source: trunk/src/SDMemTable.cc@ 485

Last change on this file since 485 was 483, checked in by mar637, 20 years ago
  • Added history support.
  • Added version keyword to SDMemTable.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 50.4 KB
Line 
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 uInt version;
88 tab.keywordSet().get("VERSION", version);
89 if (version != version_) {
90 throw(AipsError("Unsupported version of ASAP file."));
91 }
92 table_ = tab.copyToMemoryTable("dummy");
93 //cerr << "hello from C SDMemTable @ " << this << endl;
94 attach();
95}
96
97SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
98{
99 table_ = other.table_.copyToMemoryTable(String("dummy"));
100 // clear all rows()
101 if (clear) {
102 table_.removeRow(this->table_.rowNumbers());
103 IFSel_= 0;
104 beamSel_= 0;
105 polSel_= 0;
106 chanMask_.resize(0);
107 } else {
108 IFSel_= other.IFSel_;
109 beamSel_= other.beamSel_;
110 polSel_= other.polSel_;
111 chanMask_.resize(0);
112 chanMask_ = other.chanMask_;
113 }
114
115 attach();
116 //cerr << "hello from CC SDMemTable @ " << this << endl;
117}
118
119SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
120 IFSel_(0),
121 beamSel_(0),
122 polSel_(0)
123{
124 Table t = tableCommand(exprs,tab);
125 if (t.nrow() == 0)
126 throw(AipsError("Query unsuccessful."));
127 table_ = t.copyToMemoryTable("dummy");
128 attach();
129 renumber();
130}
131
132SDMemTable::~SDMemTable()
133{
134 //cerr << "goodbye from SDMemTable @ " << this << endl;
135}
136
137SDMemTable SDMemTable::getScan(Int scanID) const
138{
139 String cond("SELECT * from $1 WHERE SCANID == ");
140 cond += String::toString(scanID);
141 return SDMemTable(table_, cond);
142}
143
144SDMemTable &SDMemTable::operator=(const SDMemTable& other)
145{
146 if (this != &other) {
147 IFSel_= other.IFSel_;
148 beamSel_= other.beamSel_;
149 polSel_= other.polSel_;
150 chanMask_.resize(0);
151 chanMask_ = other.chanMask_;
152 table_ = other.table_.copyToMemoryTable(String("dummy"));
153 attach();
154 }
155 return *this;
156}
157
158SDMemTable SDMemTable::getSource(const std::string& source) const
159{
160 String cond("SELECT * from $1 WHERE SRCNAME == ");
161 cond += source;
162 return SDMemTable(table_, cond);
163}
164
165void SDMemTable::setup()
166{
167 TableDesc td("", "1", TableDesc::Scratch);
168 td.comment() = "A SDMemTable";
169 td.rwKeywordSet().define("VERSION", Int(version_));
170
171 td.addColumn(ScalarColumnDesc<Double>("TIME"));
172 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
173 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
174 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
175 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
176 td.addColumn(ArrayColumnDesc<Float>("STOKES"));
177 td.addColumn(ScalarColumnDesc<Int>("SCANID"));
178 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
179 td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
180 td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
181 td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
182 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
183 td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
184 td.addColumn(ArrayColumnDesc<Float>("TCAL"));
185 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
186 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
187 td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
188 td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
189 td.addColumn(ArrayColumnDesc<Int>("FITID"));
190
191 // Now create Table SetUp from the description.
192 SetupNewTable aNewTab("dummy", td, Table::New);
193
194 // Bind the Stokes Virtual machine to the STOKES column Because we
195 // don't know how many polarizations will be in the data at this
196 // point, we must bind the Virtual Engine regardless. The STOKES
197 // column won't be accessed if not appropriate (nPol=4)
198 SDStokesEngine::registerClass();
199 SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
200 aNewTab.bindColumn("STOKES", stokesEngine);
201
202 // Create Table
203 table_ = Table(aNewTab, Table::Memory, 0);
204 // add subtable
205 TableDesc tdf("", "1", TableDesc::Scratch);
206 tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
207 tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
208 tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
209 tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
210 tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
211 SetupNewTable fittab("fits", tdf, Table::New);
212 Table fitTable(fittab, Table::Memory);
213 table_.rwKeywordSet().defineTable("FITS", fitTable);
214
215 TableDesc tdh("", "1", TableDesc::Scratch);
216 tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
217 SetupNewTable histtab("hist", tdh, Table::New);
218 Table histTable(histtab, Table::Memory);
219 table_.rwKeywordSet().defineTable("HISTORY", histTable);
220}
221
222void SDMemTable::attach()
223{
224 timeCol_.attach(table_, "TIME");
225 srcnCol_.attach(table_, "SRCNAME");
226 specCol_.attach(table_, "SPECTRA");
227 flagsCol_.attach(table_, "FLAGTRA");
228 tsCol_.attach(table_, "TSYS");
229 stokesCol_.attach(table_, "STOKES");
230 scanCol_.attach(table_, "SCANID");
231 integrCol_.attach(table_, "INTERVAL");
232 freqidCol_.attach(table_, "FREQID");
233 restfreqidCol_.attach(table_, "RESTFREQID");
234 dirCol_.attach(table_, "DIRECTION");
235 fldnCol_.attach(table_, "FIELDNAME");
236 tcaltCol_.attach(table_, "TCALTIME");
237 tcalCol_.attach(table_, "TCAL");
238 azCol_.attach(table_, "AZIMUTH");
239 elCol_.attach(table_, "ELEVATION");
240 paraCol_.attach(table_, "PARANGLE");
241 rbeamCol_.attach(table_, "REFBEAM");
242 fitCol_.attach(table_,"FITID");
243}
244
245
246std::string SDMemTable::getSourceName(Int whichRow) const
247{
248 String name;
249 srcnCol_.get(whichRow, name);
250 return name;
251}
252
253std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
254{
255 Double tm;
256 if (whichRow > -1) {
257 timeCol_.get(whichRow, tm);
258 } else {
259 table_.keywordSet().get("UTC",tm);
260 }
261 MVTime mvt(tm);
262 if (showDate)
263 mvt.setFormat(MVTime::YMD);
264 else
265 mvt.setFormat(MVTime::TIME);
266 ostringstream oss;
