source: trunk/src/SDMemTable.cc@ 478

Last change on this file since 478 was 476, checked in by kil064, 20 years ago

move function convertInstrument to SDAttr
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 49.7 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/Quanta/MVAngle.h>
46
47#include <tables/Tables/TableParse.h>
48#include <tables/Tables/TableDesc.h>
49#include <tables/Tables/SetupNewTab.h>
50#include <tables/Tables/ScaColDesc.h>
51#include <tables/Tables/ArrColDesc.h>
52
53#include <tables/Tables/ExprNode.h>
54#include <tables/Tables/TableRecord.h>
55#include <measures/Measures/MFrequency.h>
56#include <measures/Measures/MeasTable.h>
57#include <coordinates/Coordinates/CoordinateUtil.h>
58#include <casa/Quanta/MVTime.h>
59#include <casa/Quanta/MVAngle.h>
60
61#include "SDDefs.h"
62#include "SDContainer.h"
63#include "MathUtils.h"
64#include "SDPol.h"
65#include "SDAttr.h"
66
67#include "SDMemTable.h"
68
69using namespace casa;
70using namespace asap;
71
72SDMemTable::SDMemTable() :
73 IFSel_(0),
74 beamSel_(0),
75 polSel_(0)
76{
77 setup();
78 attach();
79}
80
81SDMemTable::SDMemTable(const std::string& name) :
82 IFSel_(0),
83 beamSel_(0),
84 polSel_(0)
85{
86 Table tab(name);
87 table_ = tab.copyToMemoryTable("dummy");
88 //cerr << "hello from C SDMemTable @ " << this << endl;
89 attach();
90}
91
92SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
93{
94 IFSel_= other.IFSel_;
95 beamSel_= other.beamSel_;
96 polSel_= other.polSel_;
97 chanMask_ = other.chanMask_;
98 table_ = other.table_.copyToMemoryTable(String("dummy"));
99 // clear all rows()
100 if (clear) {
101 table_.removeRow(this->table_.rowNumbers());
102 } else {
103 IFSel_ = other.IFSel_;
104 beamSel_ = other.beamSel_;
105 polSel_ = other.polSel_;
106 }
107//
108 attach();
109 //cerr << "hello from CC SDMemTable @ " << this << endl;
110}
111
112SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
113 IFSel_(0),
114 beamSel_(0),
115 polSel_(0)
116{
117 Table t = tableCommand(exprs,tab);
118 if (t.nrow() == 0)
119 throw(AipsError("Query unsuccessful."));
120 table_ = t.copyToMemoryTable("dummy");
121 attach();
122 renumber();
123}
124
125SDMemTable::~SDMemTable()
126{
127 //cerr << "goodbye from SDMemTable @ " << this << endl;
128}
129
130SDMemTable SDMemTable::getScan(Int scanID) const
131{
132 String cond("SELECT * from $1 WHERE SCANID == ");
133 cond += String::toString(scanID);
134 return SDMemTable(table_, cond);
135}
136
137SDMemTable &SDMemTable::operator=(const SDMemTable& other)
138{
139 if (this != &other) {
140 IFSel_= other.IFSel_;
141 beamSel_= other.beamSel_;
142 polSel_= other.polSel_;
143 chanMask_.resize(0);
144 chanMask_ = other.chanMask_;
145 table_ = other.table_.copyToMemoryTable(String("dummy"));
146 attach();
147 }
148 //cerr << "hello from ASS SDMemTable @ " << this << endl;
149 return *this;
150}
151
152SDMemTable SDMemTable::getSource(const std::string& source) const
153{
154 String cond("SELECT * from $1 WHERE SRCNAME == ");
155 cond += source;
156 return SDMemTable(table_, cond);
157}
158
159void SDMemTable::setup()
160{
161 TableDesc td("", "1", TableDesc::Scratch);
162 td.comment() = "A SDMemTable";
163
164 td.addColumn(ScalarColumnDesc<Double>("TIME"));
165 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
166 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
167 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
168 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
169 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
170 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
171 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
172 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
173 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
174 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
175 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
176 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
177 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
178 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
179 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
180 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
181 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
182 td.addColumn(ArrayColumnDesc<String>("HISTORY"));
183 td.addColumn(ArrayColumnDesc<Int>("FITID"));
184
185
186 // Now create Table SetUp from the description.
187
188 SetupNewTable aNewTab("dummy", td, Table::New);
189
190 // Bind the Stokes Virtual machine to the STOKES column Because we
191 // don't know how many polarizations will be in the data at this
192 // point, we must bind the Virtual Engine regardless. The STOKES
193 // column won't be accessed if not appropriate (nPol=4)
194
195
196 SDStokesEngine::registerClass();
197 SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
198 aNewTab.bindColumn ("STOKES", stokesEngine);
199
200 // Create Table
201 table_ = Table(aNewTab, Table::Memory, 0);
202 // add subtable
203 TableDesc tdf("", "1", TableDesc::Scratch);
204 tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
205 tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
206 tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
207 tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
208 tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
209 SetupNewTable fittab("fits", tdf, Table::New);
210 Table fitTable(fittab, Table::Memory);
211 table_.rwKeywordSet().defineTable("FITS", fitTable);
212
213
214}
215
216void SDMemTable::attach()
217{
218 timeCol_.attach(table_, "TIME");
219 srcnCol_.attach(table_, "SRCNAME");
220 specCol_.attach(table_, "SPECTRA");
221 flagsCol_.attach(table_, "FLAGTRA");
222 tsCol_.attach(table_, "TSYS");
223 stokesCol_.attach(table_, "STOKES");
224 scanCol_.attach(table_, "SCANID");
225 integrCol_.attach(table_, "INTERVAL");
226 freqidCol_.attach(table_, "FREQID");
227 restfreqidCol_.attach(table_, "RESTFREQID");
228 dirCol_.attach(table_, "DIRECTION");
229 fldnCol_.attach(table_, "FIELDNAME");
230 tcaltCol_.attach(table_, "TCALTIME");
231 tcalCol_.attach(table_, "TCAL");
232 azCol_.attach(table_, "AZIMUTH");
233 elCol_.attach(table_, "ELEVATION");
234 paraCol_.attach(table_, "PARANGLE");
235 rbeamCol_.attach(table_, "REFBEAM");
236 histCol_.attach(table_, "HISTORY");
237 fitCol_.attach(table_,"FITID");
238}
239
240
241std::string SDMemTable::getSourceName(Int whichRow) const
242{
