source: trunk/src/Scantable.cpp@ 2286

Last change on this file since 2286 was 2286, checked in by Kana Sugimoto, 13 years ago

New Development: No (performance tuning)

JIRA Issue: No

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: a parameter "filename" is added to Scantable::summary. scantable.summary doesn't return a string anymore

Test Programs: sdlist unittest/ scantable.summary("summary.txt")

Put in Release Notes: Yes

Module(s): sdlist, asap.summary

Description:

scantable.summary is very slow for large data sets (in row number) often outputted
by modern telescopes. It takes > 1.5 hours to list OTF raster scan with 350,000 rows.

This was because, the methods accumulates the whole text string (~700,000 lines) and
returns it as a string. Once the summary string exceed several tens thousands lines,
elapse time increases non-linearly, may be because very massive output string starts
to overweigh the memory.

I updated scantable.summary so that it flushes the summary string more often to file/logger.
After the modification, scantable.summary could list the data mentioned above in ~ 7 minutes.
The side effect of it is that scantable.summary doesn't return summary string anymore.
(But people may not happy with sub-million lines of string anyway.)


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 101.3 KB
RevLine 
[805]1//
2// C++ Implementation: Scantable
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
[206]12#include <map>
13
[2186]14#include <atnf/PKSIO/SrcType.h>
15
[125]16#include <casa/aips.h>
[2186]17#include <casa/iomanip.h>
[80]18#include <casa/iostream.h>
[2186]19#include <casa/OS/File.h>
[805]20#include <casa/OS/Path.h>
[80]21#include <casa/Arrays/Array.h>
[2186]22#include <casa/Arrays/ArrayAccessor.h>
23#include <casa/Arrays/ArrayLogical.h>
[80]24#include <casa/Arrays/ArrayMath.h>
25#include <casa/Arrays/MaskArrMath.h>
[2186]26#include <casa/Arrays/Slice.h>
[1325]27#include <casa/Arrays/Vector.h>
[455]28#include <casa/Arrays/VectorSTLIterator.h>
[418]29#include <casa/BasicMath/Math.h>
[504]30#include <casa/BasicSL/Constants.h>
[2186]31#include <casa/Containers/RecordField.h>
32#include <casa/Logging/LogIO.h>
[286]33#include <casa/Quanta/MVAngle.h>
[2186]34#include <casa/Quanta/MVTime.h>
[902]35#include <casa/Utilities/GenSort.h>
[2]36
[2186]37#include <coordinates/Coordinates/CoordinateUtil.h>
[2]38
[1325]39// needed to avoid error in .tcc
40#include <measures/Measures/MCDirection.h>
41//
42#include <measures/Measures/MDirection.h>
[2186]43#include <measures/Measures/MEpoch.h>
[80]44#include <measures/Measures/MFrequency.h>
[2186]45#include <measures/Measures/MeasRef.h>
46#include <measures/Measures/MeasTable.h>
47#include <measures/TableMeasures/ScalarMeasColumn.h>
48#include <measures/TableMeasures/TableMeasDesc.h>
[805]49#include <measures/TableMeasures/TableMeasRefDesc.h>
50#include <measures/TableMeasures/TableMeasValueDesc.h>
[2]51
[2186]52#include <tables/Tables/ArrColDesc.h>
53#include <tables/Tables/ExprNode.h>
54#include <tables/Tables/ScaColDesc.h>
55#include <tables/Tables/SetupNewTab.h>
56#include <tables/Tables/TableCopy.h>
57#include <tables/Tables/TableDesc.h>
58#include <tables/Tables/TableIter.h>
59#include <tables/Tables/TableParse.h>
60#include <tables/Tables/TableRecord.h>
61#include <tables/Tables/TableRow.h>
62#include <tables/Tables/TableVector.h>
63
64#include "MathUtils.h"
65#include "STAttr.h"
66#include "STLineFinder.h"
67#include "STPolCircular.h"
[896]68#include "STPolLinear.h"
[913]69#include "STPolStokes.h"
[2186]70#include "Scantable.h"
[2]71
[125]72using namespace casa;
[2]73
[805]74namespace asap {
75
[896]76std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
77
78void Scantable::initFactories() {
79 if ( factories_.empty() ) {
80 Scantable::factories_["linear"] = &STPolLinear::myFactory;
[1323]81 Scantable::factories_["circular"] = &STPolCircular::myFactory;
[913]82 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
[896]83 }
84}
85
[805]86Scantable::Scantable(Table::TableType ttype) :
[852]87 type_(ttype)
[206]88{
[896]89 initFactories();
[805]90 setupMainTable();
[852]91 freqTable_ = STFrequencies(*this);
[805]92 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
[852]93 weatherTable_ = STWeather(*this);
[805]94 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
[852]95 focusTable_ = STFocus(*this);
[805]96 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
[852]97 tcalTable_ = STTcal(*this);
[805]98 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
[852]99 moleculeTable_ = STMolecules(*this);
[805]100 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
[860]101 historyTable_ = STHistory(*this);
102 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
[959]103 fitTable_ = STFit(*this);
104 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
[1881]105 table_.tableInfo().setType( "Scantable" ) ;
[805]106 originalTable_ = table_;
[322]107 attach();
[18]108}
[206]109
[805]110Scantable::Scantable(const std::string& name, Table::TableType ttype) :
[852]111 type_(ttype)
[206]112{
[896]113 initFactories();
[1819]114
[865]115 Table tab(name, Table::Update);
[1009]116 uInt version = tab.keywordSet().asuInt("VERSION");
[483]117 if (version != version_) {
[2162]118 if ( version == 2 && version_ == 3 ) {
119 // run asap2to3 command
120 LogIO os( LogOrigin( "Scantable" ) ) ;
121 string command="asap2to3" ;
122 string exec=command+" in="+name ;
123 string outname=name ;
124 if ( name.at(name.length()-1) == '/' )
125 outname = outname.substr( 0, name.length()-1 ) ;
126 outname += ".asap3" ;
127 os << LogIO::WARN
128 << name << " is incompatible data format (Scantable v2)." << endl
129 << "Running " << command << " to create " << outname << ", " << endl
130 << "which is identical to " << name << " but compatible " << endl
131 << "data format with current software version (Scantable v3)."
132 << LogIO::POST ;
133 int ret = system( string("which "+command+" > /dev/null 2>&1").c_str() ) ;
134 if ( ret != 0 )
135 throw(AipsError(command+" is not installed")) ;
136 os << LogIO::WARN
137 << "Data will be loaded from " << outname << " instead of "
138 << name << LogIO::POST ;
[2163]139 int tmp = system( exec.c_str() ) ;
140 (void) tmp;
[2162]141 tab = Table(outname, Table::Update ) ;
142 //os << "tab.tableName()=" << tab.tableName() << LogIO::POST ;
143 }
144 else {
145 throw(AipsError("Unsupported version of ASAP file."));
146 }
[483]147 }
[1009]148 if ( type_ == Table::Memory ) {
[852]149 table_ = tab.copyToMemoryTable(generateName());
[1009]150 } else {
[805]151 table_ = tab;
[1009]152 }
[1881]153 table_.tableInfo().setType( "Scantable" ) ;
[1009]154
[859]155 attachSubtables();
[805]156 originalTable_ = table_;
[329]157 attach();
[2]158}
[1819]159/*
160Scantable::Scantable(const std::string& name, Table::TableType ttype) :
161 type_(ttype)
162{
163 initFactories();
164 Table tab(name, Table::Update);
165 uInt version = tab.keywordSet().asuInt("VERSION");
166 if (version != version_) {
167 throw(AipsError("Unsupported version of ASAP file."));
168 }
169 if ( type_ == Table::Memory ) {
170 table_ = tab.copyToMemoryTable(generateName());
171 } else {
172 table_ = tab;
173 }
[2]174
[1819]175 attachSubtables();
176 originalTable_ = table_;
177 attach();
178}
179*/
180
[2163]181Scantable::Scantable( const Scantable& other, bool clear ):
182 Logger()
[206]183{
[805]184 // with or without data
[859]185 String newname = String(generateName());
[865]186 type_ = other.table_.tableType();
[859]187 if ( other.table_.tableType() == Table::Memory ) {
188 if ( clear ) {
189 table_ = TableCopy::makeEmptyMemoryTable(newname,
190 other.table_, True);
191 } else
192 table_ = other.table_.copyToMemoryTable(newname);
[16]193 } else {
[915]194 other.table_.deepCopy(newname, Table::New, False,
195 other.table_.endianFormat(),
[865]196 Bool(clear));
197 table_ = Table(newname, Table::Update);
198 table_.markForDelete();
199 }
[1881]200 table_.tableInfo().setType( "Scantable" ) ;
[1111]201 /// @todo reindex SCANNO, recompute nbeam, nif, npol
[915]202 if ( clear ) copySubtables(other);
[859]203 attachSubtables();
[805]204 originalTable_ = table_;
[322]205 attach();
[2]206}
207
[865]208void Scantable::copySubtables(const Scantable& other) {
209 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
210 TableCopy::copyRows(t, other.freqTable_.table());
211 t = table_.rwKeywordSet().asTable("FOCUS");
212 TableCopy::copyRows(t, other.focusTable_.table());
213 t = table_.rwKeywordSet().asTable("WEATHER");
214 TableCopy::copyRows(t, other.weatherTable_.table());
215 t = table_.rwKeywordSet().asTable("TCAL");
216 TableCopy::copyRows(t, other.tcalTable_.table());
217 t = table_.rwKeywordSet().asTable("MOLECULES");
218 TableCopy::copyRows(t, other.moleculeTable_.table());
219 t = table_.rwKeywordSet().asTable("HISTORY");
220 TableCopy::copyRows(t, other.historyTable_.table());
[972]221 t = table_.rwKeywordSet().asTable("FIT");
222 TableCopy::copyRows(t, other.fitTable_.table());
[865]223}
224
[859]225void Scantable::attachSubtables()
226{
227 freqTable_ = STFrequencies(table_);
228 focusTable_ = STFocus(table_);
229 weatherTable_ = STWeather(table_);
230 tcalTable_ = STTcal(table_);
231 moleculeTable_ = STMolecules(table_);
[860]232 historyTable_ = STHistory(table_);
[972]233 fitTable_ = STFit(table_);
[859]234}
235
[805]236Scantable::~Scantable()
[206]237{
[941]238 //cout << "~Scantable() " << this << endl;
[2]239}
240
[805]241void Scantable::setupMainTable()
[206]242{
[805]243 TableDesc td("", "1", TableDesc::Scratch);
244 td.comment() = "An ASAP Scantable";
[1009]245 td.rwKeywordSet().define("VERSION", uInt(version_));
[2]246
[805]247 // n Cycles
248 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
249 // new index every nBeam x nIF x nPol
250 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
[2]251
[805]252 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
253 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
[972]254 // linear, circular, stokes
[805]255 td.rwKeywordSet().define("POLTYPE", String("linear"));
256 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
[138]257
[805]258 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
259 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
[80]260
[1819]261 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
262 refbeamnoColumn.setDefault(Int(-1));
263 td.addColumn(refbeamnoColumn);
264
265 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
266 flagrowColumn.setDefault(uInt(0));
267 td.addColumn(flagrowColumn);
268
[805]269 td.addColumn(ScalarColumnDesc<Double>("TIME"));
270 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
271 TableMeasValueDesc measVal(td, "TIME");
272 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
273 mepochCol.write(td);
[483]274
[805]275 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
276
[2]277 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
[805]278 // Type of source (on=0, off=1, other=-1)
[1503]279 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
280 stypeColumn.setDefault(Int(-1));
281 td.addColumn(stypeColumn);
[805]282 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
283
284 //The actual Data Vectors
[2]285 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
286 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
[89]287 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
[805]288
289 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
290 IPosition(1,2),
291 ColumnDesc::Direct));
292 TableMeasRefDesc mdirRef(MDirection::J2000); // default
293 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
294 // the TableMeasDesc gives the column a type
295 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
[987]296 // a uder set table type e.g. GALCTIC, B1950 ...
297 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
[805]298 // writing create the measure column
299 mdirCol.write(td);
[923]300 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
301 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
[1047]302 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
[105]303
[805]304 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
[972]305 ScalarColumnDesc<Int> fitColumn("FIT_ID");
[973]306 fitColumn.setDefault(Int(-1));
[972]307 td.addColumn(fitColumn);
[805]308
309 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
310 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
311
[999]312 // columns which just get dragged along, as they aren't used in asap
313 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
314 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
315 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
316 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
317
[805]318 td.rwKeywordSet().define("OBSMODE", String(""));
319
[418]320 // Now create Table SetUp from the description.