267 oss << mvt;
268 return String(oss);
269}
270
271double SDMemTable::getInterval(Int whichRow) const
272{
273 Double intval;
274 integrCol_.get(whichRow, intval);
275 return intval;
276}
277
278bool SDMemTable::setIF(Int whichIF)
279{
280 if ( whichIF >= 0 && whichIF < nIF()) {
281 IFSel_ = whichIF;
282 return true;
283 }
284 return false;
285}
286
287bool SDMemTable::setBeam(Int whichBeam)
288{
289 if ( whichBeam >= 0 && whichBeam < nBeam()) {
290 beamSel_ = whichBeam;
291 return true;
292 }
293 return false;
294}
295
296bool SDMemTable::setPol(Int whichPol)
297{
298 if ( whichPol >= 0 && whichPol < nPol()) {
299 polSel_ = whichPol;
300 return true;
301 }
302 return false;
303}
304
305void SDMemTable::resetCursor()
306{
307 polSel_ = 0;
308 IFSel_ = 0;
309 beamSel_ = 0;
310}
311
312bool SDMemTable::setMask(std::vector<int> whichChans)
313{
314 std::vector<int>::iterator it;
315 uInt n = flagsCol_.shape(0)(3);
316 if (whichChans.empty()) {
317 chanMask_ = std::vector<bool>(n,true);
318 return true;
319 }
320 chanMask_.resize(n,true);
321 for (it = whichChans.begin(); it != whichChans.end(); ++it) {
322 if (*it < n) {
323 chanMask_[*it] = false;
324 }
325 }
326 return true;
327}
328
329std::vector<bool> SDMemTable::getMask(Int whichRow) const
330{
331
332 std::vector<bool> mask;
333
334 Array<uChar> arr;
335 flagsCol_.get(whichRow, arr);
336
337 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
338 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
339 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
340 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
341 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
342 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
343
344 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
345
346 std::vector<bool> tmp;
347 tmp = chanMask_; // WHY the fxxx do I have to make a copy here
348 std::vector<bool>::iterator miter;
349 miter = tmp.begin();
350
351 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
352 bool out =!static_cast<bool>(*i);
353 if (useUserMask) {
354 out = out && (*miter);
355 miter++;
356 }
357 mask.push_back(out);
358 }
359 return mask;
360}
361
362
363
364std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
365{
366 Array<Float> arr;
367 specCol_.get(whichRow, arr);
368 return getFloatSpectrum(arr);
369}
370
371std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow, Bool doPol,
372 Float paOffset) const
373//
374// Gets one STokes parameter depending on cursor polSel location
375// doPol=False : I,Q,U,V
376// doPol=True : I,P,PA,V ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
377//
378{
379 AlwaysAssert(asap::nAxes==4,AipsError);
380 if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
381 throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
382 }
383 Array<Float> arr;
384 stokesCol_.get(whichRow, arr);
385
386 if (doPol && (polSel_==1 || polSel_==2)) { // Q,U --> P, P.A.
387
388 // Set current cursor location
389 const IPosition& shape = arr.shape();
390 IPosition start, end;
391 getCursorSlice(start, end, shape);
392
393 // Get Q and U slices
394
395 Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
396 Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
397
398 // Compute output
399
400 Array<Float> out;
401 if (polSel_==1) { // P
402 out = SDPolUtil::polarizedIntensity(Q,U);
403 } else if (polSel_==2) { // P.A.
404 out = SDPolUtil::positionAngle(Q,U) + paOffset;
405 }
406
407 // Copy to output
408
409 IPosition vecShape(1,shape(asap::ChanAxis));
410 Vector<Float> outV = out.reform(vecShape);
411 std::vector<float> stlout;
412 outV.tovector(stlout);
413 return stlout;
414
415 } else {
416
417 // Selects at the cursor location
418 return getFloatSpectrum(arr);
419 }
420}
421
422std::vector<float> SDMemTable::getCircularSpectrum(Int whichRow,
423 Bool doRR) const
424 // Gets
425 // RR = I + V
426 // LL = I - V
427{
428 AlwaysAssert(asap::nAxes==4,AipsError);
429 if (nPol()!=4) {
430 throw (AipsError("You must have 4 polarizations to get RR or LL"));
431 }
432 Array<Float> arr;
433 stokesCol_.get(whichRow, arr);
434
435 // Set current cursor location
436
437 const IPosition& shape = arr.shape();
438 IPosition start, end;
439 getCursorSlice(start, end, shape);
440
441 // Get I and V slices
442
443 Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
444 Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
445
446 // Compute output
447
448 Array<Float> out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
449
450 // Copy to output
451
452 IPosition vecShape(1,shape(asap::ChanAxis));
453 Vector<Float> outV = out.reform(vecShape);
454 std::vector<float> stlout;
455 outV.tovector(stlout);
456
457 return stlout;
458}
459
460Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
461{
462
463// Get data
464
465 Array<Float> arr;
466 stokesCol_.get(whichRow, arr);
467
468// Set current cursor location and overwrite polarization axis
469
470 const IPosition& shape = arr.shape();
471 IPosition start(shape.nelements(),0);
472 IPosition end(shape-1);
473 if (iBeam!=-1) {
474 start(asap::BeamAxis) = iBeam;
475 end(asap::BeamAxis) = iBeam;
476 }
477 if (iIF!=-1) {
478 start(asap::IFAxis) = iIF;
479 end(asap::IFAxis) = iIF;
480 }
481
482// Get slice
483
484 return arr(start,end);
485}
486
487
488std::vector<string> SDMemTable::getCoordInfo() const
489{
490 String un;
491 Table t = table_.keywordSet().asTable("FREQUENCIES");
492 String sunit;
493 t.keywordSet().get("UNIT",sunit);
494 String dpl;
495 t.keywordSet().get("DOPPLER",dpl);
496 if (dpl == "") dpl = "RADIO";
497 String rfrm;
498 t.keywordSet().get("REFFRAME",rfrm);
499 std::vector<string> inf;
500 inf.push_back(sunit);
501 inf.push_back(rfrm);
502 inf.push_back(dpl);
503 t.keywordSet().get("BASEREFFRAME",rfrm);
504 inf.push_back(rfrm);
505 return inf;
506}
507
508void SDMemTable::setCoordInfo(std::vector<string> theinfo)
509{
510 std::vector<string>::iterator it;
511 String un,rfrm, brfrm,dpl;
512 un = theinfo[0]; // Abcissa unit
513 rfrm = theinfo[1]; // Active (or conversion) frame
514 dpl = theinfo[2]; // Doppler
515 brfrm = theinfo[3]; // Base frame
516
517 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