243 String name;
244 srcnCol_.get(whichRow, name);
245 return name;
246}
247
248std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
249{
250 Double tm;
251 if (whichRow > -1) {
252 timeCol_.get(whichRow, tm);
253 } else {
254 table_.keywordSet().get("UTC",tm);
255 }
256 MVTime mvt(tm);
257 if (showDate)
258 mvt.setFormat(MVTime::YMD);
259 else
260 mvt.setFormat(MVTime::TIME);
261 ostringstream oss;
262 oss << mvt;
263 return String(oss);
264}
265
266double SDMemTable::getInterval(Int whichRow) const
267{
268 Double intval;
269 integrCol_.get(whichRow, intval);
270 return intval;
271}
272
273bool SDMemTable::setIF(Int whichIF)
274{
275 if ( whichIF >= 0 && whichIF < nIF()) {
276 IFSel_ = whichIF;
277 return true;
278 }
279 return false;
280}
281
282bool SDMemTable::setBeam(Int whichBeam)
283{
284 if ( whichBeam >= 0 && whichBeam < nBeam()) {
285 beamSel_ = whichBeam;
286 return true;
287 }
288 return false;
289}
290
291bool SDMemTable::setPol(Int whichPol)
292{
293 if ( whichPol >= 0 && whichPol < nPol()) {
294 polSel_ = whichPol;
295 return true;
296 }
297 return false;
298}
299
300void SDMemTable::resetCursor()
301{
302 polSel_ = 0;
303 IFSel_ = 0;
304 beamSel_ = 0;
305}
306
307bool SDMemTable::setMask(std::vector<int> whichChans)
308{
309 std::vector<int>::iterator it;
310 uInt n = flagsCol_.shape(0)(3);
311 if (whichChans.empty()) {
312 chanMask_ = std::vector<bool>(n,true);
313 return true;
314 }
315 chanMask_.resize(n,true);
316 for (it = whichChans.begin(); it != whichChans.end(); ++it) {
317 if (*it < n) {
318 chanMask_[*it] = false;
319 }
320 }
321 return true;
322}
323
324std::vector<bool> SDMemTable::getMask(Int whichRow) const
325{
326
327 std::vector<bool> mask;
328
329 Array<uChar> arr;
330 flagsCol_.get(whichRow, arr);
331
332 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
333 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
334 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
335 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
336 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
337 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
338
339 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
340
341 std::vector<bool> tmp;
342 tmp = chanMask_; // WHY the fxxx do I have to make a copy here
343 std::vector<bool>::iterator miter;
344 miter = tmp.begin();
345
346 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
347 bool out =!static_cast<bool>(*i);
348 if (useUserMask) {
349 out = out && (*miter);
350 miter++;
351 }
352 mask.push_back(out);
353 }
354 return mask;
355}
356
357
358
359std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
360{
361
362 Array<Float> arr;
363 specCol_.get(whichRow, arr);
364 return getFloatSpectrum(arr);
365}
366
367std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow, Bool doPol,
368 Float paOffset) const
369//
370// Gets one STokes parameter depending on cursor polSel location
371// doPol=False : I,Q,U,V
372// doPol=True : I,P,PA,V ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
373//
374{
375 AlwaysAssert(asap::nAxes==4,AipsError);
376 if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
377 throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
378 }
379 Array<Float> arr;
380 stokesCol_.get(whichRow, arr);
381
382 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
383
384 // Set current cursor location
385 const IPosition& shape = arr.shape();
386 IPosition start, end;
387 setCursorSlice (start, end, shape);
388
389 // Get Q and U slices
390
391 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
392 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
393
394 // Compute output
395
396 Array<Float> out;
397 if (polSel_==1) { // P
398 out = SDPolUtil::polarizedIntensity(Q,U);
399 } else if (polSel_==2) { // P.A.
400 out = SDPolUtil::positionAngle(Q,U) + paOffset;
401 }
402
403 // Copy to output
404
405 IPosition vecShape(1,shape(asap::ChanAxis));
406 Vector<Float> outV = out.reform(vecShape);
407 std::vector<float> stlout;
408 outV.tovector(stlout);
409 return stlout;
410
411 } else {
412
413 // Selects at the cursor location
414 return getFloatSpectrum(arr);
415 }
416}
417
418std::vector<float> SDMemTable::getCircularSpectrum(Int whichRow,
419 Bool doRR) const
420 // Gets
421 // RR = I + V
422 // LL = I - V
423{
424 AlwaysAssert(asap::nAxes==4,AipsError);
425 if (nPol()!=4) {
426 throw (AipsError("You must have 4 polarizations to get RR or LL"));
427 }
428 Array<Float> arr;
429 stokesCol_.get(whichRow, arr);
430
431 // Set current cursor location
432
433 const IPosition& shape = arr.shape();
434 IPosition start, end;
435 setCursorSlice(start, end, shape);
436
437 // Get I and V slices
438
439 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
440 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
441
442 // Compute output
443
444 Array<Float> out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
445
446 // Copy to output
447
448 IPosition vecShape(1,shape(asap::ChanAxis));
449 Vector<Float> outV = out.reform(vecShape);
450 std::vector<float> stlout;
451 outV.tovector(stlout);
452
453 return stlout;
454}
455
456Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
457{
458
459// Get data
460
461 Array<Float> arr;
462 stokesCol_.get(whichRow, arr);
463
464// Set current cursor location and overwrite polarization axis
465
466 const IPosition& shape = arr.shape();
467 IPosition start(shape.nelements(),0);
468 IPosition end(shape-1);
469 if (iBeam!=-1) {
470 start(asap::BeamAxis) = iBeam;
471 end(asap::BeamAxis) = iBeam;
472 }
473 if (iIF!=-1) {
474 start(asap::IFAxis) = iIF;
475 end(asap::IFAxis) = iIF;
476 }
477
478// Get slice
479
480 return arr(start,end);
481}
482
483
484std::vector<string> SDMemTable::getCoordInfo() const
485{
486 String un;
487 Table t = table_.keywordSet().asTable("FREQUENCIES");
488 String sunit;
489 t.keywordSet().get("UNIT",sunit);
490 String dpl;
491 t.keywordSet().get("DOPPLER",dpl);
492 if (dpl == "") dpl = "RADIO";
493 String rfrm;
494 t.keywordSet().get("REFFRAME",rfrm);
495 std::vector<string> inf;
496 inf.push_back(sunit);
497 inf.push_back(rfrm);
498 inf.push_back(dpl);
499 t.keywordSet().get("BASEREFFRAME",rfrm);
500 inf.push_back(rfrm);
501 return inf;
502}
503
504void SDMemTable::setCoordInfo(std::vector<string> theinfo)
505{
506 std::vector<string>::iterator it;
507 String un,rfrm, brfrm,dpl;
508 un = theinfo[0]; // Abcissa unit