[859]321 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
[852]322 table_ = Table(aNewTab, type_, 0);
[805]323 originalTable_ = table_;
324}
[418]325
[805]326void Scantable::attach()
[455]327{
[805]328 timeCol_.attach(table_, "TIME");
329 srcnCol_.attach(table_, "SRCNAME");
[1068]330 srctCol_.attach(table_, "SRCTYPE");
[805]331 specCol_.attach(table_, "SPECTRA");
332 flagsCol_.attach(table_, "FLAGTRA");
[865]333 tsysCol_.attach(table_, "TSYS");
[805]334 cycleCol_.attach(table_,"CYCLENO");
335 scanCol_.attach(table_, "SCANNO");
336 beamCol_.attach(table_, "BEAMNO");
[847]337 ifCol_.attach(table_, "IFNO");
338 polCol_.attach(table_, "POLNO");
[805]339 integrCol_.attach(table_, "INTERVAL");
340 azCol_.attach(table_, "AZIMUTH");
341 elCol_.attach(table_, "ELEVATION");
342 dirCol_.attach(table_, "DIRECTION");
343 fldnCol_.attach(table_, "FIELDNAME");
344 rbeamCol_.attach(table_, "REFBEAMNO");
[455]345
[1730]346 mweatheridCol_.attach(table_,"WEATHER_ID");
[805]347 mfitidCol_.attach(table_,"FIT_ID");
348 mfreqidCol_.attach(table_, "FREQ_ID");
349 mtcalidCol_.attach(table_, "TCAL_ID");
350 mfocusidCol_.attach(table_, "FOCUS_ID");
351 mmolidCol_.attach(table_, "MOLECULE_ID");
[1819]352
353 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
354 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
355
[455]356}
357
[1819]358template<class T, class T2>
359void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
360 const String& colName,
361 const T2& defValue)
362{
363 try {
364 col.attach(table_, colName);
365 } catch (TableError& err) {
366 String errMesg = err.getMesg();
367 if (errMesg == "Table column " + colName + " is unknown") {
368 table_.addColumn(ScalarColumnDesc<T>(colName));
369 col.attach(table_, colName);
370 col.fillColumn(static_cast<T>(defValue));
371 } else {
372 throw;
373 }
374 } catch (...) {
375 throw;
376 }
377}
378
379template<class T, class T2>
380void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
381 const String& colName,
382 const Array<T2>& defValue)
383{
384 try {
385 col.attach(table_, colName);
386 } catch (TableError& err) {
387 String errMesg = err.getMesg();
388 if (errMesg == "Table column " + colName + " is unknown") {
389 table_.addColumn(ArrayColumnDesc<T>(colName));
390 col.attach(table_, colName);
391
392 int size = 0;
393 ArrayIterator<T2>& it = defValue.begin();
394 while (it != defValue.end()) {
395 ++size;
396 ++it;
397 }
398 IPosition ip(1, size);
399 Array<T>& arr(ip);
400 for (int i = 0; i < size; ++i)
401 arr[i] = static_cast<T>(defValue[i]);
402
403 col.fillColumn(arr);
404 } else {
405 throw;
406 }
407 } catch (...) {
408 throw;
409 }
410}
411
[901]412void Scantable::setHeader(const STHeader& sdh)
[206]413{
[18]414 table_.rwKeywordSet().define("nIF", sdh.nif);
415 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
416 table_.rwKeywordSet().define("nPol", sdh.npol);
417 table_.rwKeywordSet().define("nChan", sdh.nchan);
418 table_.rwKeywordSet().define("Observer", sdh.observer);
419 table_.rwKeywordSet().define("Project", sdh.project);
420 table_.rwKeywordSet().define("Obstype", sdh.obstype);
421 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
422 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
423 table_.rwKeywordSet().define("Equinox", sdh.equinox);
424 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
425 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
426 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
427 table_.rwKeywordSet().define("UTC", sdh.utc);
[206]428 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
429 table_.rwKeywordSet().define("Epoch", sdh.epoch);
[905]430 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
[50]431}
[21]432
[901]433STHeader Scantable::getHeader() const
[206]434{
[901]435 STHeader sdh;
[21]436 table_.keywordSet().get("nBeam",sdh.nbeam);
437 table_.keywordSet().get("nIF",sdh.nif);
438 table_.keywordSet().get("nPol",sdh.npol);
439 table_.keywordSet().get("nChan",sdh.nchan);
440 table_.keywordSet().get("Observer", sdh.observer);
441 table_.keywordSet().get("Project", sdh.project);
442 table_.keywordSet().get("Obstype", sdh.obstype);
443 table_.keywordSet().get("AntennaName", sdh.antennaname);
444 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
445 table_.keywordSet().get("Equinox", sdh.equinox);
446 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
447 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
448 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
449 table_.keywordSet().get("UTC", sdh.utc);
[206]450 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
451 table_.keywordSet().get("Epoch", sdh.epoch);
[905]452 table_.keywordSet().get("POLTYPE", sdh.poltype);
[21]453 return sdh;
[18]454}
[805]455
[1360]456void Scantable::setSourceType( int stype )
[1068]457{
458 if ( stype < 0 || stype > 1 )
459 throw(AipsError("Illegal sourcetype."));
460 TableVector<Int> tabvec(table_, "SRCTYPE");
461 tabvec = Int(stype);
462}
463
[845]464bool Scantable::conformant( const Scantable& other )
465{
466 return this->getHeader().conformant(other.getHeader());
467}
468
469
[50]470
[805]471std::string Scantable::formatSec(Double x) const
[206]472{
[105]473 Double xcop = x;
474 MVTime mvt(xcop/24./3600.); // make days
[365]475
[105]476 if (x < 59.95)
[281]477 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
[745]478 else if (x < 3599.95)
[281]479 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
480 else {
481 ostringstream oss;
482 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
483 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
484 return String(oss);
[745]485 }
[105]486};
487
[805]488std::string Scantable::formatDirection(const MDirection& md) const
[281]489{
490 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
491 Int prec = 7;
492
493 MVAngle mvLon(t[0]);
494 String sLon = mvLon.string(MVAngle::TIME,prec);
[987]495 uInt tp = md.getRef().getType();
496 if (tp == MDirection::GALACTIC ||
497 tp == MDirection::SUPERGAL ) {
498 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
499 }
[281]500 MVAngle mvLat(t[1]);
501 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
[380]502 return sLon + String(" ") + sLat;
[281]503}
504
505
[805]506std::string Scantable::getFluxUnit() const
[206]507{
[847]508 return table_.keywordSet().asString("FluxUnit");
[206]509}
510
[805]511void Scantable::setFluxUnit(const std::string& unit)
[218]512{
513 String tmp(unit);
514 Unit tU(tmp);
515 if (tU==Unit("K") || tU==Unit("Jy")) {
516 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
517 } else {
518 throw AipsError("Illegal unit - must be compatible with Jy or K");
519 }
520}
521
[805]522void Scantable::setInstrument(const std::string& name)
[236]523{
[805]524 bool throwIt = true;
[996]525 // create an Instrument to see if this is valid
526 STAttr::convertInstrument(name, throwIt);
[236]527 String nameU(name);
528 nameU.upcase();
529 table_.rwKeywordSet().define(String("AntennaName"), nameU);
530}
531
[1189]532void Scantable::setFeedType(const std::string& feedtype)
533{
534 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
535 std::string msg = "Illegal feed type "+ feedtype;
536 throw(casa::AipsError(msg));
537 }
538 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
539}
540
[1743]541MPosition Scantable::getAntennaPosition() const
[805]542{
543 Vector<Double> antpos;
544 table_.keywordSet().get("AntennaPosition", antpos);
545 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
546 return MPosition(mvpos);
547}
[281]548
[805]549void Scantable::makePersistent(const std::string& filename)
550{
551 String inname(filename);
552 Path path(inname);
[1111]553 /// @todo reindex SCANNO, recompute nbeam, nif, npol
[805]554 inname = path.expandedName();
[2030]555 // 2011/03/04 TN
556 // We can comment out this workaround since the essential bug is
557 // fixed in casacore (r20889 in google code).
558 table_.deepCopy(inname, Table::New);
559// // WORKAROUND !!! for Table bug
560// // Remove when fixed in casacore
561// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
562// Table tab = table_.copyToMemoryTable(generateName());
563// tab.deepCopy(inname, Table::New);
564// tab.markForDelete();
565//
566// } else {
567// table_.deepCopy(inname, Table::New);
568// }
[805]569}
570
[837]571int Scantable::nbeam( int scanno ) const
[805]572{
573 if ( scanno < 0 ) {
574 Int n;
575 table_.keywordSet().get("nBeam",n);
576 return int(n);
[105]577 } else {
[805]578 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
[888]579 Table t = table_(table_.col("SCANNO") == scanno);
580 ROTableRow row(t);
581 const TableRecord& rec = row.get(0);
582 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
583 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
584 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
585 ROTableVector<uInt> v(subt, "BEAMNO");
[805]586 return int(v.nelements());
[105]587 }
[805]588 return 0;
589}
[455]590
[837]591int Scantable::nif( int scanno ) const
[805]592{
593 if ( scanno < 0 ) {
594 Int n;
595 table_.keywordSet().get("nIF",n);
596 return int(n);
597 } else {
598 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
[888]599 Table t = table_(table_.col("SCANNO") == scanno);
600 ROTableRow row(t);
601 const TableRecord& rec = row.get(0);
602 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
603 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
604 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
605 if ( subt.nrow() == 0 ) return 0;
606 ROTableVector<uInt> v(subt, "IFNO");
[805]607 return int(v.nelements());
[2]608 }
[805]609 return 0;
610}
[321]611
[837]612int Scantable::npol( int scanno ) const
[805]613{
614 if ( scanno < 0 ) {
615 Int n;
616 table_.keywordSet().get("nPol",n);
617 return n;
618 } else {
619 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
[888]620 Table t = table_(table_.col("SCANNO") == scanno);
621 ROTableRow row(t);
622 const TableRecord& rec = row.get(0);
623 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
624 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
625 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
626 if ( subt.nrow() == 0 ) return 0;
627 ROTableVector<uInt> v(subt, "POLNO");
[805]628 return int(v.nelements());
[321]629 }
[805]630 return 0;
[2]631}
[805]632
[845]633int Scantable::ncycle( int scanno ) const
[206]634{
[805]635 if ( scanno < 0 ) {
[837]636 Block<String> cols(2);
637 cols[0] = "SCANNO";
638 cols[1] = "CYCLENO";
639 TableIterator it(table_, cols);
640 int n = 0;
641 while ( !it.pastEnd() ) {
642 ++n;
[902]643 ++it;
[837]644 }
645 return n;
[805]646 } else {
[888]647 Table t = table_(table_.col("SCANNO") == scanno);
648 ROTableRow row(t);
649 const TableRecord& rec = row.get(0);
650 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
651 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
652 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
653 if ( subt.nrow() == 0 ) return 0;
654 return int(subt.nrow());
[805]655 }
656 return 0;
[18]657}
[455]658
659
[845]660int Scantable::nrow( int scanno ) const
[805]661{
[845]662 return int(table_.nrow());
663}
664
665int Scantable::nchan( int ifno ) const
666{
667 if ( ifno < 0 ) {
[805]668 Int n;
669 table_.keywordSet().get("nChan",n);
670 return int(n);
671 } else {
[1360]672 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
673 // vary with these
[2244]674 Table t = table_(table_.col("IFNO") == ifno, 1);
[888]675 if ( t.nrow() == 0 ) return 0;
676 ROArrayColumn<Float> v(t, "SPECTRA");
[923]677 return v.shape(0)(0);
[805]678 }
679 return 0;
[18]680}
[455]681
[1111]682int Scantable::nscan() const {
683 Vector<uInt> scannos(scanCol_.getColumn());
[1148]684 uInt nout = genSort( scannos, Sort::Ascending,
[1111]685 Sort::QuickSort|Sort::NoDuplicates );
686 return int(nout);
687}
688
[923]689int Scantable::getChannels(int whichrow) const
690{
691 return specCol_.shape(whichrow)(0);
692}
[847]693
694int Scantable::getBeam(int whichrow) const
695{
696 return beamCol_(whichrow);
697}
698
[1694]699std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
[1111]700{
701 Vector<uInt> nos(col.getColumn());
[1148]702 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
703 nos.resize(n, True);
[1111]704 std::vector<uint> stlout;
705 nos.tovector(stlout);
706 return stlout;
707}
708
[847]709int Scantable::getIF(int whichrow) const
710{
711 return ifCol_(whichrow);
712}
713
714int Scantable::getPol(int whichrow) const
715{
716 return polCol_(whichrow);
717}
718
[805]719std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
720{
[1947]721 return formatTime(me, showdate, 0);
722}
723
724std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
725{
[805]726 MVTime mvt(me.getValue());
727 if (showdate)
[1947]728 //mvt.setFormat(MVTime::YMD);
729 mvt.setFormat(MVTime::YMD, prec);
[805]730 else
[1947]731 //mvt.setFormat(MVTime::TIME);
732 mvt.setFormat(MVTime::TIME, prec);
[805]733 ostringstream oss;
734 oss << mvt;
735 return String(oss);
736}
[488]737
[805]738void Scantable::calculateAZEL()
739{
740 MPosition mp = getAntennaPosition();
741 MEpoch::ROScalarColumn timeCol(table_, "TIME");
742 ostringstream oss;
743 oss << "Computed azimuth/elevation using " << endl
744 << mp << endl;
[996]745 for (Int i=0; i<nrow(); ++i) {
[805]746 MEpoch me = timeCol(i);
[987]747 MDirection md = getDirection(i);
[805]748 oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
749 << endl << " => ";
750 MeasFrame frame(mp, me);
751 Vector<Double> azel =
752 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
753 frame)
754 )().getAngle("rad").getValue();
[923]755 azCol_.put(i,Float(azel[0]));
756 elCol_.put(i,Float(azel[1]));
[805]757 oss << "azel: " << azel[0]/C::pi*180.0 << " "
758 << azel[1]/C::pi*180.0 << " (deg)" << endl;
[16]759 }
[805]760 pushLog(String(oss));
761}
[89]762
[1819]763void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
764{
765 for (uInt i=0; i<table_.nrow(); ++i) {
766 Vector<uChar> flgs = flagsCol_(i);
767 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
768 flagsCol_.put(i, flgs);
769 }
770}
771
772std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
773{
774 Vector<uChar> flags;
775 flagsCol_.get(uInt(whichrow), flags);
776 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
777 Vector<Bool> bflag(flags.shape());
778 convertArray(bflag, flags);
779 //bflag = !bflag;
780
781 std::vector<bool> mask;
782 bflag.tovector(mask);
783 return mask;
784}
785
786void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
787 Vector<uChar> flgs)
788{
789 Vector<Float> spcs = specCol_(whichrow);
790 uInt nchannel = nchan();
791 if (spcs.nelements() != nchannel) {
792 throw(AipsError("Data has incorrect number of channels"));
793 }
794 uChar userflag = 1 << 7;
795 if (unflag) {
796 userflag = 0 << 7;
797 }
798 if (clipoutside) {
799 for (uInt j = 0; j < nchannel; ++j) {
800 Float spc = spcs(j);
801 if ((spc >= uthres) || (spc <= dthres)) {
802 flgs(j) = userflag;
803 }
804 }
805 } else {
806 for (uInt j = 0; j < nchannel; ++j) {
807 Float spc = spcs(j);
808 if ((spc < uthres) && (spc > dthres)) {
809 flgs(j) = userflag;
810 }
811 }
812 }
813}
814
[1994]815
816void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
[1333]817 std::vector<bool>::const_iterator it;
818 uInt ntrue = 0;
[1994]819 if (whichrow >= int(table_.nrow()) ) {
820 throw(AipsError("Invalid row number"));
821 }
[1333]822 for (it = msk.begin(); it != msk.end(); ++it) {
823 if ( *it ) {
824 ntrue++;
825 }
826 }
[1994]827 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
828 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
[1000]829 throw(AipsError("Trying to flag whole scantable."));
[1994]830 uChar userflag = 1 << 7;
831 if ( unflag ) {
832 userflag = 0 << 7;
833 }
834 if (whichrow > -1 ) {
835 applyChanFlag(uInt(whichrow), msk, userflag);
836 } else {
[1000]837 for ( uInt i=0; i<table_.nrow(); ++i) {
[1994]838 applyChanFlag(i, msk, userflag);
[1000]839 }
[1994]840 }
841}
842
843void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
844{
845 if (whichrow >= table_.nrow() ) {
846 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
847 }
848 Vector<uChar> flgs = flagsCol_(whichrow);
849 if ( msk.size() == 0 ) {
850 flgs = flagval;
851 flagsCol_.put(whichrow, flgs);
[1000]852 return;
853 }
854 if ( int(msk.size()) != nchan() ) {
855 throw(AipsError("Mask has incorrect number of channels."));
856 }
[1994]857 if ( flgs.nelements() != msk.size() ) {
858 throw(AipsError("Mask has incorrect number of channels."
