source: trunk/src/Scantable.cpp@ 3014

Last change on this file since 3014 was 3010, checked in by WataruKawasaki, 10 years ago

New Development: No

JIRA Issue: Yes CAS-6599

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s): sd

Description: modified so that sd.scantable.stats() returns None for flagged rows and rows with all channels flagged.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 165.8 KB
RevLine 
[805]1//
2// C++ Implementation: Scantable
3//
4// Description:
5//
6//
[2791]7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005-2013
[805]8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
[206]12#include <map>
[2591]13#include <sys/time.h>
[206]14
[2186]15#include <atnf/PKSIO/SrcType.h>
16
[125]17#include <casa/aips.h>
[2186]18#include <casa/iomanip.h>
[80]19#include <casa/iostream.h>
[2186]20#include <casa/OS/File.h>
[805]21#include <casa/OS/Path.h>
[2658]22#include <casa/Logging/LogIO.h>
[80]23#include <casa/Arrays/Array.h>
[2186]24#include <casa/Arrays/ArrayAccessor.h>
25#include <casa/Arrays/ArrayLogical.h>
[80]26#include <casa/Arrays/ArrayMath.h>
27#include <casa/Arrays/MaskArrMath.h>
[2186]28#include <casa/Arrays/Slice.h>
[1325]29#include <casa/Arrays/Vector.h>
[455]30#include <casa/Arrays/VectorSTLIterator.h>
[418]31#include <casa/BasicMath/Math.h>
[504]32#include <casa/BasicSL/Constants.h>
[2186]33#include <casa/Containers/RecordField.h>
34#include <casa/Logging/LogIO.h>
[286]35#include <casa/Quanta/MVAngle.h>
[2186]36#include <casa/Quanta/MVTime.h>
[902]37#include <casa/Utilities/GenSort.h>
[2]38
[2186]39#include <coordinates/Coordinates/CoordinateUtil.h>
[2]40
[1325]41// needed to avoid error in .tcc
42#include <measures/Measures/MCDirection.h>
43//
44#include <measures/Measures/MDirection.h>
[2186]45#include <measures/Measures/MEpoch.h>
[80]46#include <measures/Measures/MFrequency.h>
[2186]47#include <measures/Measures/MeasRef.h>
48#include <measures/Measures/MeasTable.h>
49#include <measures/TableMeasures/ScalarMeasColumn.h>
50#include <measures/TableMeasures/TableMeasDesc.h>
[805]51#include <measures/TableMeasures/TableMeasRefDesc.h>
52#include <measures/TableMeasures/TableMeasValueDesc.h>
[2]53
[2186]54#include <tables/Tables/ArrColDesc.h>
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/ScaColDesc.h>
57#include <tables/Tables/SetupNewTab.h>
58#include <tables/Tables/TableCopy.h>
59#include <tables/Tables/TableDesc.h>
60#include <tables/Tables/TableIter.h>
61#include <tables/Tables/TableParse.h>
62#include <tables/Tables/TableRecord.h>
63#include <tables/Tables/TableRow.h>
64#include <tables/Tables/TableVector.h>
65
66#include "MathUtils.h"
67#include "STAttr.h"
[2737]68#include "STBaselineTable.h"
[2186]69#include "STLineFinder.h"
70#include "STPolCircular.h"
[896]71#include "STPolLinear.h"
[913]72#include "STPolStokes.h"
[2321]73#include "STUpgrade.h"
[2666]74#include "STFitter.h"
[2186]75#include "Scantable.h"
[2]76
[2462]77#define debug 1
78
[125]79using namespace casa;
[2]80
[805]81namespace asap {
82
[896]83std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
84
85void Scantable::initFactories() {
86 if ( factories_.empty() ) {
87 Scantable::factories_["linear"] = &STPolLinear::myFactory;
[1323]88 Scantable::factories_["circular"] = &STPolCircular::myFactory;
[913]89 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
[896]90 }
91}
92
[805]93Scantable::Scantable(Table::TableType ttype) :
[852]94 type_(ttype)
[206]95{
[896]96 initFactories();
[805]97 setupMainTable();
[2346]98 freqTable_ = STFrequencies(*this);
99 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
[852]100 weatherTable_ = STWeather(*this);
[805]101 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
[852]102 focusTable_ = STFocus(*this);
[805]103 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
[852]104 tcalTable_ = STTcal(*this);
[805]105 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
[852]106 moleculeTable_ = STMolecules(*this);
[805]107 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
[860]108 historyTable_ = STHistory(*this);
109 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
[959]110 fitTable_ = STFit(*this);
111 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
[1881]112 table_.tableInfo().setType( "Scantable" ) ;
[805]113 originalTable_ = table_;
[322]114 attach();
[18]115}
[206]116
[805]117Scantable::Scantable(const std::string& name, Table::TableType ttype) :
[852]118 type_(ttype)
[206]119{
[896]120 initFactories();
[1819]121
[865]122 Table tab(name, Table::Update);
[1009]123 uInt version = tab.keywordSet().asuInt("VERSION");
[483]124 if (version != version_) {
[2321]125 STUpgrade upgrader(version_);
[2162]126 LogIO os( LogOrigin( "Scantable" ) ) ;
127 os << LogIO::WARN
[2321]128 << name << " data format version " << version
129 << " is deprecated" << endl
130 << "Running upgrade."<< endl
[2162]131 << LogIO::POST ;
[2321]132 std::string outname = upgrader.upgrade(name);
[2332]133 if ( outname != name ) {
134 os << LogIO::WARN
135 << "Data will be loaded from " << outname << " instead of "
136 << name << LogIO::POST ;
137 tab = Table(outname, Table::Update ) ;
138 }
[483]139 }
[1009]140 if ( type_ == Table::Memory ) {
[852]141 table_ = tab.copyToMemoryTable(generateName());
[1009]142 } else {
[805]143 table_ = tab;
[1009]144 }
[1881]145 table_.tableInfo().setType( "Scantable" ) ;
[1009]146
[859]147 attachSubtables();
[805]148 originalTable_ = table_;
[329]149 attach();
[2]150}
[1819]151/*
152Scantable::Scantable(const std::string& name, Table::TableType ttype) :
153 type_(ttype)
154{
155 initFactories();
156 Table tab(name, Table::Update);
157 uInt version = tab.keywordSet().asuInt("VERSION");
158 if (version != version_) {
159 throw(AipsError("Unsupported version of ASAP file."));
160 }
161 if ( type_ == Table::Memory ) {
162 table_ = tab.copyToMemoryTable(generateName());
163 } else {
164 table_ = tab;
165 }
[2]166
[1819]167 attachSubtables();
168 originalTable_ = table_;
169 attach();
170}
171*/
172
[2658]173Scantable::Scantable( const Scantable& other, bool clear )
[206]174{
[805]175 // with or without data
[859]176 String newname = String(generateName());
[865]177 type_ = other.table_.tableType();
[859]178 if ( other.table_.tableType() == Table::Memory ) {
179 if ( clear ) {
180 table_ = TableCopy::makeEmptyMemoryTable(newname,
181 other.table_, True);
[2818]182 } else {
[859]183 table_ = other.table_.copyToMemoryTable(newname);
[2818]184 }
[16]185 } else {
[915]186 other.table_.deepCopy(newname, Table::New, False,
187 other.table_.endianFormat(),
[865]188 Bool(clear));
189 table_ = Table(newname, Table::Update);
190 table_.markForDelete();
191 }
[1881]192 table_.tableInfo().setType( "Scantable" ) ;
[1111]193 /// @todo reindex SCANNO, recompute nbeam, nif, npol
[2846]194 if ( clear ) copySubtables(other);
[859]195 attachSubtables();
[805]196 originalTable_ = table_;
[322]197 attach();
[2]198}
199
[865]200void Scantable::copySubtables(const Scantable& other) {
201 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
[2346]202 TableCopy::copyRows(t, other.freqTable_.table());
[865]203 t = table_.rwKeywordSet().asTable("FOCUS");
204 TableCopy::copyRows(t, other.focusTable_.table());
205 t = table_.rwKeywordSet().asTable("WEATHER");
206 TableCopy::copyRows(t, other.weatherTable_.table());
207 t = table_.rwKeywordSet().asTable("TCAL");
208 TableCopy::copyRows(t, other.tcalTable_.table());
209 t = table_.rwKeywordSet().asTable("MOLECULES");
210 TableCopy::copyRows(t, other.moleculeTable_.table());
211 t = table_.rwKeywordSet().asTable("HISTORY");
212 TableCopy::copyRows(t, other.historyTable_.table());
[972]213 t = table_.rwKeywordSet().asTable("FIT");
214 TableCopy::copyRows(t, other.fitTable_.table());
[865]215}
216
[859]217void Scantable::attachSubtables()
218{
[2346]219 freqTable_ = STFrequencies(table_);
[859]220 focusTable_ = STFocus(table_);
221 weatherTable_ = STWeather(table_);
222 tcalTable_ = STTcal(table_);
223 moleculeTable_ = STMolecules(table_);
[860]224 historyTable_ = STHistory(table_);
[972]225 fitTable_ = STFit(table_);
[859]226}
227
[805]228Scantable::~Scantable()
[206]229{
[2]230}
231
[805]232void Scantable::setupMainTable()
[206]233{
[805]234 TableDesc td("", "1", TableDesc::Scratch);
235 td.comment() = "An ASAP Scantable";
[1009]236 td.rwKeywordSet().define("VERSION", uInt(version_));
[2]237
[805]238 // n Cycles
239 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
240 // new index every nBeam x nIF x nPol
241 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
[2]242
[805]243 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
244 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
[972]245 // linear, circular, stokes
[805]246 td.rwKeywordSet().define("POLTYPE", String("linear"));
247 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
[138]248
[805]249 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
250 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
[80]251
[1819]252 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
253 refbeamnoColumn.setDefault(Int(-1));
254 td.addColumn(refbeamnoColumn);
255
256 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
257 flagrowColumn.setDefault(uInt(0));
258 td.addColumn(flagrowColumn);
259
[805]260 td.addColumn(ScalarColumnDesc<Double>("TIME"));
261 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
262 TableMeasValueDesc measVal(td, "TIME");
263 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
264 mepochCol.write(td);
[483]265
[805]266 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
267
[2]268 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
[805]269 // Type of source (on=0, off=1, other=-1)
[1503]270 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
271 stypeColumn.setDefault(Int(-1));
272 td.addColumn(stypeColumn);
[805]273 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
274
275 //The actual Data Vectors
[2]276 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
277 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
[89]278 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
[805]279
280 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
281 IPosition(1,2),
282 ColumnDesc::Direct));
283 TableMeasRefDesc mdirRef(MDirection::J2000); // default
284 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
285 // the TableMeasDesc gives the column a type
286 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
[987]287 // a uder set table type e.g. GALCTIC, B1950 ...
288 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
[805]289 // writing create the measure column
290 mdirCol.write(td);
[923]291 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
292 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
[1047]293 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
[105]294
[805]295 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
[972]296 ScalarColumnDesc<Int> fitColumn("FIT_ID");
[973]297 fitColumn.setDefault(Int(-1));
[972]298 td.addColumn(fitColumn);
[805]299
300 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
301 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
302
[999]303 // columns which just get dragged along, as they aren't used in asap
304 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
305 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
306 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
307 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
308
[805]309 td.rwKeywordSet().define("OBSMODE", String(""));
310
[418]311 // Now create Table SetUp from the description.
[859]312 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
[852]313 table_ = Table(aNewTab, type_, 0);
[805]314 originalTable_ = table_;
315}
[418]316
[805]317void Scantable::attach()
[455]318{
[805]319 timeCol_.attach(table_, "TIME");
320 srcnCol_.attach(table_, "SRCNAME");
[1068]321 srctCol_.attach(table_, "SRCTYPE");
[805]322 specCol_.attach(table_, "SPECTRA");
323 flagsCol_.attach(table_, "FLAGTRA");
[865]324 tsysCol_.attach(table_, "TSYS");
[805]325 cycleCol_.attach(table_,"CYCLENO");
326 scanCol_.attach(table_, "SCANNO");
327 beamCol_.attach(table_, "BEAMNO");
[847]328 ifCol_.attach(table_, "IFNO");
329 polCol_.attach(table_, "POLNO");
[805]330 integrCol_.attach(table_, "INTERVAL");
331 azCol_.attach(table_, "AZIMUTH");
332 elCol_.attach(table_, "ELEVATION");
333 dirCol_.attach(table_, "DIRECTION");
334 fldnCol_.attach(table_, "FIELDNAME");
335 rbeamCol_.attach(table_, "REFBEAMNO");
[455]336
[1730]337 mweatheridCol_.attach(table_,"WEATHER_ID");
[805]338 mfitidCol_.attach(table_,"FIT_ID");
339 mfreqidCol_.attach(table_, "FREQ_ID");
340 mtcalidCol_.attach(table_, "TCAL_ID");
341 mfocusidCol_.attach(table_, "FOCUS_ID");
342 mmolidCol_.attach(table_, "MOLECULE_ID");
[1819]343
344 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
345 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
346
[455]347}
348
[1819]349template<class T, class T2>
350void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
351 const String& colName,
352 const T2& defValue)
353{
354 try {
355 col.attach(table_, colName);
356 } catch (TableError& err) {
357 String errMesg = err.getMesg();
358 if (errMesg == "Table column " + colName + " is unknown") {
359 table_.addColumn(ScalarColumnDesc<T>(colName));
360 col.attach(table_, colName);
361 col.fillColumn(static_cast<T>(defValue));
362 } else {
363 throw;
364 }
365 } catch (...) {
366 throw;
367 }
368}
369
370template<class T, class T2>
371void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
372 const String& colName,
373 const Array<T2>& defValue)
374{
375 try {
376 col.attach(table_, colName);
377 } catch (TableError& err) {
378 String errMesg = err.getMesg();
379 if (errMesg == "Table column " + colName + " is unknown") {
380 table_.addColumn(ArrayColumnDesc<T>(colName));
381 col.attach(table_, colName);
382
383 int size = 0;
384 ArrayIterator<T2>& it = defValue.begin();
385 while (it != defValue.end()) {
386 ++size;
387 ++it;
388 }
389 IPosition ip(1, size);
390 Array<T>& arr(ip);
391 for (int i = 0; i < size; ++i)
392 arr[i] = static_cast<T>(defValue[i]);
393
394 col.fillColumn(arr);
395 } else {
396 throw;
397 }
398 } catch (...) {
399 throw;
400 }
401}
402
[901]403void Scantable::setHeader(const STHeader& sdh)
[206]404{
[18]405 table_.rwKeywordSet().define("nIF", sdh.nif);
406 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
407 table_.rwKeywordSet().define("nPol", sdh.npol);
408 table_.rwKeywordSet().define("nChan", sdh.nchan);
409 table_.rwKeywordSet().define("Observer", sdh.observer);
410 table_.rwKeywordSet().define("Project", sdh.project);
411 table_.rwKeywordSet().define("Obstype", sdh.obstype);
412 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
413 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
414 table_.rwKeywordSet().define("Equinox", sdh.equinox);
415 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
416 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
417 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
418 table_.rwKeywordSet().define("UTC", sdh.utc);
[206]419 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
420 table_.rwKeywordSet().define("Epoch", sdh.epoch);
[905]421 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
[50]422}
[21]423
[901]424STHeader Scantable::getHeader() const
[206]425{
[901]426 STHeader sdh;
[21]427 table_.keywordSet().get("nBeam",sdh.nbeam);
428 table_.keywordSet().get("nIF",sdh.nif);
429 table_.keywordSet().get("nPol",sdh.npol);
430 table_.keywordSet().get("nChan",sdh.nchan);
431 table_.keywordSet().get("Observer", sdh.observer);
432 table_.keywordSet().get("Project", sdh.project);
433 table_.keywordSet().get("Obstype", sdh.obstype);
434 table_.keywordSet().get("AntennaName", sdh.antennaname);
435 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
436 table_.keywordSet().get("Equinox", sdh.equinox);
437 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
438 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
439 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
440 table_.keywordSet().get("UTC", sdh.utc);
[206]441 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
442 table_.keywordSet().get("Epoch", sdh.epoch);
[905]443 table_.keywordSet().get("POLTYPE", sdh.poltype);
[21]444 return sdh;
[18]445}
[805]446
[1360]447void Scantable::setSourceType( int stype )
[1068]448{
449 if ( stype < 0 || stype > 1 )
450 throw(AipsError("Illegal sourcetype."));
451 TableVector<Int> tabvec(table_, "SRCTYPE");
452 tabvec = Int(stype);
453}
454
[2818]455void Scantable::setSourceName( const std::string& name )
456{
457 TableVector<String> tabvec(table_, "SRCNAME");
458 tabvec = name;
459}
460
[845]461bool Scantable::conformant( const Scantable& other )
462{
463 return this->getHeader().conformant(other.getHeader());
464}
465
466
[50]467
[805]468std::string Scantable::formatSec(Double x) const
[206]469{
[105]470 Double xcop = x;
471 MVTime mvt(xcop/24./3600.); // make days
[365]472
[105]473 if (x < 59.95)
[281]474 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
[745]475 else if (x < 3599.95)
[281]476 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
477 else {
478 ostringstream oss;
479 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
480 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
481 return String(oss);
[745]482 }
[105]483};
484
[2969]485 std::string Scantable::formatDirection(const MDirection& md, Int prec) const
[281]486{
487 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
[2969]488 if (prec<0)
489 prec = 7;
[281]490
[2575]491 String ref = md.getRefString();
[281]492 MVAngle mvLon(t[0]);
493 String sLon = mvLon.string(MVAngle::TIME,prec);
[987]494 uInt tp = md.getRef().getType();
495 if (tp == MDirection::GALACTIC ||
496 tp == MDirection::SUPERGAL ) {
497 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
498 }
[281]499 MVAngle mvLat(t[1]);
500 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
[2575]501 return ref + String(" ") + sLon + String(" ") + sLat;
[281]502}
503
504
[805]505std::string Scantable::getFluxUnit() const
[206]506{
[847]507 return table_.keywordSet().asString("FluxUnit");
[206]508}
509
[805]510void Scantable::setFluxUnit(const std::string& unit)
[218]511{
512 String tmp(unit);
513 Unit tU(tmp);
514 if (tU==Unit("K") || tU==Unit("Jy")) {
515 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
516 } else {
517 throw AipsError("Illegal unit - must be compatible with Jy or K");
518 }
519}
520
[805]521void Scantable::setInstrument(const std::string& name)
[236]522{
[805]523 bool throwIt = true;
[996]524 // create an Instrument to see if this is valid
525 STAttr::convertInstrument(name, throwIt);
[236]526 String nameU(name);
527 nameU.upcase();
528 table_.rwKeywordSet().define(String("AntennaName"), nameU);
529}
530
[1189]531void Scantable::setFeedType(const std::string& feedtype)
532{
533 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
534 std::string msg = "Illegal feed type "+ feedtype;
535 throw(casa::AipsError(msg));
536 }
537 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
538}
539
[1743]540MPosition Scantable::getAntennaPosition() const
[805]541{
542 Vector<Double> antpos;
543 table_.keywordSet().get("AntennaPosition", antpos);
544 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
545 return MPosition(mvpos);
546}
[281]547
[805]548void Scantable::makePersistent(const std::string& filename)
549{
550 String inname(filename);
551 Path path(inname);
[1111]552 /// @todo reindex SCANNO, recompute nbeam, nif, npol
[805]553 inname = path.expandedName();
[2030]554 // 2011/03/04 TN
555 // We can comment out this workaround since the essential bug is
556 // fixed in casacore (r20889 in google code).