509 rfrm = theinfo[1]; // Active (or conversion) frame
510 dpl = theinfo[2]; // Doppler
511 brfrm = theinfo[3]; // Base frame
512
513 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
514
515 Vector<Double> rstf;
516 t.keywordSet().get("RESTFREQS",rstf);
517
518 Bool canDo = True;
519 Unit u1("km/s");Unit u2("Hz");
520 if (Unit(un) == u1) {
521 Vector<Double> rstf;
522 t.keywordSet().get("RESTFREQS",rstf);
523 if (rstf.nelements() == 0) {
524 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
525 }
526 } else if (Unit(un) != u2 && un != "") {
527 throw(AipsError("Unit not conformant with Spectral Coordinates"));
528 }
529 t.rwKeywordSet().define("UNIT", un);
530
531 MFrequency::Types mdr;
532 if (!MFrequency::getType(mdr, rfrm)) {
533
534 Int a,b;const uInt* c;
535 const String* valid = MFrequency::allMyTypes(a, b, c);
536 String pfix = "Please specify a legal frame type. Types are\n";
537 throw(AipsError(pfix+(*valid)));
538 } else {
539 t.rwKeywordSet().define("REFFRAME",rfrm);
540 }
541
542 MDoppler::Types dtype;
543 dpl.upcase();
544 if (!MDoppler::getType(dtype, dpl)) {
545 throw(AipsError("Doppler type unknown"));
546 } else {
547 t.rwKeywordSet().define("DOPPLER",dpl);
548 }
549
550 if (!MFrequency::getType(mdr, brfrm)) {
551 Int a,b;const uInt* c;
552 const String* valid = MFrequency::allMyTypes(a, b, c);
553 String pfix = "Please specify a legal frame type. Types are\n";
554 throw(AipsError(pfix+(*valid)));
555 } else {
556 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
557 }
558}
559
560
561std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
562{
563 std::vector<double> abc(nChan());
564
565 // Get header units keyword
566 Table t = table_.keywordSet().asTable("FREQUENCIES");
567 String sunit;
568 t.keywordSet().get("UNIT",sunit);
569 if (sunit == "") sunit = "pixel";
570 Unit u(sunit);
571
572 // Easy if just wanting pixels
573 if (sunit==String("pixel")) {
574 // assume channels/pixels
575 std::vector<double>::iterator it;
576 uInt i=0;
577 for (it = abc.begin(); it != abc.end(); ++it) {
578 (*it) = Double(i++);
579 }
580 return abc;
581 }
582
583 // Continue with km/s or Hz. Get FreqIDs
584 Vector<uInt> freqIDs;
585 freqidCol_.get(whichRow, freqIDs);
586 uInt freqID = freqIDs(IFSel_);
587 restfreqidCol_.get(whichRow, freqIDs);
588 uInt restFreqID = freqIDs(IFSel_);
589
590 // Get SpectralCoordinate, set reference frame conversion,
591 // velocity conversion, and rest freq state
592
593 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
594 Vector<Double> pixel(nChan());
595 indgen(pixel);
596
597 if (u == Unit("km/s")) {
598 Vector<Double> world;
599 spc.pixelToVelocity(world,pixel);
600 std::vector<double>::iterator it;
601 uInt i = 0;
602 for (it = abc.begin(); it != abc.end(); ++it) {
603 (*it) = world[i];
604 i++;
605 }
606 } else if (u == Unit("Hz")) {
607
608 // Set world axis units
609 Vector<String> wau(1); wau = u.getName();
610 spc.setWorldAxisUnits(wau);
611
612 std::vector<double>::iterator it;
613 Double tmp;
614 uInt i = 0;
615 for (it = abc.begin(); it != abc.end(); ++it) {
616 spc.toWorld(tmp,pixel[i]);
617 (*it) = tmp;
618 i++;
619 }
620 }
621 return abc;
622}
623
624std::string SDMemTable::getAbcissaString(Int whichRow) const
625{
626 Table t = table_.keywordSet().asTable("FREQUENCIES");
627
628 String sunit;
629 t.keywordSet().get("UNIT",sunit);
630 if (sunit == "") sunit = "pixel";
631 Unit u(sunit);
632
633 Vector<uInt> freqIDs;
634 freqidCol_.get(whichRow, freqIDs);
635 uInt freqID = freqIDs(IFSel_);
636 restfreqidCol_.get(whichRow, freqIDs);
637 uInt restFreqID = freqIDs(IFSel_);
638
639 // Get SpectralCoordinate, with frame, velocity, rest freq state set
640 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
641
642 String s = "Channel";
643 if (u == Unit("km/s")) {
644 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
645 } else if (u == Unit("Hz")) {
646 Vector<String> wau(1);wau = u.getName();
647 spc.setWorldAxisUnits(wau);
648
649 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
650 }
651 return s;
652}
653
654void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
655{
656 Array<Float> arr;
657 specCol_.get(whichRow, arr);
658 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
659 throw(AipsError("Attempting to set spectrum with incorrect length."));
660 }
661
662 // Setup accessors
663 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
664 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
665 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
666 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
667 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
668 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
669
670 // Iterate
671 std::vector<float>::iterator it = spectrum.begin();
672 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
673 (*i) = Float(*it);
674 it++;
675 }
676 specCol_.put(whichRow, arr);
677}
678
679void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
680{
681 Array<Float> arr;
682 specCol_.get(whichRow, arr);
683
684 // Iterate and extract
685 spectrum.resize(arr.shape()(3));
686 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
687 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
688 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
689 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
690 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
691 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
692
693 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
694 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
695 (*va) = (*i);
696 va++;
697 }
698}
699
700
701/*
702void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
703 Array<uChar> arr;
704 flagsCol_.get(whichRow, arr);
705 mask.resize(arr.shape()(3));
706
707 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
708 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
709 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
710 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
711 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
712 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
713
714 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
715
716 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
717 std::vector<bool> tmp;
718 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
719 // iterator should work on chanMask_??