859 " Probably varying with IF. Please flag per IF"));
860 }
861 std::vector<bool>::const_iterator it;
862 uInt j = 0;
863 for (it = msk.begin(); it != msk.end(); ++it) {
864 if ( *it ) {
865 flgs(j) = flagval;
[1000]866 }
[1994]867 ++j;
[1000]868 }
[1994]869 flagsCol_.put(whichrow, flgs);
[865]870}
871
[1819]872void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
873{
874 if ( selector_.empty() && (rows.size() == table_.nrow()) )
875 throw(AipsError("Trying to flag whole scantable."));
876
877 uInt rowflag = (unflag ? 0 : 1);
878 std::vector<uInt>::const_iterator it;
879 for (it = rows.begin(); it != rows.end(); ++it)
880 flagrowCol_.put(*it, rowflag);
881}
882
[805]883std::vector<bool> Scantable::getMask(int whichrow) const
884{
885 Vector<uChar> flags;
886 flagsCol_.get(uInt(whichrow), flags);
887 Vector<Bool> bflag(flags.shape());
888 convertArray(bflag, flags);
889 bflag = !bflag;
890 std::vector<bool> mask;
891 bflag.tovector(mask);
892 return mask;
893}
[89]894
[896]895std::vector<float> Scantable::getSpectrum( int whichrow,
[902]896 const std::string& poltype ) const
[805]897{
[905]898 String ptype = poltype;
899 if (poltype == "" ) ptype = getPolType();
[902]900 if ( whichrow < 0 || whichrow >= nrow() )
901 throw(AipsError("Illegal row number."));
[896]902 std::vector<float> out;
[805]903 Vector<Float> arr;
[896]904 uInt requestedpol = polCol_(whichrow);
905 String basetype = getPolType();
[905]906 if ( ptype == basetype ) {
[896]907 specCol_.get(whichrow, arr);
908 } else {
[1598]909 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
[1586]910 basetype));
[1334]911 uInt row = uInt(whichrow);
912 stpol->setSpectra(getPolMatrix(row));
[2047]913 Float fang,fhand;
[1586]914 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
[1334]915 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
[1586]916 stpol->setPhaseCorrections(fang, fhand);
[1334]917 arr = stpol->getSpectrum(requestedpol, ptype);
[896]918 }
[902]919 if ( arr.nelements() == 0 )
920 pushLog("Not enough polarisations present to do the conversion.");
[805]921 arr.tovector(out);
922 return out;
[89]923}
[212]924
[1360]925void Scantable::setSpectrum( const std::vector<float>& spec,
[884]926 int whichrow )
927{
928 Vector<Float> spectrum(spec);
929 Vector<Float> arr;
930 specCol_.get(whichrow, arr);
931 if ( spectrum.nelements() != arr.nelements() )
[896]932 throw AipsError("The spectrum has incorrect number of channels.");
[884]933 specCol_.put(whichrow, spectrum);
934}
935
936
[805]937String Scantable::generateName()
[745]938{
[805]939 return (File::newUniqueName("./","temp")).baseName();
[212]940}
941
[805]942const casa::Table& Scantable::table( ) const
[212]943{
[805]944 return table_;
[212]945}
946
[805]947casa::Table& Scantable::table( )
[386]948{
[805]949 return table_;
[386]950}
951
[896]952std::string Scantable::getPolType() const
953{
954 return table_.keywordSet().asString("POLTYPE");
955}
956
[805]957void Scantable::unsetSelection()
[380]958{
[805]959 table_ = originalTable_;
[847]960 attach();
[805]961 selector_.reset();
[380]962}
[386]963
[805]964void Scantable::setSelection( const STSelector& selection )
[430]965{
[805]966 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
967 if ( tab.nrow() == 0 ) {
968 throw(AipsError("Selection contains no data. Not applying it."));
969 }
970 table_ = tab;
[847]971 attach();
[2084]972// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
973// vector<uint> selectedIFs = getIFNos() ;
974// Int newnIF = selectedIFs.size() ;
975// tab.rwKeywordSet().define("nIF",newnIF) ;
976// if ( newnIF != 0 ) {
977// Int newnChan = 0 ;
978// for ( Int i = 0 ; i < newnIF ; i++ ) {
979// Int nChan = nchan( selectedIFs[i] ) ;
980// if ( newnChan > nChan )
981// newnChan = nChan ;
982// }
983// tab.rwKeywordSet().define("nChan",newnChan) ;
984// }
985// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
[805]986 selector_ = selection;
[430]987}
988
[2111]989
[2163]990std::string Scantable::headerSummary()
[447]991{
[805]992 // Format header info
[2111]993// STHeader sdh;
994// sdh = getHeader();
995// sdh.print();
[805]996 ostringstream oss;
997 oss.flags(std::ios_base::left);
998 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
999 << setw(15) << "IFs:" << setw(4) << nif() << endl
[896]1000 << setw(15) << "Polarisations:" << setw(4) << npol()
1001 << "(" << getPolType() << ")" << endl
[1694]1002 << setw(15) << "Channels:" << nchan() << endl;
[805]1003 String tmp;
[860]1004 oss << setw(15) << "Observer:"
1005 << table_.keywordSet().asString("Observer") << endl;
[805]1006 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1007 table_.keywordSet().get("Project", tmp);
1008 oss << setw(15) << "Project:" << tmp << endl;
1009 table_.keywordSet().get("Obstype", tmp);
1010 oss << setw(15) << "Obs. Type:" << tmp << endl;
1011 table_.keywordSet().get("AntennaName", tmp);
1012 oss << setw(15) << "Antenna Name:" << tmp << endl;
1013 table_.keywordSet().get("FluxUnit", tmp);
1014 oss << setw(15) << "Flux Unit:" << tmp << endl;
[1819]1015 //Vector<Double> vec(moleculeTable_.getRestFrequencies());
1016 int nid = moleculeTable_.nrow();
1017 Bool firstline = True;
[805]1018 oss << setw(15) << "Rest Freqs:";
[1819]1019 for (int i=0; i<nid; i++) {
[2244]1020 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
[1819]1021 if (t.nrow() > 0) {
1022 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1023 if (vec.nelements() > 0) {
1024 if (firstline) {
1025 oss << setprecision(10) << vec << " [Hz]" << endl;
1026 firstline=False;
1027 }
1028 else{
1029 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1030 }
1031 } else {
1032 oss << "none" << endl;
1033 }
1034 }
[805]1035 }
[941]1036
1037 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
[805]1038 oss << selector_.print() << endl;
[2111]1039 return String(oss);
1040}
1041
[2286]1042 //std::string Scantable::summary( const std::string& filename )
1043void Scantable::summary( const std::string& filename )
[2111]1044{
1045 ostringstream oss;
[2286]1046 ofstream ofs;
1047 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1048
1049 if (filename != "")
1050 ofs.open( filename.c_str(), ios::out );
1051
[805]1052 oss << endl;
[2111]1053 oss << asap::SEPERATOR << endl;
1054 oss << " Scan Table Summary" << endl;
1055 oss << asap::SEPERATOR << endl;
1056
1057 // Format header info
[2163]1058 oss << headerSummary();
[2111]1059 oss << endl;
1060
[805]1061 // main table
1062 String dirtype = "Position ("
[987]1063 + getDirectionRefString()
[805]1064 + ")";
[2111]1065 oss.flags(std::ios_base::left);
[941]1066 oss << setw(5) << "Scan" << setw(15) << "Source"
[2005]1067 << setw(10) << "Time" << setw(18) << "Integration"
1068 << setw(15) << "Source Type" << endl;
[941]1069 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
[1694]1070 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
[805]1071 << setw(8) << "Frame" << setw(16)
[1694]1072 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1073 << setw(7) << "Channels"
1074 << endl;
[805]1075 oss << asap::SEPERATOR << endl;
[2286]1076
1077 // Flush summary and clear up the string
1078 ols << String(oss) << LogIO::POST;
1079 if (ofs) ofs << String(oss) << flush;
1080 oss.str("");
1081 oss.clear();
1082
1083// TableIterator iter(table_, "SCANNO");
1084// while (!iter.pastEnd()) {
1085// Table subt = iter.table();
1086// ROTableRow row(subt);
1087// MEpoch::ROScalarColumn timeCol(subt,"TIME");
1088// const TableRecord& rec = row.get(0);
1089// oss << setw(4) << std::right << rec.asuInt("SCANNO")
1090// << std::left << setw(1) << ""
1091// << setw(15) << rec.asString("SRCNAME")
1092// << setw(10) << formatTime(timeCol(0), false);
1093// // count the cycles in the scan
1094// TableIterator cyciter(subt, "CYCLENO");
1095// int nint = 0;
1096// while (!cyciter.pastEnd()) {
1097// ++nint;
1098// ++cyciter;
1099// }
1100// oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1101// << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1102// << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1103
1104// TableIterator biter(subt, "BEAMNO");
1105// while (!biter.pastEnd()) {
1106// Table bsubt = biter.table();
1107// ROTableRow brow(bsubt);
1108// const TableRecord& brec = brow.get(0);
1109// uInt row0 = bsubt.rowNumbers(table_)[0];
1110// oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1111// oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1112// TableIterator iiter(bsubt, "IFNO");
1113// while (!iiter.pastEnd()) {
1114// Table isubt = iiter.table();
1115// ROTableRow irow(isubt);
1116// const TableRecord& irec = irow.get(0);
1117// oss << setw(9) << "";
1118// oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1119// << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1120// << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1121// << endl;
1122
1123// ++iiter;
1124// }
1125// ++biter;
1126// }
1127// ++iter;
1128// }
[805]1129 TableIterator iter(table_, "SCANNO");
1130 while (!iter.pastEnd()) {
1131 Table subt = iter.table();
1132 ROTableRow row(subt);
1133 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1134 const TableRecord& rec = row.get(0);
1135 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1136 << std::left << setw(1) << ""
1137 << setw(15) << rec.asString("SRCNAME")
1138 << setw(10) << formatTime(timeCol(0), false);
1139 // count the cycles in the scan
1140 TableIterator cyciter(subt, "CYCLENO");
1141 int nint = 0;
1142 while (!cyciter.pastEnd()) {
1143 ++nint;
1144 ++cyciter;
1145 }
1146 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
[2005]1147 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1148 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
[447]1149
[805]1150 TableIterator biter(subt, "BEAMNO");
1151 while (!biter.pastEnd()) {
1152 Table bsubt = biter.table();
1153 ROTableRow brow(bsubt);
1154 const TableRecord& brec = brow.get(0);
[1000]1155 uInt row0 = bsubt.rowNumbers(table_)[0];
[941]1156 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
[987]1157 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
[805]1158 TableIterator iiter(bsubt, "IFNO");
1159 while (!iiter.pastEnd()) {
1160 Table isubt = iiter.table();
1161 ROTableRow irow(isubt);
1162 const TableRecord& irec = irow.get(0);
[1694]1163 oss << setw(9) << "";
[941]1164 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
[1694]1165 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1166 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
[1375]1167 << endl;
[447]1168
[805]1169 ++iiter;
1170 }
1171 ++biter;
1172 }
[2286]1173 // Flush summary every scan and clear up the string
1174 ols << String(oss) << LogIO::POST;
1175 if (ofs) ofs << String(oss) << flush;
1176 oss.str("");
1177 oss.clear();
1178
[805]1179 ++iter;
[447]1180 }
[2286]1181 oss << asap::SEPERATOR << endl;
1182 ols << String(oss) << LogIO::POST;
1183 if (ofs) {
1184 //ofs << String(oss) << flush;
1185 ofs.close();
1186 }
1187 // return String(oss);
[447]1188}
1189
[1947]1190// std::string Scantable::getTime(int whichrow, bool showdate) const
1191// {
1192// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1193// MEpoch me;
1194// if (whichrow > -1) {
1195// me = timeCol(uInt(whichrow));
1196// } else {
1197// Double tm;
1198// table_.keywordSet().get("UTC",tm);
1199// me = MEpoch(MVEpoch(tm));
1200// }
1201// return formatTime(me, showdate);
1202// }
1203
1204std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
[777]1205{
[805]1206 MEpoch me;
[1947]1207 me = getEpoch(whichrow);
1208 return formatTime(me, showdate, prec);
[777]1209}
[805]1210
[1411]1211MEpoch Scantable::getEpoch(int whichrow) const
1212{
1213 if (whichrow > -1) {
1214 return timeCol_(uInt(whichrow));
1215 } else {
1216 Double tm;
1217 table_.keywordSet().get("UTC",tm);
[1598]1218 return MEpoch(MVEpoch(tm));
[1411]1219 }
1220}
1221
[1068]1222std::string Scantable::getDirectionString(int whichrow) const
1223{