557 table_.deepCopy(inname, Table::New);
558// // WORKAROUND !!! for Table bug
559// // Remove when fixed in casacore
560// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
561// Table tab = table_.copyToMemoryTable(generateName());
562// tab.deepCopy(inname, Table::New);
563// tab.markForDelete();
564//
565// } else {
566// table_.deepCopy(inname, Table::New);
567// }
[805]568}
569
[837]570int Scantable::nbeam( int scanno ) const
[805]571{
572 if ( scanno < 0 ) {
573 Int n;
574 table_.keywordSet().get("nBeam",n);
575 return int(n);
[105]576 } else {
[805]577 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
[888]578 Table t = table_(table_.col("SCANNO") == scanno);
579 ROTableRow row(t);
580 const TableRecord& rec = row.get(0);
581 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
582 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
583 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
584 ROTableVector<uInt> v(subt, "BEAMNO");
[805]585 return int(v.nelements());
[105]586 }
[805]587 return 0;
588}
[455]589
[837]590int Scantable::nif( int scanno ) const
[805]591{
592 if ( scanno < 0 ) {
593 Int n;
594 table_.keywordSet().get("nIF",n);
595 return int(n);
596 } else {
597 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
[888]598 Table t = table_(table_.col("SCANNO") == scanno);
599 ROTableRow row(t);
600 const TableRecord& rec = row.get(0);
601 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
602 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
603 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
604 if ( subt.nrow() == 0 ) return 0;
605 ROTableVector<uInt> v(subt, "IFNO");
[805]606 return int(v.nelements());
[2]607 }
[805]608 return 0;
609}
[321]610
[837]611int Scantable::npol( int scanno ) const
[805]612{
613 if ( scanno < 0 ) {
614 Int n;
615 table_.keywordSet().get("nPol",n);
616 return n;
617 } else {
618 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
[888]619 Table t = table_(table_.col("SCANNO") == scanno);
620 ROTableRow row(t);
621 const TableRecord& rec = row.get(0);
622 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
623 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
624 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
625 if ( subt.nrow() == 0 ) return 0;
626 ROTableVector<uInt> v(subt, "POLNO");
[805]627 return int(v.nelements());
[321]628 }
[805]629 return 0;
[2]630}
[805]631
[845]632int Scantable::ncycle( int scanno ) const
[206]633{
[805]634 if ( scanno < 0 ) {
[837]635 Block<String> cols(2);
636 cols[0] = "SCANNO";
637 cols[1] = "CYCLENO";
638 TableIterator it(table_, cols);
639 int n = 0;
640 while ( !it.pastEnd() ) {
641 ++n;
[902]642 ++it;
[837]643 }
644 return n;
[805]645 } else {
[888]646 Table t = table_(table_.col("SCANNO") == scanno);
647 ROTableRow row(t);
648 const TableRecord& rec = row.get(0);
649 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
650 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
651 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
652 if ( subt.nrow() == 0 ) return 0;
653 return int(subt.nrow());
[805]654 }
655 return 0;
[18]656}
[455]657
658
[845]659int Scantable::nrow( int scanno ) const
[805]660{
[845]661 return int(table_.nrow());
662}
663
664int Scantable::nchan( int ifno ) const
665{
666 if ( ifno < 0 ) {
[805]667 Int n;
668 table_.keywordSet().get("nChan",n);
669 return int(n);
670 } else {
[1360]671 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
672 // vary with these
[2244]673 Table t = table_(table_.col("IFNO") == ifno, 1);
[888]674 if ( t.nrow() == 0 ) return 0;
675 ROArrayColumn<Float> v(t, "SPECTRA");
[923]676 return v.shape(0)(0);
[805]677 }
678 return 0;
[18]679}
[455]680
[1111]681int Scantable::nscan() const {
682 Vector<uInt> scannos(scanCol_.getColumn());
[1148]683 uInt nout = genSort( scannos, Sort::Ascending,
[1111]684 Sort::QuickSort|Sort::NoDuplicates );
685 return int(nout);
686}
687
[923]688int Scantable::getChannels(int whichrow) const
689{
690 return specCol_.shape(whichrow)(0);
691}
[847]692
693int Scantable::getBeam(int whichrow) const
694{
695 return beamCol_(whichrow);
696}
697
[1694]698std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
[1111]699{
700 Vector<uInt> nos(col.getColumn());
[1148]701 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
702 nos.resize(n, True);
[1111]703 std::vector<uint> stlout;
704 nos.tovector(stlout);
705 return stlout;
706}
707
[847]708int Scantable::getIF(int whichrow) const
709{
710 return ifCol_(whichrow);
711}
712
713int Scantable::getPol(int whichrow) const
714{
715 return polCol_(whichrow);
716}
717
[805]718std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
719{
[1947]720 return formatTime(me, showdate, 0);
721}
722
723std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
724{
[805]725 MVTime mvt(me.getValue());
726 if (showdate)
[1947]727 //mvt.setFormat(MVTime::YMD);
728 mvt.setFormat(MVTime::YMD, prec);
[805]729 else
[1947]730 //mvt.setFormat(MVTime::TIME);
731 mvt.setFormat(MVTime::TIME, prec);
[805]732 ostringstream oss;
733 oss << mvt;
734 return String(oss);
735}
[488]736
[805]737void Scantable::calculateAZEL()
[2658]738{
739 LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ;
[805]740 MPosition mp = getAntennaPosition();
741 MEpoch::ROScalarColumn timeCol(table_, "TIME");
742 ostringstream oss;
[2658]743 oss << mp;
744 os << "Computed azimuth/elevation using " << endl
745 << String(oss) << endl;
[996]746 for (Int i=0; i<nrow(); ++i) {
[805]747 MEpoch me = timeCol(i);
[987]748 MDirection md = getDirection(i);
[2658]749 os << " Time: " << formatTime(me,False)
750 << " Direction: " << formatDirection(md)
[805]751 << endl << " => ";
752 MeasFrame frame(mp, me);
753 Vector<Double> azel =
754 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
755 frame)
756 )().getAngle("rad").getValue();
[923]757 azCol_.put(i,Float(azel[0]));
758 elCol_.put(i,Float(azel[1]));
[2658]759 os << "azel: " << azel[0]/C::pi*180.0 << " "
760 << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST;
[16]761 }
[805]762}
[89]763
[1819]764void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
765{
[2947]766 Vector<uInt> flagrow = flagrowCol_.getColumn();
[1819]767 for (uInt i=0; i<table_.nrow(); ++i) {
[2947]768 // apply flag only when specified row is vaild
769 if (flagrow[i] == 0) {
770 Vector<uChar> flgs = flagsCol_(i);
771 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
772 flagsCol_.put(i, flgs);
773 }
[1819]774 }
775}
776
777std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
778{
779 Vector<uChar> flags;
780 flagsCol_.get(uInt(whichrow), flags);
781 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
782 Vector<Bool> bflag(flags.shape());
783 convertArray(bflag, flags);
784 //bflag = !bflag;
785
786 std::vector<bool> mask;
787 bflag.tovector(mask);
788 return mask;
789}
790
791void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
792 Vector<uChar> flgs)
793{
794 Vector<Float> spcs = specCol_(whichrow);
[2348]795 uInt nchannel = spcs.nelements();
[1819]796 if (spcs.nelements() != nchannel) {
797 throw(AipsError("Data has incorrect number of channels"));
798 }
799 uChar userflag = 1 << 7;
800 if (unflag) {
801 userflag = 0 << 7;
802 }
803 if (clipoutside) {
804 for (uInt j = 0; j < nchannel; ++j) {
805 Float spc = spcs(j);
806 if ((spc >= uthres) || (spc <= dthres)) {
807 flgs(j) = userflag;
808 }
809 }
810 } else {
811 for (uInt j = 0; j < nchannel; ++j) {
812 Float spc = spcs(j);
813 if ((spc < uthres) && (spc > dthres)) {
814 flgs(j) = userflag;
815 }
816 }
817 }
818}
819
[1994]820
821void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
[1333]822 std::vector<bool>::const_iterator it;
823 uInt ntrue = 0;
[1994]824 if (whichrow >= int(table_.nrow()) ) {
825 throw(AipsError("Invalid row number"));
826 }
[1333]827 for (it = msk.begin(); it != msk.end(); ++it) {
828 if ( *it ) {
829 ntrue++;
830 }
831 }
[1994]832 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
833 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
[1000]834 throw(AipsError("Trying to flag whole scantable."));
[1994]835 uChar userflag = 1 << 7;
836 if ( unflag ) {
837 userflag = 0 << 7;
838 }
839 if (whichrow > -1 ) {
[2947]840 // apply flag only when specified row is vaild
841 if (flagrowCol_(whichrow) == 0) {
842 applyChanFlag(uInt(whichrow), msk, userflag);
843 }
[1994]844 } else {
[2948]845 Vector<uInt> flagrow = flagrowCol_.getColumn();
[1000]846 for ( uInt i=0; i<table_.nrow(); ++i) {
[2947]847 // apply flag only when specified row is vaild
[2948]848 if (flagrow[i] == 0) {
[2947]849 applyChanFlag(i, msk, userflag);
850 }
[1000]851 }
[1994]852 }
853}
854
855void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
856{
857 if (whichrow >= table_.nrow() ) {
858 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
859 }
860 Vector<uChar> flgs = flagsCol_(whichrow);
861 if ( msk.size() == 0 ) {
862 flgs = flagval;
863 flagsCol_.put(whichrow, flgs);
[1000]864 return;
865 }
[2348]866 if ( int(msk.size()) != nchan( getIF(whichrow) ) ) {
[1000]867 throw(AipsError("Mask has incorrect number of channels."));
868 }
[1994]869 if ( flgs.nelements() != msk.size() ) {
870 throw(AipsError("Mask has incorrect number of channels."
871 " Probably varying with IF. Please flag per IF"));
872 }
873 std::vector<bool>::const_iterator it;
874 uInt j = 0;
875 for (it = msk.begin(); it != msk.end(); ++it) {
876 if ( *it ) {
877 flgs(j) = flagval;
[1000]878 }
[1994]879 ++j;
[1000]880 }
[1994]881 flagsCol_.put(whichrow, flgs);
[865]882}
883
[1819]884void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
885{
[2683]886 if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag)
[1819]887 throw(AipsError("Trying to flag whole scantable."));
888
889 uInt rowflag = (unflag ? 0 : 1);
890 std::vector<uInt>::const_iterator it;
891 for (it = rows.begin(); it != rows.end(); ++it)
892 flagrowCol_.put(*it, rowflag);
893}
894
[805]895std::vector<bool> Scantable::getMask(int whichrow) const
896{
897 Vector<uChar> flags;
898 flagsCol_.get(uInt(whichrow), flags);
899 Vector<Bool> bflag(flags.shape());
900 convertArray(bflag, flags);
901 bflag = !bflag;
902 std::vector<bool> mask;
903 bflag.tovector(mask);
904 return mask;
905}
[89]906
[896]907std::vector<float> Scantable::getSpectrum( int whichrow,
[902]908 const std::string& poltype ) const
[805]909{
[2658]910 LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ;
911
[905]912 String ptype = poltype;
913 if (poltype == "" ) ptype = getPolType();
[902]914 if ( whichrow < 0 || whichrow >= nrow() )
915 throw(AipsError("Illegal row number."));
[896]916 std::vector<float> out;
[805]917 Vector<Float> arr;
[896]918 uInt requestedpol = polCol_(whichrow);
919 String basetype = getPolType();
[905]920 if ( ptype == basetype ) {
[896]921 specCol_.get(whichrow, arr);
922 } else {
[1598]923 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
[1586]924 basetype));
[1334]925 uInt row = uInt(whichrow);
926 stpol->setSpectra(getPolMatrix(row));
[2047]927 Float fang,fhand;
[1586]928 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
[1334]929 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
[1586]930 stpol->setPhaseCorrections(fang, fhand);
[1334]931 arr = stpol->getSpectrum(requestedpol, ptype);
[896]932 }
[902]933 if ( arr.nelements() == 0 )
[2658]934
935 os << "Not enough polarisations present to do the conversion."
936 << LogIO::POST;
[805]937 arr.tovector(out);
938 return out;
[89]939}
[212]940
[1360]941void Scantable::setSpectrum( const std::vector<float>& spec,
[884]942 int whichrow )
943{
944 Vector<Float> spectrum(spec);
945 Vector<Float> arr;
946 specCol_.get(whichrow, arr);
947 if ( spectrum.nelements() != arr.nelements() )
[896]948 throw AipsError("The spectrum has incorrect number of channels.");
[884]949 specCol_.put(whichrow, spectrum);
950}
951
952
[805]953String Scantable::generateName()
[745]954{
[805]955 return (File::newUniqueName("./","temp")).baseName();
[212]956}
957
[805]958const casa::Table& Scantable::table( ) const
[212]959{
[805]960 return table_;
[212]961}
962
[805]963casa::Table& Scantable::table( )
[386]964{
[805]965 return table_;
[386]966}
967
[896]968std::string Scantable::getPolType() const
969{
970 return table_.keywordSet().asString("POLTYPE");
971}
972
[805]973void Scantable::unsetSelection()
[380]974{
[805]975 table_ = originalTable_;
[847]976 attach();
[805]977 selector_.reset();
[380]978}
[386]979
[805]980void Scantable::setSelection( const STSelector& selection )
[430]981{
[805]982 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
983 if ( tab.nrow() == 0 ) {
984 throw(AipsError("Selection contains no data. Not applying it."));
985 }
986 table_ = tab;
[847]987 attach();
[2084]988// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
989// vector<uint> selectedIFs = getIFNos() ;
990// Int newnIF = selectedIFs.size() ;
991// tab.rwKeywordSet().define("nIF",newnIF) ;
992// if ( newnIF != 0 ) {
993// Int newnChan = 0 ;
994// for ( Int i = 0 ; i < newnIF ; i++ ) {
995// Int nChan = nchan( selectedIFs[i] ) ;
996// if ( newnChan > nChan )
997// newnChan = nChan ;
998// }
999// tab.rwKeywordSet().define("nChan",newnChan) ;
1000// }
1001// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
[805]1002 selector_ = selection;
[430]1003}
1004
[2111]1005
[2163]1006std::string Scantable::headerSummary()
[447]1007{
[805]1008 // Format header info
[2111]1009// STHeader sdh;
1010// sdh = getHeader();
1011// sdh.print();
[805]1012 ostringstream oss;
1013 oss.flags(std::ios_base::left);
[2290]1014 String tmp;
1015 // Project
1016 table_.keywordSet().get("Project", tmp);
1017 oss << setw(15) << "Project:" << tmp << endl;
1018 // Observation date
1019 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1020 // Observer
1021 oss << setw(15) << "Observer:"
1022 << table_.keywordSet().asString("Observer") << endl;
1023 // Antenna Name
1024 table_.keywordSet().get("AntennaName", tmp);
1025 oss << setw(15) << "Antenna Name:" << tmp << endl;
1026 // Obs type
1027 table_.keywordSet().get("Obstype", tmp);
1028 // Records (nrow)
1029 oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
1030 oss << setw(15) << "Obs. Type:" << tmp << endl;
1031 // Beams, IFs, Polarizations, and Channels
[805]1032 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1033 << setw(15) << "IFs:" << setw(4) << nif() << endl
[896]1034 << setw(15) << "Polarisations:" << setw(4) << npol()
1035 << "(" << getPolType() << ")" << endl
[1694]1036 << setw(15) << "Channels:" << nchan() << endl;
[2290]1037 // Flux unit
1038 table_.keywordSet().get("FluxUnit", tmp);
1039 oss << setw(15) << "Flux Unit:" << tmp << endl;
1040 // Abscissa Unit
1041 oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
1042 // Selection
1043 oss << selector_.print() << endl;
1044
1045 return String(oss);
1046}
1047
1048void Scantable::summary( const std::string& filename )
1049{
1050 ostringstream oss;
1051 ofstream ofs;
1052 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1053
1054 if (filename != "")
1055 ofs.open( filename.c_str(), ios::out );
1056
1057 oss << endl;
1058 oss << asap::SEPERATOR << endl;
1059 oss << " Scan Table Summary" << endl;
1060 oss << asap::SEPERATOR << endl;
1061
1062 // Format header info
1063 oss << headerSummary();
1064 oss << endl;
1065
1066 if (table_.nrow() <= 0){
1067 oss << asap::SEPERATOR << endl;
1068 oss << "The MAIN table is empty: there are no data!!!" << endl;
1069 oss << asap::SEPERATOR << endl;
1070
1071 ols << String(oss) << LogIO::POST;
1072 if (ofs) {
1073 ofs << String(oss) << flush;
1074 ofs.close();
1075 }
1076 return;
1077 }
1078
1079
1080
1081 // main table
1082 String dirtype = "Position ("
1083 + getDirectionRefString()
1084 + ")";
1085 oss.flags(std::ios_base::left);
1086 oss << setw(5) << "Scan"
1087 << setw(15) << "Source"
1088 << setw(35) << "Time range"
1089 << setw(2) << "" << setw(7) << "Int[s]"
1090 << setw(7) << "Record"
1091 << setw(8) << "SrcType"
1092 << setw(8) << "FreqIDs"
1093 << setw(7) << "MolIDs" << endl;
1094 oss << setw(7)<< "" << setw(6) << "Beam"
1095 << setw(23) << dirtype << endl;
1096
1097 oss << asap::SEPERATOR << endl;
1098
1099 // Flush summary and clear up the string
1100 ols << String(oss) << LogIO::POST;
1101 if (ofs) ofs << String(oss) << flush;
1102 oss.str("");
1103 oss.clear();
1104
1105
1106 // Get Freq_ID map
1107 ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
1108 Int nfid = ftabIds.nrow();
1109 if (nfid <= 0){
1110 oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
1111 oss << asap::SEPERATOR << endl;
1112
1113 ols << String(oss) << LogIO::POST;
1114 if (ofs) {
1115 ofs << String(oss) << flush;
1116 ofs.close();
1117 }
1118 return;
1119 }
1120 // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
1121 // the orders are identical to ID in FREQ subtable
1122 Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
1123 Vector<Int> fIdchans(nfid,-1);
[2938]1124 Vector<Double> fIdfreq0(nfid,-1);
1125 Vector<Double> fIdfcent(nfid,-1);
[2290]1126 map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
1127 for (Int i=0; i < nfid; i++){
1128 // fidMap[freqId] returns row number in FREQ subtable
1129 fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
1130 ifNos[i] = Vector<uInt>();
1131 polNos[i] = Vector<uInt>();
1132 }
1133
1134 TableIterator iter(table_, "SCANNO");
1135
1136 // Vars for keeping track of time, freqids, molIds in a SCANNO
[2813]1137 //Vector<uInt> freqids;
1138 //Vector<uInt> molids;
[2290]1139 Vector<uInt> beamids(1,0);
1140 Vector<MDirection> beamDirs;
1141 Vector<Int> stypeids(1,0);
1142 Vector<String> stypestrs;
1143 Int nfreq(1);
1144 Int nmol(1);
1145 uInt nbeam(1);
1146 uInt nstype(1);
1147
1148 Double btime(0.0), etime(0.0);
1149 Double meanIntTim(0.0);
1150
1151 uInt currFreqId(0), ftabRow(0);
1152 Int iflen(0), pollen(0);
1153
1154 while (!iter.pastEnd()) {
1155 Table subt = iter.table();
1156 uInt snrow = subt.nrow();
1157 ROTableRow row(subt);
1158 const TableRecord& rec = row.get(0);
1159
1160 // relevant columns
1161 ROScalarColumn<Double> mjdCol(subt,"TIME");
1162 ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
1163 MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
1164
1165 ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
1166 ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
1167 ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
1168 ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
1169
1170 ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
1171 ROScalarColumn<uInt> polNoCol(subt,"POLNO");
1172
1173
1174 // Times
1175 meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
1176 minMax(btime, etime, mjdCol.getColumn());
[2969]1177 double shiftInDay(0.5*meanIntTim/C::day);
1178 btime -= shiftInDay;
1179 etime += shiftInDay;
[2290]1180
1181 // MOLECULE_ID and FREQ_ID
[2813]1182 Vector<uInt> molids(getNumbers(molIdCol));
[2290]1183 molids.shape(nmol);
1184
[2813]1185 Vector<uInt> freqids(getNumbers(freqIdCol));
[2290]1186 freqids.shape(nfreq);
1187
1188 // Add first beamid, and srcNames
1189 beamids.resize(1,False);
1190 beamDirs.resize(1,False);
1191 beamids(0)=beamCol(0);
1192 beamDirs(0)=dirCol(0);
1193 nbeam = 1;
1194
1195 stypeids.resize(1,False);
1196 stypeids(0)=stypeCol(0);
1197 nstype = 1;
1198
1199 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1200 currFreqId=freqIdCol(0);
1201 ftabRow = fidMap[currFreqId];
1202 // Assumes an identical number of channels per FREQ_ID
1203 if (fIdchans(ftabRow) < 0 ) {
1204 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1205 fIdchans(ftabRow)=(*spec).shape()(0);
1206 }
[2938]1207 if (fIdfreq0(ftabRow) < 0 ) {
1208 SpectralCoordinate spc = frequencies().getSpectralCoordinate(ftabRow);
1209 Double fs, fe;
1210 spc.toWorld(fs, 0);
1211 spc.toWorld(fe, fIdchans(ftabRow)-1);
1212 fIdfreq0(ftabRow) = fs;
1213 fIdfcent(ftabRow) = 0.5 * ( fs + fe );
1214 }
[2290]1215 // Should keep ifNos and polNos form the previous SCANNO
1216 if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
1217 ifNos[ftabRow].shape(iflen);
1218 iflen++;
1219 ifNos[ftabRow].resize(iflen,True);
1220 ifNos[ftabRow](iflen-1) = ifNoCol(0);
1221 }
1222 if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
1223 polNos[ftabRow].shape(pollen);
1224 pollen++;
1225 polNos[ftabRow].resize(pollen,True);
1226 polNos[ftabRow](pollen-1) = polNoCol(0);
1227 }
1228
1229 for (uInt i=1; i < snrow; i++){
1230 // Need to list BEAMNO and DIRECTION in the same order
1231 if ( !anyEQ(beamids,beamCol(i)) ) {
1232 nbeam++;
1233 beamids.resize(nbeam,True);
1234 beamids(nbeam-1)=beamCol(i);
1235 beamDirs.resize(nbeam,True);
1236 beamDirs(nbeam-1)=dirCol(i);
1237 }
1238
1239 // SRCTYPE is Int (getNumber takes only uInt)
1240 if ( !anyEQ(stypeids,stypeCol(i)) ) {
1241 nstype++;
1242 stypeids.resize(nstype,True);
1243 stypeids(nstype-1)=stypeCol(i);
1244 }
1245
1246 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1247 currFreqId=freqIdCol(i);
1248 ftabRow = fidMap[currFreqId];
1249 if (fIdchans(ftabRow) < 0 ) {
1250 const TableRecord& rec = row.get(i);
1251 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1252 fIdchans(ftabRow) = (*spec).shape()(0);
1253 }
[2938]1254 if (fIdfreq0(ftabRow) < 0 ) {
1255 SpectralCoordinate spc = frequencies().getSpectralCoordinate(ftabRow);
1256 Double fs, fe;
1257 spc.toWorld(fs, 0);
1258 spc.toWorld(fe, fIdchans(ftabRow)-1);
1259 fIdfreq0(ftabRow) = fs;
1260 fIdfcent(ftabRow) = 5.e-1 * ( fs + fe );
1261 }
[2290]1262 if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
1263 ifNos[ftabRow].shape(iflen);
1264 iflen++;
1265 ifNos[ftabRow].resize(iflen,True);
1266 ifNos[ftabRow](iflen-1) = ifNoCol(i);
1267 }
1268 if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
1269 polNos[ftabRow].shape(pollen);
1270 pollen++;
1271 polNos[ftabRow].resize(pollen,True);
1272 polNos[ftabRow](pollen-1) = polNoCol(i);
1273 }
1274 } // end of row iteration
1275
1276 stypestrs.resize(nstype,False);
1277 for (uInt j=0; j < nstype; j++)
1278 stypestrs(j) = SrcType::getName(stypeids(j));
1279
1280 // Format Scan summary
1281 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1282 << std::left << setw(1) << ""
1283 << setw(15) << rec.asString("SRCNAME")
[2969]1284 << setw(21) << MVTime(btime).string(MVTime::YMD,8)
1285 << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,8)
[2290]1286 << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
1287 << std::right << setw(5) << snrow << setw(2) << ""
1288 << std::left << stypestrs << setw(1) << ""
1289 << freqids << setw(1) << ""
1290 << molids << endl;
1291 // Format Beam summary
1292 for (uInt j=0; j < nbeam; j++) {
1293 oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
[2969]1294 << formatDirection(beamDirs(j),9) << endl;
[2290]1295 }
1296 // Flush summary every scan and clear up the string
1297 ols << String(oss) << LogIO::POST;
1298 if (ofs) ofs << String(oss) << flush;
1299 oss.str("");
1300 oss.clear();
1301
1302 ++iter;
1303 } // end of scan iteration
1304 oss << asap::SEPERATOR << endl;
1305
1306 // List FRECUENCIES Table (using STFrequencies.print may be slow)
1307 oss << "FREQUENCIES: " << nfreq << endl;
[2938]1308// oss << std::right << setw(5) << "ID" << setw(2) << ""
1309// << std::left << setw(5) << "IFNO" << setw(2) << ""
1310// << setw(8) << "Frame"
1311// << setw(16) << "RefVal"
1312// << setw(7) << "RefPix"
1313// << setw(15) << "Increment"
1314// << setw(9) << "Channels"
1315// << setw(6) << "POLNOs" << endl;
1316// Int tmplen;
1317// for (Int i=0; i < nfid; i++){
1318// // List row=i of FREQUENCIES subtable
1319// ifNos[i].shape(tmplen);
1320// if (tmplen >= 1) {
1321// oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
1322// << setw(3) << ifNos[i](0) << setw(1) << ""
1323// << std::left << setw(46) << frequencies().print(ftabIds(i))
1324// << setw(2) << ""
1325// << std::right << setw(8) << fIdchans[i] << setw(2) << ""
1326// << std::left << polNos[i];
1327// if (tmplen > 1) {
1328// oss << " (" << tmplen << " chains)";
1329// }
1330// oss << endl;
1331// }
1332 oss << std::right << setw(4) << "ID" << setw(2) << ""
1333 << std::left << setw(9) << "IFNO(SPW)" << setw(2) << ""
1334 << setw(8) << "#Chans"