720 std::vector<bool>::iterator miter;
721 miter = tmp.begin();
722
723 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
724 bool out =!static_cast<bool>(*i);
725 if (useUserMask) {
726 out = out && (*miter);
727 miter++;
728 }
729 (*va) = out;
730 va++;
731 }
732}
733*/
734
735MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
736 Bool toStokes) const
737{
738 // Get flags
739 Array<uChar> farr;
740 flagsCol_.get(whichRow, farr);
741
742 // Get data and convert mask to Bool
743 Array<Float> arr;
744 Array<Bool> mask;
745 if (toStokes) {
746 stokesCol_.get(whichRow, arr);
747
748 Array<Bool> tMask(farr.shape());
749 convertArray(tMask, farr);
750 mask = SDPolUtil::stokesData (tMask, True);
751 } else {
752 specCol_.get(whichRow, arr);
753 mask.resize(farr.shape());
754 convertArray(mask, farr);
755 }
756
757 return MaskedArray<Float>(arr,!mask);
758}
759
760Float SDMemTable::getTsys(Int whichRow) const
761{
762 Array<Float> arr;
763 tsCol_.get(whichRow, arr);
764 Float out;
765
766 IPosition ip(arr.shape());
767 ip(asap::BeamAxis) = beamSel_;
768 ip(asap::IFAxis) = IFSel_;
769 ip(asap::PolAxis) = polSel_;
770 ip(asap::ChanAxis)=0; // First channel only
771
772 out = arr(ip);
773 return out;
774}
775
776MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
777{
778 MDirection::Types mdr = getDirectionReference();
779 Array<Double> posit;
780 dirCol_.get(whichRow,posit);
781 Vector<Double> wpos(2);
782 Int rb;
783 rbeamCol_.get(whichRow,rb);
784 wpos[0] = posit(IPosition(2,beamSel_,0));
785 wpos[1] = posit(IPosition(2,beamSel_,1));
786 if (refBeam && rb > -1) { // use refBeam instead if it exists
787 wpos[0] = posit(IPosition(2,rb,0));
788 wpos[1] = posit(IPosition(2,rb,1));
789 }
790
791 Quantum<Double> lon(wpos[0],Unit(String("rad")));
792 Quantum<Double> lat(wpos[1],Unit(String("rad")));
793 return MDirection(lon, lat, mdr);
794}
795
796MEpoch SDMemTable::getEpoch(Int whichRow) const
797{
798 MEpoch::Types met = getTimeReference();
799
800 Double obstime;
801 timeCol_.get(whichRow,obstime);
802 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
803 return MEpoch(tm2, met);
804}
805
806MPosition SDMemTable::getAntennaPosition () const
807{
808 Vector<Double> antpos;
809 table_.keywordSet().get("AntennaPosition", antpos);
810 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
811 return MPosition(mvpos);
812}
813
814
815SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
816{
817
818 Table t = table_.keywordSet().asTable("FREQUENCIES");
819 if (freqID> t.nrow() ) {
820 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
821 }
822
823 Double rp,rv,inc;
824 String rf;
825 ROScalarColumn<Double> rpc(t, "REFPIX");
826 ROScalarColumn<Double> rvc(t, "REFVAL");
827 ROScalarColumn<Double> incc(t, "INCREMENT");
828 t.keywordSet().get("BASEREFFRAME",rf);
829
830 // Create SpectralCoordinate (units Hz)
831 MFrequency::Types mft;
832 if (!MFrequency::getType(mft, rf)) {
833 cerr << "Frequency type unknown assuming TOPO" << endl;
834 mft = MFrequency::TOPO;
835 }
836 rpc.get(freqID, rp);
837 rvc.get(freqID, rv);
838 incc.get(freqID, inc);
839
840 SpectralCoordinate spec(mft,rv,inc,rp);
841 return spec;
842}
843
844
845SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
846 uInt restFreqID,
847 uInt whichRow) const
848{
849
850 // Create basic SC
851 SpectralCoordinate spec = getSpectralCoordinate (freqID);
852
853 Table t = table_.keywordSet().asTable("FREQUENCIES");
854
855 // Set rest frequency
856 Vector<Double> restFreqIDs;
857 t.keywordSet().get("RESTFREQS",restFreqIDs);
858 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
859 spec.setRestFrequency(restFreqIDs(restFreqID),True);
860 }
861
862 // Set up frame conversion layer
863 String frm;
864 t.keywordSet().get("REFFRAME",frm);
865 if (frm == "") frm = "TOPO";
866 MFrequency::Types mtype;
867 if (!MFrequency::getType(mtype, frm)) {
868 // Should never happen
869 cerr << "Frequency type unknown assuming TOPO" << endl;
870 mtype = MFrequency::TOPO;
871 }
872
873 // Set reference frame conversion (requires row)
874 MDirection dir = getDirection(whichRow);
875 MEpoch epoch = getEpoch(whichRow);
876 MPosition pos = getAntennaPosition();
877
878 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
879 throw(AipsError("Couldn't convert frequency frame."));
880 }
881
882 // Now velocity conversion if appropriate
883 String unitStr;
884 t.keywordSet().get("UNIT",unitStr);
885
886 String dpl;
887 t.keywordSet().get("DOPPLER",dpl);
888 MDoppler::Types dtype;
889 MDoppler::getType(dtype, dpl);
890
891 // Only set velocity unit if non-blank and non-Hz
892 if (!unitStr.empty()) {
893 Unit unitU(unitStr);
894 if (unitU==Unit("Hz")) {
895 } else {
896 spec.setVelocity(unitStr, dtype);
897 }
898 }
899
900 return spec;
901}
902
903
904Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
905 uInt freqID) {
906 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
907 if (freqID > t.nrow() ) {
908 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
909 }
910 ScalarColumn<Double> rpc(t, "REFPIX");
911 ScalarColumn<Double> rvc(t, "REFVAL");
912 ScalarColumn<Double> incc(t, "INCREMENT");
913
914 rpc.put(freqID, speccord.referencePixel()[0]);
915 rvc.put(freqID, speccord.referenceValue()[0]);
916 incc.put(freqID, speccord.increment()[0]);
917
918 return True;
919}
920
921Int SDMemTable::nCoordinates() const
922{
923 return table_.keywordSet().asTable("FREQUENCIES").nrow();
924}
925
926
927std::vector<double> SDMemTable::getRestFreqs() const
928{
929 Table t = table_.keywordSet().asTable("FREQUENCIES");
930 Vector<Double> tvec;
931 t.keywordSet().get("RESTFREQS",tvec);
932 std::vector<double> stlout;
933 tvec.tovector(stlout);
934 return stlout;
935}
936
937bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
938{
939 TableDesc td("", "1", TableDesc::Scratch);
940 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
941 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
942 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
943 SetupNewTable aNewTab("freqs", td, Table::New);
944 Table aTable (aNewTab, Table::Memory, sdft.length());
945 ScalarColumn<Double> sc0(aTable, "REFPIX");
946 ScalarColumn<Double> sc1(aTable, "REFVAL");
947 ScalarColumn<Double> sc2(aTable, "INCREMENT");
948 for (uInt i=0; i < sdft.length(); ++i) {
949 sc0.put(i,sdft.referencePixel(i));
950 sc1.put(i,sdft.referenceValue(i));
951 sc2.put(i,sdft.increment(i));
952 }
953 String rf = sdft.refFrame();
954 if (rf.contains("TOPO")) rf = "TOPO";
955
956 aTable.rwKeywordSet().define("BASEREFFRAME", rf);
957 aTable.rwKeywordSet().define("REFFRAME", rf);
958 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
959 aTable.rwKeywordSet().define("UNIT", String(""));
960 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