1224 return formatDirection(getDirection(uInt(whichrow)));
1225}
1226
[1598]1227
1228SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1229 const MPosition& mp = getAntennaPosition();
1230 const MDirection& md = getDirection(whichrow);
1231 const MEpoch& me = timeCol_(whichrow);
[1819]1232 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1233 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
[1598]1234 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1235 mfreqidCol_(whichrow));
1236}
1237
[1360]1238std::vector< double > Scantable::getAbcissa( int whichrow ) const
[865]1239{
[1507]1240 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
[865]1241 std::vector<double> stlout;
1242 int nchan = specCol_(whichrow).nelements();
1243 String us = freqTable_.getUnitString();
1244 if ( us == "" || us == "pixel" || us == "channel" ) {
1245 for (int i=0; i<nchan; ++i) {
1246 stlout.push_back(double(i));
1247 }
1248 return stlout;
1249 }
[1598]1250 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
[865]1251 Vector<Double> pixel(nchan);
1252 Vector<Double> world;
1253 indgen(pixel);
1254 if ( Unit(us) == Unit("Hz") ) {
1255 for ( int i=0; i < nchan; ++i) {
1256 Double world;
1257 spc.toWorld(world, pixel[i]);
1258 stlout.push_back(double(world));
1259 }
1260 } else if ( Unit(us) == Unit("km/s") ) {
1261 Vector<Double> world;
1262 spc.pixelToVelocity(world, pixel);
1263 world.tovector(stlout);
1264 }
1265 return stlout;
1266}
[1360]1267void Scantable::setDirectionRefString( const std::string & refstr )
[987]1268{
1269 MDirection::Types mdt;
1270 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1271 throw(AipsError("Illegal Direction frame."));
1272 }
1273 if ( refstr == "" ) {
1274 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1275 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1276 } else {
1277 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1278 }
1279}
[865]1280
[1360]1281std::string Scantable::getDirectionRefString( ) const
[987]1282{
1283 return table_.keywordSet().asString("DIRECTIONREF");
1284}
1285
1286MDirection Scantable::getDirection(int whichrow ) const
1287{
1288 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1289 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1290 if ( usertype != type ) {
1291 MDirection::Types mdt;
1292 if (!MDirection::getType(mdt, usertype)) {
1293 throw(AipsError("Illegal Direction frame."));
1294 }
1295 return dirCol_.convert(uInt(whichrow), mdt);
1296 } else {
1297 return dirCol_(uInt(whichrow));
1298 }
1299}
1300
[847]1301std::string Scantable::getAbcissaLabel( int whichrow ) const
1302{
[996]1303 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
[847]1304 const MPosition& mp = getAntennaPosition();
[987]1305 const MDirection& md = getDirection(whichrow);
[847]1306 const MEpoch& me = timeCol_(whichrow);
[1819]1307 //const Double& rf = mmolidCol_(whichrow);
1308 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
[847]1309 SpectralCoordinate spc =
1310 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1311
1312 String s = "Channel";
1313 Unit u = Unit(freqTable_.getUnitString());
1314 if (u == Unit("km/s")) {
[1170]1315 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
[847]1316 } else if (u == Unit("Hz")) {
1317 Vector<String> wau(1);wau = u.getName();
1318 spc.setWorldAxisUnits(wau);
[1170]1319 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
[847]1320 }
1321 return s;
1322
1323}
1324
[1819]1325/**
1326void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
[1170]1327 const std::string& unit )
[1819]1328**/
1329void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1330 const std::string& unit )
1331
[847]1332{
[923]1333 ///@todo lookup in line table to fill in name and formattedname
[847]1334 Unit u(unit);
[1819]1335 //Quantum<Double> urf(rf, u);
1336 Quantum<Vector<Double> >urf(rf, u);
1337 Vector<String> formattedname(0);
1338 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1339
1340 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1341 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
[847]1342 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1343 tabvec = id;
1344}
1345
[1819]1346/**
1347void asap::Scantable::setRestFrequencies( const std::string& name )
[847]1348{
1349 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1350 ///@todo implement
1351}
[1819]1352**/
[2012]1353
[1819]1354void Scantable::setRestFrequencies( const vector<std::string>& name )
1355{
[2163]1356 (void) name; // suppress unused warning
[1819]1357 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1358 ///@todo implement
1359}
[847]1360
[1360]1361std::vector< unsigned int > Scantable::rownumbers( ) const
[852]1362{
1363 std::vector<unsigned int> stlout;
1364 Vector<uInt> vec = table_.rowNumbers();
1365 vec.tovector(stlout);
1366 return stlout;
1367}
1368
[865]1369
[1360]1370Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
[896]1371{
1372 ROTableRow row(table_);
1373 const TableRecord& rec = row.get(whichrow);
1374 Table t =
1375 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1376 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1377 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1378 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1379 ROArrayColumn<Float> speccol(t, "SPECTRA");
1380 return speccol.getColumn();
1381}
[865]1382
[1360]1383std::vector< std::string > Scantable::columnNames( ) const
[902]1384{
1385 Vector<String> vec = table_.tableDesc().columnNames();
1386 return mathutil::tovectorstring(vec);
1387}
[896]1388
[1360]1389MEpoch::Types Scantable::getTimeReference( ) const
[915]1390{
1391 return MEpoch::castType(timeCol_.getMeasRef().getType());
[972]1392}
[915]1393
[1360]1394void Scantable::addFit( const STFitEntry& fit, int row )
[972]1395{
[1819]1396 //cout << mfitidCol_(uInt(row)) << endl;
1397 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1398 os << mfitidCol_(uInt(row)) << LogIO::POST ;
[972]1399 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1400 mfitidCol_.put(uInt(row), id);
1401}
[915]1402
[1360]1403void Scantable::shift(int npix)
1404{
1405 Vector<uInt> fids(mfreqidCol_.getColumn());
1406 genSort( fids, Sort::Ascending,
1407 Sort::QuickSort|Sort::NoDuplicates );
1408 for (uInt i=0; i<fids.nelements(); ++i) {
[1567]1409 frequencies().shiftRefPix(npix, fids[i]);
[1360]1410 }
1411}
[987]1412
[1819]1413String Scantable::getAntennaName() const
[1391]1414{
1415 String out;
1416 table_.keywordSet().get("AntennaName", out);
[1987]1417 String::size_type pos1 = out.find("@") ;
1418 String::size_type pos2 = out.find("//") ;
1419 if ( pos2 != String::npos )
[2036]1420 out = out.substr(pos2+2,pos1-pos2-2) ;
[1987]1421 else if ( pos1 != String::npos )
1422 out = out.substr(0,pos1) ;
[1391]1423 return out;
[987]1424}
[1391]1425
[1730]1426int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
[1391]1427{
1428 String tbpath;
1429 int ret = 0;
1430 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1431 table_.keywordSet().get("GBT_GO", tbpath);
1432 Table t(tbpath,Table::Old);
1433 // check each scan if other scan of the pair exist
1434 int nscan = scanlist.size();
1435 for (int i = 0; i < nscan; i++) {
1436 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1437 if (subt.nrow()==0) {
[1819]1438 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1439 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1440 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
[1391]1441 ret = 1;
1442 break;
1443 }
1444 ROTableRow row(subt);
1445 const TableRecord& rec = row.get(0);
1446 int scan1seqn = rec.asuInt("PROCSEQN");
1447 int laston1 = rec.asuInt("LASTON");
1448 if ( rec.asuInt("PROCSIZE")==2 ) {
1449 if ( i < nscan-1 ) {
1450 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1451 if ( subt2.nrow() == 0) {
[1819]1452 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1453
1454 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1455 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
[1391]1456 ret = 1;
1457 break;
1458 }
1459 ROTableRow row2(subt2);
1460 const TableRecord& rec2 = row2.get(0);
1461 int scan2seqn = rec2.asuInt("PROCSEQN");
1462 int laston2 = rec2.asuInt("LASTON");
1463 if (scan1seqn == 1 && scan2seqn == 2) {
1464 if (laston1 == laston2) {
[1819]1465 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1466 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1467 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
[1391]1468 i +=1;
1469 }
1470 else {
[1819]1471 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1472 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1473 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
[1391]1474 }
1475 }
1476 else if (scan1seqn==2 && scan2seqn == 1) {
1477 if (laston1 == laston2) {
[1819]1478 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1479 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1480 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
[1391]1481 ret = 1;
1482 break;
1483 }
1484 }
1485 else {
[1819]1486 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1487 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1488 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
[1391]1489 ret = 1;
1490 break;
1491 }
1492 }
1493 }
1494 else {
[1819]1495 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1496 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1497 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
[1391]1498 }
1499 //if ( i >= nscan ) break;
1500 }
1501 }
1502 else {
[1819]1503 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1504 //cerr<<"No reference to GBT_GO table."<<endl;
1505 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
[1391]1506 ret = 1;
1507 }
1508 return ret;
1509}
1510
[1730]1511std::vector<double> Scantable::getDirectionVector(int whichrow) const
[1391]1512{
1513 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1514 std::vector<double> dir;
1515 Dir.tovector(dir);
1516 return dir;
1517}
1518
[1819]1519void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1520 throw( casa::AipsError )
1521{
1522 // assumed that all rows have same nChan
1523 Vector<Float> arr = specCol_( 0 ) ;
1524 int nChan = arr.nelements() ;
1525
1526 // if nmin < 0 or nmax < 0, nothing to do
1527 if ( nmin < 0 ) {
1528 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1529 }
1530 if ( nmax < 0 ) {
1531 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1532 }
1533
1534 // if nmin > nmax, exchange values
1535 if ( nmin > nmax ) {
1536 int tmp = nmax ;
1537 nmax = nmin ;
1538 nmin = tmp ;
1539 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1540 os << "Swap values. Applied range is ["
1541 << nmin << ", " << nmax << "]" << LogIO::POST ;
1542 }
1543
1544 // if nmin exceeds nChan, nothing to do
1545 if ( nmin >= nChan ) {
1546 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1547 }
1548
1549 // if nmax exceeds nChan, reset nmax to nChan
1550 if ( nmax >= nChan ) {
1551 if ( nmin == 0 ) {
1552 // nothing to do
1553 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1554 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1555 return ;
1556 }
1557 else {
1558 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1559 os << "Specified maximum exceeds nChan. Applied range is ["
1560 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1561 nmax = nChan - 1 ;
1562 }
1563 }
1564
1565 // reshape specCol_ and flagCol_
1566 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1567 reshapeSpectrum( nmin, nmax, irow ) ;
1568 }
1569
1570 // update FREQUENCIES subtable
1571 Double refpix ;
1572 Double refval ;
1573 Double increment ;
1574 int freqnrow = freqTable_.table().nrow() ;
1575 Vector<uInt> oldId( freqnrow ) ;
1576 Vector<uInt> newId( freqnrow ) ;
1577 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1578 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1579 /***
1580 * need to shift refpix to nmin
1581 * note that channel nmin in old index will be channel 0 in new one