[2290]1335 << setw(8) << "Frame"
[2938]1336 << setw(12) << "Ch0[MHz]"
1337 << setw(14) << "ChanWid[kHz]"
1338 << setw(14) << "Center[MHz]"
[2290]1339 << setw(6) << "POLNOs" << endl;
1340 Int tmplen;
1341 for (Int i=0; i < nfid; i++){
1342 // List row=i of FREQUENCIES subtable
1343 ifNos[i].shape(tmplen);
[2938]1344 Double refpix, refval, increment ;
[2531]1345 if (tmplen >= 1) {
[2938]1346 freqTable_.getEntry( refpix, refval, increment, ftabIds(i) ) ;
1347 oss << std::right << setw(4) << ftabIds(i) << setw(2) << ""
1348 << std::left << setw(9) << ifNos[i](0) << setw(2) << ""
1349 << std::right << setw(6) << fIdchans[i] << setw(2) << ""
1350 << setw(6) << frequencies().getFrameString(true)
1351 << setw(2) << ""
1352 << setw(10) << std::setprecision(9) << (fIdfreq0[i]*1.e-6) << setw(2) << ""
1353 << setw(12) << (increment*1.e-3) << setw(2) << ""
1354 << setw(12) << (fIdfcent[i]*1.e-6) << setw(2) << ""
[2531]1355 << std::left << polNos[i];
1356 if (tmplen > 1) {
1357 oss << " (" << tmplen << " chains)";
1358 }
1359 oss << endl;
[2290]1360 }
[2531]1361
[2290]1362 }
1363 oss << asap::SEPERATOR << endl;
1364
1365 // List MOLECULES Table (currently lists all rows)
1366 oss << "MOLECULES: " << endl;
1367 if (molecules().nrow() <= 0) {
1368 oss << " MOLECULES subtable is empty: there are no data" << endl;
1369 } else {
1370 ROTableRow row(molecules().table());
1371 oss << std::right << setw(5) << "ID"
1372 << std::left << setw(3) << ""
1373 << setw(18) << "RestFreq"
1374 << setw(15) << "Name" << endl;
1375 for (Int i=0; i < molecules().nrow(); i++){
1376 const TableRecord& rec=row.get(i);
1377 oss << std::right << setw(5) << rec.asuInt("ID")
1378 << std::left << setw(3) << ""
1379 << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
1380 << rec.asArrayString("NAME") << endl;
1381 }
1382 }
1383 oss << asap::SEPERATOR << endl;
1384 ols << String(oss) << LogIO::POST;
1385 if (ofs) {
1386 ofs << String(oss) << flush;
1387 ofs.close();
1388 }
1389 // return String(oss);
1390}
1391
1392
1393std::string Scantable::oldheaderSummary()
1394{
1395 // Format header info
1396// STHeader sdh;
1397// sdh = getHeader();
1398// sdh.print();
1399 ostringstream oss;
1400 oss.flags(std::ios_base::left);
1401 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1402 << setw(15) << "IFs:" << setw(4) << nif() << endl
1403 << setw(15) << "Polarisations:" << setw(4) << npol()
1404 << "(" << getPolType() << ")" << endl
1405 << setw(15) << "Channels:" << nchan() << endl;
[805]1406 String tmp;
[860]1407 oss << setw(15) << "Observer:"
1408 << table_.keywordSet().asString("Observer") << endl;
[805]1409 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1410 table_.keywordSet().get("Project", tmp);
1411 oss << setw(15) << "Project:" << tmp << endl;
1412 table_.keywordSet().get("Obstype", tmp);
1413 oss << setw(15) << "Obs. Type:" << tmp << endl;
1414 table_.keywordSet().get("AntennaName", tmp);
1415 oss << setw(15) << "Antenna Name:" << tmp << endl;
1416 table_.keywordSet().get("FluxUnit", tmp);
1417 oss << setw(15) << "Flux Unit:" << tmp << endl;
[1819]1418 int nid = moleculeTable_.nrow();
1419 Bool firstline = True;
[805]1420 oss << setw(15) << "Rest Freqs:";
[1819]1421 for (int i=0; i<nid; i++) {
[2244]1422 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
[1819]1423 if (t.nrow() > 0) {
1424 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1425 if (vec.nelements() > 0) {
1426 if (firstline) {
1427 oss << setprecision(10) << vec << " [Hz]" << endl;
1428 firstline=False;
1429 }
1430 else{
1431 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1432 }
1433 } else {
1434 oss << "none" << endl;
1435 }
1436 }
[805]1437 }
[941]1438
1439 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
[805]1440 oss << selector_.print() << endl;
[2111]1441 return String(oss);
1442}
1443
[2286]1444 //std::string Scantable::summary( const std::string& filename )
[2290]1445void Scantable::oldsummary( const std::string& filename )
[2111]1446{
1447 ostringstream oss;
[2286]1448 ofstream ofs;
1449 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1450
1451 if (filename != "")
1452 ofs.open( filename.c_str(), ios::out );
1453
[805]1454 oss << endl;
[2111]1455 oss << asap::SEPERATOR << endl;
1456 oss << " Scan Table Summary" << endl;
1457 oss << asap::SEPERATOR << endl;
1458
1459 // Format header info
[2290]1460 oss << oldheaderSummary();
[2111]1461 oss << endl;
1462
[805]1463 // main table
1464 String dirtype = "Position ("
[987]1465 + getDirectionRefString()
[805]1466 + ")";
[2111]1467 oss.flags(std::ios_base::left);
[941]1468 oss << setw(5) << "Scan" << setw(15) << "Source"
[2005]1469 << setw(10) << "Time" << setw(18) << "Integration"
1470 << setw(15) << "Source Type" << endl;
[941]1471 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
[1694]1472 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
[805]1473 << setw(8) << "Frame" << setw(16)
[1694]1474 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1475 << setw(7) << "Channels"
1476 << endl;
[805]1477 oss << asap::SEPERATOR << endl;
[2286]1478
1479 // Flush summary and clear up the string
1480 ols << String(oss) << LogIO::POST;
1481 if (ofs) ofs << String(oss) << flush;
1482 oss.str("");
1483 oss.clear();
1484
[805]1485 TableIterator iter(table_, "SCANNO");
1486 while (!iter.pastEnd()) {
1487 Table subt = iter.table();
1488 ROTableRow row(subt);
1489 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1490 const TableRecord& rec = row.get(0);
1491 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1492 << std::left << setw(1) << ""
1493 << setw(15) << rec.asString("SRCNAME")
1494 << setw(10) << formatTime(timeCol(0), false);
1495 // count the cycles in the scan
1496 TableIterator cyciter(subt, "CYCLENO");
1497 int nint = 0;
1498 while (!cyciter.pastEnd()) {
1499 ++nint;
1500 ++cyciter;
1501 }
1502 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
[2005]1503 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1504 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
[447]1505
[805]1506 TableIterator biter(subt, "BEAMNO");
1507 while (!biter.pastEnd()) {
1508 Table bsubt = biter.table();
1509 ROTableRow brow(bsubt);
1510 const TableRecord& brec = brow.get(0);
[1000]1511 uInt row0 = bsubt.rowNumbers(table_)[0];
[941]1512 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
[987]1513 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
[805]1514 TableIterator iiter(bsubt, "IFNO");
1515 while (!iiter.pastEnd()) {
1516 Table isubt = iiter.table();
1517 ROTableRow irow(isubt);
1518 const TableRecord& irec = irow.get(0);
[1694]1519 oss << setw(9) << "";
[941]1520 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
[1694]1521 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1522 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
[1375]1523 << endl;
[447]1524
[805]1525 ++iiter;
1526 }
1527 ++biter;
1528 }
[2286]1529 // Flush summary every scan and clear up the string
1530 ols << String(oss) << LogIO::POST;
1531 if (ofs) ofs << String(oss) << flush;
1532 oss.str("");
1533 oss.clear();
1534
[805]1535 ++iter;
[447]1536 }
[2286]1537 oss << asap::SEPERATOR << endl;
1538 ols << String(oss) << LogIO::POST;
1539 if (ofs) {
[2290]1540 ofs << String(oss) << flush;
[2286]1541 ofs.close();
1542 }
1543 // return String(oss);
[447]1544}
1545
[1947]1546// std::string Scantable::getTime(int whichrow, bool showdate) const
1547// {
1548// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1549// MEpoch me;
1550// if (whichrow > -1) {
1551// me = timeCol(uInt(whichrow));
1552// } else {
1553// Double tm;
1554// table_.keywordSet().get("UTC",tm);
1555// me = MEpoch(MVEpoch(tm));
1556// }
1557// return formatTime(me, showdate);
1558// }
1559
1560std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
[777]1561{
[805]1562 MEpoch me;
[1947]1563 me = getEpoch(whichrow);
1564 return formatTime(me, showdate, prec);
[777]1565}
[805]1566
[1411]1567MEpoch Scantable::getEpoch(int whichrow) const
1568{
1569 if (whichrow > -1) {
1570 return timeCol_(uInt(whichrow));
1571 } else {
1572 Double tm;
1573 table_.keywordSet().get("UTC",tm);
[1598]1574 return MEpoch(MVEpoch(tm));
[1411]1575 }
1576}
1577
[1068]1578std::string Scantable::getDirectionString(int whichrow) const
1579{
1580 return formatDirection(getDirection(uInt(whichrow)));
1581}
1582
[1598]1583
1584SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1585 const MPosition& mp = getAntennaPosition();
1586 const MDirection& md = getDirection(whichrow);
1587 const MEpoch& me = timeCol_(whichrow);
[1819]1588 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1589 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
[2346]1590 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
[1598]1591 mfreqidCol_(whichrow));
1592}
1593
[1360]1594std::vector< double > Scantable::getAbcissa( int whichrow ) const
[865]1595{
[1507]1596 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
[865]1597 std::vector<double> stlout;
1598 int nchan = specCol_(whichrow).nelements();
[2346]1599 String us = freqTable_.getUnitString();
[865]1600 if ( us == "" || us == "pixel" || us == "channel" ) {
1601 for (int i=0; i<nchan; ++i) {
1602 stlout.push_back(double(i));
1603 }
1604 return stlout;
1605 }
[1598]1606 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
[865]1607 Vector<Double> pixel(nchan);
1608 Vector<Double> world;
1609 indgen(pixel);
1610 if ( Unit(us) == Unit("Hz") ) {
1611 for ( int i=0; i < nchan; ++i) {
1612 Double world;
1613 spc.toWorld(world, pixel[i]);
1614 stlout.push_back(double(world));
1615 }
1616 } else if ( Unit(us) == Unit("km/s") ) {
1617 Vector<Double> world;
1618 spc.pixelToVelocity(world, pixel);
1619 world.tovector(stlout);
1620 }
1621 return stlout;
1622}
[1360]1623void Scantable::setDirectionRefString( const std::string & refstr )
[987]1624{
1625 MDirection::Types mdt;
1626 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1627 throw(AipsError("Illegal Direction frame."));
1628 }
1629 if ( refstr == "" ) {
1630 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1631 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1632 } else {
1633 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1634 }
1635}
[865]1636
[1360]1637std::string Scantable::getDirectionRefString( ) const
[987]1638{
1639 return table_.keywordSet().asString("DIRECTIONREF");
1640}
1641
1642MDirection Scantable::getDirection(int whichrow ) const
1643{
1644 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1645 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1646 if ( usertype != type ) {
1647 MDirection::Types mdt;
1648 if (!MDirection::getType(mdt, usertype)) {
1649 throw(AipsError("Illegal Direction frame."));
1650 }
1651 return dirCol_.convert(uInt(whichrow), mdt);
1652 } else {
1653 return dirCol_(uInt(whichrow));
1654 }
1655}
1656
[847]1657std::string Scantable::getAbcissaLabel( int whichrow ) const
1658{
[996]1659 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
[847]1660 const MPosition& mp = getAntennaPosition();
[987]1661 const MDirection& md = getDirection(whichrow);
[847]1662 const MEpoch& me = timeCol_(whichrow);
[1819]1663 //const Double& rf = mmolidCol_(whichrow);
1664 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
[847]1665 SpectralCoordinate spc =
[2346]1666 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
[847]1667
1668 String s = "Channel";
[2346]1669 Unit u = Unit(freqTable_.getUnitString());
[847]1670 if (u == Unit("km/s")) {
[1170]1671 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
[847]1672 } else if (u == Unit("Hz")) {
1673 Vector<String> wau(1);wau = u.getName();
1674 spc.setWorldAxisUnits(wau);
[1170]1675 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
[847]1676 }
1677 return s;
1678
1679}
1680
[1819]1681/**
1682void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
[1170]1683 const std::string& unit )
[1819]1684**/
1685void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1686 const std::string& unit )
1687
[847]1688{
[923]1689 ///@todo lookup in line table to fill in name and formattedname
[847]1690 Unit u(unit);
[1819]1691 //Quantum<Double> urf(rf, u);
1692 Quantum<Vector<Double> >urf(rf, u);
1693 Vector<String> formattedname(0);
1694 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1695
1696 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1697 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
[847]1698 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1699 tabvec = id;
1700}
1701
[1819]1702/**
1703void asap::Scantable::setRestFrequencies( const std::string& name )
[847]1704{
1705 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1706 ///@todo implement
1707}
[1819]1708**/
[2012]1709
[1819]1710void Scantable::setRestFrequencies( const vector<std::string>& name )
1711{
[2163]1712 (void) name; // suppress unused warning
[1819]1713 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1714 ///@todo implement
1715}
[847]1716
[1360]1717std::vector< unsigned int > Scantable::rownumbers( ) const
[852]1718{
1719 std::vector<unsigned int> stlout;
1720 Vector<uInt> vec = table_.rowNumbers();
1721 vec.tovector(stlout);
1722 return stlout;
1723}
1724
[865]1725
[1360]1726Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
[896]1727{
1728 ROTableRow row(table_);
1729 const TableRecord& rec = row.get(whichrow);
1730 Table t =
1731 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1732 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1733 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1734 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1735 ROArrayColumn<Float> speccol(t, "SPECTRA");
1736 return speccol.getColumn();
1737}
[865]1738
[1360]1739std::vector< std::string > Scantable::columnNames( ) const
[902]1740{
1741 Vector<String> vec = table_.tableDesc().columnNames();
1742 return mathutil::tovectorstring(vec);
1743}
[896]1744
[1360]1745MEpoch::Types Scantable::getTimeReference( ) const
[915]1746{
1747 return MEpoch::castType(timeCol_.getMeasRef().getType());
[972]1748}
[915]1749
[1360]1750void Scantable::addFit( const STFitEntry& fit, int row )
[972]1751{
[1819]1752 //cout << mfitidCol_(uInt(row)) << endl;
1753 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1754 os << mfitidCol_(uInt(row)) << LogIO::POST ;
[972]1755 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1756 mfitidCol_.put(uInt(row), id);
1757}
[915]1758
[1360]1759void Scantable::shift(int npix)
1760{
1761 Vector<uInt> fids(mfreqidCol_.getColumn());
1762 genSort( fids, Sort::Ascending,
1763 Sort::QuickSort|Sort::NoDuplicates );
1764 for (uInt i=0; i<fids.nelements(); ++i) {
[1567]1765 frequencies().shiftRefPix(npix, fids[i]);
[1360]1766 }
1767}
[987]1768
[1819]1769String Scantable::getAntennaName() const
[1391]1770{
1771 String out;
1772 table_.keywordSet().get("AntennaName", out);
[1987]1773 String::size_type pos1 = out.find("@") ;
1774 String::size_type pos2 = out.find("//") ;
1775 if ( pos2 != String::npos )
[2036]1776 out = out.substr(pos2+2,pos1-pos2-2) ;
[1987]1777 else if ( pos1 != String::npos )
1778 out = out.substr(0,pos1) ;
[1391]1779 return out;
[987]1780}
[1391]1781
[1730]1782int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
[1391]1783{
1784 String tbpath;
1785 int ret = 0;
1786 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1787 table_.keywordSet().get("GBT_GO", tbpath);
1788 Table t(tbpath,Table::Old);
1789 // check each scan if other scan of the pair exist
1790 int nscan = scanlist.size();
1791 for (int i = 0; i < nscan; i++) {
[2869]1792 Table subt = t( t.col("SCAN") == scanlist[i] );
[1391]1793 if (subt.nrow()==0) {
[1819]1794 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1795 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1796 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
[1391]1797 ret = 1;
1798 break;
1799 }
1800 ROTableRow row(subt);
1801 const TableRecord& rec = row.get(0);
1802 int scan1seqn = rec.asuInt("PROCSEQN");
1803 int laston1 = rec.asuInt("LASTON");
1804 if ( rec.asuInt("PROCSIZE")==2 ) {
1805 if ( i < nscan-1 ) {
[2869]1806 Table subt2 = t( t.col("SCAN") == scanlist[i+1] );
[1391]1807 if ( subt2.nrow() == 0) {
[1819]1808 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1809
1810 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1811 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
[1391]1812 ret = 1;
1813 break;
1814 }
1815 ROTableRow row2(subt2);
1816 const TableRecord& rec2 = row2.get(0);
1817 int scan2seqn = rec2.asuInt("PROCSEQN");
1818 int laston2 = rec2.asuInt("LASTON");
1819 if (scan1seqn == 1 && scan2seqn == 2) {
1820 if (laston1 == laston2) {
[1819]1821 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1822 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1823 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
[1391]1824 i +=1;
1825 }
1826 else {
[1819]1827 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1828 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1829 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
[1391]1830 }
1831 }
1832 else if (scan1seqn==2 && scan2seqn == 1) {
1833 if (laston1 == laston2) {
[1819]1834 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1835 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1836 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
[1391]1837 ret = 1;
1838 break;
1839 }
1840 }
1841 else {
[1819]1842 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1843 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1844 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
[1391]1845 ret = 1;
1846 break;
1847 }
1848 }
1849 }
1850 else {
[1819]1851 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1852 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1853 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
[1391]1854 }
1855 //if ( i >= nscan ) break;
1856 }
1857 }
1858 else {
[1819]1859 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1860 //cerr<<"No reference to GBT_GO table."<<endl;
1861 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
[1391]1862 ret = 1;
1863 }
1864 return ret;
1865}
1866
[1730]1867std::vector<double> Scantable::getDirectionVector(int whichrow) const
[1391]1868{
1869 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1870 std::vector<double> dir;
1871 Dir.tovector(dir);
1872 return dir;
1873}
1874
[1819]1875void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1876 throw( casa::AipsError )
1877{
1878 // assumed that all rows have same nChan
1879 Vector<Float> arr = specCol_( 0 ) ;
1880 int nChan = arr.nelements() ;
1881
1882 // if nmin < 0 or nmax < 0, nothing to do
1883 if ( nmin < 0 ) {
1884 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1885 }
1886 if ( nmax < 0 ) {
1887 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1888 }
1889
1890 // if nmin > nmax, exchange values
1891 if ( nmin > nmax ) {
1892 int tmp = nmax ;
1893 nmax = nmin ;
1894 nmin = tmp ;
1895 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1896 os << "Swap values. Applied range is ["
1897 << nmin << ", " << nmax << "]" << LogIO::POST ;
1898 }
1899
1900 // if nmin exceeds nChan, nothing to do
1901 if ( nmin >= nChan ) {
1902 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1903 }
1904
1905 // if nmax exceeds nChan, reset nmax to nChan
[2672]1906 if ( nmax >= nChan-1 ) {
[1819]1907 if ( nmin == 0 ) {
1908 // nothing to do
1909 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1910 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1911 return ;
1912 }
1913 else {
1914 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1915 os << "Specified maximum exceeds nChan. Applied range is ["
1916 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1917 nmax = nChan - 1 ;
1918 }
1919 }
1920
1921 // reshape specCol_ and flagCol_
1922 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1923 reshapeSpectrum( nmin, nmax, irow ) ;
1924 }
1925
1926 // update FREQUENCIES subtable
[2908]1927 Vector<uInt> freqIdArray = mfreqidCol_.getColumn();
1928 uInt numFreqId = GenSort<uInt>::sort(freqIdArray, Sort::Ascending,
1929 Sort::HeapSort | Sort::NoDuplicates);
[1819]1930 Double refpix ;
1931 Double refval ;
1932 Double increment ;
[2908]1933 for (uInt irow = 0; irow < numFreqId; irow++) {
1934 freqTable_.getEntry( refpix, refval, increment, freqIdArray[irow] ) ;
[1819]1935 /***
1936 * need to shift refpix to nmin
1937 * note that channel nmin in old index will be channel 0 in new one
1938 ***/
1939 refval = refval - ( refpix - nmin ) * increment ;
1940 refpix = 0 ;
[2908]1941 freqTable_.setEntry( refpix, refval, increment, freqIdArray[irow] ) ;
[1819]1942 }
1943
1944 // update nchan
1945 int newsize = nmax - nmin + 1 ;
1946 table_.rwKeywordSet().define( "nChan", newsize ) ;
1947
1948 // update bandwidth
1949 // assumed all spectra in the scantable have same bandwidth
1950 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1951
1952 return ;
1953}
1954
1955void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1956{
1957 // reshape specCol_ and flagCol_
1958 Vector<Float> oldspec = specCol_( irow ) ;
1959 Vector<uChar> oldflag = flagsCol_( irow ) ;
[2475]1960 Vector<Float> oldtsys = tsysCol_( irow ) ;
[1819]1961 uInt newsize = nmax - nmin + 1 ;
[2475]1962 Slice slice( nmin, newsize, 1 ) ;
1963 specCol_.put( irow, oldspec( slice ) ) ;
1964 flagsCol_.put( irow, oldflag( slice ) ) ;
1965 if ( oldspec.size() == oldtsys.size() )
1966 tsysCol_.put( irow, oldtsys( slice ) ) ;
[1819]1967
1968 return ;
1969}
1970
[2435]1971void asap::Scantable::regridSpecChannel( double dnu, int nChan )
1972{
1973 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1974 os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ;
1975 int freqnrow = freqTable_.table().nrow() ;
1976 Vector<bool> firstTime( freqnrow, true ) ;
1977 double oldincr, factor;
1978 uInt currId;
1979 Double refpix ;
1980 Double refval ;
1981 Double increment ;
1982 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1983 currId = mfreqidCol_(irow);
1984 vector<double> abcissa = getAbcissa( irow ) ;
1985 if (nChan < 0) {
1986 int oldsize = abcissa.size() ;
1987 double bw = (abcissa[oldsize-1]-abcissa[0]) + \
1988 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ;
1989 nChan = int( ceil( abs(bw/dnu) ) ) ;
1990 }
1991 // actual regridding
1992 regridChannel( nChan, dnu, irow ) ;
[2433]1993
[2435]1994 // update FREQUENCIES subtable
1995 if (firstTime[currId]) {
1996 oldincr = abcissa[1]-abcissa[0] ;
1997 factor = dnu/oldincr ;
1998 firstTime[currId] = false ;
1999 freqTable_.getEntry( refpix, refval, increment, currId ) ;
[2463]2000
[2437]2001 //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ;
[2463]2002 if (factor > 0 ) {
[2462]2003 refpix = (refpix + 0.5)/factor - 0.5;
2004 } else {
[2463]2005 refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5;
[2462]2006 }
[2435]2007 freqTable_.setEntry( refpix, refval, increment*factor, currId ) ;
[2463]2008 //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ;
2009 //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ;
[2435]2010 }
2011 }
2012}
2013
[1819]2014void asap::Scantable::regridChannel( int nChan, double dnu )
2015{
2016 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
2017 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
2018 // assumed that all rows have same nChan
2019 Vector<Float> arr = specCol_( 0 ) ;
2020 int oldsize = arr.nelements() ;
2021
2022 // if oldsize == nChan, nothing to do
2023 if ( oldsize == nChan ) {
2024 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
2025 return ;
2026 }
2027
2028 // if oldChan < nChan, unphysical operation
2029 if ( oldsize < nChan ) {
2030 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
2031 return ;
2032 }
2033
[2433]2034 // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary)
[1819]2035 vector<string> coordinfo = getCoordInfo() ;
2036 string oldinfo = coordinfo[0] ;
2037 coordinfo[0] = "Hz" ;
2038 setCoordInfo( coordinfo ) ;
2039 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
2040 regridChannel( nChan, dnu, irow ) ;
2041 }
2042 coordinfo[0] = oldinfo ;
2043 setCoordInfo( coordinfo ) ;
2044
2045
2046 // NOTE: this method does not update metadata such as
2047 // FREQUENCIES subtable, nChan, Bandwidth, etc.