961 Vector<Double> rfvec;
962 String rfunit;
963 sdft.restFrequencies(rfvec,rfunit);
964 Quantum<Vector<Double> > q(rfvec, rfunit);
965 rfvec.resize();
966 rfvec = q.getValue("Hz");
967 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
968 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
969 return true;
970}
971
972bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
973{
974 TableDesc td("", "1", TableDesc::Scratch);
975 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
976 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
977 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
978 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
979 td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
980 SetupNewTable aNewTab("fits", td, Table::New);
981 Table aTable(aNewTab, Table::Memory);
982 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
983 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
984 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
985 ArrayColumn<Bool> sc3(aTable, "PARMASK");
986 ArrayColumn<String> sc4(aTable, "FRAMEINFO");
987 for (uInt i; i<sdft.length(); ++i) {
988 const Vector<Double>& parms = sdft.getParameters(i);
989 const Vector<Bool>& parmask = sdft.getParameterMask(i);
990 const Vector<String>& funcs = sdft.getFunctions(i);
991 const Vector<Int>& comps = sdft.getComponents(i);
992 const Vector<String>& finfo = sdft.getFrameInfo(i);
993 sc0.put(i,funcs);
994 sc1.put(i,comps);
995 sc3.put(i,parmask);
996 sc2.put(i,parms);
997 sc4.put(i,finfo);
998 }
999 table_.rwKeywordSet().defineTable("FITS", aTable);
1000 return true;
1001}
1002
1003SDFitTable SDMemTable::getSDFitTable() const
1004{
1005 const Table& t = table_.keywordSet().asTable("FITS");
1006 Vector<Double> parms;
1007 Vector<Bool> parmask;
1008 Vector<String> funcs;
1009 Vector<String> finfo;
1010 Vector<Int> comps;
1011 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1012 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1013 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1014 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1015 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1016 uInt n = t.nrow();
1017 SDFitTable sdft;
1018 for (uInt i=0; i<n; ++i) {
1019 parmaskCol.get(i, parmask);
1020 parmsCol.get(i, parms);
1021 funcsCol.get(i, funcs);
1022 compsCol.get(i, comps);
1023 finfoCol.get(i, finfo);
1024 sdft.addFit(parms, parmask, funcs, comps, finfo);
1025 }
1026 return sdft;
1027}
1028
1029SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1030 Array<Int> fitid;
1031 fitCol_.get(whichRow, fitid);
1032 if (fitid.nelements() == 0) return SDFitTable();
1033
1034 IPosition shp = fitid.shape();
1035 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1036 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1037
1038 // reform the output array slice to be of dim=1
1039 Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1040
1041 const Table& t = table_.keywordSet().asTable("FITS");
1042 Vector<Double> parms;
1043 Vector<Bool> parmask;
1044 Vector<String> funcs;
1045 Vector<String> finfo;
1046 Vector<Int> comps;
1047 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1048 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1049 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1050 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1051 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1052 if (t.nrow() == 0) return SDFitTable();
1053 SDFitTable sdft;
1054 Int k=-1;
1055 for (uInt i=0; i< tmp.nelements(); ++i) {
1056 k = tmp[i];
1057 if ( k > -1 && k < t.nrow() ) {
1058 parms.resize();
1059 parmsCol.get(k, parms);
1060 parmask.resize();
1061 parmaskCol.get(k, parmask);
1062 funcs.resize();
1063 funcsCol.get(k, funcs);
1064 comps.resize();
1065 compsCol.get(k, comps);
1066 finfo.resize();
1067 finfoCol.get(k, finfo);
1068 sdft.addFit(parms, parmask, funcs, comps, finfo);
1069 }
1070 }
1071 return sdft;
1072}
1073
1074void SDMemTable::addFit(uInt whichRow,
1075 const Vector<Double>& p, const Vector<Bool>& m,
1076 const Vector<String>& f, const Vector<Int>& c)
1077{
1078 if (whichRow >= nRow()) {
1079 throw(AipsError("Specified row out of range"));
1080 }
1081 Table t = table_.keywordSet().asTable("FITS");
1082 uInt nrow = t.nrow();
1083 t.addRow();
1084 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1085 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1086 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1087 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1088 ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1089 parmsCol.put(nrow, p);
1090 parmaskCol.put(nrow, m);
1091 compsCol.put(nrow, c);
1092 funcsCol.put(nrow, f);
1093 Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1094 finfoCol.put(nrow, fi);
1095
1096 Array<Int> fitarr;
1097 fitCol_.get(whichRow, fitarr);
1098
1099 Array<Int> newarr; // The new Array containing the fitid
1100 Int pos =-1; // The fitid position in the array
1101 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1102 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1103 arr = -1;
1104 newarr.reference(arr);
1105 pos = 0;
1106 } else {
1107 IPosition shp = fitarr.shape();
1108 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1109 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1110 // reform the output array slice to be of dim=1
1111 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1112 const Vector<Int>& fits = tmp;
1113 VectorSTLIterator<Int> it(fits);
1114 Int i = 0;
1115 while (it != fits.end()) {
1116 if (*it == -1) {
1117 pos = i;
1118 break;
1119 }
1120 ++i;
1121 ++it;
1122 };
1123 }
1124 if (pos == -1) {
1125 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1126 pos = fitarr.shape()[3]; // the new element position
1127 } else {
1128 if (fitarr.nelements() > 0)
1129 newarr = fitarr;
1130 }
1131 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1132 fitCol_.put(whichRow, newarr);
1133
1134}
1135
1136SDFrequencyTable SDMemTable::getSDFreqTable() const
1137{
1138 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1139 SDFrequencyTable sdft;
1140
1141 // Add refpix/refval/incr. What are the units ? Hz I suppose
1142 // but it's nowhere described...
1143 Vector<Double> refPix, refVal, incr;
1144 ScalarColumn<Double> refPixCol(t, "REFPIX");
1145 ScalarColumn<Double> refValCol(t, "REFVAL");
1146 ScalarColumn<Double> incrCol(t, "INCREMENT");
1147 refPix = refPixCol.getColumn();
1148 refVal = refValCol.getColumn();
1149 incr = incrCol.getColumn();
1150
1151 uInt n = refPix.nelements();
1152 for (uInt i=0; i<n; i++) {
1153 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1154 }
1155
1156 // Frequency reference frame. I don't know if this
1157 // is the correct frame. It might be 'REFFRAME'
1158 // rather than 'BASEREFFRAME' ?