1582 ***/
1583 refval = refval - ( refpix - nmin ) * increment ;
1584 refpix = 0 ;
1585 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1586 }
1587
1588 // update nchan
1589 int newsize = nmax - nmin + 1 ;
1590 table_.rwKeywordSet().define( "nChan", newsize ) ;
1591
1592 // update bandwidth
1593 // assumed all spectra in the scantable have same bandwidth
1594 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1595
1596 return ;
1597}
1598
1599void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1600{
1601 // reshape specCol_ and flagCol_
1602 Vector<Float> oldspec = specCol_( irow ) ;
1603 Vector<uChar> oldflag = flagsCol_( irow ) ;
1604 uInt newsize = nmax - nmin + 1 ;
1605 specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ;
1606 flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ;
1607
1608 return ;
1609}
1610
1611void asap::Scantable::regridChannel( int nChan, double dnu )
1612{
1613 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1614 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1615 // assumed that all rows have same nChan
1616 Vector<Float> arr = specCol_( 0 ) ;
1617 int oldsize = arr.nelements() ;
1618
1619 // if oldsize == nChan, nothing to do
1620 if ( oldsize == nChan ) {
1621 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1622 return ;
1623 }
1624
1625 // if oldChan < nChan, unphysical operation
1626 if ( oldsize < nChan ) {
1627 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1628 return ;
1629 }
1630
1631 // change channel number for specCol_ and flagCol_
1632 Vector<Float> newspec( nChan, 0 ) ;
1633 Vector<uChar> newflag( nChan, false ) ;
1634 vector<string> coordinfo = getCoordInfo() ;
1635 string oldinfo = coordinfo[0] ;
1636 coordinfo[0] = "Hz" ;
1637 setCoordInfo( coordinfo ) ;
1638 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1639 regridChannel( nChan, dnu, irow ) ;
1640 }
1641 coordinfo[0] = oldinfo ;
1642 setCoordInfo( coordinfo ) ;
1643
1644
1645 // NOTE: this method does not update metadata such as
1646 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1647
1648 return ;
1649}
1650
1651void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1652{
1653 // logging
1654 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1655 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1656
1657 Vector<Float> oldspec = specCol_( irow ) ;
1658 Vector<uChar> oldflag = flagsCol_( irow ) ;
1659 Vector<Float> newspec( nChan, 0 ) ;
1660 Vector<uChar> newflag( nChan, false ) ;
1661
1662 // regrid
1663 vector<double> abcissa = getAbcissa( irow ) ;
1664 int oldsize = abcissa.size() ;
1665 double olddnu = abcissa[1] - abcissa[0] ;
1666 //int refChan = 0 ;
1667 //double frac = 0.0 ;
1668 //double wedge = 0.0 ;
1669 //double pile = 0.0 ;
1670 int ichan = 0 ;
1671 double wsum = 0.0 ;
1672 Vector<Float> zi( nChan+1 ) ;
1673 Vector<Float> yi( oldsize + 1 ) ;
[2133]1674 zi[0] = abcissa[0] - 0.5 * olddnu ;
1675 zi[1] = zi[1] + dnu ;
[1819]1676 for ( int ii = 2 ; ii < nChan ; ii++ )
[2133]1677 zi[ii] = zi[0] + dnu * ii ;
1678 zi[nChan] = zi[nChan-1] + dnu ;
[1819]1679 yi[0] = abcissa[0] - 0.5 * olddnu ;
1680 yi[1] = abcissa[1] + 0.5 * olddnu ;
1681 for ( int ii = 2 ; ii < oldsize ; ii++ )
1682 yi[ii] = abcissa[ii-1] + olddnu ;
1683 yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ;
1684 if ( dnu > 0.0 ) {
1685 for ( int ii = 0 ; ii < nChan ; ii++ ) {
1686 double zl = zi[ii] ;
1687 double zr = zi[ii+1] ;
1688 for ( int j = ichan ; j < oldsize ; j++ ) {
1689 double yl = yi[j] ;
1690 double yr = yi[j+1] ;
1691 if ( yl <= zl ) {
1692 if ( yr <= zl ) {
1693 continue ;
1694 }
1695 else if ( yr <= zr ) {
1696 newspec[ii] += oldspec[j] * ( yr - zl ) ;
1697 newflag[ii] = newflag[ii] || oldflag[j] ;
1698 wsum += ( yr - zl ) ;
1699 }
1700 else {
1701 newspec[ii] += oldspec[j] * dnu ;
1702 newflag[ii] = newflag[ii] || oldflag[j] ;
1703 wsum += dnu ;
1704 ichan = j ;
1705 break ;
1706 }
1707 }
1708 else if ( yl < zr ) {
1709 if ( yr <= zr ) {
1710 newspec[ii] += oldspec[j] * ( yr - yl ) ;
1711 newflag[ii] = newflag[ii] || oldflag[j] ;
1712 wsum += ( yr - yl ) ;
1713 }
1714 else {
1715 newspec[ii] += oldspec[j] * ( zr - yl ) ;
1716 newflag[ii] = newflag[ii] || oldflag[j] ;
1717 wsum += ( zr - yl ) ;
1718 ichan = j ;
1719 break ;
1720 }
1721 }
1722 else {
1723 ichan = j - 1 ;
1724 break ;
1725 }
1726 }
[2133]1727 if ( wsum != 0.0 )
1728 newspec[ii] /= wsum ;
[1819]1729 wsum = 0.0 ;
1730 }
1731 }
1732 else if ( dnu < 0.0 ) {
1733 for ( int ii = 0 ; ii < nChan ; ii++ ) {
1734 double zl = zi[ii] ;
1735 double zr = zi[ii+1] ;
1736 for ( int j = ichan ; j < oldsize ; j++ ) {
1737 double yl = yi[j] ;
1738 double yr = yi[j+1] ;
1739 if ( yl >= zl ) {
1740 if ( yr >= zl ) {
1741 continue ;
1742 }
1743 else if ( yr >= zr ) {
1744 newspec[ii] += oldspec[j] * abs( yr - zl ) ;
1745 newflag[ii] = newflag[ii] || oldflag[j] ;
1746 wsum += abs( yr - zl ) ;
1747 }
1748 else {
1749 newspec[ii] += oldspec[j] * abs( dnu ) ;
1750 newflag[ii] = newflag[ii] || oldflag[j] ;
1751 wsum += abs( dnu ) ;
1752 ichan = j ;
1753 break ;
1754 }
1755 }
1756 else if ( yl > zr ) {
1757 if ( yr >= zr ) {
1758 newspec[ii] += oldspec[j] * abs( yr - yl ) ;
1759 newflag[ii] = newflag[ii] || oldflag[j] ;
1760 wsum += abs( yr - yl ) ;
1761 }
1762 else {
1763 newspec[ii] += oldspec[j] * abs( zr - yl ) ;
1764 newflag[ii] = newflag[ii] || oldflag[j] ;
1765 wsum += abs( zr - yl ) ;
1766 ichan = j ;
1767 break ;
1768 }
1769 }
1770 else {
1771 ichan = j - 1 ;
1772 break ;
1773 }
1774 }
[2133]1775 if ( wsum != 0.0 )
1776 newspec[ii] /= wsum ;
[1819]1777 wsum = 0.0 ;
1778 }
1779 }
1780// * ichan = 0
1781// ***/
1782// //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
1783// pile += dnu ;
1784// wedge = olddnu * ( refChan + 1 ) ;
1785// while ( wedge < pile ) {
1786// newspec[0] += olddnu * oldspec[refChan] ;
1787// newflag[0] = newflag[0] || oldflag[refChan] ;
1788// //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
1789// refChan++ ;
1790// wedge += olddnu ;
1791// wsum += olddnu ;
1792// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
1793// }
1794// frac = ( wedge - pile ) / olddnu ;
1795// wsum += ( 1.0 - frac ) * olddnu ;
1796// newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
1797// newflag[0] = newflag[0] || oldflag[refChan] ;
1798// //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
1799// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
1800// newspec[0] /= wsum ;
1801// //ofs << "newspec[0] = " << newspec[0] << endl ;
1802// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
1803
1804// /***
1805// * ichan = 1 - nChan-2
1806// ***/
1807// for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
1808// pile += dnu ;
1809// newspec[ichan] += frac * olddnu * oldspec[refChan] ;
1810// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
1811// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
1812// refChan++ ;
1813// wedge += olddnu ;
1814// wsum = frac * olddnu ;
1815// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
1816// while ( wedge < pile ) {
1817// newspec[ichan] += olddnu * oldspec[refChan] ;
1818// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
1819// //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
1820// refChan++ ;
1821// wedge += olddnu ;
1822// wsum += olddnu ;
1823// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
1824// }
1825// frac = ( wedge - pile ) / olddnu ;
1826// wsum += ( 1.0 - frac ) * olddnu ;
1827// newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
1828// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
1829// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
1830// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
1831// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
1832// newspec[ichan] /= wsum ;
1833// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
1834// }
1835
1836// /***
1837// * ichan = nChan-1
1838// ***/
1839// // NOTE: Assumed that all spectra have the same bandwidth
1840// pile += dnu ;
1841// newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
1842// newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
1843// //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
1844// refChan++ ;
1845// wedge += olddnu ;
1846// wsum = frac * olddnu ;
1847// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
1848// for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
1849// newspec[nChan-1] += olddnu * oldspec[jchan] ;
1850// newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
1851// wsum += olddnu ;
1852// //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
1853// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
1854// }
1855// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
1856// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
1857// newspec[nChan-1] /= wsum ;
1858// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
1859
1860// // ofs.close() ;
1861
[2032]1862 specCol_.put( irow, newspec ) ;
1863 flagsCol_.put( irow, newflag ) ;
[1819]1864
1865 return ;
1866}
1867
[1730]1868std::vector<float> Scantable::getWeather(int whichrow) const
1869{
1870 std::vector<float> out(5);
1871 //Float temperature, pressure, humidity, windspeed, windaz;
1872 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
1873 mweatheridCol_(uInt(whichrow)));
1874
1875
1876 return out;
[1391]1877}
[1730]1878
[2047]1879bool Scantable::getFlagtraFast(uInt whichrow)
[1907]1880{
1881 uChar flag;
1882 Vector<uChar> flags;
[2047]1883 flagsCol_.get(whichrow, flags);
[2012]1884 flag = flags[0];
[2047]1885 for (uInt i = 1; i < flags.size(); ++i) {
[2012]1886 flag &= flags[i];
1887 }
1888 return ((flag >> 7) == 1);
1889}
1890
[2277]1891void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
[2047]1892{
[2193]1893 try {
1894 ofstream ofs;
1895 String coordInfo = "";
1896 bool hasSameNchan = true;
1897 bool outTextFile = false;
[2047]1898
[2193]1899 if (blfile != "") {
1900 ofs.open(blfile.c_str(), ios::out | ios::app);
1901 if (ofs) outTextFile = true;
1902 }
[2047]1903
[2193]1904 if (outLogger || outTextFile) {
1905 coordInfo = getCoordInfo()[0];
1906 if (coordInfo == "") coordInfo = "channel";
1907 hasSameNchan = hasSameNchanOverIFs();
1908 }
[2047]1909
[2193]1910 Fitter fitter = Fitter();
1911 fitter.setExpression("poly", order);
1912 //fitter.setIterClipping(thresClip, nIterClip);
[2047]1913
[2193]1914 int nRow = nrow();
1915 std::vector<bool> chanMask;
1916 bool showProgress;
1917 int minNRow;
1918 parseProgressInfo(progressInfo, showProgress, minNRow);
[2047]1919
[2193]1920 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
1921 chanMask = getCompositeChanMask(whichrow, mask);
1922 fitBaseline(chanMask, whichrow, fitter);
1923 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
[2277]1924 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
[2193]1925 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
1926 }
1927
1928 if (outTextFile) ofs.close();
1929
1930 } catch (...) {
1931 throw;
[2047]1932 }
1933}
1934
[2189]1935void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
[2047]1936{
[2193]1937 try {
1938 ofstream ofs;
1939 String coordInfo = "";
1940 bool hasSameNchan = true;
1941 bool outTextFile = false;
[2047]1942
[2193]1943 if (blfile != "") {
1944 ofs.open(blfile.c_str(), ios::out | ios::app);
1945 if (ofs) outTextFile = true;
1946 }
[2047]1947
[2193]1948 if (outLogger || outTextFile) {
1949 coordInfo = getCoordInfo()[0];
1950 if (coordInfo == "") coordInfo = "channel";
1951 hasSameNchan = hasSameNchanOverIFs();
1952 }
[2047]1953
[2193]1954 Fitter fitter = Fitter();
1955 fitter.setExpression("poly", order);
1956 //fitter.setIterClipping(thresClip, nIterClip);
[2047]1957
[2193]1958 int nRow = nrow();
1959 std::vector<bool> chanMask;
1960 int minEdgeSize = getIFNos().size()*2;
1961 STLineFinder lineFinder = STLineFinder();
1962 lineFinder.setOptions(threshold, 3, chanAvgLimit);
[2047]1963
[2193]1964 bool showProgress;
1965 int minNRow;