2048
2049 return ;
2050}
2051
2052void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
2053{
2054 // logging
2055 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
2056 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
2057
2058 Vector<Float> oldspec = specCol_( irow ) ;
2059 Vector<uChar> oldflag = flagsCol_( irow ) ;
[2431]2060 Vector<Float> oldtsys = tsysCol_( irow ) ;
[1819]2061 Vector<Float> newspec( nChan, 0 ) ;
[2431]2062 Vector<uChar> newflag( nChan, true ) ;
2063 Vector<Float> newtsys ;
2064 bool regridTsys = false ;
2065 if (oldtsys.size() == oldspec.size()) {
2066 regridTsys = true ;
2067 newtsys.resize(nChan,false) ;
2068 newtsys = 0 ;
2069 }
[1819]2070
2071 // regrid
2072 vector<double> abcissa = getAbcissa( irow ) ;
2073 int oldsize = abcissa.size() ;
2074 double olddnu = abcissa[1] - abcissa[0] ;
[2462]2075 //int ichan = 0 ;
[1819]2076 double wsum = 0.0 ;
[2433]2077 Vector<double> zi( nChan+1 ) ;
2078 Vector<double> yi( oldsize + 1 ) ;
[1819]2079 yi[0] = abcissa[0] - 0.5 * olddnu ;
[2431]2080 for ( int ii = 1 ; ii < oldsize ; ii++ )
[2433]2081 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2082 yi[oldsize] = abcissa[oldsize-1] \
2083 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
[2462]2084 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2085 zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2086 for ( int ii = 1 ; ii < nChan ; ii++ )
2087 zi[ii] = zi[0] + dnu * ii ;
2088 zi[nChan] = zi[nChan-1] + dnu ;
2089 // Access zi and yi in ascending order
2090 int izs = ((dnu > 0) ? 0 : nChan ) ;
2091 int ize = ((dnu > 0) ? nChan : 0 ) ;
2092 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2093 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2094 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2095 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2096 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2097 int ii = izs ;
2098 while (ii != ize) {
2099 // always zl < zr
2100 double zl = zi[ii] ;
2101 double zr = zi[ii+izincr] ;
2102 // Need to access smaller index for the new spec, flag, and tsys.
2103 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2104 int i = min(ii, ii+izincr) ;
2105 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2106 int jj = ichan ;
2107 while (jj != iye) {
2108 // always yl < yr
2109 double yl = yi[jj] ;
2110 double yr = yi[jj+iyincr] ;
2111 // Need to access smaller index for the original spec, flag, and tsys.
2112 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2113 int j = min(jj, jj+iyincr) ;
2114 if ( yr <= zl ) {
2115 jj += iyincr ;
2116 continue ;
[1819]2117 }
[2462]2118 else if ( yl <= zl ) {
2119 if ( yr < zr ) {
2120 if (!oldflag[j]) {
2121 newspec[i] += oldspec[j] * ( yr - zl ) ;
2122 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2123 wsum += ( yr - zl ) ;
2124 }
[2950]2125 newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ;
[2462]2126 }
2127 else {
2128 if (!oldflag[j]) {
2129 newspec[i] += oldspec[j] * abs(dnu) ;
2130 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2131 wsum += abs(dnu) ;
2132 }
[2950]2133 newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ;
[2462]2134 ichan = jj ;
2135 break ;
2136 }
[2431]2137 }
[2462]2138 else if ( yl < zr ) {
2139 if ( yr <= zr ) {
2140 if (!oldflag[j]) {
2141 newspec[i] += oldspec[j] * ( yr - yl ) ;
2142 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2143 wsum += ( yr - yl ) ;
2144 }
[2950]2145 newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ;
[2462]2146 }
2147 else {
2148 if (!oldflag[j]) {
2149 newspec[i] += oldspec[j] * ( zr - yl ) ;
2150 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2151 wsum += ( zr - yl ) ;
2152 }
[2950]2153 newflag[i] = (newflag[i] && oldflag[j]) ? 1 << 7 : 0 ;
[2462]2154 ichan = jj ;
2155 break ;
2156 }
[1819]2157 }
[2462]2158 else {
2159 ichan = jj - iyincr ;
2160 break ;
[2431]2161 }
[2462]2162 jj += iyincr ;
[1819]2163 }
[2462]2164 if ( wsum != 0.0 ) {
2165 newspec[i] /= wsum ;
2166 if (regridTsys) newtsys[i] /= wsum ;
2167 }
2168 wsum = 0.0 ;
2169 ii += izincr ;
[1819]2170 }
[2462]2171// if ( dnu > 0.0 ) {
2172// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2173// double zl = zi[ii] ;
2174// double zr = zi[ii+1] ;
2175// for ( int j = ichan ; j < oldsize ; j++ ) {
2176// double yl = yi[j] ;
2177// double yr = yi[j+1] ;
2178// if ( yl <= zl ) {
2179// if ( yr <= zl ) {
2180// continue ;
2181// }
2182// else if ( yr <= zr ) {
2183// if (!oldflag[j]) {
2184// newspec[ii] += oldspec[j] * ( yr - zl ) ;
2185// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ;
2186// wsum += ( yr - zl ) ;
2187// }
2188// newflag[ii] = newflag[ii] && oldflag[j] ;
2189// }
2190// else {
2191// if (!oldflag[j]) {
2192// newspec[ii] += oldspec[j] * dnu ;
2193// if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ;
2194// wsum += dnu ;
2195// }
2196// newflag[ii] = newflag[ii] && oldflag[j] ;
2197// ichan = j ;
2198// break ;
2199// }
2200// }
2201// else if ( yl < zr ) {
2202// if ( yr <= zr ) {
2203// if (!oldflag[j]) {
2204// newspec[ii] += oldspec[j] * ( yr - yl ) ;
2205// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ;
2206// wsum += ( yr - yl ) ;
2207// }
2208// newflag[ii] = newflag[ii] && oldflag[j] ;
2209// }
2210// else {
2211// if (!oldflag[j]) {
2212// newspec[ii] += oldspec[j] * ( zr - yl ) ;
2213// if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ;
2214// wsum += ( zr - yl ) ;
2215// }
2216// newflag[ii] = newflag[ii] && oldflag[j] ;
2217// ichan = j ;
2218// break ;
2219// }
2220// }
2221// else {
2222// ichan = j - 1 ;
2223// break ;
2224// }
2225// }
2226// if ( wsum != 0.0 ) {
2227// newspec[ii] /= wsum ;
2228// if (regridTsys) newtsys[ii] /= wsum ;
2229// }
2230// wsum = 0.0 ;
2231// }
[1819]2232// }
[2462]2233// else if ( dnu < 0.0 ) {
2234// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2235// double zl = zi[ii] ;
2236// double zr = zi[ii+1] ;
2237// for ( int j = ichan ; j < oldsize ; j++ ) {
2238// double yl = yi[j] ;
2239// double yr = yi[j+1] ;
2240// if ( yl >= zl ) {
2241// if ( yr >= zl ) {
2242// continue ;
2243// }
2244// else if ( yr >= zr ) {
2245// if (!oldflag[j]) {
2246// newspec[ii] += oldspec[j] * abs( yr - zl ) ;
2247// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ;
2248// wsum += abs( yr - zl ) ;
2249// }
2250// newflag[ii] = newflag[ii] && oldflag[j] ;
2251// }
2252// else {
2253// if (!oldflag[j]) {
2254// newspec[ii] += oldspec[j] * abs( dnu ) ;
2255// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ;
2256// wsum += abs( dnu ) ;
2257// }
2258// newflag[ii] = newflag[ii] && oldflag[j] ;
2259// ichan = j ;
2260// break ;
2261// }
2262// }
2263// else if ( yl > zr ) {
2264// if ( yr >= zr ) {
2265// if (!oldflag[j]) {
2266// newspec[ii] += oldspec[j] * abs( yr - yl ) ;
2267// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ;
2268// wsum += abs( yr - yl ) ;
2269// }
2270// newflag[ii] = newflag[ii] && oldflag[j] ;
2271// }
2272// else {
2273// if (!oldflag[j]) {
2274// newspec[ii] += oldspec[j] * abs( zr - yl ) ;
2275// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ;
2276// wsum += abs( zr - yl ) ;
2277// }
2278// newflag[ii] = newflag[ii] && oldflag[j] ;
2279// ichan = j ;
2280// break ;
2281// }
2282// }
2283// else {
2284// ichan = j - 1 ;
2285// break ;
2286// }
2287// }
2288// if ( wsum != 0.0 ) {
2289// newspec[ii] /= wsum ;
2290// if (regridTsys) newtsys[ii] /= wsum ;
2291// }
2292// wsum = 0.0 ;
[1819]2293// }
2294// }
[2462]2295// // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
2296// // pile += dnu ;
2297// // wedge = olddnu * ( refChan + 1 ) ;
2298// // while ( wedge < pile ) {
2299// // newspec[0] += olddnu * oldspec[refChan] ;
2300// // newflag[0] = newflag[0] || oldflag[refChan] ;
2301// // //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
2302// // refChan++ ;
2303// // wedge += olddnu ;
2304// // wsum += olddnu ;
2305// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2306// // }
2307// // frac = ( wedge - pile ) / olddnu ;
2308// // wsum += ( 1.0 - frac ) * olddnu ;
2309// // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2310// // newflag[0] = newflag[0] || oldflag[refChan] ;
2311// // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
2312// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2313// // newspec[0] /= wsum ;
2314// // //ofs << "newspec[0] = " << newspec[0] << endl ;
2315// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
[1819]2316
[2462]2317// // /***
2318// // * ichan = 1 - nChan-2
2319// // ***/
2320// // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
2321// // pile += dnu ;
2322// // newspec[ichan] += frac * olddnu * oldspec[refChan] ;
2323// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2324// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
2325// // refChan++ ;
2326// // wedge += olddnu ;
2327// // wsum = frac * olddnu ;
2328// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2329// // while ( wedge < pile ) {
2330// // newspec[ichan] += olddnu * oldspec[refChan] ;
2331// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2332// // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
2333// // refChan++ ;
2334// // wedge += olddnu ;
2335// // wsum += olddnu ;
2336// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2337// // }
2338// // frac = ( wedge - pile ) / olddnu ;
2339// // wsum += ( 1.0 - frac ) * olddnu ;
2340// // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2341// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2342// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
2343// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2344// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2345// // newspec[ichan] /= wsum ;
2346// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
2347// // }
[1819]2348
[2462]2349// // /***
2350// // * ichan = nChan-1
2351// // ***/
2352// // // NOTE: Assumed that all spectra have the same bandwidth
2353// // pile += dnu ;
2354// // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
2355// // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
2356// // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2357// // refChan++ ;
2358// // wedge += olddnu ;
2359// // wsum = frac * olddnu ;
2360// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2361// // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
2362// // newspec[nChan-1] += olddnu * oldspec[jchan] ;
2363// // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
2364// // wsum += olddnu ;
2365// // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2366// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2367// // }
2368// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2369// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2370// // newspec[nChan-1] /= wsum ;
2371// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
[1819]2372
[2462]2373// // // ofs.close() ;
2374
[2032]2375 specCol_.put( irow, newspec ) ;
2376 flagsCol_.put( irow, newflag ) ;
[2431]2377 if (regridTsys) tsysCol_.put( irow, newtsys );
[1819]2378
2379 return ;
2380}
2381
[2595]2382void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow )
2383{
2384 Vector<Float> oldspec = specCol_( irow ) ;
2385 Vector<uChar> oldflag = flagsCol_( irow ) ;
2386 Vector<Float> oldtsys = tsysCol_( irow ) ;
2387 Vector<Float> newspec( nChan, 0 ) ;
2388 Vector<uChar> newflag( nChan, true ) ;
2389 Vector<Float> newtsys ;
2390 bool regridTsys = false ;
2391 if (oldtsys.size() == oldspec.size()) {
2392 regridTsys = true ;
2393 newtsys.resize(nChan,false) ;
2394 newtsys = 0 ;
2395 }
2396
2397 // regrid
2398 vector<double> abcissa = getAbcissa( irow ) ;
2399 int oldsize = abcissa.size() ;
2400 double olddnu = abcissa[1] - abcissa[0] ;
2401 //int ichan = 0 ;
2402 double wsum = 0.0 ;
2403 Vector<double> zi( nChan+1 ) ;
2404 Vector<double> yi( oldsize + 1 ) ;
2405 Block<uInt> count( nChan, 0 ) ;
2406 yi[0] = abcissa[0] - 0.5 * olddnu ;
2407 for ( int ii = 1 ; ii < oldsize ; ii++ )
2408 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2409 yi[oldsize] = abcissa[oldsize-1] \
2410 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2411// cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ;
2412// cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ;
2413// cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ;
2414
2415 // do not regrid if input parameters are almost same as current
2416 // spectral setup
2417 double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ;
2418 double oldfmin = min( yi[0], yi[oldsize] ) ;
2419 double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ;
2420 double nChanDiff = nChan - oldsize ;
2421 double eps = 1.0e-8 ;
2422 if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps )
2423 return ;
2424
2425 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2426 //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2427 if ( dnu > 0 )
2428 zi[0] = fmin - 0.5 * dnu ;
2429 else
2430 zi[0] = fmin + nChan * abs(dnu) ;
2431 for ( int ii = 1 ; ii < nChan ; ii++ )
2432 zi[ii] = zi[0] + dnu * ii ;
2433 zi[nChan] = zi[nChan-1] + dnu ;
2434 // Access zi and yi in ascending order
2435 int izs = ((dnu > 0) ? 0 : nChan ) ;
2436 int ize = ((dnu > 0) ? nChan : 0 ) ;
2437 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2438 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2439 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2440 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2441 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2442 int ii = izs ;
2443 while (ii != ize) {
2444 // always zl < zr
2445 double zl = zi[ii] ;
2446 double zr = zi[ii+izincr] ;
2447 // Need to access smaller index for the new spec, flag, and tsys.
2448 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2449 int i = min(ii, ii+izincr) ;
2450 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2451 int jj = ichan ;
2452 while (jj != iye) {
2453 // always yl < yr
2454 double yl = yi[jj] ;
2455 double yr = yi[jj+iyincr] ;
2456 // Need to access smaller index for the original spec, flag, and tsys.
2457 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2458 int j = min(jj, jj+iyincr) ;
2459 if ( yr <= zl ) {
2460 jj += iyincr ;
2461 continue ;
2462 }
2463 else if ( yl <= zl ) {
2464 if ( yr < zr ) {
2465 if (!oldflag[j]) {
2466 newspec[i] += oldspec[j] * ( yr - zl ) ;
2467 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2468 wsum += ( yr - zl ) ;
2469 count[i]++ ;
2470 }
2471 newflag[i] = newflag[i] && oldflag[j] ;
2472 }
2473 else {
2474 if (!oldflag[j]) {
2475 newspec[i] += oldspec[j] * abs(dnu) ;
2476 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2477 wsum += abs(dnu) ;
2478 count[i]++ ;
2479 }
2480 newflag[i] = newflag[i] && oldflag[j] ;
2481 ichan = jj ;
2482 break ;
2483 }
2484 }
2485 else if ( yl < zr ) {
2486 if ( yr <= zr ) {
2487 if (!oldflag[j]) {
2488 newspec[i] += oldspec[j] * ( yr - yl ) ;
2489 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2490 wsum += ( yr - yl ) ;
2491 count[i]++ ;
2492 }
2493 newflag[i] = newflag[i] && oldflag[j] ;
2494 }
2495 else {
2496 if (!oldflag[j]) {
2497 newspec[i] += oldspec[j] * ( zr - yl ) ;
2498 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2499 wsum += ( zr - yl ) ;
2500 count[i]++ ;
2501 }
2502 newflag[i] = newflag[i] && oldflag[j] ;
2503 ichan = jj ;
2504 break ;
2505 }
2506 }
2507 else {
2508 //ichan = jj - iyincr ;
2509 break ;
2510 }
2511 jj += iyincr ;
2512 }
2513 if ( wsum != 0.0 ) {
2514 newspec[i] /= wsum ;
2515 if (regridTsys) newtsys[i] /= wsum ;
2516 }
2517 wsum = 0.0 ;
2518 ii += izincr ;
2519 }
2520
2521 // flag out channels without data
2522 // this is tentative since there is no specific definition
2523 // on bit flag...
2524 uChar noData = 1 << 7 ;
2525 for ( Int i = 0 ; i < nChan ; i++ ) {
2526 if ( count[i] == 0 )
2527 newflag[i] = noData ;
2528 }
2529
2530 specCol_.put( irow, newspec ) ;
2531 flagsCol_.put( irow, newflag ) ;
2532 if (regridTsys) tsysCol_.put( irow, newtsys );
2533
2534 return ;
2535}
2536
[1730]2537std::vector<float> Scantable::getWeather(int whichrow) const
2538{
2539 std::vector<float> out(5);
2540 //Float temperature, pressure, humidity, windspeed, windaz;
2541 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
2542 mweatheridCol_(uInt(whichrow)));
2543
2544
2545 return out;
[1391]2546}
[1730]2547
[2831]2548bool Scantable::isAllChannelsFlagged(uInt whichrow)
[1907]2549{
[2831]2550 uInt rflag;
2551 flagrowCol_.get(whichrow, rflag);
2552 if (rflag > 0)
2553 return true;
[1907]2554 uChar flag;
2555 Vector<uChar> flags;
[2047]2556 flagsCol_.get(whichrow, flags);
[2012]2557 flag = flags[0];
[2047]2558 for (uInt i = 1; i < flags.size(); ++i) {
[2012]2559 flag &= flags[i];
2560 }
[2837]2561 // return ((flag >> 7) == 1);
2562 return (flag > 0);
[2012]2563}
2564
[2811]2565std::vector<std::string> Scantable::applyBaselineTable(const std::string& bltable, const bool returnfitresult, const std::string& outbltable, const bool outbltableexists, const bool overwrite)
[2047]2566{
[2773]2567 STBaselineTable btin = STBaselineTable(bltable);
[2767]2568
[2773]2569 Vector<Bool> applyCol = btin.getApply();
[2767]2570 int nRowBl = applyCol.size();
2571 if (nRowBl != nrow()) {
2572 throw(AipsError("Scantable and bltable have different number of rows."));
2573 }
2574
2575 std::vector<std::string> res;
2576 res.clear();
2577
2578 bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite));
2579 bool bltableidentical = (bltable == outbltable);
[2773]2580 STBaselineTable btout = STBaselineTable(*this);
2581 ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME");
2582 Vector<Double> timeSecCol = tcol.getColumn();
[2767]2583
2584 for (int whichrow = 0; whichrow < nRowBl; ++whichrow) {
2585 if (applyCol[whichrow]) {
2586 std::vector<float> spec = getSpectrum(whichrow);
2587
[2773]2588 std::vector<bool> mask = btin.getMask(whichrow); //use mask_bltable only
[2767]2589
[2773]2590 STBaselineFunc::FuncName ftype = btin.getFunctionName(whichrow);
2591 std::vector<int> fpar = btin.getFuncParam(whichrow);
[2767]2592 std::vector<float> params;
2593 float rms;
2594 std::vector<float> resfit = doApplyBaselineTable(spec, mask, ftype, fpar, params, rms);
2595 setSpectrum(resfit, whichrow);
2596
[2811]2597 if (returnfitresult) {
2598 res.push_back(packFittingResults(whichrow, params, rms));
2599 }
[2767]2600
2601 if (outBaselineTable) {
2602 if (outbltableexists) {
2603 if (overwrite) {
2604 if (bltableidentical) {
[2773]2605 btin.setresult(uInt(whichrow), Vector<Float>(params), Float(rms));
[2767]2606 } else {
[2773]2607 btout.setresult(uInt(whichrow), Vector<Float>(params), Float(rms));
[2767]2608 }
2609 }
2610 } else {
[2773]2611 btout.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
2612 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
2613 true, ftype, fpar, std::vector<float>(),
2614 getMaskListFromMask(mask), params, rms, spec.size(),
2615 3.0, 0, 0.0, 0, std::vector<int>());
[2767]2616 }
2617 }
2618 }
2619 }
2620
2621 if (outBaselineTable) {
2622 if (bltableidentical) {
[2773]2623 btin.save(outbltable);
[2767]2624 } else {
[2773]2625 btout.save(outbltable);
[2767]2626 }
2627 }
2628
2629 return res;
2630}
2631
[2811]2632std::vector<std::string> Scantable::subBaseline(const std::vector<std::string>& blInfoList, const bool returnfitresult, const std::string& outbltable, const bool outbltableexists, const bool overwrite)
[2767]2633{
2634 int nRowBl = blInfoList.size();
2635 int nRowSt = nrow();
2636
2637 std::vector<std::string> res;
2638 res.clear();
2639
2640 bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite));
2641 if ((outbltable != "") && outbltableexists && !overwrite) {
2642 throw(AipsError("Cannot overwrite bltable. Set overwrite=True."));
2643 }
2644
[2883]2645 STBaselineTable* btp;
[2773]2646 ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME");
2647 Vector<Double> timeSecCol = tcol.getColumn();
[2767]2648
[2883]2649 if (outBaselineTable) {
2650 if (outbltableexists) {
2651 btp = new STBaselineTable((String)outbltable);
2652 } else {
2653 btp = new STBaselineTable(*this);
[3009]2654 // for (int i = 0; i < nRowSt; ++i) {
2655 // btp->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i),
2656 // 0, timeSecCol[i]);
2657 // btp->setApply(i, false);
2658 // }
[2767]2659 }
[3009]2660 int nrow = btp->nrow();
2661 for (int i = nrow; i < nRowSt; ++i) {
2662 btp->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i),
2663 0, timeSecCol[i]);
2664 btp->setApply(i, false);
2665 }
[2767]2666 }
2667
2668 for (int i = 0; i < nRowBl; ++i) {
2669 int irow;
2670 STBaselineFunc::FuncName ftype;
2671 std::vector<bool> mask;
2672 std::vector<int> fpar;
2673 float clipth;
2674 int clipn;
2675 bool uself;
2676 float lfth;
2677 std::vector<int> lfedge;
2678 int lfavg;
2679 parseBlInfo(blInfoList[i], irow, ftype, fpar, mask, clipth, clipn, uself, lfth, lfedge, lfavg);
2680
2681 if (irow < nRowSt) {
2682 std::vector<float> spec = getSpectrum(irow);
2683 std::vector<float> params;
2684 float rms;
2685 std::vector<bool> finalmask;
[3009]2686 Bool doApply = True;
2687
2688 if (flagrowCol_(irow) == 0) {
2689 std::vector<float> resfit = doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, clipth, clipn, uself, irow, lfth, lfedge, lfavg);
2690 setSpectrum(resfit, irow);
2691 }
2692 else {
2693 doApply = False;
2694 }
[2767]2695
[2811]2696 if (returnfitresult) {
2697 res.push_back(packFittingResults(irow, params, rms));
2698 }
2699
[2767]2700 if (outBaselineTable) {
2701 Vector<Int> fparam(fpar.size());
2702 for (uInt j = 0; j < fparam.size(); ++j) {
2703 fparam[j] = (Int)fpar[j];
2704 }
2705
[2883]2706 btp->setdata(uInt(irow),
[2767]2707 uInt(getScan(irow)), uInt(getCycle(irow)),
2708 uInt(getBeam(irow)), uInt(getIF(irow)), uInt(getPol(irow)),
[3009]2709 uInt(0), timeSecCol[irow], doApply, ftype, fparam,
[2773]2710 Vector<Float>(), getMaskListFromMask(finalmask), Vector<Float>(params),
[2767]2711 Float(rms), uInt(spec.size()), Float(clipth), uInt(clipn),
2712 Float(0.0), uInt(0), Vector<uInt>());
2713 }
2714
2715 }
2716 }
2717
2718 if (outBaselineTable) {
[2883]2719 btp->save(outbltable);
[2767]2720 }
2721
[2883]2722 delete btp;
[2767]2723 return res;
2724}
2725
[2773]2726std::vector<float> Scantable::doApplyBaselineTable(std::vector<float>& spec,
2727 std::vector<bool>& mask,
2728 const STBaselineFunc::FuncName ftype,
2729 std::vector<int>& fpar,
2730 std::vector<float>& params,
2731 float&rms)
[2767]2732{
2733 std::vector<bool> finalmask;
2734 std::vector<int> lfedge;
2735 return doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, 0.0, 0, false, 0, 0.0, lfedge, 0);
2736}
2737
[2774]2738std::vector<float> Scantable::doSubtractBaseline(std::vector<float>& spec,
2739 std::vector<bool>& mask,
2740 const STBaselineFunc::FuncName ftype,
2741 std::vector<int>& fpar,
2742 std::vector<float>& params,
2743 float&rms,
2744 std::vector<bool>& finalmask,
2745 float clipth,
2746 int clipn,
2747 bool uself,
2748 int irow,
2749 float lfth,
2750 std::vector<int>& lfedge,
2751 int lfavg)
[2767]2752{
2753 if (uself) {
2754 STLineFinder lineFinder = STLineFinder();
[2774]2755 initLineFinder(lfedge, lfth, lfavg, lineFinder);
[2767]2756 std::vector<int> currentEdge;
[2774]2757 mask = getCompositeChanMask(irow, mask, lfedge, currentEdge, lineFinder);
[2946]2758 } else {
2759 mask = getCompositeChanMask(irow, mask);
[2767]2760 }
2761
2762 std::vector<float> res;
2763 if (ftype == STBaselineFunc::Polynomial) {
2764 res = doPolynomialFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn);
2765 } else if (ftype == STBaselineFunc::Chebyshev) {
2766 res = doChebyshevFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn);
2767 } else if (ftype == STBaselineFunc::CSpline) {
2768 if (fpar.size() > 1) { // reading from baseline table in which pieceEdges are already calculated and stored.