1159 String baseFrame;
1160 t.keywordSet().get("BASEREFFRAME",baseFrame);
1161 sdft.setRefFrame(baseFrame);
1162
1163 // Equinox
1164 Float equinox;
1165 t.keywordSet().get("EQUINOX", equinox);
1166 sdft.setEquinox(equinox);
1167
1168 // Rest Frequency
1169 Vector<Double> restFreqs;
1170 t.keywordSet().get("RESTFREQS", restFreqs);
1171 for (uInt i=0; i<restFreqs.nelements(); i++) {
1172 sdft.addRestFrequency(restFreqs[i]);
1173 }
1174 sdft.setRestFrequencyUnit(String("Hz"));
1175
1176 return sdft;
1177}
1178
1179bool SDMemTable::putSDContainer(const SDContainer& sdc)
1180{
1181 uInt rno = table_.nrow();
1182 table_.addRow();
1183
1184 timeCol_.put(rno, sdc.timestamp);
1185 srcnCol_.put(rno, sdc.sourcename);
1186 fldnCol_.put(rno, sdc.fieldname);
1187 specCol_.put(rno, sdc.getSpectrum());
1188 flagsCol_.put(rno, sdc.getFlags());
1189 tsCol_.put(rno, sdc.getTsys());
1190 scanCol_.put(rno, sdc.scanid);
1191 integrCol_.put(rno, sdc.interval);
1192 freqidCol_.put(rno, sdc.getFreqMap());
1193 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1194 dirCol_.put(rno, sdc.getDirection());
1195 rbeamCol_.put(rno, sdc.refbeam);
1196 tcalCol_.put(rno, sdc.tcal);
1197 tcaltCol_.put(rno, sdc.tcaltime);
1198 azCol_.put(rno, sdc.azimuth);
1199 elCol_.put(rno, sdc.elevation);
1200 paraCol_.put(rno, sdc.parangle);
1201 histCol_.put(rno, sdc.getHistory());
1202 fitCol_.put(rno, sdc.getFitMap());
1203 return true;
1204}
1205
1206SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1207{
1208 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1209 timeCol_.get(whichRow, sdc.timestamp);
1210 srcnCol_.get(whichRow, sdc.sourcename);
1211 integrCol_.get(whichRow, sdc.interval);
1212 scanCol_.get(whichRow, sdc.scanid);
1213 fldnCol_.get(whichRow, sdc.fieldname);
1214 rbeamCol_.get(whichRow, sdc.refbeam);
1215 azCol_.get(whichRow, sdc.azimuth);
1216 elCol_.get(whichRow, sdc.elevation);
1217 paraCol_.get(whichRow, sdc.parangle);
1218 Vector<Float> tc;
1219 tcalCol_.get(whichRow, tc);
1220 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1221 tcaltCol_.get(whichRow, sdc.tcaltime);
1222
1223 Array<Float> spectrum;
1224 Array<Float> tsys;
1225 Array<uChar> flagtrum;
1226 Vector<uInt> fmap;
1227 Array<Double> direction;
1228 Vector<String> histo;
1229 Array<Int> fits;
1230
1231 specCol_.get(whichRow, spectrum);
1232 sdc.putSpectrum(spectrum);
1233 flagsCol_.get(whichRow, flagtrum);
1234 sdc.putFlags(flagtrum);
1235 tsCol_.get(whichRow, tsys);
1236 sdc.putTsys(tsys);
1237 freqidCol_.get(whichRow, fmap);
1238 sdc.putFreqMap(fmap);
1239 restfreqidCol_.get(whichRow, fmap);
1240 sdc.putRestFreqMap(fmap);
1241 dirCol_.get(whichRow, direction);
1242 sdc.putDirection(direction);
1243 histCol_.get(whichRow, histo);
1244 sdc.putHistory(histo);
1245 fitCol_.get(whichRow, fits);
1246 sdc.putFitMap(fits);
1247 return sdc;
1248}
1249
1250bool SDMemTable::putSDHeader(const SDHeader& sdh)
1251{
1252 table_.rwKeywordSet().define("nIF", sdh.nif);
1253 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
1254 table_.rwKeywordSet().define("nPol", sdh.npol);
1255 table_.rwKeywordSet().define("nChan", sdh.nchan);
1256 table_.rwKeywordSet().define("Observer", sdh.observer);
1257 table_.rwKeywordSet().define("Project", sdh.project);
1258 table_.rwKeywordSet().define("Obstype", sdh.obstype);
1259 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
1260 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
1261 table_.rwKeywordSet().define("Equinox", sdh.equinox);
1262 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
1263 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
1264 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
1265 table_.rwKeywordSet().define("UTC", sdh.utc);
1266 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
1267 table_.rwKeywordSet().define("Epoch", sdh.epoch);
1268 return true;
1269}
1270
1271SDHeader SDMemTable::getSDHeader() const
1272{
1273 SDHeader sdh;
1274 table_.keywordSet().get("nBeam",sdh.nbeam);
1275 table_.keywordSet().get("nIF",sdh.nif);
1276 table_.keywordSet().get("nPol",sdh.npol);
1277 table_.keywordSet().get("nChan",sdh.nchan);
1278 table_.keywordSet().get("Observer", sdh.observer);
1279 table_.keywordSet().get("Project", sdh.project);
1280 table_.keywordSet().get("Obstype", sdh.obstype);
1281 table_.keywordSet().get("AntennaName", sdh.antennaname);
1282 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
1283 table_.keywordSet().get("Equinox", sdh.equinox);
1284 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
1285 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
1286 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
1287 table_.keywordSet().get("UTC", sdh.utc);
1288 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
1289 table_.keywordSet().get("Epoch", sdh.epoch);
1290 return sdh;
1291}
1292void SDMemTable::makePersistent(const std::string& filename)
1293{
1294 table_.deepCopy(filename,Table::New);
1295}
1296
1297Int SDMemTable::nScan() const {
1298 Int n = 0;
1299 Int previous = -1;Int current=0;
1300 for (uInt i=0; i< scanCol_.nrow();i++) {
1301 scanCol_.getScalar(i,current);
1302 if (previous != current) {
1303 previous = current;
1304 n++;
1305 }
1306 }
1307 return n;
1308}
1309
1310String SDMemTable::formatSec(Double x) const
1311{
1312 Double xcop = x;
1313 MVTime mvt(xcop/24./3600.); // make days
1314
1315 if (x < 59.95)
1316 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1317 else if (x < 3599.95)
1318 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1319 else {
1320 ostringstream oss;
1321 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1322 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1323 return String(oss);
1324 }
1325};
1326
1327String SDMemTable::formatDirection(const MDirection& md) const
1328{
1329 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1330 Int prec = 7;
1331
1332 MVAngle mvLon(t[0]);
1333 String sLon = mvLon.string(MVAngle::TIME,prec);
1334 MVAngle mvLat(t[1]);
1335 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1336 return sLon + String(" ") + sLat;
1337}
1338
1339
1340std::string SDMemTable::getFluxUnit() const
1341{
1342 String tmp;
1343 table_.keywordSet().get("FluxUnit", tmp);
1344 return tmp;
1345}
1346
1347void SDMemTable::setFluxUnit(const std::string& unit)
1348{