1966 parseProgressInfo(progressInfo, showProgress, minNRow);
[2189]1967
[2193]1968 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2047]1969
[2193]1970 //-------------------------------------------------------
1971 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
1972 //-------------------------------------------------------
1973 int edgeSize = edge.size();
1974 std::vector<int> currentEdge;
1975 if (edgeSize >= 2) {
1976 int idx = 0;
1977 if (edgeSize > 2) {
1978 if (edgeSize < minEdgeSize) {
1979 throw(AipsError("Length of edge element info is less than that of IFs"));
1980 }
1981 idx = 2 * getIF(whichrow);
[2047]1982 }
[2193]1983 currentEdge.push_back(edge[idx]);
1984 currentEdge.push_back(edge[idx+1]);
1985 } else {
1986 throw(AipsError("Wrong length of edge element"));
[2047]1987 }
[2193]1988 lineFinder.setData(getSpectrum(whichrow));
1989 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
1990 chanMask = lineFinder.getMask();
1991 //-------------------------------------------------------
1992
1993 fitBaseline(chanMask, whichrow, fitter);
1994 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
1995
1996 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
1997 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[2047]1998 }
1999
[2193]2000 if (outTextFile) ofs.close();
[2047]2001
[2193]2002 } catch (...) {
2003 throw;
[2047]2004 }
2005}
2006
[2189]2007void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
[2081]2008{
[2193]2009 try {
2010 ofstream ofs;
2011 String coordInfo = "";
2012 bool hasSameNchan = true;
2013 bool outTextFile = false;
[2012]2014
[2193]2015 if (blfile != "") {
2016 ofs.open(blfile.c_str(), ios::out | ios::app);
2017 if (ofs) outTextFile = true;
2018 }
[2012]2019
[2193]2020 if (outLogger || outTextFile) {
2021 coordInfo = getCoordInfo()[0];
2022 if (coordInfo == "") coordInfo = "channel";
2023 hasSameNchan = hasSameNchanOverIFs();
2024 }
[2012]2025
[2193]2026 //Fitter fitter = Fitter();
2027 //fitter.setExpression("cspline", nPiece);
2028 //fitter.setIterClipping(thresClip, nIterClip);
[2012]2029
[2193]2030 int nRow = nrow();
2031 std::vector<bool> chanMask;
2032 bool showProgress;
2033 int minNRow;
2034 parseProgressInfo(progressInfo, showProgress, minNRow);
[2012]2035
[2193]2036 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2037 chanMask = getCompositeChanMask(whichrow, mask);
2038 //fitBaseline(chanMask, whichrow, fitter);
2039 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2040 std::vector<int> pieceEdges;
2041 std::vector<float> params;
2042 int nClipped = 0;
2043 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2044 setSpectrum(res, whichrow);
2045 //
[2012]2046
[2193]2047 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
2048 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2049 }
2050
2051 if (outTextFile) ofs.close();
2052
2053 } catch (...) {
2054 throw;
[2012]2055 }
2056}
2057
[2189]2058void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
[2012]2059{
[2193]2060 try {
2061 ofstream ofs;
2062 String coordInfo = "";
2063 bool hasSameNchan = true;
2064 bool outTextFile = false;
[2012]2065
[2193]2066 if (blfile != "") {
2067 ofs.open(blfile.c_str(), ios::out | ios::app);
2068 if (ofs) outTextFile = true;
2069 }
[2012]2070
[2193]2071 if (outLogger || outTextFile) {
2072 coordInfo = getCoordInfo()[0];
2073 if (coordInfo == "") coordInfo = "channel";
2074 hasSameNchan = hasSameNchanOverIFs();
2075 }
[2012]2076
[2193]2077 //Fitter fitter = Fitter();
2078 //fitter.setExpression("cspline", nPiece);
2079 //fitter.setIterClipping(thresClip, nIterClip);
[2012]2080
[2193]2081 int nRow = nrow();
2082 std::vector<bool> chanMask;
2083 int minEdgeSize = getIFNos().size()*2;
2084 STLineFinder lineFinder = STLineFinder();
2085 lineFinder.setOptions(threshold, 3, chanAvgLimit);
[2012]2086
[2193]2087 bool showProgress;
2088 int minNRow;
2089 parseProgressInfo(progressInfo, showProgress, minNRow);
[2189]2090
[2193]2091 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2012]2092
[2193]2093 //-------------------------------------------------------
2094 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2095 //-------------------------------------------------------
2096 int edgeSize = edge.size();
2097 std::vector<int> currentEdge;
2098 if (edgeSize >= 2) {
2099 int idx = 0;
2100 if (edgeSize > 2) {
2101 if (edgeSize < minEdgeSize) {
2102 throw(AipsError("Length of edge element info is less than that of IFs"));
2103 }
2104 idx = 2 * getIF(whichrow);
[2012]2105 }
[2193]2106 currentEdge.push_back(edge[idx]);
2107 currentEdge.push_back(edge[idx+1]);
2108 } else {
2109 throw(AipsError("Wrong length of edge element"));
[2012]2110 }
[2193]2111 lineFinder.setData(getSpectrum(whichrow));
2112 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2113 chanMask = lineFinder.getMask();
2114 //-------------------------------------------------------
2115
2116
2117 //fitBaseline(chanMask, whichrow, fitter);
2118 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2119 std::vector<int> pieceEdges;
2120 std::vector<float> params;
2121 int nClipped = 0;
2122 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2123 setSpectrum(res, whichrow);
2124 //
2125
2126 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
2127 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[1907]2128 }
[2012]2129
[2193]2130 if (outTextFile) ofs.close();
[2012]2131
[2193]2132 } catch (...) {
2133 throw;
[2012]2134 }
[1730]2135}
[1907]2136
[2193]2137std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
[2081]2138{
2139 if (data.size() != mask.size()) {
2140 throw(AipsError("data and mask sizes are not identical"));
2141 }
[2012]2142 if (nPiece < 1) {
[2094]2143 throw(AipsError("number of the sections must be one or more"));
[2012]2144 }
2145
2146 int nChan = data.size();
2147 std::vector<int> maskArray;
2148 std::vector<int> x;
2149 for (int i = 0; i < nChan; ++i) {
2150 maskArray.push_back(mask[i] ? 1 : 0);
2151 if (mask[i]) {
2152 x.push_back(i);
2153 }
2154 }
2155
[2081]2156 int initNData = x.size();
[2193]2157 if (initNData < nPiece) {
2158 throw(AipsError("too few non-flagged channels"));
2159 }
[2081]2160
2161 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
[2064]2162 std::vector<double> invEdge;
2163 idxEdge.clear();
2164 idxEdge.push_back(x[0]);
[2012]2165 for (int i = 1; i < nPiece; ++i) {
[2047]2166 int valX = x[nElement*i];
[2064]2167 idxEdge.push_back(valX);
2168 invEdge.push_back(1.0/(double)valX);
[2012]2169 }
[2064]2170 idxEdge.push_back(x[x.size()-1]+1);
2171
[2081]2172 int nData = initNData;
2173 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
2174
2175 std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1, residual;
[2012]2176 for (int i = 0; i < nChan; ++i) {
[2064]2177 double di = (double)i;
2178 double dD = (double)data[i];
2179 x1.push_back(di);
2180 x2.push_back(di*di);
2181 x3.push_back(di*di*di);
2182 z1.push_back(dD);
2183 x1z1.push_back(dD*di);
2184 x2z1.push_back(dD*di*di);
2185 x3z1.push_back(dD*di*di*di);
[2012]2186 r1.push_back(0.0);
[2081]2187 residual.push_back(0.0);
[2012]2188 }
2189
2190 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
[2064]2191 // xMatrix : horizontal concatenation of
2192 // the least-sq. matrix (left) and an
2193 // identity matrix (right).
2194 // the right part is used to calculate the inverse matrix of the left part.
[2012]2195 double xMatrix[nDOF][2*nDOF];
2196 double zMatrix[nDOF];
2197 for (int i = 0; i < nDOF; ++i) {
2198 for (int j = 0; j < 2*nDOF; ++j) {
2199 xMatrix[i][j] = 0.0;
2200 }
2201 xMatrix[i][nDOF+i] = 1.0;
2202 zMatrix[i] = 0.0;
2203 }
2204
2205 for (int n = 0; n < nPiece; ++n) {
[2193]2206 int nUseDataInPiece = 0;
[2064]2207 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2208
[2012]2209 if (maskArray[i] == 0) continue;
[2064]2210
[2012]2211 xMatrix[0][0] += 1.0;
[2064]2212 xMatrix[0][1] += x1[i];
2213 xMatrix[0][2] += x2[i];
2214 xMatrix[0][3] += x3[i];
2215 xMatrix[1][1] += x2[i];
2216 xMatrix[1][2] += x3[i];
2217 xMatrix[1][3] += x2[i]*x2[i];
2218 xMatrix[2][2] += x2[i]*x2[i];
2219 xMatrix[2][3] += x3[i]*x2[i];
2220 xMatrix[3][3] += x3[i]*x3[i];
[2012]2221 zMatrix[0] += z1[i];
[2064]2222 zMatrix[1] += x1z1[i];
2223 zMatrix[2] += x2z1[i];
2224 zMatrix[3] += x3z1[i];
2225
[2012]2226 for (int j = 0; j < n; ++j) {
[2064]2227 double q = 1.0 - x1[i]*invEdge[j];
[2012]2228 q = q*q*q;
2229 xMatrix[0][j+4] += q;
[2064]2230 xMatrix[1][j+4] += q*x1[i];
2231 xMatrix[2][j+4] += q*x2[i];
2232 xMatrix[3][j+4] += q*x3[i];
[2012]2233 for (int k = 0; k < j; ++k) {
[2064]2234 double r = 1.0 - x1[i]*invEdge[k];
[2012]2235 r = r*r*r;
2236 xMatrix[k+4][j+4] += r*q;
2237 }
2238 xMatrix[j+4][j+4] += q*q;
2239 zMatrix[j+4] += q*z1[i];
2240 }
[2064]2241
[2193]2242 nUseDataInPiece++;
[2012]2243 }
[2193]2244
2245 if (nUseDataInPiece < 1) {
2246 std::vector<string> suffixOfPieceNumber(4);
2247 suffixOfPieceNumber[0] = "th";
2248 suffixOfPieceNumber[1] = "st";
2249 suffixOfPieceNumber[2] = "nd";
2250 suffixOfPieceNumber[3] = "rd";
2251 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
2252 ostringstream oss;
2253 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
2254 oss << " piece of the spectrum. can't execute fitting anymore.";
2255 throw(AipsError(String(oss)));
2256 }
[2012]2257 }
2258
2259 for (int i = 0; i < nDOF; ++i) {
2260 for (int j = 0; j < i; ++j) {
2261 xMatrix[i][j] = xMatrix[j][i];
2262 }
2263 }
2264
2265 std::vector<double> invDiag;
2266 for (int i = 0; i < nDOF; ++i) {
2267 invDiag.push_back(1.0/xMatrix[i][i]);
2268 for (int j = 0; j < nDOF; ++j) {
2269 xMatrix[i][j] *= invDiag[i];
2270 }
2271 }
2272
2273 for (int k = 0; k < nDOF; ++k) {
2274 for (int i = 0; i < nDOF; ++i) {
2275 if (i != k) {
2276 double factor1 = xMatrix[k][k];
2277 double factor2 = xMatrix[i][k];
2278 for (int j = k; j < 2*nDOF; ++j) {
2279 xMatrix[i][j] *= factor1;
2280 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2281 xMatrix[i][j] /= factor1;
2282 }
2283 }
2284 }
2285 double xDiag = xMatrix[k][k];
2286 for (int j = k; j < 2*nDOF; ++j) {
2287 xMatrix[k][j] /= xDiag;
2288 }
2289 }
2290
2291 for (int i = 0; i < nDOF; ++i) {
2292 for (int j = 0; j < nDOF; ++j) {
2293 xMatrix[i][nDOF+j] *= invDiag[j];
2294 }
2295 }
2296 //compute a vector y which consists of the coefficients of the best-fit spline curves
2297 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
2298 //cubic terms for the other pieces (in case nPiece>1).
2299 std::vector<double> y;
[2058]2300 y.clear();
[2012]2301 for (int i = 0; i < nDOF; ++i) {
2302 y.push_back(0.0);
2303 for (int j = 0; j < nDOF; ++j) {
2304 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2305 }
2306 }
2307
2308 double a0 = y[0];
2309 double a1 = y[1];
2310 double a2 = y[2];
2311 double a3 = y[3];
2312 params.clear();
2313
2314 for (int n = 0; n < nPiece; ++n) {
[2064]2315 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2316 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
[2081]2317 residual[i] = z1[i] - r1[i];
[2012]2318 }
2319 params.push_back(a0);
2320 params.push_back(a1);
2321 params.push_back(a2);
2322 params.push_back(a3);
2323
2324 if (n == nPiece-1) break;
2325
2326 double d = y[4+n];
[2064]2327 double iE = invEdge[n];
2328 a0 += d;
2329 a1 -= 3.0*d*iE;
2330 a2 += 3.0*d*iE*iE;
2331 a3 -= d*iE*iE*iE;
[2012]2332 }
2333
2334 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2335 break;
2336 } else {
2337 double stdDev = 0.0;
2338 for (int i = 0; i < nChan; ++i) {
[2081]2339 stdDev += residual[i]*residual[i]*(double)maskArray[i];
[2012]2340 }
2341 stdDev = sqrt(stdDev/(double)nData);
2342
2343 double thres = stdDev * thresClip;
2344 int newNData = 0;
2345 for (int i = 0; i < nChan; ++i) {
[2081]2346 if (abs(residual[i]) >= thres) {
[2012]2347 maskArray[i] = 0;
2348 }
2349 if (maskArray[i] > 0) {
2350 newNData++;
2351 }
2352 }
[2081]2353 if (newNData == nData) {
[2064]2354 break; //no more flag to add. iteration stops.