2769 res = doCubicSplineFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn);
2770 } else { // usual cspline fitting by giving nPiece only. fpar will be replaced with pieceEdges.
2771 res = doCubicSplineFitting(spec, mask, fpar[0], fpar, params, rms, finalmask, clipth, clipn);
2772 }
2773 } else if (ftype == STBaselineFunc::Sinusoid) {
2774 res = doSinusoidFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn);
2775 }
2776
2777 return res;
2778}
2779
2780std::string Scantable::packFittingResults(const int irow, const std::vector<float>& params, const float rms)
2781{
2782 // returned value: "irow:params[0],params[1],..,params[n-1]:rms"
2783 ostringstream os;
2784 os << irow << ':';
2785 for (uInt i = 0; i < params.size(); ++i) {
2786 if (i > 0) {
2787 os << ',';
2788 }
2789 os << params[i];
2790 }
2791 os << ':' << rms;
2792
2793 return os.str();
2794}
2795
2796void Scantable::parseBlInfo(const std::string& blInfo, int& irow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF)
2797{
2798 // The baseline info to be parsed must be column-delimited string like
2799 // "0:chebyshev:5:3,5,169,174,485,487" where the elements are
2800 // row number, funcType, funcOrder, maskList, clipThreshold, clipNIter,
2801 // useLineFinder, lfThreshold, lfEdge and lfChanAvgLimit.
2802
2803 std::vector<string> res = splitToStringList(blInfo, ':');
2804 if (res.size() < 4) {
2805 throw(AipsError("baseline info has bad format")) ;
2806 }
2807
2808 string ftype0, fpar0, masklist0, uself0, edge0;
2809 std::vector<int> masklist;
2810
2811 stringstream ss;
2812 ss << res[0];
2813 ss >> irow;
2814 ss.clear(); ss.str("");
2815
2816 ss << res[1];
2817 ss >> ftype0;
2818 if (ftype0 == "poly") {
2819 ftype = STBaselineFunc::Polynomial;
2820 } else if (ftype0 == "cspline") {
2821 ftype = STBaselineFunc::CSpline;
2822 } else if (ftype0 == "sinusoid") {
2823 ftype = STBaselineFunc::Sinusoid;
2824 } else if (ftype0 == "chebyshev") {
2825 ftype = STBaselineFunc::Chebyshev;
2826 } else {
2827 throw(AipsError("invalid function type."));
2828 }
2829 ss.clear(); ss.str("");
2830
2831 ss << res[2];
2832 ss >> fpar0;
2833 fpar = splitToIntList(fpar0, ',');
2834 ss.clear(); ss.str("");
2835
2836 ss << res[3];
2837 ss >> masklist0;
2838 mask = getMaskFromMaskList(nchan(getIF(irow)), splitToIntList(masklist0, ','));
[2883]2839 ss.clear(); ss.str("");
[2767]2840
2841 ss << res[4];
2842 ss >> thresClip;
2843 ss.clear(); ss.str("");
2844
2845 ss << res[5];
2846 ss >> nIterClip;
2847 ss.clear(); ss.str("");
2848
2849 ss << res[6];
2850 ss >> uself0;
2851 if (uself0 == "true") {
2852 useLineFinder = true;
2853 } else {
2854 useLineFinder = false;
2855 }
2856 ss.clear(); ss.str("");
2857
2858 if (useLineFinder) {
2859 ss << res[7];
2860 ss >> thresLF;
2861 ss.clear(); ss.str("");
2862
2863 ss << res[8];
2864 ss >> edge0;
2865 edgeLF = splitToIntList(edge0, ',');
2866 ss.clear(); ss.str("");
2867
2868 ss << res[9];
2869 ss >> avgLF;
2870 ss.clear(); ss.str("");
2871 }
2872
2873}
2874
2875std::vector<int> Scantable::splitToIntList(const std::string& s, const char delim)
2876{
2877 istringstream iss(s);
2878 string tmp;
2879 int tmpi;
2880 std::vector<int> res;
2881 stringstream ss;
2882 while (getline(iss, tmp, delim)) {
2883 ss << tmp;
2884 ss >> tmpi;
2885 res.push_back(tmpi);
2886 ss.clear(); ss.str("");
2887 }
2888
2889 return res;
2890}
2891
2892std::vector<string> Scantable::splitToStringList(const std::string& s, const char delim)
2893{
2894 istringstream iss(s);
2895 std::string tmp;
2896 std::vector<string> res;
2897 while (getline(iss, tmp, delim)) {
2898 res.push_back(tmp);
2899 }
2900
2901 return res;
2902}
2903
2904std::vector<bool> Scantable::getMaskFromMaskList(const int nchan, const std::vector<int>& masklist)
2905{
2906 if (masklist.size() % 2 != 0) {
2907 throw(AipsError("masklist must have even number of elements."));
2908 }
2909
2910 std::vector<bool> res(nchan);
2911
2912 for (int i = 0; i < nchan; ++i) {
2913 res[i] = false;
2914 }
2915 for (uInt j = 0; j < masklist.size(); j += 2) {
[3009]2916 for (int i = masklist[j]; i <= min(nchan-1, masklist[j+1]); ++i) {
[2767]2917 res[i] = true;
2918 }
2919 }
2920
2921 return res;
2922}
2923
[2773]2924Vector<uInt> Scantable::getMaskListFromMask(const std::vector<bool>& mask)
[2767]2925{
[2773]2926 std::vector<int> masklist;
2927 masklist.clear();
2928
2929 for (uInt i = 0; i < mask.size(); ++i) {
2930 if (mask[i]) {
2931 if ((i == 0)||(i == mask.size()-1)) {
2932 masklist.push_back(i);
2933 } else {
2934 if ((mask[i])&&(!mask[i-1])) {
2935 masklist.push_back(i);
2936 }
2937 if ((mask[i])&&(!mask[i+1])) {
2938 masklist.push_back(i);
2939 }
2940 }
2941 }
2942 }
2943
2944 Vector<uInt> res(masklist.size());
2945 for (uInt i = 0; i < masklist.size(); ++i) {
2946 res[i] = (uInt)masklist[i];
2947 }
2948
2949 return res;
2950}
2951
2952void Scantable::initialiseBaselining(const std::string& blfile,
2953 ofstream& ofs,
2954 const bool outLogger,
2955 bool& outTextFile,
2956 bool& csvFormat,
2957 String& coordInfo,
2958 bool& hasSameNchan,
2959 const std::string& progressInfo,
2960 bool& showProgress,
2961 int& minNRow,
2962 Vector<Double>& timeSecCol)
2963{
2964 csvFormat = false;
2965 outTextFile = false;
2966
2967 if (blfile != "") {
2968 csvFormat = (blfile.substr(0, 1) == "T");
2969 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2970 if (ofs) outTextFile = true;
2971 }
2972
2973 coordInfo = "";
2974 hasSameNchan = true;
2975
2976 if (outLogger || outTextFile) {
2977 coordInfo = getCoordInfo()[0];
2978 if (coordInfo == "") coordInfo = "channel";
2979 hasSameNchan = hasSameNchanOverIFs();
2980 }
2981
2982 parseProgressInfo(progressInfo, showProgress, minNRow);
2983
2984 ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME");
2985 timeSecCol = tcol.getColumn();
2986}
2987
2988void Scantable::finaliseBaselining(const bool outBaselineTable,
2989 STBaselineTable* pbt,
2990 const string& bltable,
2991 const bool outTextFile,
2992 ofstream& ofs)
2993{
2994 if (outBaselineTable) {
2995 pbt->save(bltable);
2996 }
2997
2998 if (outTextFile) ofs.close();
2999}
3000
3001void Scantable::initLineFinder(const std::vector<int>& edge,
3002 const float threshold,
3003 const int chanAvgLimit,
3004 STLineFinder& lineFinder)
3005{
[2774]3006 if ((edge.size() > 2) && (edge.size() < getIFNos().size()*2)) {
[2773]3007 throw(AipsError("Length of edge element info is less than that of IFs"));
3008 }
3009
3010 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3011}
3012
3013void Scantable::polyBaseline(const std::vector<bool>& mask, int order,
3014 float thresClip, int nIterClip,
3015 bool getResidual,
3016 const std::string& progressInfo,
3017 const bool outLogger, const std::string& blfile,
3018 const std::string& bltable)
3019{
[2774]3020 /****
[2767]3021 double TimeStart = mathutil::gettimeofday_sec();
[2774]3022 ****/
[2767]3023
[2193]3024 try {
3025 ofstream ofs;
[2773]3026 String coordInfo;
3027 bool hasSameNchan, outTextFile, csvFormat, showProgress;
[2193]3028 int minNRow;
[2767]3029 int nRow = nrow();
[2773]3030 std::vector<bool> chanMask, finalChanMask;
[2767]3031 float rms;
[2773]3032 bool outBaselineTable = (bltable != "");
3033 STBaselineTable bt = STBaselineTable(*this);
3034 Vector<Double> timeSecCol;
[2767]3035
[2773]3036 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3037 coordInfo, hasSameNchan,
3038 progressInfo, showProgress, minNRow,
3039 timeSecCol);
[2767]3040
[2773]3041 std::vector<int> nChanNos;
3042 std::vector<std::vector<std::vector<double> > > modelReservoir;
3043 modelReservoir = getPolynomialModelReservoir(order,
3044 &Scantable::getNormalPolynomial,
3045 nChanNos);
[2968]3046 int nModel = modelReservoir.size();
[2773]3047
[2193]3048 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2767]3049 std::vector<float> sp = getSpectrum(whichrow);
[2193]3050 chanMask = getCompositeChanMask(whichrow, mask);
[2968]3051 std::vector<float> params;
[2773]3052
[2968]3053 if (flagrowCol_(whichrow) == 0) {
3054 int nClipped = 0;
3055 std::vector<float> res;
3056 res = doLeastSquareFitting(sp, chanMask,
[2773]3057 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3058 params, rms, finalChanMask,
3059 nClipped, thresClip, nIterClip, getResidual);
[2767]3060
[2968]3061 if (outBaselineTable) {
3062 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3063 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3064 true, STBaselineFunc::Polynomial, order, std::vector<float>(),
3065 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3066 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3067 } else {
3068 setSpectrum(res, whichrow);
3069 }
3070
3071 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3072 coordInfo, hasSameNchan, ofs, "polyBaseline()",
3073 params, nClipped);
[2767]3074 } else {
[2968]3075 if (outBaselineTable) {
3076 params.resize(nModel);
3077 for (uInt i = 0; i < params.size(); ++i) {
3078 params[i] = 0.0;
3079 }
3080 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3081 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3082 true, STBaselineFunc::Polynomial, order, std::vector<float>(),
3083 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
3084 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3085 }
[2767]3086 }
3087
[2193]3088 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3089 }
3090
[2773]3091 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2193]3092
3093 } catch (...) {
3094 throw;
[2047]3095 }
[2767]3096
[2774]3097 /****
[2767]3098 double TimeEnd = mathutil::gettimeofday_sec();
3099 double elapse1 = TimeEnd - TimeStart;
3100 std::cout << "poly-new : " << elapse1 << " (sec.)" << endl;
[2774]3101 ****/
[2047]3102}
3103
[2773]3104void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order,
3105 float thresClip, int nIterClip,
3106 const std::vector<int>& edge,
3107 float threshold, int chanAvgLimit,
3108 bool getResidual,
3109 const std::string& progressInfo,
3110 const bool outLogger, const std::string& blfile,
3111 const std::string& bltable)
[2047]3112{
[2193]3113 try {
3114 ofstream ofs;
[2773]3115 String coordInfo;
3116 bool hasSameNchan, outTextFile, csvFormat, showProgress;
[2767]3117 int minNRow;
3118 int nRow = nrow();
[2773]3119 std::vector<bool> chanMask, finalChanMask;
[2767]3120 float rms;
[2773]3121 bool outBaselineTable = (bltable != "");
3122 STBaselineTable bt = STBaselineTable(*this);
3123 Vector<Double> timeSecCol;
3124 STLineFinder lineFinder = STLineFinder();
[2189]3125
[2773]3126 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3127 coordInfo, hasSameNchan,
3128 progressInfo, showProgress, minNRow,
3129 timeSecCol);
[2767]3130
[2773]3131 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3132
3133 std::vector<int> nChanNos;
3134 std::vector<std::vector<std::vector<double> > > modelReservoir;
3135 modelReservoir = getPolynomialModelReservoir(order,
3136 &Scantable::getNormalPolynomial,
3137 nChanNos);
[2968]3138 int nModel = modelReservoir.size();
[2773]3139
[2193]3140 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2767]3141 std::vector<float> sp = getSpectrum(whichrow);
[2193]3142 std::vector<int> currentEdge;
[2773]3143 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
[2968]3144 std::vector<float> params;
[2193]3145
[2968]3146 if (flagrowCol_(whichrow) == 0) {
3147 int nClipped = 0;
3148 std::vector<float> res;
3149 res = doLeastSquareFitting(sp, chanMask,
[2773]3150 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3151 params, rms, finalChanMask,
3152 nClipped, thresClip, nIterClip, getResidual);
[2193]3153
[2968]3154 if (outBaselineTable) {
3155 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3156 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3157 true, STBaselineFunc::Polynomial, order, std::vector<float>(),
3158 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3159 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3160 } else {
3161 setSpectrum(res, whichrow);
3162 }
3163
3164 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3165 coordInfo, hasSameNchan, ofs, "autoPolyBaseline()",
3166 params, nClipped);
[2767]3167 } else {
[2968]3168 if (outBaselineTable) {
3169 params.resize(nModel);
3170 for (uInt i = 0; i < params.size(); ++i) {
3171 params[i] = 0.0;
3172 }
3173 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3174 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3175 true, STBaselineFunc::Polynomial, order, std::vector<float>(),
3176 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
3177 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3178 }
[2767]3179 }
3180
[2193]3181 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[2047]3182 }
3183
[2773]3184 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2767]3185
[2193]3186 } catch (...) {
3187 throw;
[2047]3188 }
3189}
3190
[2773]3191void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order,
3192 float thresClip, int nIterClip,
3193 bool getResidual,
3194 const std::string& progressInfo,
3195 const bool outLogger, const std::string& blfile,
3196 const std::string& bltable)
[2645]3197{
[2774]3198 /*
[2767]3199 double TimeStart = mathutil::gettimeofday_sec();
[2774]3200 */
[2767]3201
[2645]3202 try {
3203 ofstream ofs;
[2773]3204 String coordInfo;
3205 bool hasSameNchan, outTextFile, csvFormat, showProgress;
[2645]3206 int minNRow;
3207 int nRow = nrow();
[2773]3208 std::vector<bool> chanMask, finalChanMask;
[2737]3209 float rms;
[2773]3210 bool outBaselineTable = (bltable != "");
3211 STBaselineTable bt = STBaselineTable(*this);
3212 Vector<Double> timeSecCol;
[2737]3213
[2773]3214 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3215 coordInfo, hasSameNchan,
3216 progressInfo, showProgress, minNRow,
3217 timeSecCol);
[2737]3218
[2773]3219 std::vector<int> nChanNos;
3220 std::vector<std::vector<std::vector<double> > > modelReservoir;
3221 modelReservoir = getPolynomialModelReservoir(order,
3222 &Scantable::getChebyshevPolynomial,
3223 nChanNos);
[2968]3224 int nModel = modelReservoir.size();
[2773]3225
[2645]3226 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3227 std::vector<float> sp = getSpectrum(whichrow);
3228 chanMask = getCompositeChanMask(whichrow, mask);
[2968]3229 std::vector<float> params;
[2773]3230
[2968]3231 if (flagrowCol_(whichrow) == 0) {
3232 int nClipped = 0;
3233 std::vector<float> res;
3234 res = doLeastSquareFitting(sp, chanMask,
[2773]3235 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3236 params, rms, finalChanMask,
3237 nClipped, thresClip, nIterClip, getResidual);
[2645]3238
[2968]3239 if (outBaselineTable) {
3240 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3241 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3242 true, STBaselineFunc::Chebyshev, order, std::vector<float>(),
3243 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3244 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3245 } else {
3246 setSpectrum(res, whichrow);
3247 }
3248
3249 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3250 coordInfo, hasSameNchan, ofs, "chebyshevBaseline()",
3251 params, nClipped);
[2737]3252 } else {
[2968]3253 if (outBaselineTable) {
3254 params.resize(nModel);
3255 for (uInt i = 0; i < params.size(); ++i) {
3256 params[i] = 0.0;
3257 }
3258 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3259 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3260 true, STBaselineFunc::Chebyshev, order, std::vector<float>(),
3261 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
3262 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3263 }
[2737]3264 }
3265
[2645]3266 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3267 }
3268
[2773]3269 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2737]3270
[2645]3271 } catch (...) {
3272 throw;
3273 }
[2767]3274
[2774]3275 /*
[2767]3276 double TimeEnd = mathutil::gettimeofday_sec();
3277 double elapse1 = TimeEnd - TimeStart;
3278 std::cout << "cheby : " << elapse1 << " (sec.)" << endl;
[2774]3279 */
[2645]3280}
3281
[2773]3282void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order,
3283 float thresClip, int nIterClip,
3284 const std::vector<int>& edge,
3285 float threshold, int chanAvgLimit,
3286 bool getResidual,
3287 const std::string& progressInfo,
3288 const bool outLogger, const std::string& blfile,
3289 const std::string& bltable)
[2767]3290{
3291 try {
3292 ofstream ofs;
[2773]3293 String coordInfo;
3294 bool hasSameNchan, outTextFile, csvFormat, showProgress;
[2767]3295 int minNRow;
3296 int nRow = nrow();
[2773]3297 std::vector<bool> chanMask, finalChanMask;
[2767]3298 float rms;
[2773]3299 bool outBaselineTable = (bltable != "");
3300 STBaselineTable bt = STBaselineTable(*this);
3301 Vector<Double> timeSecCol;
3302 STLineFinder lineFinder = STLineFinder();
[2767]3303
[2773]3304 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3305 coordInfo, hasSameNchan,
3306 progressInfo, showProgress, minNRow,
3307 timeSecCol);
[2767]3308
[2773]3309 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3310
3311 std::vector<int> nChanNos;
3312 std::vector<std::vector<std::vector<double> > > modelReservoir;
3313 modelReservoir = getPolynomialModelReservoir(order,
3314 &Scantable::getChebyshevPolynomial,
3315 nChanNos);
[2968]3316 int nModel = modelReservoir.size();
[2773]3317
[2767]3318 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3319 std::vector<float> sp = getSpectrum(whichrow);
3320 std::vector<int> currentEdge;
[2773]3321 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
[2968]3322 std::vector<float> params;
[2767]3323
[2968]3324 if (flagrowCol_(whichrow) == 0) {
3325 int nClipped = 0;
3326 std::vector<float> res;
3327 res = doLeastSquareFitting(sp, chanMask,
[2773]3328 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3329 params, rms, finalChanMask,
3330 nClipped, thresClip, nIterClip, getResidual);
[2767]3331
[2968]3332 if (outBaselineTable) {
3333 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3334 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3335 true, STBaselineFunc::Chebyshev, order, std::vector<float>(),
3336 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3337 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3338 } else {
3339 setSpectrum(res, whichrow);
3340 }
3341
3342 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3343 coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()",
3344 params, nClipped);
[2767]3345 } else {
[2968]3346 if (outBaselineTable) {
3347 params.resize(nModel);
3348 for (uInt i = 0; i < params.size(); ++i) {
3349 params[i] = 0.0;
3350 }
3351 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3352 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3353 true, STBaselineFunc::Chebyshev, order, std::vector<float>(),
3354 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
3355 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3356 }
[2767]3357 }
3358
3359 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3360 }
3361
[2773]3362 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2767]3363
3364 } catch (...) {
3365 throw;
3366 }
3367}
3368
[2774]3369double Scantable::calculateModelSelectionCriteria(const std::string& valname,
3370 const std::string& blfunc,
3371 int order,
3372 const std::vector<bool>& inMask,
3373 int whichrow,
3374 bool useLineFinder,
3375 const std::vector<int>& edge,
3376 float threshold,
3377 int chanAvgLimit)
[2713]3378{
[2767]3379 std::vector<float> sp = getSpectrum(whichrow);
3380 std::vector<bool> chanMask;
3381 chanMask.clear();
3382
[2713]3383 if (useLineFinder) {
[2774]3384 STLineFinder lineFinder = STLineFinder();
3385 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
[2713]3386 std::vector<int> currentEdge;
[2774]3387 chanMask = getCompositeChanMask(whichrow, inMask, edge, currentEdge, lineFinder);
[2713]3388 } else {
[2767]3389 chanMask = getCompositeChanMask(whichrow, inMask);
[2713]3390 }
3391
[2767]3392 return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order);
[2713]3393}
3394
3395double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order)
3396{
3397 int nparam;
3398 std::vector<float> params;
[2737]3399 std::vector<bool> finalChanMask;
3400 float rms;
[2713]3401 int nClipped = 0;
3402 std::vector<float> res;
[2767]3403 if (blfunc == "poly") {
[2713]3404 nparam = order + 1;
[2767]3405 res = doPolynomialFitting(spec, mask, order, params, rms, finalChanMask, nClipped);
3406 } else if (blfunc == "chebyshev") {
3407 nparam = order + 1;
3408 res = doChebyshevFitting(spec, mask, order, params, rms, finalChanMask, nClipped);
3409 } else if (blfunc == "cspline") {
3410 std::vector<int> pieceEdges;//(order+1); //order = npiece
3411 nparam = order + 3;
3412 res = doCubicSplineFitting(spec, mask, order, false, pieceEdges, params, rms, finalChanMask, nClipped);
[2713]3413 } else if (blfunc == "sinusoid") {
3414 std::vector<int> nWaves;
3415 nWaves.clear();
3416 for (int i = 0; i <= order; ++i) {
3417 nWaves.push_back(i);
3418 }
3419 nparam = 2*order + 1; // order = nwave
[2767]3420 res = doSinusoidFitting(spec, mask, nWaves, params, rms, finalChanMask, nClipped);
[2713]3421 } else {
[2767]3422 throw(AipsError("blfunc must be poly, chebyshev, cspline or sinusoid."));
[2713]3423 }
3424
3425 double msq = 0.0;
3426 int nusedchan = 0;
3427 int nChan = res.size();
3428 for (int i = 0; i < nChan; ++i) {
3429 if (mask[i]) {
3430 msq += (double)res[i]*(double)res[i];
3431 nusedchan++;
3432 }
3433 }
3434 if (nusedchan == 0) {
3435 throw(AipsError("all channels masked."));
3436 }
3437 msq /= (double)nusedchan;
3438
3439 nparam++; //add 1 for sigma of Gaussian distribution
3440 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
3441
3442 if (valname.find("aic") == 0) {
3443 // Original Akaike Information Criterion (AIC)
3444 double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam;
3445
[2767]3446 // Corrected AIC by Sugiura(1978) (AICc)
[2713]3447 if (valname == "aicc") {
3448 if (nusedchan - nparam - 1 <= 0) {
3449 throw(AipsError("channel size is too small to calculate AICc."));
3450 }
3451 aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1);
3452 }
3453
3454 return aic;
3455
3456 } else if (valname == "bic") {
3457 // Bayesian Information Criterion (BIC)
3458 double bic = nusedchan * log(msq) + nparam * log((double)nusedchan);
3459 return bic;
3460
3461 } else if (valname == "gcv") {
3462 // Generalised Cross Validation
3463 double x = 1.0 - (double)nparam / (double)nusedchan;
3464 double gcv = msq / (x * x);
3465 return gcv;
3466
3467 } else {
3468 throw(AipsError("valname must be aic, aicc, bic or gcv."));
3469 }
3470}
3471
[2767]3472double Scantable::getNormalPolynomial(int n, double x) {
3473 if (n == 0) {
3474 return 1.0;
3475 } else if (n > 0) {
3476 double res = 1.0;
3477 for (int i = 0; i < n; ++i) {
3478 res *= x;
[2645]3479 }
[2767]3480 return res;
3481 } else {
3482 if (x == 0.0) {
3483 throw(AipsError("infinity result: x=0 given for negative power."));
3484 } else {
3485 return pow(x, (double)n);
[2645]3486 }
3487 }
3488}
3489
3490double Scantable::getChebyshevPolynomial(int n, double x) {
3491 if ((x < -1.0)||(x > 1.0)) {
3492 throw(AipsError("out of definition range (-1 <= x <= 1)."));
[2713]3493 } else if (x == 1.0) {
3494 return 1.0;
3495 } else if (x == 0.0) {
3496 double res;
3497 if (n%2 == 0) {
3498 if (n%4 == 0) {
3499 res = 1.0;
3500 } else {
3501 res = -1.0;
3502 }
3503 } else {
3504 res = 0.0;
3505 }
3506 return res;
3507 } else if (x == -1.0) {
3508 double res = (n%2 == 0 ? 1.0 : -1.0);
3509 return res;
[2645]3510 } else if (n < 0) {
3511 throw(AipsError("the order must be zero or positive."));
3512 } else if (n == 0) {
3513 return 1.0;
3514 } else if (n == 1) {
3515 return x;
3516 } else {
[2880]3517 double res[n+1];
3518 for (int i = 0; i < n+1; ++i) {
3519 double res0 = 0.0;
3520 if (i == 0) {
3521 res0 = 1.0;
3522 } else if (i == 1) {
3523 res0 = x;
3524 } else {
3525 res0 = 2.0 * x * res[i-1] - res[i-2];
[2645]3526 }
[2880]3527 res[i] = res0;
[2645]3528 }
[2880]3529 return res[n];
[2645]3530 }
3531}
3532
[2773]3533std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data,
3534 const std::vector<bool>& mask,
3535 int order,
3536 std::vector<float>& params,
3537 float& rms,
3538 std::vector<bool>& finalmask,
3539 float clipth,
3540 int clipn)
[2645]3541{
[2767]3542 int nClipped = 0;
3543 return doPolynomialFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn);
3544}
3545
[2773]3546std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data,
3547 const std::vector<bool>& mask,
3548 int order,
3549 std::vector<float>& params,
3550 float& rms,
3551 std::vector<bool>& finalMask,
3552 int& nClipped,
3553 float thresClip,
3554 int nIterClip,
3555 bool getResidual)
[2767]3556{
[2773]3557 return doLeastSquareFitting(data, mask,
3558 getPolynomialModel(order, data.size(), &Scantable::getNormalPolynomial),
3559 params, rms, finalMask,
3560 nClipped, thresClip, nIterClip,
3561 getResidual);
[2767]3562}
3563
[2773]3564std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data,
3565 const std::vector<bool>& mask,
3566 int order,
3567 std::vector<float>& params,
3568 float& rms,
3569 std::vector<bool>& finalmask,
3570 float clipth,
3571 int clipn)
[2767]3572{
3573 int nClipped = 0;
3574 return doChebyshevFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn);
3575}
3576
[2773]3577std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data,
3578 const std::vector<bool>& mask,
3579 int order,
3580 std::vector<float>& params,
3581 float& rms,
3582 std::vector<bool>& finalMask,
3583 int& nClipped,
3584 float thresClip,
3585 int nIterClip,
3586 bool getResidual)
[2767]3587{
[2773]3588 return doLeastSquareFitting(data, mask,
3589 getPolynomialModel(order, data.size(), &Scantable::getChebyshevPolynomial),
3590 params, rms, finalMask,
3591 nClipped, thresClip, nIterClip,
3592 getResidual);
[2767]3593}
3594
[2773]3595std::vector<std::vector<double> > Scantable::getPolynomialModel(int order, int nchan, double (Scantable::*pfunc)(int, double))
[2767]3596{
[2773]3597 // model : contains model values for computing the least-square matrix.