1349 String tmp(unit);
1350 Unit tU(tmp);
1351 if (tU==Unit("K") || tU==Unit("Jy")) {
1352 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1353 } else {
1354 throw AipsError("Illegal unit - must be compatible with Jy or K");
1355 }
1356}
1357
1358
1359void SDMemTable::setInstrument(const std::string& name)
1360{
1361 Bool throwIt = True;
1362 Instrument ins = SDAttr::convertInstrument(name, throwIt);
1363 String nameU(name);
1364 nameU.upcase();
1365 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1366}
1367
1368std::string SDMemTable::summary(bool verbose) const {
1369
1370 // Format header info
1371 ostringstream oss;
1372 oss << endl;
1373 oss << "--------------------------------------------------------------------------------" << endl;
1374 oss << " Scan Table Summary" << endl;
1375 oss << "--------------------------------------------------------------------------------" << endl;
1376 oss.flags(std::ios_base::left);
1377 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1378 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1379 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1380 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1381 oss << endl;
1382 String tmp;
1383 table_.keywordSet().get("Observer", tmp);
1384 oss << setw(15) << "Observer:" << tmp << endl;
1385 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1386 table_.keywordSet().get("Project", tmp);
1387 oss << setw(15) << "Project:" << tmp << endl;
1388 table_.keywordSet().get("Obstype", tmp);
1389 oss << setw(15) << "Obs. Type:" << tmp << endl;
1390 table_.keywordSet().get("AntennaName", tmp);
1391 oss << setw(15) << "Antenna Name:" << tmp << endl;
1392 table_.keywordSet().get("FluxUnit", tmp);
1393 oss << setw(15) << "Flux Unit:" << tmp << endl;
1394 Table t = table_.keywordSet().asTable("FREQUENCIES");
1395 Vector<Double> vec;
1396 t.keywordSet().get("RESTFREQS",vec);
1397 oss << setw(15) << "Rest Freqs:";
1398 if (vec.nelements() > 0) {
1399 oss << setprecision(0) << vec << " [Hz]" << endl;
1400 } else {
1401 oss << "None set" << endl;
1402 }
1403 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1404 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1405 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1406 oss << endl;
1407
1408 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1409 oss << setw(5) << "Scan"
1410 << setw(15) << "Source"
1411 << setw(24) << dirtype
1412 << setw(10) << "Time"
1413 << setw(18) << "Integration"
1414 << setw(7) << "FreqIDs" << endl;
1415 oss << "--------------------------------------------------------------------------------" << endl;
1416
1417 // Generate list of scan start and end integrations
1418 Vector<Int> scanIDs = scanCol_.getColumn();
1419 Vector<uInt> startInt, endInt;
1420 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1421
1422 const uInt nScans = startInt.nelements();
1423 String name;
1424 Vector<uInt> freqIDs, listFQ;
1425 uInt nInt;
1426
1427 for (uInt i=0; i<nScans; i++) {
1428 // Get things from first integration of scan
1429 String time = getTime(startInt(i),False);
1430 String tInt = formatSec(Double(getInterval(startInt(i))));
1431 String posit = formatDirection(getDirection(startInt(i),True));
1432 srcnCol_.getScalar(startInt(i),name);
1433
1434 // Find all the FreqIDs in this scan
1435 listFQ.resize(0);
1436 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1437 freqidCol_.get(j, freqIDs);
1438 for (uInt k=0; k<freqIDs.nelements(); k++) {
1439 mathutil::addEntry(listFQ, freqIDs(k));
1440 }
1441 }
1442
1443 nInt = endInt(i) - startInt(i) + 1;
1444 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1445 << setw(15) << name
1446 << setw(24) << posit
1447 << setw(10) << time
1448 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1449 << setw(6) << tInt
1450 << " " << listFQ << endl;
1451 }
1452 oss << endl;
1453 oss << "Table contains " << table_.nrow() << " integration(s) in "
1454 << nScans << " scan(s)." << endl;
1455
1456 // Frequency Table
1457 if (verbose) {
1458 std::vector<string> info = getCoordInfo();
1459 SDFrequencyTable sdft = getSDFreqTable();
1460 oss << endl << endl;
1461 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1462 oss << "--------------------------------------------------------------------------------" << endl;
1463 for (uInt i=0; i<sdft.length(); i++) {
1464 oss << setw(8) << i << setw(8)
1465 << info[3] << setw(16) << setprecision(8)
1466 << sdft.referenceValue(i) << setw(10)
1467 << sdft.referencePixel(i) << setw(12)
1468 << sdft.increment(i) << endl;
1469 }
1470 oss << "--------------------------------------------------------------------------------" << endl;
1471 }
1472 return String(oss);
1473}
1474
1475Int SDMemTable::nBeam() const
1476{
1477 Int n;
1478 table_.keywordSet().get("nBeam",n);
1479 return n;
1480}
1481
1482Int SDMemTable::nIF() const {
1483 Int n;
1484 table_.keywordSet().get("nIF",n);
1485 return n;
1486}
1487
1488Int SDMemTable::nPol() const {
1489 Int n;
1490 table_.keywordSet().get("nPol",n);
1491 return n;
1492}
1493
1494Int SDMemTable::nChan() const {
1495 Int n;
1496 table_.keywordSet().get("nChan",n);
1497 return n;
1498}
1499
1500bool SDMemTable::appendHistory(const std::string& hist, int whichRow)
1501{
1502 Vector<String> history;
1503 histCol_.get(whichRow, history);
1504 history.resize(history.nelements()+1,True);
1505 history[history.nelements()-1] = hist;
1506 histCol_.put(whichRow, history);
1507}
1508
1509std::vector<std::string> SDMemTable::history(int whichRow) const
1510{
1511 Vector<String> history;
1512 histCol_.get(whichRow, history);
1513 std::vector<std::string> stlout = mathutil::tovectorstring(history);
1514 return stlout;
1515}
1516/*
1517void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1518
1519 std::vector<int>::iterator it;
1520 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1521 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1522 j.reset(j.begin(uInt(*it)));
1523 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1524 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1525 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1526 iii != iii.end(); ++iii) {
1527 (*iii) =
1528 }
1529 }
1530 }
1531 }
1532
1533}
1534*/
1535void SDMemTable::flag(int whichRow)
1536{
1537 Array<uChar> arr;
1538 flagsCol_.get(whichRow, arr);