518
519 Vector<Double> rstf;
520 t.keywordSet().get("RESTFREQS",rstf);
521
522 Bool canDo = True;
523 Unit u1("km/s");Unit u2("Hz");
524 if (Unit(un) == u1) {
525 Vector<Double> rstf;
526 t.keywordSet().get("RESTFREQS",rstf);
527 if (rstf.nelements() == 0) {
528 throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
529 }
530 } else if (Unit(un) != u2 && un != "") {
531 throw(AipsError("Unit not conformant with Spectral Coordinates"));
532 }
533 t.rwKeywordSet().define("UNIT", un);
534
535 MFrequency::Types mdr;
536 if (!MFrequency::getType(mdr, rfrm)) {
537
538 Int a,b;const uInt* c;
539 const String* valid = MFrequency::allMyTypes(a, b, c);
540 String pfix = "Please specify a legal frame type. Types are\n";
541 throw(AipsError(pfix+(*valid)));
542 } else {
543 t.rwKeywordSet().define("REFFRAME",rfrm);
544 }
545
546 MDoppler::Types dtype;
547 dpl.upcase();
548 if (!MDoppler::getType(dtype, dpl)) {
549 throw(AipsError("Doppler type unknown"));
550 } else {
551 t.rwKeywordSet().define("DOPPLER",dpl);
552 }
553
554 if (!MFrequency::getType(mdr, brfrm)) {
555 Int a,b;const uInt* c;
556 const String* valid = MFrequency::allMyTypes(a, b, c);
557 String pfix = "Please specify a legal frame type. Types are\n";
558 throw(AipsError(pfix+(*valid)));
559 } else {
560 t.rwKeywordSet().define("BASEREFFRAME",brfrm);
561 }
562}
563
564
565std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
566{
567 std::vector<double> abc(nChan());
568
569 // Get header units keyword
570 Table t = table_.keywordSet().asTable("FREQUENCIES");
571 String sunit;
572 t.keywordSet().get("UNIT",sunit);
573 if (sunit == "") sunit = "pixel";
574 Unit u(sunit);
575
576 // Easy if just wanting pixels
577 if (sunit==String("pixel")) {
578 // assume channels/pixels
579 std::vector<double>::iterator it;
580 uInt i=0;
581 for (it = abc.begin(); it != abc.end(); ++it) {
582 (*it) = Double(i++);
583 }
584 return abc;
585 }
586
587 // Continue with km/s or Hz. Get FreqIDs
588 Vector<uInt> freqIDs;
589 freqidCol_.get(whichRow, freqIDs);
590 uInt freqID = freqIDs(IFSel_);
591 restfreqidCol_.get(whichRow, freqIDs);
592 uInt restFreqID = freqIDs(IFSel_);
593
594 // Get SpectralCoordinate, set reference frame conversion,
595 // velocity conversion, and rest freq state
596
597 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
598 Vector<Double> pixel(nChan());
599 indgen(pixel);
600
601 if (u == Unit("km/s")) {
602 Vector<Double> world;
603 spc.pixelToVelocity(world,pixel);
604 std::vector<double>::iterator it;
605 uInt i = 0;
606 for (it = abc.begin(); it != abc.end(); ++it) {
607 (*it) = world[i];
608 i++;
609 }
610 } else if (u == Unit("Hz")) {
611
612 // Set world axis units
613 Vector<String> wau(1); wau = u.getName();
614 spc.setWorldAxisUnits(wau);
615
616 std::vector<double>::iterator it;
617 Double tmp;
618 uInt i = 0;
619 for (it = abc.begin(); it != abc.end(); ++it) {
620 spc.toWorld(tmp,pixel[i]);
621 (*it) = tmp;
622 i++;
623 }
624 }
625 return abc;
626}
627
628std::string SDMemTable::getAbcissaString(Int whichRow) const
629{
630 Table t = table_.keywordSet().asTable("FREQUENCIES");
631
632 String sunit;
633 t.keywordSet().get("UNIT",sunit);
634 if (sunit == "") sunit = "pixel";
635 Unit u(sunit);
636
637 Vector<uInt> freqIDs;
638 freqidCol_.get(whichRow, freqIDs);
639 uInt freqID = freqIDs(IFSel_);
640 restfreqidCol_.get(whichRow, freqIDs);
641 uInt restFreqID = freqIDs(IFSel_);
642
643 // Get SpectralCoordinate, with frame, velocity, rest freq state set
644 SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
645
646 String s = "Channel";
647 if (u == Unit("km/s")) {
648 s = CoordinateUtil::axisLabel(spc,0,True,True,True);
649 } else if (u == Unit("Hz")) {
650 Vector<String> wau(1);wau = u.getName();
651 spc.setWorldAxisUnits(wau);
652
653 s = CoordinateUtil::axisLabel(spc,0,True,True,False);
654 }
655 return s;
656}
657
658void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
659{
660 Array<Float> arr;
661 specCol_.get(whichRow, arr);
662 if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
663 throw(AipsError("Attempting to set spectrum with incorrect length."));
664 }
665
666 // Setup accessors
667 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
668 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
669 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
670 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
671 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
672 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
673
674 // Iterate
675 std::vector<float>::iterator it = spectrum.begin();
676 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
677 (*i) = Float(*it);
678 it++;
679 }
680 specCol_.put(whichRow, arr);
681}
682
683void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
684{
685 Array<Float> arr;
686 specCol_.get(whichRow, arr);
687
688 // Iterate and extract
689 spectrum.resize(arr.shape()(3));
690 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
691 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
692 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
693 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
694 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
695 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
696
697 ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
698 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
699 (*va) = (*i);
700 va++;
701 }
702}
703
704
705/*
706void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
707 Array<uChar> arr;
708 flagsCol_.get(whichRow, arr);
709 mask.resize(arr.shape()(3));
710
711 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
712 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
713 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
714 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
715 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
716 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
717
718 Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
719
720 ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
721 std::vector<bool> tmp;
722 tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
723 // iterator should work on chanMask_??
