363 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1364 return String(oss);
1365 }
1366};
1367
1368String SDMemTable::formatDirection(const MDirection& md) const
1369{
1370 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1371 Int prec = 7;
1372
1373 MVAngle mvLon(t[0]);
1374 String sLon = mvLon.string(MVAngle::TIME,prec);
1375 MVAngle mvLat(t[1]);
1376 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1377 return sLon + String(" ") + sLat;
1378}
1379
1380
1381std::string SDMemTable::getFluxUnit() const
1382{
1383 String tmp;
1384 table_.keywordSet().get("FluxUnit", tmp);
1385 return tmp;
1386}
1387
1388void SDMemTable::setFluxUnit(const std::string& unit)
1389{
1390 String tmp(unit);
1391 Unit tU(tmp);
1392 if (tU==Unit("K") || tU==Unit("Jy")) {
1393 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1394 } else {
1395 throw AipsError("Illegal unit - must be compatible with Jy or K");
1396 }
1397}
1398
1399
1400void SDMemTable::setInstrument(const std::string& name)
1401{
1402 Bool throwIt = True;
1403 Instrument ins = SDAttr::convertInstrument(name, throwIt);
1404 String nameU(name);
1405 nameU.upcase();
1406 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1407}
1408
1409std::string SDMemTable::summary(bool verbose) const {
1410
1411 // Format header info
1412 ostringstream oss;
1413 oss << endl;
1414 oss << "--------------------------------------------------------------------------------" << endl;
1415 oss << " Scan Table Summary" << endl;
1416 oss << "--------------------------------------------------------------------------------" << endl;
1417 oss.flags(std::ios_base::left);
1418 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1419 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1420 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1421 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1422 oss << endl;
1423 String tmp;
1424 table_.keywordSet().get("Observer", tmp);
1425 oss << setw(15) << "Observer:" << tmp << endl;
1426 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1427 table_.keywordSet().get("Project", tmp);
1428 oss << setw(15) << "Project:" << tmp << endl;
1429 table_.keywordSet().get("Obstype", tmp);
1430 oss << setw(15) << "Obs. Type:" << tmp << endl;
1431 table_.keywordSet().get("AntennaName", tmp);
1432 oss << setw(15) << "Antenna Name:" << tmp << endl;
1433 table_.keywordSet().get("FluxUnit", tmp);
1434 oss << setw(15) << "Flux Unit:" << tmp << endl;
1435 Table t = table_.keywordSet().asTable("FREQUENCIES");
1436 Vector<Double> vec;
1437 t.keywordSet().get("RESTFREQS",vec);
1438 oss << setw(15) << "Rest Freqs:";
1439 if (vec.nelements() > 0) {
1440 oss << setprecision(0) << vec << " [Hz]" << endl;
1441 } else {
1442 oss << "None set" << endl;
1443 }
1444 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1445 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1446 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1447 oss << endl;
1448
1449 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1450 oss << setw(5) << "Scan"
1451 << setw(15) << "Source"
1452 << setw(24) << dirtype
1453 << setw(10) << "Time"
1454 << setw(18) << "Integration"
1455 << setw(7) << "FreqIDs" << endl;
1456 oss << "--------------------------------------------------------------------------------" << endl;
1457
1458 // Generate list of scan start and end integrations
1459 Vector<Int> scanIDs = scanCol_.getColumn();
1460 Vector<uInt> startInt, endInt;
1461 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1462
1463 const uInt nScans = startInt.nelements();
1464 String name;
1465 Vector<uInt> freqIDs, listFQ;
1466 uInt nInt;
1467
1468 for (uInt i=0; i<nScans; i++) {
1469 // Get things from first integration of scan
1470 String time = getTime(startInt(i),False);
1471 String tInt = formatSec(Double(getInterval(startInt(i))));
1472 String posit = formatDirection(getDirection(startInt(i),True));
1473 srcnCol_.getScalar(startInt(i),name);
1474
1475 // Find all the FreqIDs in this scan
1476 listFQ.resize(0);
1477 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1478 freqidCol_.get(j, freqIDs);
1479 for (uInt k=0; k<freqIDs.nelements(); k++) {
1480 mathutil::addEntry(listFQ, freqIDs(k));
1481 }
1482 }
1483
1484 nInt = endInt(i) - startInt(i) + 1;
1485 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1486 << setw(15) << name
1487 << setw(24) << posit
1488 << setw(10) << time
1489 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1490 << setw(6) << tInt
1491 << " " << listFQ << endl;
1492 }
1493 oss << endl;
1494 oss << "Table contains " << table_.nrow() << " integration(s) in "
1495 << nScans << " scan(s)." << endl;
1496
1497 // Frequency Table
1498 if (verbose) {
1499 std::vector<string> info = getCoordInfo();