1539
1540 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1541 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1542 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1543 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1544 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1545 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1546
1547 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1548 (*i) = uChar(True);
1549 }
1550
1551 flagsCol_.put(whichRow, arr);
1552}
1553
1554MDirection::Types SDMemTable::getDirectionReference() const
1555{
1556 Float eq;
1557 table_.keywordSet().get("Equinox",eq);
1558 std::map<float,string> mp;
1559 mp[2000.0] = "J2000";
1560 mp[1950.0] = "B1950";
1561 MDirection::Types mdr;
1562 if (!MDirection::getType(mdr, mp[eq])) {
1563 mdr = MDirection::J2000;
1564 cerr << "Unknown equinox using J2000" << endl;
1565 }
1566
1567 return mdr;
1568}
1569
1570MEpoch::Types SDMemTable::getTimeReference() const
1571{
1572 MEpoch::Types met;
1573 String ep;
1574 table_.keywordSet().get("Epoch",ep);
1575 if (!MEpoch::getType(met, ep)) {
1576 cerr << "Epoch type unknown - using UTC" << endl;
1577 met = MEpoch::UTC;
1578 }
1579
1580 return met;
1581}
1582
1583
1584Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1585 const String& sUnit,
1586 const vector<string>& lines,
1587 const String& source,
1588 Int whichIF)
1589{
1590 const Int nIFs = nIF();
1591 if (whichIF>=nIFs) {
1592 throw(AipsError("Illegal IF index"));
1593 }
1594
1595 // Find vector of restfrequencies
1596 // Double takes precedence over String
1597 Unit unit;
1598 Vector<Double> restFreqs;
1599 if (restFreqsIn.nelements()>0) {
1600 restFreqs.resize(restFreqsIn.nelements());
1601 restFreqs = restFreqsIn;
1602 unit = Unit(sUnit);
1603 } else if (lines.size()>0) {
1604 const uInt nLines = lines.size();
1605 unit = Unit("Hz");
1606 restFreqs.resize(nLines);
1607 MFrequency lineFreq;
1608 for (uInt i=0; i<nLines; i++) {
1609 String tS(lines[i]);
1610 tS.upcase();
1611 if (MeasTable::Line(lineFreq, tS)) {
1612 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1613 } else {
1614 String s = String(lines[i]) +
1615 String(" is an unrecognized spectral line");
1616 throw(AipsError(s));
1617 }
1618 }
1619 } else {
1620 throw(AipsError("You have not specified any rest frequencies or lines"));
1621 }
1622
1623 // If multiple restfreqs, must be length nIF. In this
1624 // case we will just replace the rest frequencies
1625 const uInt nRestFreqs = restFreqs.nelements();
1626 Int idx = -1;
1627 SDFrequencyTable sdft = getSDFreqTable();
1628
1629 if (nRestFreqs>1) {
1630 // Replace restFreqs, one per IF
1631 if (nRestFreqs != nIFs) {
1632 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1633 }
1634 cout << "Replacing rest frequencies with given list, one per IF" << endl;
1635 sdft.deleteRestFrequencies();
1636 for (uInt i=0; i<nRestFreqs; i++) {
1637 Quantum<Double> rf(restFreqs[i], unit);
1638 sdft.addRestFrequency(rf.getValue("Hz"));
1639 }
1640 } else {
1641
1642 // Add new rest freq
1643 Quantum<Double> rf(restFreqs[0], unit);
1644 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1645 cout << "Selecting given rest frequency" << endl;
1646 }
1647
1648 // Replace
1649 Bool empty = source.empty();
1650 Bool ok = False;
1651 if (putSDFreqTable(sdft)) {
1652 const uInt nRow = table_.nrow();
1653 String srcName;
1654 Vector<uInt> restFreqIDs;
1655 for (uInt i=0; i<nRow; i++) {
1656 srcnCol_.get(i, srcName);
1657 restfreqidCol_.get(i,restFreqIDs);
1658
1659 if (idx==-1) {
1660 // Replace vector of restFreqs; one per IF.
1661 // No selection possible
1662 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1663 } else {
1664 // Set RestFreqID for selected data
1665 if (empty || source==srcName) {
1666 if (whichIF<0) {
1667 restFreqIDs = idx;
1668 } else {
1669 restFreqIDs[whichIF] = idx;
1670 }
1671 }
1672 }
1673 restfreqidCol_.put(i,restFreqIDs);
1674 }
1675 ok = True;
1676 } else {
1677 ok = False;
1678 }
1679
1680 return ok;
1681}
1682
1683void SDMemTable::spectralLines() const
1684{
1685 Vector<String> lines = MeasTable::Lines();
1686 MFrequency lineFreq;
1687 Double freq;
1688
1689 cout.flags(std::ios_base::left);
1690 cout << "Line Frequency (Hz)" << endl;
1691 cout << "-----------------------" << endl;
1692 for (uInt i=0; i<lines.nelements(); i++) {
1693 MeasTable::Line(lineFreq, lines[i]);
1694 freq = lineFreq.getValue().getValue(); // Hz
1695 cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1696 }
1697}
1698
1699void SDMemTable::renumber()
1700{
1701 uInt nRow = scanCol_.nrow();
1702 Int newscanid = 0;
1703 Int cIdx;// the current scanid
1704 // get the first scanid
1705 scanCol_.getScalar(0,cIdx);
1706 Int pIdx = cIdx;// the scanid of the previous row
1707 for (uInt i=0; i<nRow;++i) {
1708 scanCol_.getScalar(i,cIdx);
1709 if (pIdx == cIdx) {
1710 // renumber
1711 scanCol_.put(i,newscanid);
1712 } else {
1713 ++newscanid;
1714 pIdx = cIdx; // store scanid
1715 --i; // don't increment next loop
1716 }
1717 }
1718}
1719
1720
1721void SDMemTable::setCursorSlice(IPosition& start, IPosition& end,
1722 const IPosition& shape) const
1723{
1724 const uInt nDim = shape.nelements();
1725 start.resize(nDim);
1726 end.resize(nDim);
1727
1728 start(asap::BeamAxis) = beamSel_;
1729 end(asap::BeamAxis) = beamSel_;
1730 start(asap::IFAxis) = IFSel_;
1731 end(asap::IFAxis) = IFSel_;
1732
1733 start(asap::PolAxis) = polSel_;
1734 end(asap::PolAxis) = polSel_;
1735
1736 start(asap::ChanAxis) = 0;
1737 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1738}
1739
1740
1741std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1742 // Get spectrum at cursor location
1743{
1744
1745 // Setup accessors
1746 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1747 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1748
1749 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1750 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1751
1752 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1753 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1754
1755 std::vector<float> spectrum;
1756 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1757 spectrum.push_back(*i);
1758 }
1759 return spectrum;
1760}
1761
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