3598 // model.size() is nmodel and model[*].size() is nchan.
3599 // Each model element are as follows:
3600 //
3601 // (for normal polynomials)
3602 // model[0] = {1.0, 1.0, 1.0, ..., 1.0},
3603 // model[1] = {0.0, 1.0, 2.0, ..., (nchan-1)}
3604 // model[n-1] = ...,
3605 // model[n] = {0.0^n, 1.0^n, 2.0^n, ..., (nchan-1)^n}
3606 // where (0 <= n <= order)
3607 //
3608 // (for Chebyshev polynomials)
3609 // model[0] = {T0(-1), T0(2/(nchan-1)-1), T0(4/(nchan-1)-1), ..., T0(1)},
3610 // model[n-1] = ...,
3611 // model[n] = {Tn(-1), Tn(2/(nchan-1)-1), Tn(4/(nchan-1)-1), ..., Tn(1)}
3612 // where (0 <= n <= order),
3613
3614 int nmodel = order + 1;
3615 std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan));
3616
3617 double stretch, shift;
3618 if (pfunc == &Scantable::getChebyshevPolynomial) {
3619 stretch = 2.0/(double)(nchan - 1);
3620 shift = -1.0;
3621 } else {
3622 stretch = 1.0;
3623 shift = 0.0;
[2645]3624 }
[2773]3625
3626 for (int i = 0; i < nmodel; ++i) {
3627 for (int j = 0; j < nchan; ++j) {
3628 model[i][j] = (this->*pfunc)(i, stretch*(double)j + shift);
3629 }
[2645]3630 }
3631
[2773]3632 return model;
3633}
3634
3635std::vector<std::vector<std::vector<double> > > Scantable::getPolynomialModelReservoir(int order,
3636 double (Scantable::*pfunc)(int, double),
3637 std::vector<int>& nChanNos)
3638{
3639 std::vector<std::vector<std::vector<double> > > res;
3640 res.clear();
3641 nChanNos.clear();
3642
3643 std::vector<uint> ifNos = getIFNos();
3644 for (uint i = 0; i < ifNos.size(); ++i) {
3645 int currNchan = nchan(ifNos[i]);
3646 bool hasDifferentNchan = (i == 0);
3647 for (uint j = 0; j < i; ++j) {
3648 if (currNchan != nchan(ifNos[j])) {
3649 hasDifferentNchan = true;
3650 break;
3651 }
3652 }
3653 if (hasDifferentNchan) {
3654 res.push_back(getPolynomialModel(order, currNchan, pfunc));
3655 nChanNos.push_back(currNchan);
3656 }
3657 }
3658
3659 return res;
3660}
3661
3662std::vector<float> Scantable::doLeastSquareFitting(const std::vector<float>& data,
3663 const std::vector<bool>& mask,
3664 const std::vector<std::vector<double> >& model,
3665 std::vector<float>& params,
3666 float& rms,
3667 std::vector<bool>& finalMask,
3668 int& nClipped,
3669 float thresClip,
3670 int nIterClip,
3671 bool getResidual)
3672{
3673 int nDOF = model.size();
[2645]3674 int nChan = data.size();
[2737]3675
[2773]3676 if (nDOF == 0) {
3677 throw(AipsError("no model data given"));
3678 }
3679 if (nChan < 2) {
3680 throw(AipsError("data size is too few"));
3681 }
3682 if (nChan != (int)mask.size()) {
3683 throw(AipsError("data and mask sizes are not identical"));
3684 }
3685 for (int i = 0; i < nDOF; ++i) {
3686 if (nChan != (int)model[i].size()) {
3687 throw(AipsError("data and model sizes are not identical"));
3688 }
3689 }
3690
3691 params.clear();
3692 params.resize(nDOF);
3693
[2737]3694 finalMask.clear();
3695 finalMask.resize(nChan);
3696
[2773]3697 std::vector<int> maskArray(nChan);
3698 int j = 0;
[2645]3699 for (int i = 0; i < nChan; ++i) {
[2773]3700 maskArray[i] = mask[i] ? 1 : 0;
[2890]3701 if (isnan(data[i])) maskArray[i] = 0;
3702 if (isinf(data[i])) maskArray[i] = 0;
3703
3704 finalMask[i] = (maskArray[i] == 1);
3705 if (finalMask[i]) {
3706 j++;
3707 }
3708
3709 /*
3710 maskArray[i] = mask[i] ? 1 : 0;
[2645]3711 if (mask[i]) {
[2773]3712 j++;
[2645]3713 }
[2737]3714 finalMask[i] = mask[i];
[2890]3715 */
[2645]3716 }
3717
[2773]3718 int initNData = j;
[2645]3719 int nData = initNData;
3720
[2773]3721 std::vector<double> z1(nChan), r1(nChan), residual(nChan);
[2645]3722 for (int i = 0; i < nChan; ++i) {
[2773]3723 z1[i] = (double)data[i];
3724 r1[i] = 0.0;
3725 residual[i] = 0.0;
[2645]3726 }
3727
3728 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3729 // xMatrix : horizontal concatenation of
3730 // the least-sq. matrix (left) and an
3731 // identity matrix (right).
3732 // the right part is used to calculate the inverse matrix of the left part.
3733 double xMatrix[nDOF][2*nDOF];
3734 double zMatrix[nDOF];
3735 for (int i = 0; i < nDOF; ++i) {
3736 for (int j = 0; j < 2*nDOF; ++j) {
3737 xMatrix[i][j] = 0.0;
3738 }
3739 xMatrix[i][nDOF+i] = 1.0;
3740 zMatrix[i] = 0.0;
3741 }
3742
3743 int nUseData = 0;
3744 for (int k = 0; k < nChan; ++k) {
3745 if (maskArray[k] == 0) continue;
3746
3747 for (int i = 0; i < nDOF; ++i) {
3748 for (int j = i; j < nDOF; ++j) {
[2773]3749 xMatrix[i][j] += model[i][k] * model[j][k];
[2645]3750 }
[2773]3751 zMatrix[i] += z1[k] * model[i][k];
[2645]3752 }
3753
3754 nUseData++;
3755 }
3756
3757 if (nUseData < 1) {
3758 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3759 }
3760
3761 for (int i = 0; i < nDOF; ++i) {
3762 for (int j = 0; j < i; ++j) {
3763 xMatrix[i][j] = xMatrix[j][i];
3764 }
3765 }
3766
[2890]3767 //compute inverse matrix of the left half of xMatrix
[2773]3768 std::vector<double> invDiag(nDOF);
[2645]3769 for (int i = 0; i < nDOF; ++i) {
[2773]3770 invDiag[i] = 1.0 / xMatrix[i][i];
[2645]3771 for (int j = 0; j < nDOF; ++j) {
3772 xMatrix[i][j] *= invDiag[i];
3773 }
3774 }
3775
3776 for (int k = 0; k < nDOF; ++k) {
3777 for (int i = 0; i < nDOF; ++i) {
3778 if (i != k) {
3779 double factor1 = xMatrix[k][k];
[2773]3780 double invfactor1 = 1.0 / factor1;
[2645]3781 double factor2 = xMatrix[i][k];
3782 for (int j = k; j < 2*nDOF; ++j) {
3783 xMatrix[i][j] *= factor1;
3784 xMatrix[i][j] -= xMatrix[k][j]*factor2;
[2773]3785 xMatrix[i][j] *= invfactor1;
[2645]3786 }
3787 }
3788 }
[2773]3789 double invXDiag = 1.0 / xMatrix[k][k];
[2645]3790 for (int j = k; j < 2*nDOF; ++j) {
[2773]3791 xMatrix[k][j] *= invXDiag;
[2645]3792 }
3793 }
3794
3795 for (int i = 0; i < nDOF; ++i) {
3796 for (int j = 0; j < nDOF; ++j) {
3797 xMatrix[i][nDOF+j] *= invDiag[j];
3798 }
3799 }
[2773]3800 //compute a vector y in which coefficients of the best-fit
3801 //model functions are stored.
3802 //in case of polynomials, y consists of (a0,a1,a2,...)
3803 //where ai is the coefficient of the term x^i.
3804 //in case of sinusoids, y consists of (a0,s1,c1,s2,c2,...)
3805 //where a0 is constant term and s* and c* are of sine
3806 //and cosine functions, respectively.
3807 std::vector<double> y(nDOF);
[2645]3808 for (int i = 0; i < nDOF; ++i) {
[2773]3809 y[i] = 0.0;
[2645]3810 for (int j = 0; j < nDOF; ++j) {
3811 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3812 }
[2773]3813 params[i] = (float)y[i];
[2645]3814 }
3815
3816 for (int i = 0; i < nChan; ++i) {
3817 r1[i] = y[0];
3818 for (int j = 1; j < nDOF; ++j) {
[2773]3819 r1[i] += y[j]*model[j][i];
[2645]3820 }
3821 residual[i] = z1[i] - r1[i];
3822 }
3823
[2737]3824 double stdDev = 0.0;
3825 for (int i = 0; i < nChan; ++i) {
[2890]3826 if (maskArray[i] == 0) continue;
3827 stdDev += residual[i]*residual[i];
[2737]3828 }
3829 stdDev = sqrt(stdDev/(double)nData);
3830 rms = (float)stdDev;
3831
[2645]3832 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3833 break;
3834 } else {
[2737]3835
[2645]3836 double thres = stdDev * thresClip;
3837 int newNData = 0;
3838 for (int i = 0; i < nChan; ++i) {
3839 if (abs(residual[i]) >= thres) {
3840 maskArray[i] = 0;
[2737]3841 finalMask[i] = false;
[2645]3842 }
3843 if (maskArray[i] > 0) {
3844 newNData++;
3845 }
3846 }
3847 if (newNData == nData) {
[2890]3848 break; //no more flag to add. stop iteration.
[2645]3849 } else {
3850 nData = newNData;
3851 }
[2737]3852
[2645]3853 }
3854 }
3855
3856 nClipped = initNData - nData;
3857
[2773]3858 std::vector<float> result(nChan);
[2645]3859 if (getResidual) {
3860 for (int i = 0; i < nChan; ++i) {
[2773]3861 result[i] = (float)residual[i];
[2645]3862 }
3863 } else {
3864 for (int i = 0; i < nChan; ++i) {
[2773]3865 result[i] = (float)r1[i];
[2645]3866 }
3867 }
3868
3869 return result;
[2890]3870} //xMatrix
[2645]3871
[2773]3872void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece,
3873 float thresClip, int nIterClip,
3874 bool getResidual,
3875 const std::string& progressInfo,
3876 const bool outLogger, const std::string& blfile,
3877 const std::string& bltable)
[2081]3878{
[2774]3879 /****
[2773]3880 double TimeStart = mathutil::gettimeofday_sec();
[2774]3881 ****/
[2773]3882
[2193]3883 try {
3884 ofstream ofs;
[2773]3885 String coordInfo;
3886 bool hasSameNchan, outTextFile, csvFormat, showProgress;
[2193]3887 int minNRow;
[2344]3888 int nRow = nrow();
[2773]3889 std::vector<bool> chanMask, finalChanMask;
[2767]3890 float rms;
[2773]3891 bool outBaselineTable = (bltable != "");
3892 STBaselineTable bt = STBaselineTable(*this);
3893 Vector<Double> timeSecCol;
[2344]3894
[2773]3895 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3896 coordInfo, hasSameNchan,
3897 progressInfo, showProgress, minNRow,
3898 timeSecCol);
[2767]3899
[2773]3900 std::vector<int> nChanNos;
3901 std::vector<std::vector<std::vector<double> > > modelReservoir;
3902 modelReservoir = getPolynomialModelReservoir(3,
3903 &Scantable::getNormalPolynomial,
3904 nChanNos);
[2968]3905 int nDOF = nPiece + 3;
[2767]3906
[2193]3907 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2591]3908 std::vector<float> sp = getSpectrum(whichrow);
[2193]3909 chanMask = getCompositeChanMask(whichrow, mask);
[2773]3910 std::vector<int> pieceEdges;
3911 std::vector<float> params;
[2591]3912
[2968]3913 if (flagrowCol_(whichrow) == 0) {
3914 int nClipped = 0;
3915 std::vector<float> res;
3916 res = doCubicSplineLeastSquareFitting(sp, chanMask,
3917 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3918 nPiece, false, pieceEdges, params, rms, finalChanMask,
3919 nClipped, thresClip, nIterClip, getResidual);
3920
3921 if (outBaselineTable) {
3922 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3923 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3924 true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(),
3925 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3926 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3927 } else {
3928 setSpectrum(res, whichrow);
3929 }
3930
3931 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3932 coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()",
3933 pieceEdges, params, nClipped);
[2767]3934 } else {
[2968]3935 if (outBaselineTable) {
3936 pieceEdges.resize(nPiece+1);
3937 for (uInt i = 0; i < pieceEdges.size(); ++i) {
3938 pieceEdges[i] = 0;
3939 }
3940 params.resize(nDOF);
3941 for (uInt i = 0; i < params.size(); ++i) {
3942 params[i] = 0.0;
3943 }
3944 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3945 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3946 true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(),
3947 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
3948 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3949 }
[2767]3950 }
[2591]3951
[2193]3952 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3953 }
[2344]3954
[2773]3955 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2767]3956
[2193]3957 } catch (...) {
3958 throw;
[2012]3959 }
[2773]3960
[2774]3961 /****
[2773]3962 double TimeEnd = mathutil::gettimeofday_sec();
3963 double elapse1 = TimeEnd - TimeStart;
3964 std::cout << "cspline-new : " << elapse1 << " (sec.)" << endl;
[2774]3965 ****/
[2012]3966}
3967
[2773]3968void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece,
3969 float thresClip, int nIterClip,
3970 const std::vector<int>& edge,
3971 float threshold, int chanAvgLimit,
3972 bool getResidual,
3973 const std::string& progressInfo,
3974 const bool outLogger, const std::string& blfile,
3975 const std::string& bltable)
[2012]3976{
[2193]3977 try {
3978 ofstream ofs;
[2773]3979 String coordInfo;
3980 bool hasSameNchan, outTextFile, csvFormat, showProgress;
[2767]3981 int minNRow;
3982 int nRow = nrow();
[2773]3983 std::vector<bool> chanMask, finalChanMask;
[2767]3984 float rms;
[2773]3985 bool outBaselineTable = (bltable != "");
3986 STBaselineTable bt = STBaselineTable(*this);
3987 Vector<Double> timeSecCol;
3988 STLineFinder lineFinder = STLineFinder();
[2189]3989
[2773]3990 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3991 coordInfo, hasSameNchan,
3992 progressInfo, showProgress, minNRow,
3993 timeSecCol);
[2767]3994
[2773]3995 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3996
3997 std::vector<int> nChanNos;
3998 std::vector<std::vector<std::vector<double> > > modelReservoir;
3999 modelReservoir = getPolynomialModelReservoir(3,
4000 &Scantable::getNormalPolynomial,
4001 nChanNos);
[2968]4002 int nDOF = nPiece + 3;
[2773]4003
[2193]4004 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2591]4005 std::vector<float> sp = getSpectrum(whichrow);
[2193]4006 std::vector<int> currentEdge;
[2773]4007 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
4008 std::vector<int> pieceEdges;
4009 std::vector<float> params;
[2193]4010
[2968]4011 if (flagrowCol_(whichrow) == 0) {
4012 int nClipped = 0;
4013 std::vector<float> res;
4014 res = doCubicSplineLeastSquareFitting(sp, chanMask,
4015 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
4016 nPiece, false, pieceEdges, params, rms, finalChanMask,
4017 nClipped, thresClip, nIterClip, getResidual);
4018
4019 if (outBaselineTable) {
4020 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4021 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4022 true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(),
4023 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
4024 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
4025 } else {
4026 setSpectrum(res, whichrow);
4027 }
4028
4029 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
4030 coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()",
4031 pieceEdges, params, nClipped);
[2767]4032 } else {
[2968]4033 if (outBaselineTable) {
4034 pieceEdges.resize(nPiece+1);
4035 for (uInt i = 0; i < pieceEdges.size(); ++i) {
4036 pieceEdges[i] = 0;
4037 }
4038 params.resize(nDOF);
4039 for (uInt i = 0; i < params.size(); ++i) {
4040 params[i] = 0.0;
4041 }
4042 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4043 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4044 true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(),
4045 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
4046 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
4047 }
[2767]4048 }
4049
[2193]4050 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[1907]4051 }
[2012]4052
[2773]4053 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2767]4054
[2193]4055 } catch (...) {
4056 throw;
[2012]4057 }
[1730]4058}
[1907]4059
[2773]4060std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data,
4061 const std::vector<bool>& mask,
4062 std::vector<int>& idxEdge,
4063 std::vector<float>& params,
4064 float& rms,
4065 std::vector<bool>& finalmask,
4066 float clipth,
4067 int clipn)
[2081]4068{
[2767]4069 int nClipped = 0;
4070 return doCubicSplineFitting(data, mask, idxEdge.size()-1, true, idxEdge, params, rms, finalmask, nClipped, clipth, clipn);
4071}
4072
[2773]4073std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data,
4074 const std::vector<bool>& mask,
4075 int nPiece,
4076 std::vector<int>& idxEdge,
4077 std::vector<float>& params,
4078 float& rms,
4079 std::vector<bool>& finalmask,
4080 float clipth,
4081 int clipn)
[2767]4082{
4083 int nClipped = 0;
4084 return doCubicSplineFitting(data, mask, nPiece, false, idxEdge, params, rms, finalmask, nClipped, clipth, clipn);
4085}
4086
[2773]4087std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data,
4088 const std::vector<bool>& mask,
4089 int nPiece,
4090 bool useGivenPieceBoundary,
4091 std::vector<int>& idxEdge,
4092 std::vector<float>& params,
4093 float& rms,
4094 std::vector<bool>& finalMask,
4095 int& nClipped,
4096 float thresClip,
4097 int nIterClip,
4098 bool getResidual)
[2767]4099{
[2773]4100 return doCubicSplineLeastSquareFitting(data, mask,
4101 getPolynomialModel(3, data.size(), &Scantable::getNormalPolynomial),
4102 nPiece, useGivenPieceBoundary, idxEdge,
4103 params, rms, finalMask,
4104 nClipped, thresClip, nIterClip,
4105 getResidual);
4106}
4107
4108std::vector<float> Scantable::doCubicSplineLeastSquareFitting(const std::vector<float>& data,
4109 const std::vector<bool>& mask,
4110 const std::vector<std::vector<double> >& model,
4111 int nPiece,
4112 bool useGivenPieceBoundary,
4113 std::vector<int>& idxEdge,
4114 std::vector<float>& params,
4115 float& rms,
4116 std::vector<bool>& finalMask,
4117 int& nClipped,
4118 float thresClip,
4119 int nIterClip,
4120 bool getResidual)
4121{
4122 int nDOF = nPiece + 3; //number of independent parameters to solve, namely, 4+(nPiece-1).