724 std::vector<bool>::iterator miter;
725 miter = tmp.begin();
726
727 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
728 bool out =!static_cast<bool>(*i);
729 if (useUserMask) {
730 out = out && (*miter);
731 miter++;
732 }
733 (*va) = out;
734 va++;
735 }
736}
737*/
738
739MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
740 Bool toStokes) const
741{
742 // Get flags
743 Array<uChar> farr;
744 flagsCol_.get(whichRow, farr);
745
746 // Get data and convert mask to Bool
747 Array<Float> arr;
748 Array<Bool> mask;
749 if (toStokes) {
750 stokesCol_.get(whichRow, arr);
751
752 Array<Bool> tMask(farr.shape());
753 convertArray(tMask, farr);
754 mask = SDPolUtil::stokesData (tMask, True);
755 } else {
756 specCol_.get(whichRow, arr);
757 mask.resize(farr.shape());
758 convertArray(mask, farr);
759 }
760
761 return MaskedArray<Float>(arr,!mask);
762}
763
764Float SDMemTable::getTsys(Int whichRow) const
765{
766 Array<Float> arr;
767 tsCol_.get(whichRow, arr);
768 Float out;
769
770 IPosition ip(arr.shape());
771 ip(asap::BeamAxis) = beamSel_;
772 ip(asap::IFAxis) = IFSel_;
773 ip(asap::PolAxis) = polSel_;
774 ip(asap::ChanAxis)=0; // First channel only
775
776 out = arr(ip);
777 return out;
778}
779
780MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
781{
782 MDirection::Types mdr = getDirectionReference();
783 Array<Double> posit;
784 dirCol_.get(whichRow,posit);
785 Vector<Double> wpos(2);
786 Int rb;
787 rbeamCol_.get(whichRow,rb);
788 wpos[0] = posit(IPosition(2,beamSel_,0));
789 wpos[1] = posit(IPosition(2,beamSel_,1));
790 if (refBeam && rb > -1) { // use refBeam instead if it exists
791 wpos[0] = posit(IPosition(2,rb,0));
792 wpos[1] = posit(IPosition(2,rb,1));
793 }
794
795 Quantum<Double> lon(wpos[0],Unit(String("rad")));
796 Quantum<Double> lat(wpos[1],Unit(String("rad")));
797 return MDirection(lon, lat, mdr);
798}
799
800MEpoch SDMemTable::getEpoch(Int whichRow) const
801{
802 MEpoch::Types met = getTimeReference();
803
804 Double obstime;
805 timeCol_.get(whichRow,obstime);
806 MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
807 return MEpoch(tm2, met);
808}
809
810MPosition SDMemTable::getAntennaPosition () const
811{
812 Vector<Double> antpos;
813 table_.keywordSet().get("AntennaPosition", antpos);
814 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
815 return MPosition(mvpos);
816}
817
818
819SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
820{
821
822 Table t = table_.keywordSet().asTable("FREQUENCIES");
823 if (freqID> t.nrow() ) {
824 throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
825 }
826
827 Double rp,rv,inc;
828 String rf;
829 ROScalarColumn<Double> rpc(t, "REFPIX");
830 ROScalarColumn<Double> rvc(t, "REFVAL");
831 ROScalarColumn<Double> incc(t, "INCREMENT");
832 t.keywordSet().get("BASEREFFRAME",rf);
833
834 // Create SpectralCoordinate (units Hz)
835 MFrequency::Types mft;
836 if (!MFrequency::getType(mft, rf)) {
837 cerr << "Frequency type unknown assuming TOPO" << endl;
838 mft = MFrequency::TOPO;
839 }
840 rpc.get(freqID, rp);
841 rvc.get(freqID, rv);
842 incc.get(freqID, inc);
843
844 SpectralCoordinate spec(mft,rv,inc,rp);
845 return spec;
846}
847
848
849SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
850 uInt restFreqID,
851 uInt whichRow) const
852{
853
854 // Create basic SC
855 SpectralCoordinate spec = getSpectralCoordinate (freqID);
856
857 Table t = table_.keywordSet().asTable("FREQUENCIES");
858
859 // Set rest frequency
860 Vector<Double> restFreqIDs;
861 t.keywordSet().get("RESTFREQS",restFreqIDs);
862 if (restFreqID < restFreqIDs.nelements()) { // Should always be true
863 spec.setRestFrequency(restFreqIDs(restFreqID),True);
864 }
865
866 // Set up frame conversion layer
867 String frm;
868 t.keywordSet().get("REFFRAME",frm);
869 if (frm == "") frm = "TOPO";
870 MFrequency::Types mtype;
871 if (!MFrequency::getType(mtype, frm)) {
872 // Should never happen
873 cerr << "Frequency type unknown assuming TOPO" << endl;
874 mtype = MFrequency::TOPO;
875 }
876
877 // Set reference frame conversion (requires row)
878 MDirection dir = getDirection(whichRow);
879 MEpoch epoch = getEpoch(whichRow);
880 MPosition pos = getAntennaPosition();
881
882 if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
883 throw(AipsError("Couldn't convert frequency frame."));
884 }
885
886 // Now velocity conversion if appropriate
887 String unitStr;
888 t.keywordSet().get("UNIT",unitStr);
889
890 String dpl;
891 t.keywordSet().get("DOPPLER",dpl);
892 MDoppler::Types dtype;
893 MDoppler::getType(dtype, dpl);
894
895 // Only set velocity unit if non-blank and non-Hz
896 if (!unitStr.empty()) {
897 Unit unitU(unitStr);
898 if (unitU==Unit("Hz")) {
899 } else {
900 spec.setVelocity(unitStr, dtype);
901 }
902 }
903
904 return spec;
905}
906
907
908Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
909 uInt freqID) {
910 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
911 if (freqID > t.nrow() ) {
912 throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
913 }
914 ScalarColumn<Double> rpc(t, "REFPIX");
915 ScalarColumn<Double> rvc(t, "REFVAL");
916 ScalarColumn<Double> incc(t, "INCREMENT");
917
918 rpc.put(freqID, speccord.referencePixel()[0]);
919 rvc.put(freqID, speccord.referenceValue()[0]);
920 incc.put(freqID, speccord.increment()[0]);
921
922 return True;
923}
924
925Int SDMemTable::nCoordinates() const
926{
927 return table_.keywordSet().asTable("FREQUENCIES").nrow();
928}
929
930
931std::vector<double> SDMemTable::getRestFreqs() const
932{
933 Table t = table_.keywordSet().asTable("FREQUENCIES");
934 Vector<Double> tvec;
935 t.keywordSet().get("RESTFREQS",tvec);
936 std::vector<double> stlout;
937 tvec.tovector(stlout);
938 return stlout;
939}
940
941bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
942{
943 TableDesc td("", "1", TableDesc::Scratch);
944 td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
945 td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
946 td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
947 SetupNewTable aNewTab("freqs", td, Table::New);
948 Table aTable (aNewTab, Table::Memory, sdft.length());
949 ScalarColumn<Double> sc0(aTable, "REFPIX");
950 ScalarColumn<Double> sc1(aTable, "REFVAL");
951 ScalarColumn<Double> sc2(aTable, "INCREMENT");
952 for (uInt i=0; i < sdft.length(); ++i) {
953 sc0.put(i,sdft.referencePixel(i));
954 sc1.put(i,sdft.referenceValue(i));
955 sc2.put(i,sdft.increment(i));
956 }
957 String rf = sdft.refFrame();
958 if (rf.contains("TOPO")) rf = "TOPO";
959
960 aTable.rwKeywordSet().define("BASEREFFRAME", rf);
961 aTable.rwKeywordSet().define("REFFRAME", rf);
962 aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
963 aTable.rwKeywordSet().define("UNIT", String(""));
964 aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