1500 SDFrequencyTable sdft = getSDFreqTable();
1501 oss << endl << endl;
1502 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1503 oss << "--------------------------------------------------------------------------------" << endl;
1504 for (uInt i=0; i<sdft.length(); i++) {
1505 oss << setw(8) << i << setw(8)
1506 << info[3] << setw(16) << setprecision(8)
1507 << sdft.referenceValue(i) << setw(10)
1508 << sdft.referencePixel(i) << setw(12)
1509 << sdft.increment(i) << endl;
1510 }
1511 oss << "--------------------------------------------------------------------------------" << endl;
1512 }
1513 return String(oss);
1514}
1515/*
1516std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1517 ostringstream oss;
1518 Vector<Int> scanIDs = scanCol_.getColumn();
1519 Vector<uInt> startInt, endInt;
1520 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1521 const uInt nScans = startInt.nelements();
1522 std::vector<int>::const_iterator it(whichScans);
1523 return String(oss);
1524}
1525*/
1526Int SDMemTable::nBeam() const
1527{
1528 Int n;
1529 table_.keywordSet().get("nBeam",n);
1530 return n;
1531}
1532
1533Int SDMemTable::nIF() const {
1534 Int n;
1535 table_.keywordSet().get("nIF",n);
1536 return n;
1537}
1538
1539Int SDMemTable::nPol() const {
1540 Int n;
1541 table_.keywordSet().get("nPol",n);
1542 return n;
1543}
1544
1545Int SDMemTable::nChan() const {
1546 Int n;
1547 table_.keywordSet().get("nChan",n);
1548 return n;
1549}
1550
1551Table SDMemTable::getHistoryTable() const
1552{
1553 return table_.keywordSet().asTable("HISTORY");
1554}
1555
1556void SDMemTable::appendToHistoryTable(const Table& otherHist)
1557{
1558 Table t = table_.rwKeywordSet().asTable("HISTORY");
1559 const String sep = "--------------------------------------------------------------------------------";
1560 addHistory(sep);
1561 TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
1562 addHistory(sep);
1563}
1564
1565void SDMemTable::addHistory(const std::string& hist)
1566{
1567 Table t = table_.rwKeywordSet().asTable("HISTORY");
1568 uInt nrow = t.nrow();
1569 t.addRow();
1570 ScalarColumn<String> itemCol(t, "ITEM");
1571 itemCol.put(nrow, hist);
1572}
1573
1574std::vector<std::string> SDMemTable::getHistory() const
1575{
1576 Vector<String> history;
1577 const Table& t = table_.keywordSet().asTable("HISTORY");
1578 uInt nrow = t.nrow();
1579 ROScalarColumn<String> itemCol(t, "ITEM");
1580 std::vector<std::string> stlout;
1581 String hist;
1582 for (uInt i=0; i<nrow; ++i) {
1583 itemCol.get(i, hist);
1584 stlout.push_back(hist);
1585 }
1586 return stlout;
1587}
1588
1589
1590/*
1591 void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1592
1593 std::vector<int>::iterator it;
1594 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1595 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1596 j.reset(j.begin(uInt(*it)));
1597 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1598 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1599 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1600 iii != iii.end(); ++iii) {
1601 (*iii) =
1602 }
1603 }
1604 }
1605 }
1606
1607}
1608*/
1609void SDMemTable::flag(int whichRow)
1610 {
1611 Array<uChar> arr;
1612 flagsCol_.get(whichRow, arr);
1613
1614 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1615 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1616 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1617 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1618 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1619 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1620
1621 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1622 (*i) = uChar(True);
1623 }
1624
1625 flagsCol_.put(whichRow, arr);
1626}
1627
1628MDirection::Types SDMemTable::getDirectionReference() const
1629{
1630 Float eq;
1631 table_.keywordSet().get("Equinox",eq);
1632 std::map<float,string> mp;
1633 mp[2000.0] = "J2000";
1634 mp[1950.0] = "B1950";
1635 MDirection::Types mdr;
1636 if (!MDirection::getType(mdr, mp[eq])) {
1637 mdr = MDirection::J2000;
1638 cerr << "Unknown equinox using J2000" << endl;
1639 }
1640
1641 return mdr;
1642}
1643
1644MEpoch::Types SDMemTable::getTimeReference() const
1645{
1646 MEpoch::Types met;
1647 String ep;
1648 table_.keywordSet().get("Epoch",ep);
1649 if (!MEpoch::getType(met, ep)) {
1650 cerr << "Epoch type unknown - using UTC" << endl;
1651 met = MEpoch::UTC;
1652 }
1653
1654 return met;
1655}
1656
1657
1658Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1659 const String& sUnit,
1660 const vector<string>& lines,
1661 const String& source,
1662 Int whichIF)
1663{
1664 const Int nIFs = nIF();
1665 if (whichIF>=nIFs) {
1666 throw(AipsError("Illegal IF index"));
1667 }
1668
1669 // Find vector of restfrequencies