4123 int nModel = model.size();
4124 int nChan = data.size();
4125
4126 if (nModel != 4) {
4127 throw(AipsError("model size must be 4."));
[2081]4128 }
[2012]4129 if (nPiece < 1) {
[2094]4130 throw(AipsError("number of the sections must be one or more"));
[2012]4131 }
[2773]4132 if (nChan < 2*nPiece) {
4133 throw(AipsError("data size is too few"));
4134 }
4135 if (nChan != (int)mask.size()) {
4136 throw(AipsError("data and mask sizes are not identical"));
4137 }
4138 for (int i = 0; i < nModel; ++i) {
4139 if (nChan != (int)model[i].size()) {
4140 throw(AipsError("data and model sizes are not identical"));
4141 }
4142 }
[2012]4143
[2773]4144 params.clear();
4145 params.resize(nPiece*nModel);
[2767]4146
4147 finalMask.clear();
4148 finalMask.resize(nChan);
4149
[2344]4150 std::vector<int> maskArray(nChan);
4151 std::vector<int> x(nChan);
4152 int j = 0;
[2012]4153 for (int i = 0; i < nChan; ++i) {
[2344]4154 maskArray[i] = mask[i] ? 1 : 0;
[2890]4155 if (isnan(data[i])) maskArray[i] = 0;
4156 if (isinf(data[i])) maskArray[i] = 0;
4157
4158 finalMask[i] = (maskArray[i] == 1);
4159 if (finalMask[i]) {
4160 x[j] = i;
4161 j++;
4162 }
4163
4164 /*
4165 maskArray[i] = mask[i] ? 1 : 0;
[2012]4166 if (mask[i]) {
[2344]4167 x[j] = i;
4168 j++;
[2012]4169 }
[2767]4170 finalMask[i] = mask[i];
[2890]4171 */
[2012]4172 }
[2773]4173
[2344]4174 int initNData = j;
[2773]4175 int nData = initNData;
[2012]4176
[2193]4177 if (initNData < nPiece) {
4178 throw(AipsError("too few non-flagged channels"));
4179 }
[2081]4180
4181 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
[2344]4182 std::vector<double> invEdge(nPiece-1);
[2767]4183
4184 if (useGivenPieceBoundary) {
4185 if ((int)idxEdge.size() != nPiece+1) {
4186 throw(AipsError("pieceEdge.size() must be equal to nPiece+1."));
4187 }
4188 } else {
4189 idxEdge.clear();
4190 idxEdge.resize(nPiece+1);
4191 idxEdge[0] = x[0];
4192 }
[2012]4193 for (int i = 1; i < nPiece; ++i) {
[2047]4194 int valX = x[nElement*i];
[2767]4195 if (!useGivenPieceBoundary) {
4196 idxEdge[i] = valX;
4197 }
[2344]4198 invEdge[i-1] = 1.0/(double)valX;
[2012]4199 }
[2767]4200 if (!useGivenPieceBoundary) {
4201 idxEdge[nPiece] = x[initNData-1]+1;
4202 }
[2064]4203
[2773]4204 std::vector<double> z1(nChan), r1(nChan), residual(nChan);
[2012]4205 for (int i = 0; i < nChan; ++i) {
[2773]4206 z1[i] = (double)data[i];
4207 r1[i] = 0.0;
[2344]4208 residual[i] = 0.0;
[2012]4209 }
4210
4211 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
[2064]4212 // xMatrix : horizontal concatenation of
4213 // the least-sq. matrix (left) and an
4214 // identity matrix (right).
4215 // the right part is used to calculate the inverse matrix of the left part.
[2767]4216
[2012]4217 double xMatrix[nDOF][2*nDOF];
4218 double zMatrix[nDOF];
4219 for (int i = 0; i < nDOF; ++i) {
4220 for (int j = 0; j < 2*nDOF; ++j) {
4221 xMatrix[i][j] = 0.0;
4222 }
4223 xMatrix[i][nDOF+i] = 1.0;
4224 zMatrix[i] = 0.0;
4225 }
4226
4227 for (int n = 0; n < nPiece; ++n) {
[2193]4228 int nUseDataInPiece = 0;
[2773]4229 for (int k = idxEdge[n]; k < idxEdge[n+1]; ++k) {
[2064]4230
[2773]4231 if (maskArray[k] == 0) continue;
[2064]4232
[2773]4233 for (int i = 0; i < nModel; ++i) {
4234 for (int j = i; j < nModel; ++j) {
4235 xMatrix[i][j] += model[i][k] * model[j][k];
4236 }
4237 zMatrix[i] += z1[k] * model[i][k];
4238 }
[2064]4239
[2773]4240 for (int i = 0; i < n; ++i) {
4241 double q = 1.0 - model[1][k]*invEdge[i];
[2012]4242 q = q*q*q;
[2773]4243 for (int j = 0; j < nModel; ++j) {
4244 xMatrix[j][i+nModel] += q * model[j][k];
4245 }
4246 for (int j = 0; j < i; ++j) {
4247 double r = 1.0 - model[1][k]*invEdge[j];
[2012]4248 r = r*r*r;
[2773]4249 xMatrix[j+nModel][i+nModel] += r*q;
[2012]4250 }
[2773]4251 xMatrix[i+nModel][i+nModel] += q*q;
4252 zMatrix[i+nModel] += q*z1[k];
[2012]4253 }
[2064]4254
[2193]4255 nUseDataInPiece++;
[2012]4256 }
[2193]4257
4258 if (nUseDataInPiece < 1) {
4259 std::vector<string> suffixOfPieceNumber(4);
4260 suffixOfPieceNumber[0] = "th";
4261 suffixOfPieceNumber[1] = "st";
4262 suffixOfPieceNumber[2] = "nd";
4263 suffixOfPieceNumber[3] = "rd";
4264 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
4265 ostringstream oss;
4266 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
4267 oss << " piece of the spectrum. can't execute fitting anymore.";
4268 throw(AipsError(String(oss)));
4269 }
[2012]4270 }
4271
4272 for (int i = 0; i < nDOF; ++i) {
4273 for (int j = 0; j < i; ++j) {
4274 xMatrix[i][j] = xMatrix[j][i];
4275 }
4276 }
4277
[2344]4278 std::vector<double> invDiag(nDOF);
[2012]4279 for (int i = 0; i < nDOF; ++i) {
[2773]4280 invDiag[i] = 1.0 / xMatrix[i][i];
[2012]4281 for (int j = 0; j < nDOF; ++j) {
4282 xMatrix[i][j] *= invDiag[i];
4283 }
4284 }
4285
4286 for (int k = 0; k < nDOF; ++k) {
4287 for (int i = 0; i < nDOF; ++i) {
4288 if (i != k) {
4289 double factor1 = xMatrix[k][k];
[2773]4290 double invfactor1 = 1.0 / factor1;
[2012]4291 double factor2 = xMatrix[i][k];
4292 for (int j = k; j < 2*nDOF; ++j) {
4293 xMatrix[i][j] *= factor1;
4294 xMatrix[i][j] -= xMatrix[k][j]*factor2;
[2773]4295 xMatrix[i][j] *= invfactor1;
[2012]4296 }
4297 }
4298 }
[2773]4299 double invXDiag = 1.0 / xMatrix[k][k];
[2012]4300 for (int j = k; j < 2*nDOF; ++j) {
[2773]4301 xMatrix[k][j] *= invXDiag;
[2012]4302 }
4303 }
4304
4305 for (int i = 0; i < nDOF; ++i) {
4306 for (int j = 0; j < nDOF; ++j) {
4307 xMatrix[i][nDOF+j] *= invDiag[j];
4308 }
4309 }
[2767]4310
[2012]4311 //compute a vector y which consists of the coefficients of the best-fit spline curves
4312 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
4313 //cubic terms for the other pieces (in case nPiece>1).
[2344]4314 std::vector<double> y(nDOF);
[2012]4315 for (int i = 0; i < nDOF; ++i) {
[2344]4316 y[i] = 0.0;
[2012]4317 for (int j = 0; j < nDOF; ++j) {
4318 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
4319 }
4320 }
4321
[2773]4322 std::vector<double> a(nModel);
4323 for (int i = 0; i < nModel; ++i) {
4324 a[i] = y[i];
4325 }
[2012]4326
[2344]4327 int j = 0;
[2012]4328 for (int n = 0; n < nPiece; ++n) {
[2064]4329 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
[2773]4330 r1[i] = 0.0;
4331 for (int j = 0; j < nModel; ++j) {
4332 r1[i] += a[j] * model[j][i];
4333 }
[2012]4334 }
[2773]4335 for (int i = 0; i < nModel; ++i) {
4336 params[j+i] = a[i];
4337 }
4338 j += nModel;
[2012]4339
4340 if (n == nPiece-1) break;
4341
[2773]4342 double d = y[n+nModel];
[2064]4343 double iE = invEdge[n];
[2773]4344 a[0] += d;
4345 a[1] -= 3.0 * d * iE;
4346 a[2] += 3.0 * d * iE * iE;
4347 a[3] -= d * iE * iE * iE;
[2012]4348 }
4349
[2344]4350 //subtract constant value for masked regions at the edge of spectrum
4351 if (idxEdge[0] > 0) {
4352 int n = idxEdge[0];
4353 for (int i = 0; i < idxEdge[0]; ++i) {
4354 //--cubic extrapolate--
4355 //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i];
4356 //--linear extrapolate--
4357 //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n];
4358 //--constant--
4359 r1[i] = r1[n];
4360 }
4361 }
[2767]4362
[2344]4363 if (idxEdge[nPiece] < nChan) {
4364 int n = idxEdge[nPiece]-1;
4365 for (int i = idxEdge[nPiece]; i < nChan; ++i) {
4366 //--cubic extrapolate--
4367 //int m = 4*(nPiece-1);
4368 //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i];
4369 //--linear extrapolate--
4370 //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n];
4371 //--constant--
4372 r1[i] = r1[n];
4373 }
4374 }
4375
4376 for (int i = 0; i < nChan; ++i) {
4377 residual[i] = z1[i] - r1[i];
4378 }
4379
[2767]4380 double stdDev = 0.0;
4381 for (int i = 0; i < nChan; ++i) {
[2890]4382 if (maskArray[i] == 0) continue;
4383 stdDev += residual[i]*residual[i];
[2767]4384 }
4385 stdDev = sqrt(stdDev/(double)nData);
4386 rms = (float)stdDev;
4387
[2012]4388 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
4389 break;
4390 } else {
4391
4392 double thres = stdDev * thresClip;
4393 int newNData = 0;
4394 for (int i = 0; i < nChan; ++i) {
[2081]4395 if (abs(residual[i]) >= thres) {
[2012]4396 maskArray[i] = 0;
[2767]4397 finalMask[i] = false;
[2012]4398 }
4399 if (maskArray[i] > 0) {
4400 newNData++;
4401 }
4402 }
[2081]4403 if (newNData == nData) {
[2064]4404 break; //no more flag to add. iteration stops.
[2012]4405 } else {
[2081]4406 nData = newNData;
[2012]4407 }
[2767]4408
[2012]4409 }
4410 }
4411
[2193]4412 nClipped = initNData - nData;
4413
[2344]4414 std::vector<float> result(nChan);
[2058]4415 if (getResidual) {
4416 for (int i = 0; i < nChan; ++i) {
[2344]4417 result[i] = (float)residual[i];
[2058]4418 }
4419 } else {
4420 for (int i = 0; i < nChan; ++i) {
[2344]4421 result[i] = (float)r1[i];
[2058]4422 }
[2012]4423 }
4424
[2058]4425 return result;
[2012]4426}
4427
[2773]4428std::vector<int> Scantable::selectWaveNumbers(const std::vector<int>& addNWaves,
4429 const std::vector<int>& rejectNWaves)
[2081]4430{
[2773]4431 std::vector<bool> chanMask;
[2767]4432 std::string fftMethod;
4433 std::string fftThresh;
4434
[2773]4435 return selectWaveNumbers(0, chanMask, false, fftMethod, fftThresh, addNWaves, rejectNWaves);
4436}
4437
4438std::vector<int> Scantable::selectWaveNumbers(const int whichrow,
4439 const std::vector<bool>& chanMask,
4440 const bool applyFFT,
4441 const std::string& fftMethod,
4442 const std::string& fftThresh,
4443 const std::vector<int>& addNWaves,
4444 const std::vector<int>& rejectNWaves)
4445{
4446 std::vector<int> nWaves;
[2186]4447 nWaves.clear();
4448
4449 if (applyFFT) {
4450 string fftThAttr;
4451 float fftThSigma;
4452 int fftThTop;
[2773]4453 parseFFTThresholdInfo(fftThresh, fftThAttr, fftThSigma, fftThTop);
[2186]4454 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
4455 }
4456
[2411]4457 addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves);
[2773]4458
4459 return nWaves;
[2186]4460}
4461
[2773]4462int Scantable::getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos)
4463{
4464 int idx = -1;
4465 for (uint i = 0; i < nChanNos.size(); ++i) {
4466 if (nChan == nChanNos[i]) {
4467 idx = i;
4468 break;
4469 }
4470 }
4471
4472 if (idx < 0) {
4473 throw(AipsError("nChan not found in nChhanNos."));
4474 }
4475
4476 return idx;
4477}
4478
[2767]4479void Scantable::parseFFTInfo(const std::string& fftInfo, bool& applyFFT, std::string& fftMethod, std::string& fftThresh)
4480{
4481 istringstream iss(fftInfo);
4482 std::string tmp;
4483 std::vector<string> res;
4484 while (getline(iss, tmp, ',')) {
4485 res.push_back(tmp);
4486 }
4487 if (res.size() < 3) {
4488 throw(AipsError("wrong value in 'fftinfo' parameter")) ;
4489 }
4490 applyFFT = (res[0] == "true");
4491 fftMethod = res[1];
4492 fftThresh = res[2];
4493}
4494
[2773]4495void Scantable::parseFFTThresholdInfo(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
[2186]4496{
4497 uInt idxSigma = fftThresh.find("sigma");
4498 uInt idxTop = fftThresh.find("top");
4499
4500 if (idxSigma == fftThresh.size() - 5) {
4501 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
4502 is >> fftThSigma;
4503 fftThAttr = "sigma";
4504 } else if (idxTop == 0) {
4505 std::istringstream is(fftThresh.substr(3));
4506 is >> fftThTop;
4507 fftThAttr = "top";
4508 } else {
4509 bool isNumber = true;
4510 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
4511 char ch = (fftThresh.substr(i, 1).c_str())[0];
4512 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
4513 isNumber = false;
4514 break;
4515 }
4516 }
4517 if (isNumber) {
4518 std::istringstream is(fftThresh);
4519 is >> fftThSigma;
4520 fftThAttr = "sigma";
4521 } else {
4522 throw(AipsError("fftthresh has a wrong value"));
4523 }
4524 }
4525}
4526
4527void Scantable::doSelectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftMethod, const float fftThSigma, const int fftThTop, const std::string& fftThAttr, std::vector<int>& nWaves)
4528{
4529 std::vector<float> fspec;
4530 if (fftMethod == "fft") {
4531 fspec = execFFT(whichrow, chanMask, false, true);
4532 //} else if (fftMethod == "lsp") {
4533 // fspec = lombScarglePeriodogram(whichrow);
4534 }
4535
4536 if (fftThAttr == "sigma") {
4537 float mean = 0.0;
4538 float mean2 = 0.0;
4539 for (uInt i = 0; i < fspec.size(); ++i) {
4540 mean += fspec[i];
4541 mean2 += fspec[i]*fspec[i];
4542 }
4543 mean /= float(fspec.size());
4544 mean2 /= float(fspec.size());
4545 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
4546
4547 for (uInt i = 0; i < fspec.size(); ++i) {
4548 if (fspec[i] >= thres) {
4549 nWaves.push_back(i);
4550 }
4551 }
4552
4553 } else if (fftThAttr == "top") {
4554 for (int i = 0; i < fftThTop; ++i) {
4555 float max = 0.0;
4556 int maxIdx = 0;
4557 for (uInt j = 0; j < fspec.size(); ++j) {
4558 if (fspec[j] > max) {
4559 max = fspec[j];
4560 maxIdx = j;
4561 }
4562 }
4563 nWaves.push_back(maxIdx);
4564 fspec[maxIdx] = 0.0;
4565 }
4566
4567 }
4568
4569 if (nWaves.size() > 1) {
4570 sort(nWaves.begin(), nWaves.end());
4571 }
4572}
4573
[2411]4574void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
[2186]4575{
[2411]4576 std::vector<int> tempAddNWaves, tempRejectNWaves;
[2767]4577 tempAddNWaves.clear();
4578 tempRejectNWaves.clear();
4579
[2186]4580 for (uInt i = 0; i < addNWaves.size(); ++i) {
[2411]4581 tempAddNWaves.push_back(addNWaves[i]);
4582 }
4583 if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) {
4584 setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves);
4585 }
4586
4587 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
4588 tempRejectNWaves.push_back(rejectNWaves[i]);
4589 }
4590 if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) {
4591 setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves);
4592 }
4593
4594 for (uInt i = 0; i < tempAddNWaves.size(); ++i) {
[2186]4595 bool found = false;
4596 for (uInt j = 0; j < nWaves.size(); ++j) {
[2411]4597 if (nWaves[j] == tempAddNWaves[i]) {
[2186]4598 found = true;
4599 break;
4600 }
4601 }
[2411]4602 if (!found) nWaves.push_back(tempAddNWaves[i]);
[2186]4603 }
4604
[2411]4605 for (uInt i = 0; i < tempRejectNWaves.size(); ++i) {
[2186]4606 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
[2411]4607 if (*j == tempRejectNWaves[i]) {
[2186]4608 j = nWaves.erase(j);
4609 } else {
4610 ++j;
4611 }
4612 }
4613 }
4614
4615 if (nWaves.size() > 1) {
4616 sort(nWaves.begin(), nWaves.end());
4617 unique(nWaves.begin(), nWaves.end());
4618 }
4619}
4620
[2411]4621void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves)
4622{
[2767]4623 int val = nWaves[0];
4624 int nyquistFreq = nchan(getIF(whichrow))/2+1;
4625 nWaves.clear();
4626 if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759
4627 nWaves.push_back(0);
[2411]4628 }
[2767]4629 while (val <= nyquistFreq) {
4630 nWaves.push_back(val);
4631 val++;
4632 }
[2411]4633}
4634
[2773]4635void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo,
4636 const std::vector<int>& addNWaves,
4637 const std::vector<int>& rejectNWaves,
4638 float thresClip, int nIterClip,
4639 bool getResidual,
4640 const std::string& progressInfo,
4641 const bool outLogger, const std::string& blfile,
4642 const std::string& bltable)
[2186]4643{
[2774]4644 /****
[2773]4645 double TimeStart = mathutil::gettimeofday_sec();
[2774]4646 ****/
[2773]4647
[2193]4648 try {
4649 ofstream ofs;
[2773]4650 String coordInfo;
4651 bool hasSameNchan, outTextFile, csvFormat, showProgress;
4652 int minNRow;
4653 int nRow = nrow();
4654 std::vector<bool> chanMask, finalChanMask;
4655 float rms;
4656 bool outBaselineTable = (bltable != "");
4657 STBaselineTable bt = STBaselineTable(*this);
4658 Vector<Double> timeSecCol;
[2012]4659
[2773]4660 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
4661 coordInfo, hasSameNchan,
4662 progressInfo, showProgress, minNRow,
4663 timeSecCol);
[2012]4664
[2773]4665 bool applyFFT;
4666 std::string fftMethod, fftThresh;
4667 parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh);
[2012]4668
[2193]4669 std::vector<int> nWaves;
[2773]4670 std::vector<int> nChanNos;
4671 std::vector<std::vector<std::vector<double> > > modelReservoir;
4672 if (!applyFFT) {
4673 nWaves = selectWaveNumbers(addNWaves, rejectNWaves);
4674 modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos);
4675 }
[2012]4676
[2193]4677 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2767]4678 std::vector<float> sp = getSpectrum(whichrow);
[2193]4679 chanMask = getCompositeChanMask(whichrow, mask);
[2773]4680 std::vector<std::vector<double> > model;
4681 if (applyFFT) {
4682 nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh,
4683 addNWaves, rejectNWaves);
4684 model = getSinusoidModel(nWaves, sp.size());
4685 } else {
4686 model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)];
4687 }
[2968]4688 int nModel = modelReservoir.size();
[2186]4689
[2767]4690 std::vector<float> params;
[2968]4691
4692 if (flagrowCol_(whichrow) == 0) {
4693 int nClipped = 0;
4694 std::vector<float> res;
4695 res = doLeastSquareFitting(sp, chanMask, model,
[2773]4696 params, rms, finalChanMask,
4697 nClipped, thresClip, nIterClip, getResidual);
[2767]4698
[2968]4699 if (outBaselineTable) {
4700 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4701 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4702 true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(),
4703 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
4704 thresClip, nIterClip, 0.0, 0, std::vector<int>());
4705 } else {
4706 setSpectrum(res, whichrow);
4707 }
4708
4709 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
4710 coordInfo, hasSameNchan, ofs, "sinusoidBaseline()",
4711 params, nClipped);
[2767]4712 } else {
[2968]4713 if (outBaselineTable) {
4714 params.resize(nModel);
4715 for (uInt i = 0; i < params.size(); ++i) {
4716 params[i] = 0.0;
4717 }
4718 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4719 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4720 true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(),
4721 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
4722 thresClip, nIterClip, 0.0, 0, std::vector<int>());
4723 }
[2186]4724 }
[2193]4725
4726 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[2186]4727 }
4728
[2773]4729 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2767]4730
[2193]4731 } catch (...) {
4732 throw;
[1931]4733 }
[2773]4734
[2774]4735 /****
[2773]4736 double TimeEnd = mathutil::gettimeofday_sec();
4737 double elapse1 = TimeEnd - TimeStart;
4738 std::cout << "sinusoid-old : " << elapse1 << " (sec.)" << endl;
[2774]4739 ****/
[1907]4740}
4741
[2773]4742void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo,
4743 const std::vector<int>& addNWaves,
4744 const std::vector<int>& rejectNWaves,
4745 float thresClip, int nIterClip,
4746 const std::vector<int>& edge,
4747 float threshold, int chanAvgLimit,
4748 bool getResidual,
4749 const std::string& progressInfo,
4750 const bool outLogger, const std::string& blfile,
4751 const std::string& bltable)
[2012]4752{
[2193]4753 try {
4754 ofstream ofs;
[2773]4755 String coordInfo;
4756 bool hasSameNchan, outTextFile, csvFormat, showProgress;
4757 int minNRow;
4758 int nRow = nrow();
4759 std::vector<bool> chanMask, finalChanMask;
4760 float rms;
4761 bool outBaselineTable = (bltable != "");
4762 STBaselineTable bt = STBaselineTable(*this);
4763 Vector<Double> timeSecCol;
4764 STLineFinder lineFinder = STLineFinder();
[2012]4765
[2773]4766 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
4767 coordInfo, hasSameNchan,
4768 progressInfo, showProgress, minNRow,
4769 timeSecCol);
[2012]4770
[2773]4771 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
[2012]4772
[2773]4773 bool applyFFT;
4774 string fftMethod, fftThresh;
4775 parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh);
[2012]4776
[2193]4777 std::vector<int> nWaves;
[2773]4778 std::vector<int> nChanNos;
4779 std::vector<std::vector<std::vector<double> > > modelReservoir;
4780 if (!applyFFT) {
4781 nWaves = selectWaveNumbers(addNWaves, rejectNWaves);
4782 modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos);
4783 }
[2186]4784
[2193]4785 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2767]4786 std::vector<float> sp = getSpectrum(whichrow);
[2193]4787 std::vector<int> currentEdge;
[2773]4788 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
4789 std::vector<std::vector<double> > model;
4790 if (applyFFT) {
4791 nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh,
4792 addNWaves, rejectNWaves);
4793 model = getSinusoidModel(nWaves, sp.size());
[2193]4794 } else {
[2773]4795 model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)];
[2012]4796 }
[2968]4797 int nModel = modelReservoir.size();
[2193]4798
4799 std::vector<float> params;
[2968]4800
4801 if (flagrowCol_(whichrow) == 0) {
4802 int nClipped = 0;
4803 std::vector<float> res;
4804 res = doLeastSquareFitting(sp, chanMask, model,
[2773]4805 params, rms, finalChanMask,
4806 nClipped, thresClip, nIterClip, getResidual);
[2193]4807
[2968]4808 if (outBaselineTable) {
4809 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4810 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4811 true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(),
4812 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
4813 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
4814 } else {
4815 setSpectrum(res, whichrow);
4816 }
4817
4818 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
4819 coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()",
4820 params, nClipped);
[2767]4821 } else {
[2968]4822 if (outBaselineTable) {
4823 params.resize(nModel);
4824 for (uInt i = 0; i < params.size(); ++i) {
4825 params[i] = 0.0;
4826 }
4827 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4828 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4829 true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(),
4830 getMaskListFromMask(chanMask), params, 0.0, sp.size(),
4831 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
4832 }
[2767]4833 }
4834
[2193]4835 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[2012]4836 }
4837
[2773]4838 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
[2767]4839
[2193]4840 } catch (...) {
4841 throw;
[2047]4842 }
4843}
4844
[2773]4845std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data,
4846 const std::vector<bool>& mask,
4847 const std::vector<int>& waveNumbers,
4848 std::vector<float>& params,
4849 float& rms,
4850 std::vector<bool>& finalmask,
4851 float clipth,
4852 int clipn)
[2081]4853{
[2767]4854 int nClipped = 0;
4855 return doSinusoidFitting(data, mask, waveNumbers, params, rms, finalmask, nClipped, clipth, clipn);
4856}
4857
[2773]4858std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data,
4859 const std::vector<bool>& mask,
4860 const std::vector<int>& waveNumbers,
4861 std::vector<float>& params,
4862 float& rms,
4863 std::vector<bool>& finalMask,
4864 int& nClipped,
4865 float thresClip,
4866 int nIterClip,
4867 bool getResidual)
[2767]4868{
[2773]4869 return doLeastSquareFitting(data, mask,
4870 getSinusoidModel(waveNumbers, data.size()),
4871 params, rms, finalMask,
4872 nClipped, thresClip, nIterClip,
4873 getResidual);
4874}
4875
4876std::vector<std::vector<std::vector<double> > > Scantable::getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
4877 std::vector<int>& nChanNos)
4878{
4879 std::vector<std::vector<std::vector<double> > > res;
4880 res.clear();
4881 nChanNos.clear();
4882
4883 std::vector<uint> ifNos = getIFNos();
4884 for (uint i = 0; i < ifNos.size(); ++i) {
4885 int currNchan = nchan(ifNos[i]);
4886 bool hasDifferentNchan = (i == 0);
4887 for (uint j = 0; j < i; ++j) {
4888 if (currNchan != nchan(ifNos[j])) {
4889 hasDifferentNchan = true;
4890 break;
4891 }
4892 }
4893 if (hasDifferentNchan) {
4894 res.push_back(getSinusoidModel(waveNumbers, currNchan));
4895 nChanNos.push_back(currNchan);
4896 }
[2047]4897 }
[2773]4898
4899 return res;
4900}
4901
4902std::vector<std::vector<double> > Scantable::getSinusoidModel(const std::vector<int>& waveNumbers, int nchan)
4903{
4904 // model : contains elemental values for computing the least-square matrix.