965 Vector<Double> rfvec;
966 String rfunit;
967 sdft.restFrequencies(rfvec,rfunit);
968 Quantum<Vector<Double> > q(rfvec, rfunit);
969 rfvec.resize();
970 rfvec = q.getValue("Hz");
971 aTable.rwKeywordSet().define("RESTFREQS", rfvec);
972 table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
973 return true;
974}
975
976bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
977{
978 TableDesc td("", "1", TableDesc::Scratch);
979 td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
980 td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
981 td.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
982 td.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
983 td.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
984 SetupNewTable aNewTab("fits", td, Table::New);
985 Table aTable(aNewTab, Table::Memory);
986 ArrayColumn<String> sc0(aTable, "FUNCTIONS");
987 ArrayColumn<Int> sc1(aTable, "COMPONENTS");
988 ArrayColumn<Double> sc2(aTable, "PARAMETERS");
989 ArrayColumn<Bool> sc3(aTable, "PARMASK");
990 ArrayColumn<String> sc4(aTable, "FRAMEINFO");
991 for (uInt i; i<sdft.length(); ++i) {
992 const Vector<Double>& parms = sdft.getParameters(i);
993 const Vector<Bool>& parmask = sdft.getParameterMask(i);
994 const Vector<String>& funcs = sdft.getFunctions(i);
995 const Vector<Int>& comps = sdft.getComponents(i);
996 const Vector<String>& finfo = sdft.getFrameInfo(i);
997 sc0.put(i,funcs);
998 sc1.put(i,comps);
999 sc3.put(i,parmask);
1000 sc2.put(i,parms);
1001 sc4.put(i,finfo);
1002 }
1003 table_.rwKeywordSet().defineTable("FITS", aTable);
1004 return true;
1005}
1006
1007SDFitTable SDMemTable::getSDFitTable() const
1008{
1009 const Table& t = table_.keywordSet().asTable("FITS");
1010 Vector<Double> parms;
1011 Vector<Bool> parmask;
1012 Vector<String> funcs;
1013 Vector<String> finfo;
1014 Vector<Int> comps;
1015 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1016 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1017 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1018 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1019 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1020 uInt n = t.nrow();
1021 SDFitTable sdft;
1022 for (uInt i=0; i<n; ++i) {
1023 parmaskCol.get(i, parmask);
1024 parmsCol.get(i, parms);
1025 funcsCol.get(i, funcs);
1026 compsCol.get(i, comps);
1027 finfoCol.get(i, finfo);
1028 sdft.addFit(parms, parmask, funcs, comps, finfo);
1029 }
1030 return sdft;
1031}
1032
1033SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
1034 Array<Int> fitid;
1035 fitCol_.get(whichRow, fitid);
1036 if (fitid.nelements() == 0) return SDFitTable();
1037
1038 IPosition shp = fitid.shape();
1039 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1040 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1041
1042 // reform the output array slice to be of dim=1
1043 Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
1044
1045 const Table& t = table_.keywordSet().asTable("FITS");
1046 Vector<Double> parms;
1047 Vector<Bool> parmask;
1048 Vector<String> funcs;
1049 Vector<String> finfo;
1050 Vector<Int> comps;
1051 ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
1052 ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
1053 ROArrayColumn<Int> compsCol(t, "COMPONENTS");
1054 ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
1055 ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
1056 if (t.nrow() == 0) return SDFitTable();
1057 SDFitTable sdft;
1058 Int k=-1;
1059 for (uInt i=0; i< tmp.nelements(); ++i) {
1060 k = tmp[i];
1061 if ( k > -1 && k < t.nrow() ) {
1062 parms.resize();
1063 parmsCol.get(k, parms);
1064 parmask.resize();
1065 parmaskCol.get(k, parmask);
1066 funcs.resize();
1067 funcsCol.get(k, funcs);
1068 comps.resize();
1069 compsCol.get(k, comps);
1070 finfo.resize();
1071 finfoCol.get(k, finfo);
1072 sdft.addFit(parms, parmask, funcs, comps, finfo);
1073 }
1074 }
1075 return sdft;
1076}
1077
1078void SDMemTable::addFit(uInt whichRow,
1079 const Vector<Double>& p, const Vector<Bool>& m,
1080 const Vector<String>& f, const Vector<Int>& c)
1081{
1082 if (whichRow >= nRow()) {
1083 throw(AipsError("Specified row out of range"));
1084 }
1085 Table t = table_.keywordSet().asTable("FITS");
1086 uInt nrow = t.nrow();
1087 t.addRow();
1088 ArrayColumn<Double> parmsCol(t, "PARAMETERS");
1089 ArrayColumn<Bool> parmaskCol(t, "PARMASK");
1090 ArrayColumn<Int> compsCol(t, "COMPONENTS");
1091 ArrayColumn<String> funcsCol(t, "FUNCTIONS");
1092 ArrayColumn<String> finfoCol(t, "FRAMEINFO");
1093 parmsCol.put(nrow, p);
1094 parmaskCol.put(nrow, m);
1095 compsCol.put(nrow, c);
1096 funcsCol.put(nrow, f);
1097 Vector<String> fi = mathutil::toVectorString(getCoordInfo());
1098 finfoCol.put(nrow, fi);
1099
1100 Array<Int> fitarr;
1101 fitCol_.get(whichRow, fitarr);
1102
1103 Array<Int> newarr; // The new Array containing the fitid
1104 Int pos =-1; // The fitid position in the array
1105 if ( fitarr.nelements() == 0 ) { // no fits at all in this row
1106 Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
1107 arr = -1;
1108 newarr.reference(arr);
1109 pos = 0;
1110 } else {
1111 IPosition shp = fitarr.shape();
1112 IPosition start(4, beamSel_, IFSel_, polSel_,0);
1113 IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
1114 // reform the output array slice to be of dim=1
1115 Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
1116 const Vector<Int>& fits = tmp;
1117 VectorSTLIterator<Int> it(fits);
1118 Int i = 0;
1119 while (it != fits.end()) {
1120 if (*it == -1) {
1121 pos = i;
1122 break;
1123 }
1124 ++i;
1125 ++it;
1126 };
1127 }
1128 if (pos == -1) {
1129 mathutil::extendLastArrayAxis(newarr,fitarr, -1);
1130 pos = fitarr.shape()[3]; // the new element position
1131 } else {
1132 if (fitarr.nelements() > 0)
1133 newarr = fitarr;
1134 }
1135 newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
1136 fitCol_.put(whichRow, newarr);
1137
1138}
1139
1140SDFrequencyTable SDMemTable::getSDFreqTable() const
1141{
1142 const Table& t = table_.keywordSet().asTable("FREQUENCIES");
1143 SDFrequencyTable sdft;
1144
1145 // Add refpix/refval/incr. What are the units ? Hz I suppose
1146 // but it's nowhere described...
1147 Vector<Double> refPix, refVal, incr;
1148 ScalarColumn<Double> refPixCol(t, "REFPIX");
1149 ScalarColumn<Double> refValCol(t, "REFVAL");
1150 ScalarColumn<Double> incrCol(t, "INCREMENT");
1151 refPix = refPixCol.getColumn();
1152 refVal = refValCol.getColumn();
1153 incr = incrCol.getColumn();
1154
1155 uInt n = refPix.nelements();
1156 for (uInt i=0; i<n; i++) {
1157 sdft.addFrequency(refPix[i], refVal[i], incr[i]);
1158 }
1159
1160 // Frequency reference frame. I don't know if this
1161 // is the correct frame. It might be 'REFFRAME'
1162 // rather than 'BASEREFFRAME' ?