[2012]2355 } else {
[2081]2356 nData = newNData;
[2012]2357 }
2358 }
2359 }
2360
[2193]2361 nClipped = initNData - nData;
2362
[2058]2363 std::vector<float> result;
2364 if (getResidual) {
2365 for (int i = 0; i < nChan; ++i) {
[2081]2366 result.push_back((float)residual[i]);
[2058]2367 }
2368 } else {
2369 for (int i = 0; i < nChan; ++i) {
2370 result.push_back((float)r1[i]);
2371 }
[2012]2372 }
2373
[2058]2374 return result;
[2012]2375}
2376
[2186]2377 void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
[2081]2378{
[2186]2379 nWaves.clear();
2380
2381 if (applyFFT) {
2382 string fftThAttr;
2383 float fftThSigma;
2384 int fftThTop;
2385 parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
2386 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
2387 }
2388
2389 addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves);
2390}
2391
2392void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
2393{
2394 uInt idxSigma = fftThresh.find("sigma");
2395 uInt idxTop = fftThresh.find("top");
2396
2397 if (idxSigma == fftThresh.size() - 5) {
2398 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
2399 is >> fftThSigma;
2400 fftThAttr = "sigma";
2401 } else if (idxTop == 0) {
2402 std::istringstream is(fftThresh.substr(3));
2403 is >> fftThTop;
2404 fftThAttr = "top";
2405 } else {
2406 bool isNumber = true;
2407 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
2408 char ch = (fftThresh.substr(i, 1).c_str())[0];
2409 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
2410 isNumber = false;
2411 break;
2412 }
2413 }
2414 if (isNumber) {
2415 std::istringstream is(fftThresh);
2416 is >> fftThSigma;
2417 fftThAttr = "sigma";
2418 } else {
2419 throw(AipsError("fftthresh has a wrong value"));
2420 }
2421 }
2422}
2423
2424void 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)
2425{
2426 std::vector<float> fspec;
2427 if (fftMethod == "fft") {
2428 fspec = execFFT(whichrow, chanMask, false, true);
2429 //} else if (fftMethod == "lsp") {
2430 // fspec = lombScarglePeriodogram(whichrow);
2431 }
2432
2433 if (fftThAttr == "sigma") {
2434 float mean = 0.0;
2435 float mean2 = 0.0;
2436 for (uInt i = 0; i < fspec.size(); ++i) {
2437 mean += fspec[i];
2438 mean2 += fspec[i]*fspec[i];
2439 }
2440 mean /= float(fspec.size());
2441 mean2 /= float(fspec.size());
2442 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
2443
2444 for (uInt i = 0; i < fspec.size(); ++i) {
2445 if (fspec[i] >= thres) {
2446 nWaves.push_back(i);
2447 }
2448 }
2449
2450 } else if (fftThAttr == "top") {
2451 for (int i = 0; i < fftThTop; ++i) {
2452 float max = 0.0;
2453 int maxIdx = 0;
2454 for (uInt j = 0; j < fspec.size(); ++j) {
2455 if (fspec[j] > max) {
2456 max = fspec[j];
2457 maxIdx = j;
2458 }
2459 }
2460 nWaves.push_back(maxIdx);
2461 fspec[maxIdx] = 0.0;
2462 }
2463
2464 }
2465
2466 if (nWaves.size() > 1) {
2467 sort(nWaves.begin(), nWaves.end());
2468 }
2469}
2470
2471void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
2472{
2473 for (uInt i = 0; i < addNWaves.size(); ++i) {
2474 bool found = false;
2475 for (uInt j = 0; j < nWaves.size(); ++j) {
2476 if (nWaves[j] == addNWaves[i]) {
2477 found = true;
2478 break;
2479 }
2480 }
2481 if (!found) nWaves.push_back(addNWaves[i]);
2482 }
2483
2484 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
2485 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
2486 if (*j == rejectNWaves[i]) {
2487 j = nWaves.erase(j);
2488 } else {
2489 ++j;
2490 }
2491 }
2492 }
2493
2494 if (nWaves.size() > 1) {
2495 sort(nWaves.begin(), nWaves.end());
2496 unique(nWaves.begin(), nWaves.end());
2497 }
2498}
2499
[2189]2500void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
[2186]2501{
[2193]2502 try {
2503 ofstream ofs;
2504 String coordInfo = "";
2505 bool hasSameNchan = true;
2506 bool outTextFile = false;
[2012]2507
[2193]2508 if (blfile != "") {
2509 ofs.open(blfile.c_str(), ios::out | ios::app);
2510 if (ofs) outTextFile = true;
2511 }
[2012]2512
[2193]2513 if (outLogger || outTextFile) {
2514 coordInfo = getCoordInfo()[0];
2515 if (coordInfo == "") coordInfo = "channel";
2516 hasSameNchan = hasSameNchanOverIFs();
2517 }
[2012]2518
[2193]2519 //Fitter fitter = Fitter();
2520 //fitter.setExpression("sinusoid", nWaves);
2521 //fitter.setIterClipping(thresClip, nIterClip);
[2012]2522
[2193]2523 int nRow = nrow();
2524 std::vector<bool> chanMask;
2525 std::vector<int> nWaves;
[2012]2526
[2193]2527 bool showProgress;
2528 int minNRow;
2529 parseProgressInfo(progressInfo, showProgress, minNRow);
[2189]2530
[2193]2531 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2532 chanMask = getCompositeChanMask(whichrow, mask);
2533 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
[2186]2534
[2193]2535 //FOR DEBUGGING------------
2536 if (whichrow < 0) {// == nRow -1) {
2537 cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
2538 if (applyFFT) {
[2186]2539 cout << "[ ";
2540 for (uInt j = 0; j < nWaves.size(); ++j) {
2541 cout << nWaves[j] << ", ";
2542 }
2543 cout << " ] " << endl;
[2193]2544 }
2545 cout << flush;
[2186]2546 }
[2193]2547 //-------------------------
2548
2549 //fitBaseline(chanMask, whichrow, fitter);
2550 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2551 std::vector<float> params;
2552 int nClipped = 0;
2553 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
2554 setSpectrum(res, whichrow);
2555 //
2556
2557 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
2558 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[2186]2559 }
2560
[2193]2561 if (outTextFile) ofs.close();
[2012]2562
[2193]2563 } catch (...) {
2564 throw;
[1931]2565 }
[1907]2566}
2567
[2189]2568void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
[2012]2569{
[2193]2570 try {
2571 ofstream ofs;
2572 String coordInfo = "";
2573 bool hasSameNchan = true;
2574 bool outTextFile = false;
[2012]2575
[2193]2576 if (blfile != "") {
2577 ofs.open(blfile.c_str(), ios::out | ios::app);
2578 if (ofs) outTextFile = true;
2579 }
[2012]2580
[2193]2581 if (outLogger || outTextFile) {
2582 coordInfo = getCoordInfo()[0];
2583 if (coordInfo == "") coordInfo = "channel";
2584 hasSameNchan = hasSameNchanOverIFs();
2585 }
[2012]2586
[2193]2587 //Fitter fitter = Fitter();
2588 //fitter.setExpression("sinusoid", nWaves);
2589 //fitter.setIterClipping(thresClip, nIterClip);
[2012]2590
[2193]2591 int nRow = nrow();
2592 std::vector<bool> chanMask;
2593 std::vector<int> nWaves;
[2186]2594
[2193]2595 int minEdgeSize = getIFNos().size()*2;
2596 STLineFinder lineFinder = STLineFinder();
2597 lineFinder.setOptions(threshold, 3, chanAvgLimit);
[2012]2598
[2193]2599 bool showProgress;
2600 int minNRow;
2601 parseProgressInfo(progressInfo, showProgress, minNRow);
[2189]2602
[2193]2603 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
[2012]2604
[2193]2605 //-------------------------------------------------------
2606 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2607 //-------------------------------------------------------
2608 int edgeSize = edge.size();
2609 std::vector<int> currentEdge;
2610 if (edgeSize >= 2) {
2611 int idx = 0;
2612 if (edgeSize > 2) {
2613 if (edgeSize < minEdgeSize) {
2614 throw(AipsError("Length of edge element info is less than that of IFs"));
2615 }
2616 idx = 2 * getIF(whichrow);
[2012]2617 }
[2193]2618 currentEdge.push_back(edge[idx]);
2619 currentEdge.push_back(edge[idx+1]);
2620 } else {
2621 throw(AipsError("Wrong length of edge element"));
[2012]2622 }
[2193]2623 lineFinder.setData(getSpectrum(whichrow));
2624 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2625 chanMask = lineFinder.getMask();
2626 //-------------------------------------------------------
2627
2628 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
2629
2630 //fitBaseline(chanMask, whichrow, fitter);
2631 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2632 std::vector<float> params;
2633 int nClipped = 0;
2634 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
2635 setSpectrum(res, whichrow);
2636 //
2637
2638 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
2639 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
[2012]2640 }
2641
[2193]2642 if (outTextFile) ofs.close();
[2012]2643
[2193]2644 } catch (...) {
2645 throw;
[2047]2646 }
2647}
2648
[2193]2649std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
[2081]2650{
[2047]2651 if (data.size() != mask.size()) {
[2081]2652 throw(AipsError("data and mask sizes are not identical"));
[2047]2653 }
[2081]2654 if (data.size() < 2) {
2655 throw(AipsError("data size is too short"));
2656 }
2657 if (waveNumbers.size() == 0) {
[2186]2658 throw(AipsError("no wave numbers given"));
[2081]2659 }
2660 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
2661 nWaves.reserve(waveNumbers.size());
2662 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
2663 sort(nWaves.begin(), nWaves.end());
2664 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
2665 nWaves.erase(end_it, nWaves.end());
2666
2667 int minNWaves = nWaves[0];
2668 if (minNWaves < 0) {
[2058]2669 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
2670 }
[2081]2671 bool hasConstantTerm = (minNWaves == 0);
[2047]2672
2673 int nChan = data.size();
2674 std::vector<int> maskArray;
2675 std::vector<int> x;
2676 for (int i = 0; i < nChan; ++i) {
2677 maskArray.push_back(mask[i] ? 1 : 0);
2678 if (mask[i]) {
2679 x.push_back(i);
2680 }
2681 }
2682
[2081]2683 int initNData = x.size();
[2047]2684
[2081]2685 int nData = initNData;
2686 int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
2687
2688 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
[2186]2689 double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK)
[2081]2690
2691 // xArray : contains elemental values for computing the least-square matrix.
2692 // xArray.size() is nDOF and xArray[*].size() is nChan.
2693 // Each xArray element are as follows:
2694 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
2695 // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
2696 // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
2697 // where (1 <= n <= nMaxWavesInSW),
2698 // or,
2699 // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
2700 // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
2701 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
2702 std::vector<std::vector<double> > xArray;
2703 if (hasConstantTerm) {
2704 std::vector<double> xu;
2705 for (int j = 0; j < nChan; ++j) {
2706 xu.push_back(1.0);
2707 }
2708 xArray.push_back(xu);
2709 }
2710 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
2711 double xFactor = baseXFactor*(double)nWaves[i];
2712 std::vector<double> xs, xc;
2713 xs.clear();
2714 xc.clear();
2715 for (int j = 0; j < nChan; ++j) {
2716 xs.push_back(sin(xFactor*(double)j));
2717 xc.push_back(cos(xFactor*(double)j));
2718 }
2719 xArray.push_back(xs);
2720 xArray.push_back(xc);
2721 }
2722
2723 std::vector<double> z1, r1, residual;
[2047]2724 for (int i = 0; i < nChan; ++i) {
[2081]2725 z1.push_back((double)data[i]);
[2047]2726 r1.push_back(0.0);
[2081]2727 residual.push_back(0.0);
[2047]2728 }
2729
2730 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
[2081]2731 // xMatrix : horizontal concatenation of
2732 // the least-sq. matrix (left) and an
2733 // identity matrix (right).
2734 // the right part is used to calculate the inverse matrix of the left part.
[2047]2735 double xMatrix[nDOF][2*nDOF];
2736 double zMatrix[nDOF];
2737 for (int i = 0; i < nDOF; ++i) {
2738 for (int j = 0; j < 2*nDOF; ++j) {
2739 xMatrix[i][j] = 0.0;
[2012]2740 }
[2047]2741 xMatrix[i][nDOF+i] = 1.0;
2742 zMatrix[i] = 0.0;
2743 }
2744
[2193]2745 int nUseData = 0;
[2081]2746 for (int k = 0; k < nChan; ++k) {
2747 if (maskArray[k] == 0) continue;
2748
2749 for (int i = 0; i < nDOF; ++i) {
2750 for (int j = i; j < nDOF; ++j) {
2751 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
2752 }
2753 zMatrix[i] += z1[k] * xArray[i][k];
2754 }
[2193]2755
2756 nUseData++;
[2047]2757 }
2758
[2193]2759 if (nUseData < 1) {
2760 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
2761 }
2762
[2047]2763 for (int i = 0; i < nDOF; ++i) {
2764 for (int j = 0; j < i; ++j) {
2765 xMatrix[i][j] = xMatrix[j][i];
[2012]2766 }
2767 }
2768
[2047]2769 std::vector<double> invDiag;
2770 for (int i = 0; i < nDOF; ++i) {
2771 invDiag.push_back(1.0/xMatrix[i][i]);
2772 for (int j = 0; j < nDOF; ++j) {
2773 xMatrix[i][j] *= invDiag[i];
2774 }
2775 }
2776
2777 for (int k = 0; k < nDOF; ++k) {
2778 for (int i = 0; i < nDOF; ++i) {
2779 if (i != k) {
2780 double factor1 = xMatrix[k][k];
2781 double factor2 = xMatrix[i][k];
2782 for (int j = k; j < 2*nDOF; ++j) {
2783 xMatrix[i][j] *= factor1;
2784 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2785 xMatrix[i][j] /= factor1;
2786 }
2787 }
2788 }
2789 double xDiag = xMatrix[k][k];
2790 for (int j = k; j < 2*nDOF; ++j) {
2791 xMatrix[k][j] /= xDiag;
2792 }
2793 }
2794
2795 for (int i = 0; i < nDOF; ++i) {
2796 for (int j = 0; j < nDOF; ++j) {
2797 xMatrix[i][nDOF+j] *= invDiag[j];
2798 }
2799 }
2800 //compute a vector y which consists of the coefficients of the sinusoids forming the
[2081]2801 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
2802 //and cosine functions, respectively.
[2047]2803 std::vector<double> y;
[2081]2804 params.clear();
[2047]2805 for (int i = 0; i < nDOF; ++i) {
2806 y.push_back(0.0);
2807 for (int j = 0; j < nDOF; ++j) {
2808 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2809 }
[2081]2810 params.push_back(y[i]);
[2047]2811 }
2812
2813 for (int i = 0; i < nChan; ++i) {
[2081]2814 r1[i] = y[0];
2815 for (int j = 1; j < nDOF; ++j) {
2816 r1[i] += y[j]*xArray[j][i];
2817 }
2818 residual[i] = z1[i] - r1[i];
[2047]2819 }
2820
2821 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2822 break;
2823 } else {
2824 double stdDev = 0.0;
2825 for (int i = 0; i < nChan; ++i) {
[2081]2826 stdDev += residual[i]*residual[i]*(double)maskArray[i];
[2047]2827 }
2828 stdDev = sqrt(stdDev/(double)nData);
2829
2830 double thres = stdDev * thresClip;
2831 int newNData = 0;
2832 for (int i = 0; i < nChan; ++i) {
[2081]2833 if (abs(residual[i]) >= thres) {
[2047]2834 maskArray[i] = 0;
2835 }
2836 if (maskArray[i] > 0) {
2837 newNData++;
2838 }
2839 }
[2081]2840 if (newNData == nData) {
2841 break; //no more flag to add. iteration stops.