1670 // Double takes precedence over String
1671 Unit unit;
1672 Vector<Double> restFreqs;
1673 if (restFreqsIn.nelements()>0) {
1674 restFreqs.resize(restFreqsIn.nelements());
1675 restFreqs = restFreqsIn;
1676 unit = Unit(sUnit);
1677 } else if (lines.size()>0) {
1678 const uInt nLines = lines.size();
1679 unit = Unit("Hz");
1680 restFreqs.resize(nLines);
1681 MFrequency lineFreq;
1682 for (uInt i=0; i<nLines; i++) {
1683 String tS(lines[i]);
1684 tS.upcase();
1685 if (MeasTable::Line(lineFreq, tS)) {
1686 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1687 } else {
1688 String s = String(lines[i]) +
1689 String(" is an unrecognized spectral line");
1690 throw(AipsError(s));
1691 }
1692 }
1693 } else {
1694 throw(AipsError("You have not specified any rest frequencies or lines"));
1695 }
1696
1697 // If multiple restfreqs, must be length nIF. In this
1698 // case we will just replace the rest frequencies
1699 const uInt nRestFreqs = restFreqs.nelements();
1700 Int idx = -1;
1701 SDFrequencyTable sdft = getSDFreqTable();
1702
1703 if (nRestFreqs>1) {
1704 // Replace restFreqs, one per IF
1705 if (nRestFreqs != nIFs) {
1706 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1707 }
1708 cout << "Replacing rest frequencies with given list, one per IF" << endl;
1709 sdft.deleteRestFrequencies();
1710 for (uInt i=0; i<nRestFreqs; i++) {
1711 Quantum<Double> rf(restFreqs[i], unit);
1712 sdft.addRestFrequency(rf.getValue("Hz"));
1713 }
1714 } else {
1715
1716 // Add new rest freq
1717 Quantum<Double> rf(restFreqs[0], unit);
1718 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1719 cout << "Selecting given rest frequency" << endl;
1720 }
1721
1722 // Replace
1723 Bool empty = source.empty();
1724 Bool ok = False;
1725 if (putSDFreqTable(sdft)) {
1726 const uInt nRow = table_.nrow();
1727 String srcName;
1728 Vector<uInt> restFreqIDs;
1729 for (uInt i=0; i<nRow; i++) {
1730 srcnCol_.get(i, srcName);
1731 restfreqidCol_.get(i,restFreqIDs);
1732
1733 if (idx==-1) {
1734 // Replace vector of restFreqs; one per IF.
1735 // No selection possible
1736 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1737 } else {
1738 // Set RestFreqID for selected data
1739 if (empty || source==srcName) {
1740 if (whichIF<0) {
1741 restFreqIDs = idx;
1742 } else {
1743 restFreqIDs[whichIF] = idx;
1744 }
1745 }
1746 }
1747 restfreqidCol_.put(i,restFreqIDs);
1748 }
1749 ok = True;
1750 } else {
1751 ok = False;
1752 }
1753
1754 return ok;
1755}
1756
1757void SDMemTable::spectralLines() const
1758{
1759 Vector<String> lines = MeasTable::Lines();
1760 MFrequency lineFreq;
1761 Double freq;
1762
1763 cout.flags(std::ios_base::left);
1764 cout << "Line Frequency (Hz)" << endl;
1765 cout << "-----------------------" << endl;
1766 for (uInt i=0; i<lines.nelements(); i++) {
1767 MeasTable::Line(lineFreq, lines[i]);
1768 freq = lineFreq.getValue().getValue(); // Hz
1769 cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1770 }
1771}
1772
1773void SDMemTable::renumber()
1774{
1775 uInt nRow = scanCol_.nrow();
1776 Int newscanid = 0;
1777 Int cIdx;// the current scanid
1778 // get the first scanid
1779 scanCol_.getScalar(0,cIdx);
1780 Int pIdx = cIdx;// the scanid of the previous row
1781 for (uInt i=0; i<nRow;++i) {
1782 scanCol_.getScalar(i,cIdx);
1783 if (pIdx == cIdx) {
1784 // renumber
1785 scanCol_.put(i,newscanid);
1786 } else {
1787 ++newscanid;
1788 pIdx = cIdx; // store scanid
1789 --i; // don't increment next loop
1790 }
1791 }
1792}
1793
1794
1795void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1796 const IPosition& shape) const
1797{
1798 const uInt nDim = shape.nelements();
1799 start.resize(nDim);
1800 end.resize(nDim);
1801
1802 start(asap::BeamAxis) = beamSel_;
1803 end(asap::BeamAxis) = beamSel_;
1804 start(asap::IFAxis) = IFSel_;
1805 end(asap::IFAxis) = IFSel_;
1806
1807 start(asap::PolAxis) = polSel_;
1808 end(asap::PolAxis) = polSel_;
1809
1810 start(asap::ChanAxis) = 0;
1811 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1812}
1813
1814
1815std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1816 // Get spectrum at cursor location
1817{
1818
1819 // Setup accessors
1820 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1821 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1822
1823 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1824 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1825
1826 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1827 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1828
1829 std::vector<float> spectrum;
1830 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1831 spectrum.push_back(*i);
1832 }
1833 return spectrum;
1834}
1835
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