1163 String baseFrame;
1164 t.keywordSet().get("BASEREFFRAME",baseFrame);
1165 sdft.setRefFrame(baseFrame);
1166
1167 // Equinox
1168 Float equinox;
1169 t.keywordSet().get("EQUINOX", equinox);
1170 sdft.setEquinox(equinox);
1171
1172 // Rest Frequency
1173 Vector<Double> restFreqs;
1174 t.keywordSet().get("RESTFREQS", restFreqs);
1175 for (uInt i=0; i<restFreqs.nelements(); i++) {
1176 sdft.addRestFrequency(restFreqs[i]);
1177 }
1178 sdft.setRestFrequencyUnit(String("Hz"));
1179
1180 return sdft;
1181}
1182
1183bool SDMemTable::putSDContainer(const SDContainer& sdc)
1184{
1185 uInt rno = table_.nrow();
1186 table_.addRow();
1187
1188 timeCol_.put(rno, sdc.timestamp);
1189 srcnCol_.put(rno, sdc.sourcename);
1190 fldnCol_.put(rno, sdc.fieldname);
1191 specCol_.put(rno, sdc.getSpectrum());
1192 flagsCol_.put(rno, sdc.getFlags());
1193 tsCol_.put(rno, sdc.getTsys());
1194 scanCol_.put(rno, sdc.scanid);
1195 integrCol_.put(rno, sdc.interval);
1196 freqidCol_.put(rno, sdc.getFreqMap());
1197 restfreqidCol_.put(rno, sdc.getRestFreqMap());
1198 dirCol_.put(rno, sdc.getDirection());
1199 rbeamCol_.put(rno, sdc.refbeam);
1200 tcalCol_.put(rno, sdc.tcal);
1201 tcaltCol_.put(rno, sdc.tcaltime);
1202 azCol_.put(rno, sdc.azimuth);
1203 elCol_.put(rno, sdc.elevation);
1204 paraCol_.put(rno, sdc.parangle);
1205 fitCol_.put(rno, sdc.getFitMap());
1206 return true;
1207}
1208
1209SDContainer SDMemTable::getSDContainer(uInt whichRow) const
1210{
1211 SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
1212 timeCol_.get(whichRow, sdc.timestamp);
1213 srcnCol_.get(whichRow, sdc.sourcename);
1214 integrCol_.get(whichRow, sdc.interval);
1215 scanCol_.get(whichRow, sdc.scanid);
1216 fldnCol_.get(whichRow, sdc.fieldname);
1217 rbeamCol_.get(whichRow, sdc.refbeam);
1218 azCol_.get(whichRow, sdc.azimuth);
1219 elCol_.get(whichRow, sdc.elevation);
1220 paraCol_.get(whichRow, sdc.parangle);
1221 Vector<Float> tc;
1222 tcalCol_.get(whichRow, tc);
1223 sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
1224 tcaltCol_.get(whichRow, sdc.tcaltime);
1225
1226 Array<Float> spectrum;
1227 Array<Float> tsys;
1228 Array<uChar> flagtrum;
1229 Vector<uInt> fmap;
1230 Array<Double> direction;
1231 Array<Int> fits;
1232
1233 specCol_.get(whichRow, spectrum);
1234 sdc.putSpectrum(spectrum);
1235 flagsCol_.get(whichRow, flagtrum);
1236 sdc.putFlags(flagtrum);
1237 tsCol_.get(whichRow, tsys);
1238 sdc.putTsys(tsys);
1239 freqidCol_.get(whichRow, fmap);
1240 sdc.putFreqMap(fmap);
1241 restfreqidCol_.get(whichRow, fmap);
1242 sdc.putRestFreqMap(fmap);
1243 dirCol_.get(whichRow, direction);
1244 sdc.putDirection(direction);
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}
1297
1298Int SDMemTable::nScan() const {
1299 Int n = 0;
1300 Int previous = -1;Int current=0;
1301 for (uInt i=0; i< scanCol_.nrow();i++) {
1302 scanCol_.getScalar(i,current);
1303 if (previous != current) {
1304 previous = current;
1305 n++;
1306 }
1307 }
1308 return n;
1309}
1310
1311String SDMemTable::formatSec(Double x) const
1312{
1313 Double xcop = x;
1314 MVTime mvt(xcop/24./3600.); // make days
1315
1316 if (x < 59.95)
1317 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
1318 else if (x < 3599.95)
1319 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
1320 else {
1321 ostringstream oss;
1322 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
1323 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
1324 return String(oss);
1325 }
1326};
1327
1328String SDMemTable::formatDirection(const MDirection& md) const
1329{
1330 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
1331 Int prec = 7;
1332
1333 MVAngle mvLon(t[0]);
1334 String sLon = mvLon.string(MVAngle::TIME,prec);
1335 MVAngle mvLat(t[1]);
1336 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
1337 return sLon + String(" ") + sLat;
1338}
1339
1340
1341std::string SDMemTable::getFluxUnit() const
1342{
1343 String tmp;
1344 table_.keywordSet().get("FluxUnit", tmp);
1345 return tmp;
1346}
1347
1348void SDMemTable::setFluxUnit(const std::string& unit)
1349{
1350 String tmp(unit);
1351 Unit tU(tmp);
1352 if (tU==Unit("K") || tU==Unit("Jy")) {
1353 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
1354 } else {
1355 throw AipsError("Illegal unit - must be compatible with Jy or K");
1356 }
1357}
1358
1359
1360void SDMemTable::setInstrument(const std::string& name)
1361{
1362 Bool throwIt = True;
1363 Instrument ins = SDAttr::convertInstrument(name, throwIt);
1364 String nameU(name);
1365 nameU.upcase();
1366 table_.rwKeywordSet().define(String("AntennaName"), nameU);
1367}
1368
1369std::string SDMemTable::summary(bool verbose) const {
1370
1371 // Format header info
1372 ostringstream oss;
1373 oss << endl;
1374 oss << "--------------------------------------------------------------------------------" << endl;
1375 oss << " Scan Table Summary" << endl;
1376 oss << "--------------------------------------------------------------------------------" << endl;
1377 oss.flags(std::ios_base::left);
1378 oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
1379 << setw(15) << "IFs:" << setw(4) << nIF() << endl
1380 << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
1381 << setw(15) << "Channels:" << setw(4) << nChan() << endl;
1382 oss << endl;
1383 String tmp;
1384 table_.keywordSet().get("Observer", tmp);
1385 oss << setw(15) << "Observer:" << tmp << endl;
1386 oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
1387 table_.keywordSet().get("Project", tmp);
1388 oss << setw(15) << "Project:" << tmp << endl;
1389 table_.keywordSet().get("Obstype", tmp);
1390 oss << setw(15) << "Obs. Type:" << tmp << endl;
1391 table_.keywordSet().get("AntennaName", tmp);
1392 oss << setw(15) << "Antenna Name:" << tmp << endl;