4905 // model.size() is nmodel and model[*].size() is nchan.
4906 // Each model element are as follows:
4907 // model[0] = {1.0, 1.0, 1.0, ..., 1.0},
4908 // model[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nchan])},
4909 // model[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nchan])},
4910 // where (1 <= n <= nMaxWavesInSW),
4911 // or,
4912 // model[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nchan])},
4913 // model[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nchan])},
4914 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
4915
[2081]4916 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
4917 nWaves.reserve(waveNumbers.size());
4918 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
4919 sort(nWaves.begin(), nWaves.end());
4920 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
4921 nWaves.erase(end_it, nWaves.end());
4922
4923 int minNWaves = nWaves[0];
4924 if (minNWaves < 0) {
[2058]4925 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
4926 }
[2081]4927 bool hasConstantTerm = (minNWaves == 0);
[2773]4928 int nmodel = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
[2047]4929
[2773]4930 std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan));
[2767]4931
[2773]4932 if (hasConstantTerm) {
4933 for (int j = 0; j < nchan; ++j) {
4934 model[0][j] = 1.0;
[2047]4935 }
4936 }
4937
[2081]4938 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
[2773]4939 double stretch0 = 2.0*PI/(double)(nchan-1);
[2081]4940
4941 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
[2773]4942 int sidx = hasConstantTerm ? 2*i-1 : 2*i;
4943 int cidx = sidx + 1;
4944 double stretch = stretch0*(double)nWaves[i];
[2081]4945
[2773]4946 for (int j = 0; j < nchan; ++j) {
4947 model[sidx][j] = sin(stretch*(double)j);
4948 model[cidx][j] = cos(stretch*(double)j);
[2047]4949 }
[2012]4950 }
4951
[2773]4952 return model;
[2012]4953}
4954
[2773]4955std::vector<bool> Scantable::getCompositeChanMask(int whichrow,
4956 const std::vector<bool>& inMask)
[2047]4957{
[2186]4958 std::vector<bool> mask = getMask(whichrow);
4959 uInt maskSize = mask.size();
[2410]4960 if (inMask.size() != 0) {
4961 if (maskSize != inMask.size()) {
4962 throw(AipsError("mask sizes are not the same."));
4963 }
4964 for (uInt i = 0; i < maskSize; ++i) {
4965 mask[i] = mask[i] && inMask[i];
4966 }
[2047]4967 }
4968
[2186]4969 return mask;
[2047]4970}
4971
[2773]4972std::vector<bool> Scantable::getCompositeChanMask(int whichrow,
4973 const std::vector<bool>& inMask,
4974 const std::vector<int>& edge,
4975 std::vector<int>& currEdge,
4976 STLineFinder& lineFinder)
[2047]4977{
[2773]4978 std::vector<uint> ifNos = getIFNos();
[2774]4979 if ((edge.size() > 2) && (edge.size() < ifNos.size()*2)) {
[2773]4980 throw(AipsError("Length of edge element info is less than that of IFs"));
[2047]4981 }
4982
[2774]4983 uint idx = 0;
4984 if (edge.size() > 2) {
4985 int ifVal = getIF(whichrow);
4986 bool foundIF = false;
4987 for (uint i = 0; i < ifNos.size(); ++i) {
4988 if (ifVal == (int)ifNos[i]) {
4989 idx = 2*i;
4990 foundIF = true;
4991 break;
4992 }
[2773]4993 }
[2774]4994 if (!foundIF) {
4995 throw(AipsError("bad IF number"));
4996 }
[2773]4997 }
4998
4999 currEdge.clear();
5000 currEdge.resize(2);
5001 currEdge[0] = edge[idx];
5002 currEdge[1] = edge[idx+1];
5003
[2047]5004 lineFinder.setData(getSpectrum(whichrow));
[2773]5005 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currEdge, whichrow);
[2047]5006 return lineFinder.getMask();
5007}
5008
5009/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
[2773]5010void Scantable::outputFittingResult(bool outLogger,
5011 bool outTextFile,
5012 bool csvFormat,
5013 const std::vector<bool>& chanMask,
5014 int whichrow,
5015 const casa::String& coordInfo,
5016 bool hasSameNchan,
5017 ofstream& ofs,
5018 const casa::String& funcName,
5019 const std::vector<int>& edge,
5020 const std::vector<float>& params,
5021 const int nClipped)
[2186]5022{
[2047]5023 if (outLogger || outTextFile) {
5024 float rms = getRms(chanMask, whichrow);
5025 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
[2081]5026 std::vector<bool> fixed;
5027 fixed.clear();
[2047]5028
5029 if (outLogger) {
5030 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
[2773]5031 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped,
5032 masklist, whichrow, false, csvFormat) << LogIO::POST ;
[2047]5033 }
5034 if (outTextFile) {
[2773]5035 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped,
5036 masklist, whichrow, true, csvFormat) << flush;
[2047]5037 }
5038 }
5039}
5040
[2773]5041/* for poly/chebyshev/sinusoid. */
5042void Scantable::outputFittingResult(bool outLogger,
5043 bool outTextFile,
5044 bool csvFormat,
5045 const std::vector<bool>& chanMask,
5046 int whichrow,
5047 const casa::String& coordInfo,
5048 bool hasSameNchan,
5049 ofstream& ofs,
5050 const casa::String& funcName,
5051 const std::vector<float>& params,
5052 const int nClipped)
[2186]5053{
[2047]5054 if (outLogger || outTextFile) {
5055 float rms = getRms(chanMask, whichrow);
5056 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
[2081]5057 std::vector<bool> fixed;
5058 fixed.clear();
[2047]5059
5060 if (outLogger) {
5061 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
[2773]5062 ols << formatBaselineParams(params, fixed, rms, nClipped,
5063 masklist, whichrow, false, csvFormat) << LogIO::POST ;
[2047]5064 }
5065 if (outTextFile) {
[2773]5066 ofs << formatBaselineParams(params, fixed, rms, nClipped,
5067 masklist, whichrow, true, csvFormat) << flush;
[2047]5068 }
5069 }
5070}
5071
[2189]5072void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
[2186]5073{
[2189]5074 int idxDelimiter = progressInfo.find(",");
5075 if (idxDelimiter < 0) {
5076 throw(AipsError("wrong value in 'showprogress' parameter")) ;
5077 }
5078 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
5079 std::istringstream is(progressInfo.substr(idxDelimiter+1));
5080 is >> minNRow;
5081}
5082
5083void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
5084{
5085 if (showProgress && (nTotal >= nTotalThreshold)) {
[2186]5086 int nInterval = int(floor(double(nTotal)/100.0));
5087 if (nInterval == 0) nInterval++;
5088
[2193]5089 if (nProcessed % nInterval == 0) {
[2189]5090 printf("\r"); //go to the head of line
[2186]5091 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
[2189]5092 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
5093 printf("\x1b[39m\x1b[0m"); //set default attributes
[2186]5094 fflush(NULL);
5095 }
[2193]5096
[2186]5097 if (nProcessed == nTotal - 1) {
5098 printf("\r\x1b[K"); //clear
5099 fflush(NULL);
5100 }
[2193]5101
[2186]5102 }
5103}
5104
5105std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
5106{
5107 std::vector<bool> mask = getMask(whichrow);
5108
5109 if (inMask.size() > 0) {
5110 uInt maskSize = mask.size();
5111 if (maskSize != inMask.size()) {
5112 throw(AipsError("mask sizes are not the same."));
5113 }
5114 for (uInt i = 0; i < maskSize; ++i) {
5115 mask[i] = mask[i] && inMask[i];
5116 }
5117 }
5118
5119 Vector<Float> spec = getSpectrum(whichrow);
5120 mathutil::doZeroOrderInterpolation(spec, mask);
5121
5122 FFTServer<Float,Complex> ffts;
5123 Vector<Complex> fftres;
5124 ffts.fft0(fftres, spec);
5125
5126 std::vector<float> res;
5127 float norm = float(2.0/double(spec.size()));
5128
5129 if (getRealImag) {
5130 for (uInt i = 0; i < fftres.size(); ++i) {
5131 res.push_back(real(fftres[i])*norm);
5132 res.push_back(imag(fftres[i])*norm);
5133 }
5134 } else {
5135 for (uInt i = 0; i < fftres.size(); ++i) {
5136 res.push_back(abs(fftres[i])*norm);
5137 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
5138 }
5139 }
5140
5141 return res;
5142}
5143
5144
5145float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
5146{
[2591]5147 /****
[2737]5148 double ms1TimeStart, ms1TimeEnd;
[2591]5149 double elapse1 = 0.0;
5150 ms1TimeStart = mathutil::gettimeofday_sec();
5151 ****/
5152
[2012]5153 Vector<Float> spec;
5154 specCol_.get(whichrow, spec);
5155
[2591]5156 /****
5157 ms1TimeEnd = mathutil::gettimeofday_sec();
5158 elapse1 = ms1TimeEnd - ms1TimeStart;
5159 std::cout << "rm1 : " << elapse1 << " (sec.)" << endl;
5160 ****/
5161
[2737]5162 return (float)doGetRms(mask, spec);
5163}
5164
5165double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec)
5166{
5167 double mean = 0.0;
5168 double smean = 0.0;
[2012]5169 int n = 0;
[2047]5170 for (uInt i = 0; i < spec.nelements(); ++i) {
[2012]5171 if (mask[i]) {
[2737]5172 double val = (double)spec[i];
5173 mean += val;
5174 smean += val*val;
[2012]5175 n++;
5176 }
5177 }
5178
[2737]5179 mean /= (double)n;
5180 smean /= (double)n;
[2012]5181
5182 return sqrt(smean - mean*mean);
5183}
5184
[2641]5185std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const
[2012]5186{
[2641]5187 if (verbose) {
5188 ostringstream oss;
[2012]5189
[2641]5190 if (csvformat) {
5191 oss << getScan(whichrow) << ",";
5192 oss << getBeam(whichrow) << ",";
5193 oss << getIF(whichrow) << ",";
5194 oss << getPol(whichrow) << ",";
5195 oss << getCycle(whichrow) << ",";
5196 String commaReplacedMasklist = masklist;
5197 string::size_type pos = 0;
5198 while (pos = commaReplacedMasklist.find(","), pos != string::npos) {
5199 commaReplacedMasklist.replace(pos, 1, ";");
5200 pos++;
5201 }
5202 oss << commaReplacedMasklist << ",";
5203 } else {
5204 oss << " Scan[" << getScan(whichrow) << "]";
5205 oss << " Beam[" << getBeam(whichrow) << "]";
5206 oss << " IF[" << getIF(whichrow) << "]";
5207 oss << " Pol[" << getPol(whichrow) << "]";
5208 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
5209 oss << "Fitter range = " << masklist << endl;
5210 oss << "Baseline parameters" << endl;
5211 }
[2012]5212 oss << flush;
[2641]5213
5214 return String(oss);
[2012]5215 }
5216
[2641]5217 return "";
[2012]5218}
5219
[2641]5220std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const
[2012]5221{
[2641]5222 if (verbose) {
5223 ostringstream oss;
[2012]5224
[2641]5225 if (csvformat) {
5226 oss << rms << ",";
5227 if (nClipped >= 0) {
5228 oss << nClipped;
5229 }
5230 } else {
5231 oss << "Results of baseline fit" << endl;
5232 oss << " rms = " << setprecision(6) << rms << endl;
5233 if (nClipped >= 0) {
5234 oss << " Number of clipped channels = " << nClipped << endl;
5235 }
5236 for (int i = 0; i < 60; ++i) {
5237 oss << "-";
5238 }
[2193]5239 }
[2131]5240 oss << endl;
[2094]5241 oss << flush;
[2641]5242
5243 return String(oss);
[2012]5244 }
5245
[2641]5246 return "";
[2012]5247}
5248
[2186]5249std::string Scantable::formatBaselineParams(const std::vector<float>& params,
5250 const std::vector<bool>& fixed,
5251 float rms,
[2193]5252 int nClipped,
[2186]5253 const std::string& masklist,
5254 int whichrow,
5255 bool verbose,
[2641]5256 bool csvformat,
[2186]5257 int start, int count,
5258 bool resetparamid) const
[2047]5259{
[2064]5260 int nParam = (int)(params.size());
[2047]5261
[2064]5262 if (nParam < 1) {
5263 return(" Not fitted");
5264 } else {
5265
5266 ostringstream oss;
[2641]5267 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
[2064]5268
5269 if (start < 0) start = 0;
5270 if (count < 0) count = nParam;
5271 int end = start + count;
5272 if (end > nParam) end = nParam;
5273 int paramidoffset = (resetparamid) ? (-start) : 0;
5274
5275 for (int i = start; i < end; ++i) {
5276 if (i > start) {
[2047]5277 oss << ",";
5278 }
[2064]5279 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
[2641]5280 if (csvformat) {
5281 oss << params[i] << sFix;
5282 } else {
5283 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
5284 }
[2047]5285 }
[2064]5286
[2641]5287 if (csvformat) {
5288 oss << ",";
[2644]5289 } else {
5290 oss << endl;
[2641]5291 }
5292 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
[2064]5293
5294 return String(oss);
[2047]5295 }
5296
5297}
5298
[2641]5299std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose, bool csvformat) const
[2012]5300{
[2064]5301 int nOutParam = (int)(params.size());
5302 int nPiece = (int)(ranges.size()) - 1;
[2012]5303
[2064]5304 if (nOutParam < 1) {
5305 return(" Not fitted");
5306 } else if (nPiece < 0) {
[2641]5307 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat);
[2064]5308 } else if (nPiece < 1) {
5309 return(" Bad count of the piece edge info");
5310 } else if (nOutParam % nPiece != 0) {
5311 return(" Bad count of the output baseline parameters");
5312 } else {
5313
5314 int nParam = nOutParam / nPiece;
5315
5316 ostringstream oss;
[2641]5317 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
[2064]5318
[2641]5319 if (csvformat) {
5320 for (int i = 0; i < nPiece; ++i) {
5321 oss << ranges[i] << "," << (ranges[i+1]-1) << ",";
5322 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
5323 }
5324 } else {
5325 stringstream ss;
5326 ss << ranges[nPiece] << flush;
5327 int wRange = ss.str().size() * 2 + 5;
[2064]5328
[2641]5329 for (int i = 0; i < nPiece; ++i) {
5330 ss.str("");
5331 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
5332 oss << left << setw(wRange) << ss.str();
5333 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
[2644]5334 //oss << endl;
[2641]5335 }
[2012]5336 }
[2064]5337
[2641]5338 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
[2064]5339
5340 return String(oss);
[2012]5341 }
5342
5343}
5344
[2047]5345bool Scantable::hasSameNchanOverIFs()
[2012]5346{
[2047]5347 int nIF = nif(-1);
5348 int nCh;
5349 int totalPositiveNChan = 0;
5350 int nPositiveNChan = 0;
[2012]5351
[2047]5352 for (int i = 0; i < nIF; ++i) {
5353 nCh = nchan(i);
5354 if (nCh > 0) {
5355 totalPositiveNChan += nCh;
5356 nPositiveNChan++;
[2012]5357 }
5358 }
5359
[2047]5360 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
[2012]5361}
5362
[2047]5363std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
[2012]5364{
[2427]5365 if (mask.size() <= 0) {
5366 throw(AipsError("The mask elements should be > 0"));
[2012]5367 }
[2047]5368 int IF = getIF(whichrow);
5369 if (mask.size() != (uInt)nchan(IF)) {
[2012]5370 throw(AipsError("Number of channels in scantable != number of mask elements"));
5371 }
5372
[2047]5373 if (verbose) {
[2012]5374 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
5375 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
5376 if (!hasSameNchan) {
[2047]5377 logOs << endl << "This mask is only valid for IF=" << IF;
[2012]5378 }
5379 logOs << LogIO::POST;
5380 }
5381
5382 std::vector<double> abcissa = getAbcissa(whichrow);
[2047]5383 std::vector<int> edge = getMaskEdgeIndices(mask);
5384
[2012]5385 ostringstream oss;
5386 oss.setf(ios::fixed);
5387 oss << setprecision(1) << "[";
[2047]5388 for (uInt i = 0; i < edge.size(); i+=2) {
[2012]5389 if (i > 0) oss << ",";
[2047]5390 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
[2012]5391 }
5392 oss << "]" << flush;
5393
5394 return String(oss);
5395}
5396
[2047]5397std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
[2012]5398{
[2427]5399 if (mask.size() <= 0) {
5400 throw(AipsError("The mask elements should be > 0"));
[2012]5401 }
5402
[2047]5403 std::vector<int> out, startIndices, endIndices;
5404 int maskSize = mask.size();
[2012]5405
[2047]5406 startIndices.clear();
5407 endIndices.clear();
5408
5409 if (mask[0]) {
5410 startIndices.push_back(0);
[2012]5411 }
[2047]5412 for (int i = 1; i < maskSize; ++i) {
5413 if ((!mask[i-1]) && mask[i]) {
5414 startIndices.push_back(i);
5415 } else if (mask[i-1] && (!mask[i])) {
5416 endIndices.push_back(i-1);
5417 }
[2012]5418 }
[2047]5419 if (mask[maskSize-1]) {
5420 endIndices.push_back(maskSize-1);
5421 }
[2012]5422
[2047]5423 if (startIndices.size() != endIndices.size()) {
5424 throw(AipsError("Inconsistent Mask Size: bad data?"));
5425 }
5426 for (uInt i = 0; i < startIndices.size(); ++i) {
5427 if (startIndices[i] > endIndices[i]) {
5428 throw(AipsError("Mask start index > mask end index"));
[2012]5429 }
5430 }
5431
[2047]5432 out.clear();
5433 for (uInt i = 0; i < startIndices.size(); ++i) {
5434 out.push_back(startIndices[i]);
5435 out.push_back(endIndices[i]);
5436 }
5437
[2012]5438 return out;
5439}
5440
[2791]5441void Scantable::setTsys(const std::vector<float>& newvals, int whichrow) {
5442 Vector<Float> tsys(newvals);
5443 if (whichrow > -1) {
5444 if (tsysCol_.shape(whichrow) != tsys.shape())
5445 throw(AipsError("Given Tsys values are not of the same shape"));
5446 tsysCol_.put(whichrow, tsys);
5447 } else {
5448 tsysCol_.fillColumn(tsys);
5449 }
5450}
5451
[2161]5452vector<float> Scantable::getTsysSpectrum( int whichrow ) const
5453{
5454 Vector<Float> tsys( tsysCol_(whichrow) ) ;
5455 vector<float> stlTsys ;
5456 tsys.tovector( stlTsys ) ;
5457 return stlTsys ;
5458}
[2012]5459
[2591]5460vector<uint> Scantable::getMoleculeIdColumnData() const
5461{
5462 Vector<uInt> molIds(mmolidCol_.getColumn());
5463 vector<uint> res;
5464 molIds.tovector(res);
5465 return res;
5466}
[2012]5467
[2591]5468void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids)
5469{
5470 Vector<uInt> molIds(molids);
5471 Vector<uInt> arr(mmolidCol_.getColumn());
5472 if ( molIds.nelements() != arr.nelements() )
5473 throw AipsError("The input data size must be the number of rows.");
5474 mmolidCol_.putColumn(molIds);
[1907]5475}
[2591]5476
5477
[2888]5478std::vector<uint> Scantable::getRootTableRowNumbers() const
5479{
5480 Vector<uInt> rowIds(table_.rowNumbers());
5481 vector<uint> res;
5482 rowIds.tovector(res);
5483 return res;
5484}
5485
5486
[2789]5487void Scantable::dropXPol()
5488{
5489 if (npol() <= 2) {
5490 return;
5491 }
5492 if (!selector_.empty()) {
5493 throw AipsError("Can only operate with empty selection");
5494 }
5495 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
5496 Table tab = tableCommand(taql, table_);
5497 table_ = tab;
5498 table_.rwKeywordSet().define("nPol", Int(2));
5499 originalTable_ = table_;
5500 attach();
[2591]5501}
[2789]5502
5503}
[1819]5504//namespace asap
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