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