1393 table_.keywordSet().get("FluxUnit", tmp);
1394 oss << setw(15) << "Flux Unit:" << tmp << endl;
1395 Table t = table_.keywordSet().asTable("FREQUENCIES");
1396 Vector<Double> vec;
1397 t.keywordSet().get("RESTFREQS",vec);
1398 oss << setw(15) << "Rest Freqs:";
1399 if (vec.nelements() > 0) {
1400 oss << setprecision(0) << vec << " [Hz]" << endl;
1401 } else {
1402 oss << "None set" << endl;
1403 }
1404 oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
1405 oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
1406 << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
1407 oss << endl;
1408
1409 String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
1410 oss << setw(5) << "Scan"
1411 << setw(15) << "Source"
1412 << setw(24) << dirtype
1413 << setw(10) << "Time"
1414 << setw(18) << "Integration"
1415 << setw(7) << "FreqIDs" << endl;
1416 oss << "--------------------------------------------------------------------------------" << endl;
1417
1418 // Generate list of scan start and end integrations
1419 Vector<Int> scanIDs = scanCol_.getColumn();
1420 Vector<uInt> startInt, endInt;
1421 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1422
1423 const uInt nScans = startInt.nelements();
1424 String name;
1425 Vector<uInt> freqIDs, listFQ;
1426 uInt nInt;
1427
1428 for (uInt i=0; i<nScans; i++) {
1429 // Get things from first integration of scan
1430 String time = getTime(startInt(i),False);
1431 String tInt = formatSec(Double(getInterval(startInt(i))));
1432 String posit = formatDirection(getDirection(startInt(i),True));
1433 srcnCol_.getScalar(startInt(i),name);
1434
1435 // Find all the FreqIDs in this scan
1436 listFQ.resize(0);
1437 for (uInt j=startInt(i); j<endInt(i)+1; j++) {
1438 freqidCol_.get(j, freqIDs);
1439 for (uInt k=0; k<freqIDs.nelements(); k++) {
1440 mathutil::addEntry(listFQ, freqIDs(k));
1441 }
1442 }
1443
1444 nInt = endInt(i) - startInt(i) + 1;
1445 oss << setw(3) << std::right << i << std::left << setw(2) << " "
1446 << setw(15) << name
1447 << setw(24) << posit
1448 << setw(10) << time
1449 << setw(3) << std::right << nInt << setw(3) << " x " << std::left
1450 << setw(6) << tInt
1451 << " " << listFQ << endl;
1452 }
1453 oss << endl;
1454 oss << "Table contains " << table_.nrow() << " integration(s) in "
1455 << nScans << " scan(s)." << endl;
1456
1457 // Frequency Table
1458 if (verbose) {
1459 std::vector<string> info = getCoordInfo();
1460 SDFrequencyTable sdft = getSDFreqTable();
1461 oss << endl << endl;
1462 oss << "FreqID Frame RefFreq(Hz) RefPix Increment(Hz)" << endl;
1463 oss << "--------------------------------------------------------------------------------" << endl;
1464 for (uInt i=0; i<sdft.length(); i++) {
1465 oss << setw(8) << i << setw(8)
1466 << info[3] << setw(16) << setprecision(8)
1467 << sdft.referenceValue(i) << setw(10)
1468 << sdft.referencePixel(i) << setw(12)
1469 << sdft.increment(i) << endl;
1470 }
1471 oss << "--------------------------------------------------------------------------------" << endl;
1472 }
1473 return String(oss);
1474}
1475/*
1476std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
1477 ostringstream oss;
1478 Vector<Int> scanIDs = scanCol_.getColumn();
1479 Vector<uInt> startInt, endInt;
1480 mathutil::scanBoundaries(startInt, endInt, scanIDs);
1481 const uInt nScans = startInt.nelements();
1482 std::vector<int>::const_iterator it(whichScans);
1483 return String(oss);
1484}
1485*/
1486Int SDMemTable::nBeam() const
1487{
1488 Int n;
1489 table_.keywordSet().get("nBeam",n);
1490 return n;
1491}
1492
1493Int SDMemTable::nIF() const {
1494 Int n;
1495 table_.keywordSet().get("nIF",n);
1496 return n;
1497}
1498
1499Int SDMemTable::nPol() const {
1500 Int n;
1501 table_.keywordSet().get("nPol",n);
1502 return n;
1503}
1504
1505Int SDMemTable::nChan() const {
1506 Int n;
1507 table_.keywordSet().get("nChan",n);
1508 return n;
1509}
1510
1511void SDMemTable::addHistory(const std::string& hist)
1512{
1513 Table t = table_.rwKeywordSet().asTable("HISTORY");
1514 uInt nrow = t.nrow();
1515 t.addRow();
1516 ScalarColumn<String> itemCol(t, "ITEM");
1517 itemCol.put(nrow, hist);
1518}
1519
1520std::vector<std::string> SDMemTable::getHistory() const
1521{
1522 Vector<String> history;
1523 const Table& t = table_.keywordSet().asTable("HISTORY");
1524 uInt nrow = t.nrow();
1525 ROScalarColumn<String> itemCol(t, "ITEM");
1526 std::vector<std::string> stlout;
1527 String hist;
1528 for (uInt i=0; i<nrow; ++i) {
1529 itemCol.get(i, hist);
1530 stlout.push_back(hist);
1531 }
1532 return stlout;
1533}
1534/*
1535 void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
1536
1537 std::vector<int>::iterator it;
1538 ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
1539 for (it = whichChans.begin(); it != whichChans.end(); it++) {
1540 j.reset(j.begin(uInt(*it)));
1541 for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
1542 for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
1543 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
1544 iii != iii.end(); ++iii) {
1545 (*iii) =
1546 }
1547 }
1548 }
1549 }
1550
1551}
1552*/
1553void SDMemTable::flag(int whichRow)
1554 {
1555 Array<uChar> arr;
1556 flagsCol_.get(whichRow, arr);
1557
1558 ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
1559 aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
1560 ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
1561 aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
1562 ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
1563 aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
1564
1565 for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1566 (*i) = uChar(True);
1567 }
1568
1569 flagsCol_.put(whichRow, arr);
1570}
1571
1572MDirection::Types SDMemTable::getDirectionReference() const