[2047]2842 } else {
[2081]2843 nData = newNData;
[2047]2844 }
2845 }
[2012]2846 }
2847
[2193]2848 nClipped = initNData - nData;
2849
[2058]2850 std::vector<float> result;
2851 if (getResidual) {
2852 for (int i = 0; i < nChan; ++i) {
[2081]2853 result.push_back((float)residual[i]);
[2058]2854 }
2855 } else {
2856 for (int i = 0; i < nChan; ++i) {
2857 result.push_back((float)r1[i]);
2858 }
[2047]2859 }
2860
[2058]2861 return result;
[2012]2862}
2863
[2047]2864void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
2865{
[2081]2866 std::vector<double> dAbcissa = getAbcissa(whichrow);
2867 std::vector<float> abcissa;
2868 for (uInt i = 0; i < dAbcissa.size(); ++i) {
2869 abcissa.push_back((float)dAbcissa[i]);
[2047]2870 }
2871 std::vector<float> spec = getSpectrum(whichrow);
[2012]2872
[2081]2873 fitter.setData(abcissa, spec, mask);
[2047]2874 fitter.lfit();
2875}
2876
2877std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
2878{
[2186]2879 std::vector<bool> mask = getMask(whichrow);
2880 uInt maskSize = mask.size();
2881 if (maskSize != inMask.size()) {
2882 throw(AipsError("mask sizes are not the same."));
[2047]2883 }
[2186]2884 for (uInt i = 0; i < maskSize; ++i) {
2885 mask[i] = mask[i] && inMask[i];
[2047]2886 }
2887
[2186]2888 return mask;
[2047]2889}
2890
2891/*
2892std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
2893{
2894 int edgeSize = edge.size();
2895 std::vector<int> currentEdge;
2896 if (edgeSize >= 2) {
2897 int idx = 0;
2898 if (edgeSize > 2) {
2899 if (edgeSize < minEdgeSize) {
2900 throw(AipsError("Length of edge element info is less than that of IFs"));
2901 }
2902 idx = 2 * getIF(whichrow);
2903 }
2904 currentEdge.push_back(edge[idx]);
2905 currentEdge.push_back(edge[idx+1]);
2906 } else {
2907 throw(AipsError("Wrong length of edge element"));
2908 }
2909
2910 lineFinder.setData(getSpectrum(whichrow));
2911 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
2912
2913 return lineFinder.getMask();
2914}
2915*/
2916
2917/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
[2186]2918void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter)
2919{
[2047]2920 if (outLogger || outTextFile) {
2921 std::vector<float> params = fitter.getParameters();
2922 std::vector<bool> fixed = fitter.getFixedParameters();
2923 float rms = getRms(chanMask, whichrow);
2924 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
2925
2926 if (outLogger) {
2927 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
[2193]2928 ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ;
[2047]2929 }
2930 if (outTextFile) {
[2193]2931 ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush;
[2047]2932 }
2933 }
2934}
2935
2936/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
[2193]2937void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped)
[2186]2938{
[2047]2939 if (outLogger || outTextFile) {
2940 float rms = getRms(chanMask, whichrow);
2941 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
[2081]2942 std::vector<bool> fixed;
2943 fixed.clear();
[2047]2944
2945 if (outLogger) {
2946 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
[2193]2947 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
[2047]2948 }
2949 if (outTextFile) {
[2193]2950 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
[2047]2951 }
2952 }
2953}
2954
2955/* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
[2193]2956void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped)
[2186]2957{
[2047]2958 if (outLogger || outTextFile) {
2959 float rms = getRms(chanMask, whichrow);
2960 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
[2081]2961 std::vector<bool> fixed;
2962 fixed.clear();
[2047]2963
2964 if (outLogger) {
2965 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
[2193]2966 ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
[2047]2967 }
2968 if (outTextFile) {
[2193]2969 ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
[2047]2970 }
2971 }
2972}
2973
[2189]2974void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
[2186]2975{
[2189]2976 int idxDelimiter = progressInfo.find(",");
2977 if (idxDelimiter < 0) {
2978 throw(AipsError("wrong value in 'showprogress' parameter")) ;
2979 }
2980 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
2981 std::istringstream is(progressInfo.substr(idxDelimiter+1));
2982 is >> minNRow;
2983}
2984
2985void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
2986{
2987 if (showProgress && (nTotal >= nTotalThreshold)) {
[2186]2988 int nInterval = int(floor(double(nTotal)/100.0));
2989 if (nInterval == 0) nInterval++;
2990
[2193]2991 if (nProcessed % nInterval == 0) {
[2189]2992 printf("\r"); //go to the head of line
[2186]2993 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
[2189]2994 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
2995 printf("\x1b[39m\x1b[0m"); //set default attributes
[2186]2996 fflush(NULL);
2997 }
[2193]2998
[2186]2999 if (nProcessed == nTotal - 1) {
3000 printf("\r\x1b[K"); //clear
3001 fflush(NULL);
3002 }
[2193]3003
[2186]3004 }
3005}
3006
3007std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
3008{
3009 std::vector<bool> mask = getMask(whichrow);
3010
3011 if (inMask.size() > 0) {
3012 uInt maskSize = mask.size();
3013 if (maskSize != inMask.size()) {
3014 throw(AipsError("mask sizes are not the same."));
3015 }
3016 for (uInt i = 0; i < maskSize; ++i) {
3017 mask[i] = mask[i] && inMask[i];
3018 }
3019 }
3020
3021 Vector<Float> spec = getSpectrum(whichrow);
3022 mathutil::doZeroOrderInterpolation(spec, mask);
3023
3024 FFTServer<Float,Complex> ffts;
3025 Vector<Complex> fftres;
3026 ffts.fft0(fftres, spec);
3027
3028 std::vector<float> res;
3029 float norm = float(2.0/double(spec.size()));
3030
3031 if (getRealImag) {
3032 for (uInt i = 0; i < fftres.size(); ++i) {
3033 res.push_back(real(fftres[i])*norm);
3034 res.push_back(imag(fftres[i])*norm);
3035 }
3036 } else {
3037 for (uInt i = 0; i < fftres.size(); ++i) {
3038 res.push_back(abs(fftres[i])*norm);
3039 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
3040 }
3041 }
3042
3043 return res;
3044}
3045
3046
3047float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
3048{
[2012]3049 Vector<Float> spec;
3050 specCol_.get(whichrow, spec);
3051
3052 float mean = 0.0;
3053 float smean = 0.0;
3054 int n = 0;
[2047]3055 for (uInt i = 0; i < spec.nelements(); ++i) {
[2012]3056 if (mask[i]) {
3057 mean += spec[i];
3058 smean += spec[i]*spec[i];
3059 n++;
3060 }
3061 }
3062
3063 mean /= (float)n;
3064 smean /= (float)n;
3065
3066 return sqrt(smean - mean*mean);
3067}
3068
3069
[2186]3070std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
[2012]3071{
3072 ostringstream oss;
3073
3074 if (verbose) {
3075 oss << " Scan[" << getScan(whichrow) << "]";
3076 oss << " Beam[" << getBeam(whichrow) << "]";
3077 oss << " IF[" << getIF(whichrow) << "]";
3078 oss << " Pol[" << getPol(whichrow) << "]";
3079 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
3080 oss << "Fitter range = " << masklist << endl;
3081 oss << "Baseline parameters" << endl;
3082 oss << flush;
3083 }
3084
3085 return String(oss);
3086}
3087
[2193]3088std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const
[2012]3089{
3090 ostringstream oss;
3091
3092 if (verbose) {
3093 oss << "Results of baseline fit" << endl;
3094 oss << " rms = " << setprecision(6) << rms << endl;
[2193]3095 if (nClipped >= 0) {
3096 oss << " Number of clipped channels = " << nClipped << endl;
3097 }
[2094]3098 for (int i = 0; i < 60; ++i) {
3099 oss << "-";
3100 }
[2131]3101 oss << endl;
[2094]3102 oss << flush;
[2012]3103 }
3104
3105 return String(oss);
3106}
3107
[2186]3108std::string Scantable::formatBaselineParams(const std::vector<float>& params,
3109 const std::vector<bool>& fixed,
3110 float rms,
[2193]3111 int nClipped,
[2186]3112 const std::string& masklist,
3113 int whichrow,
3114 bool verbose,
3115 int start, int count,
3116 bool resetparamid) const
[2047]3117{
[2064]3118 int nParam = (int)(params.size());
[2047]3119
[2064]3120 if (nParam < 1) {
3121 return(" Not fitted");
3122 } else {
3123
3124 ostringstream oss;
3125 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3126
3127 if (start < 0) start = 0;
3128 if (count < 0) count = nParam;
3129 int end = start + count;
3130 if (end > nParam) end = nParam;
3131 int paramidoffset = (resetparamid) ? (-start) : 0;
3132
3133 for (int i = start; i < end; ++i) {
3134 if (i > start) {
[2047]3135 oss << ",";
3136 }
[2064]3137 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
3138 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
[2047]3139 }
[2064]3140
3141 oss << endl;
[2193]3142 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
[2064]3143
3144 return String(oss);
[2047]3145 }
3146
3147}
3148
[2193]3149 std::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) const
[2012]3150{
[2064]3151 int nOutParam = (int)(params.size());
3152 int nPiece = (int)(ranges.size()) - 1;
[2012]3153
[2064]3154 if (nOutParam < 1) {
3155 return(" Not fitted");
3156 } else if (nPiece < 0) {
[2193]3157 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose);
[2064]3158 } else if (nPiece < 1) {
3159 return(" Bad count of the piece edge info");
3160 } else if (nOutParam % nPiece != 0) {
3161 return(" Bad count of the output baseline parameters");
3162 } else {
3163
3164 int nParam = nOutParam / nPiece;
3165
3166 ostringstream oss;
3167 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3168
3169 stringstream ss;
3170 ss << ranges[nPiece] << flush;
3171 int wRange = ss.str().size() * 2 + 5;
3172
3173 for (int i = 0; i < nPiece; ++i) {
[2047]3174 ss.str("");
[2064]3175 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
3176 oss << left << setw(wRange) << ss.str();
[2193]3177 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true);
[2012]3178 }
[2064]3179
[2193]3180 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
[2064]3181
3182 return String(oss);
[2012]3183 }
3184
3185}
3186
[2047]3187bool Scantable::hasSameNchanOverIFs()
[2012]3188{
[2047]3189 int nIF = nif(-1);
3190 int nCh;
3191 int totalPositiveNChan = 0;
3192 int nPositiveNChan = 0;
[2012]3193
[2047]3194 for (int i = 0; i < nIF; ++i) {
3195 nCh = nchan(i);
3196 if (nCh > 0) {
3197 totalPositiveNChan += nCh;
3198 nPositiveNChan++;
[2012]3199 }
3200 }
3201
[2047]3202 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
[2012]3203}
3204
[2047]3205std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
[2012]3206{
3207 if (mask.size() < 2) {
3208 throw(AipsError("The mask elements should be > 1"));
3209 }
[2047]3210 int IF = getIF(whichrow);
3211 if (mask.size() != (uInt)nchan(IF)) {
[2012]3212 throw(AipsError("Number of channels in scantable != number of mask elements"));
3213 }
3214
[2047]3215 if (verbose) {
[2012]3216 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
3217 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
3218 if (!hasSameNchan) {
[2047]3219 logOs << endl << "This mask is only valid for IF=" << IF;
[2012]3220 }
3221 logOs << LogIO::POST;
3222 }
3223
3224 std::vector<double> abcissa = getAbcissa(whichrow);
[2047]3225 std::vector<int> edge = getMaskEdgeIndices(mask);
3226
[2012]3227 ostringstream oss;
3228 oss.setf(ios::fixed);
3229 oss << setprecision(1) << "[";
[2047]3230 for (uInt i = 0; i < edge.size(); i+=2) {
[2012]3231 if (i > 0) oss << ",";
[2047]3232 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
[2012]3233 }
3234 oss << "]" << flush;
3235
3236 return String(oss);
3237}
3238
[2047]3239std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
[2012]3240{
[2047]3241 if (mask.size() < 2) {
3242 throw(AipsError("The mask elements should be > 1"));
[2012]3243 }
3244
[2047]3245 std::vector<int> out, startIndices, endIndices;
3246 int maskSize = mask.size();
[2012]3247
[2047]3248 startIndices.clear();
3249 endIndices.clear();
3250
3251 if (mask[0]) {
3252 startIndices.push_back(0);
[2012]3253 }
[2047]3254 for (int i = 1; i < maskSize; ++i) {
3255 if ((!mask[i-1]) && mask[i]) {
3256 startIndices.push_back(i);
3257 } else if (mask[i-1] && (!mask[i])) {
3258 endIndices.push_back(i-1);
3259 }
[2012]3260 }
[2047]3261 if (mask[maskSize-1]) {
3262 endIndices.push_back(maskSize-1);
3263 }
[2012]3264
[2047]3265 if (startIndices.size() != endIndices.size()) {
3266 throw(AipsError("Inconsistent Mask Size: bad data?"));
3267 }
3268 for (uInt i = 0; i < startIndices.size(); ++i) {
3269 if (startIndices[i] > endIndices[i]) {
3270 throw(AipsError("Mask start index > mask end index"));
[2012]3271 }
3272 }
3273
[2047]3274 out.clear();
3275 for (uInt i = 0; i < startIndices.size(); ++i) {
3276 out.push_back(startIndices[i]);
3277 out.push_back(endIndices[i]);
3278 }
3279
[2012]3280 return out;
3281}
3282
[2161]3283vector<float> Scantable::getTsysSpectrum( int whichrow ) const
3284{
3285 Vector<Float> tsys( tsysCol_(whichrow) ) ;
3286 vector<float> stlTsys ;
3287 tsys.tovector( stlTsys ) ;
3288 return stlTsys ;
3289}
[2012]3290
3291
[1907]3292}
[1819]3293//namespace asap
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