1573{
1574 Float eq;
1575 table_.keywordSet().get("Equinox",eq);
1576 std::map<float,string> mp;
1577 mp[2000.0] = "J2000";
1578 mp[1950.0] = "B1950";
1579 MDirection::Types mdr;
1580 if (!MDirection::getType(mdr, mp[eq])) {
1581 mdr = MDirection::J2000;
1582 cerr << "Unknown equinox using J2000" << endl;
1583 }
1584
1585 return mdr;
1586}
1587
1588MEpoch::Types SDMemTable::getTimeReference() const
1589{
1590 MEpoch::Types met;
1591 String ep;
1592 table_.keywordSet().get("Epoch",ep);
1593 if (!MEpoch::getType(met, ep)) {
1594 cerr << "Epoch type unknown - using UTC" << endl;
1595 met = MEpoch::UTC;
1596 }
1597
1598 return met;
1599}
1600
1601
1602Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
1603 const String& sUnit,
1604 const vector<string>& lines,
1605 const String& source,
1606 Int whichIF)
1607{
1608 const Int nIFs = nIF();
1609 if (whichIF>=nIFs) {
1610 throw(AipsError("Illegal IF index"));
1611 }
1612
1613 // Find vector of restfrequencies
1614 // Double takes precedence over String
1615 Unit unit;
1616 Vector<Double> restFreqs;
1617 if (restFreqsIn.nelements()>0) {
1618 restFreqs.resize(restFreqsIn.nelements());
1619 restFreqs = restFreqsIn;
1620 unit = Unit(sUnit);
1621 } else if (lines.size()>0) {
1622 const uInt nLines = lines.size();
1623 unit = Unit("Hz");
1624 restFreqs.resize(nLines);
1625 MFrequency lineFreq;
1626 for (uInt i=0; i<nLines; i++) {
1627 String tS(lines[i]);
1628 tS.upcase();
1629 if (MeasTable::Line(lineFreq, tS)) {
1630 restFreqs[i] = lineFreq.getValue().getValue(); // Hz
1631 } else {
1632 String s = String(lines[i]) +
1633 String(" is an unrecognized spectral line");
1634 throw(AipsError(s));
1635 }
1636 }
1637 } else {
1638 throw(AipsError("You have not specified any rest frequencies or lines"));
1639 }
1640
1641 // If multiple restfreqs, must be length nIF. In this
1642 // case we will just replace the rest frequencies
1643 const uInt nRestFreqs = restFreqs.nelements();
1644 Int idx = -1;
1645 SDFrequencyTable sdft = getSDFreqTable();
1646
1647 if (nRestFreqs>1) {
1648 // Replace restFreqs, one per IF
1649 if (nRestFreqs != nIFs) {
1650 throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
1651 }
1652 cout << "Replacing rest frequencies with given list, one per IF" << endl;
1653 sdft.deleteRestFrequencies();
1654 for (uInt i=0; i<nRestFreqs; i++) {
1655 Quantum<Double> rf(restFreqs[i], unit);
1656 sdft.addRestFrequency(rf.getValue("Hz"));
1657 }
1658 } else {
1659
1660 // Add new rest freq
1661 Quantum<Double> rf(restFreqs[0], unit);
1662 idx = sdft.addRestFrequency(rf.getValue("Hz"));
1663 cout << "Selecting given rest frequency" << endl;
1664 }
1665
1666 // Replace
1667 Bool empty = source.empty();
1668 Bool ok = False;
1669 if (putSDFreqTable(sdft)) {
1670 const uInt nRow = table_.nrow();
1671 String srcName;
1672 Vector<uInt> restFreqIDs;
1673 for (uInt i=0; i<nRow; i++) {
1674 srcnCol_.get(i, srcName);
1675 restfreqidCol_.get(i,restFreqIDs);
1676
1677 if (idx==-1) {
1678 // Replace vector of restFreqs; one per IF.
1679 // No selection possible
1680 for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
1681 } else {
1682 // Set RestFreqID for selected data
1683 if (empty || source==srcName) {
1684 if (whichIF<0) {
1685 restFreqIDs = idx;
1686 } else {
1687 restFreqIDs[whichIF] = idx;
1688 }
1689 }
1690 }
1691 restfreqidCol_.put(i,restFreqIDs);
1692 }
1693 ok = True;
1694 } else {
1695 ok = False;
1696 }
1697
1698 return ok;
1699}
1700
1701void SDMemTable::spectralLines() const
1702{
1703 Vector<String> lines = MeasTable::Lines();
1704 MFrequency lineFreq;
1705 Double freq;
1706
1707 cout.flags(std::ios_base::left);
1708 cout << "Line Frequency (Hz)" << endl;
1709 cout << "-----------------------" << endl;
1710 for (uInt i=0; i<lines.nelements(); i++) {
1711 MeasTable::Line(lineFreq, lines[i]);
1712 freq = lineFreq.getValue().getValue(); // Hz
1713 cout << setw(11) << lines[i] << setprecision(10) << freq << endl;
1714 }
1715}
1716
1717void SDMemTable::renumber()
1718{
1719 uInt nRow = scanCol_.nrow();
1720 Int newscanid = 0;
1721 Int cIdx;// the current scanid
1722 // get the first scanid
1723 scanCol_.getScalar(0,cIdx);
1724 Int pIdx = cIdx;// the scanid of the previous row
1725 for (uInt i=0; i<nRow;++i) {
1726 scanCol_.getScalar(i,cIdx);
1727 if (pIdx == cIdx) {
1728 // renumber
1729 scanCol_.put(i,newscanid);
1730 } else {
1731 ++newscanid;
1732 pIdx = cIdx; // store scanid
1733 --i; // don't increment next loop
1734 }
1735 }
1736}
1737
1738
1739void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
1740 const IPosition& shape) const
1741{
1742 const uInt nDim = shape.nelements();
1743 start.resize(nDim);
1744 end.resize(nDim);
1745
1746 start(asap::BeamAxis) = beamSel_;
1747 end(asap::BeamAxis) = beamSel_;
1748 start(asap::IFAxis) = IFSel_;
1749 end(asap::IFAxis) = IFSel_;
1750
1751 start(asap::PolAxis) = polSel_;
1752 end(asap::PolAxis) = polSel_;
1753
1754 start(asap::ChanAxis) = 0;
1755 end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
1756}
1757
1758
1759std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
1760 // Get spectrum at cursor location
1761{
1762
1763 // Setup accessors
1764 ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
1765 aa0.reset(aa0.begin(uInt(beamSel_))); // Beam selection
1766
1767 ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
1768 aa1.reset(aa1.begin(uInt(IFSel_))); // IF selection
1769
1770 ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
1771 aa2.reset(aa2.begin(uInt(polSel_))); // Pol selection
1772
1773 std::vector<float> spectrum;
1774 for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
1775 spectrum.push_back(*i);
1776 }
1777 return spectrum;
1778}
1779
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