source: trunk/src/Scantable.h@ 2648

Last change on this file since 2648 was 2645, checked in by WataruKawasaki, 12 years ago

New Development: Yes

JIRA Issue: Yes CAS-4145

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: Yes

Module(s): scantable

Description: added scantable methods [auto_]chebyshev_baseline() to subtract baseline using Chebyshev polynomials.
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  • Property svn:keywords set to Author Date Id Revision
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1//
2// C++ Interface: 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#ifndef ASAPSCANTABLE_H
13#define ASAPSCANTABLE_H
14
15// STL
16#include <fstream>
17#include <iostream>
18#include <sstream>
19#include <string>
20#include <vector>
21// AIPS++
22#include <casa/aips.h>
23#include <casa/Arrays/MaskedArray.h>
24#include <casa/Arrays/Vector.h>
25#include <casa/BasicSL/String.h>
26#include <casa/Containers/Record.h>
27#include <casa/Exceptions/Error.h>
28#include <casa/Quanta/Quantum.h>
29#include <casa/Utilities/CountedPtr.h>
30
31#include <coordinates/Coordinates/SpectralCoordinate.h>
32
33#include <measures/TableMeasures/ScalarMeasColumn.h>
34
35#include <scimath/Mathematics/FFTServer.h>
36
37#include <tables/Tables/ArrayColumn.h>
38#include <tables/Tables/ScalarColumn.h>
39#include <tables/Tables/Table.h>
40
41#include "Logger.h"
42#include "MathUtils.h"
43#include "STFit.h"
44#include "STFitEntry.h"
45#include "STFitter.h"
46#include "STFocus.h"
47#include "STFrequencies.h"
48#include "STHeader.h"
49#include "STHistory.h"
50#include "STMolecules.h"
51#include "STPol.h"
52#include "STSelector.h"
53#include "STTcal.h"
54#include "STWeather.h"
55
56namespace asap {
57
58/**
59 * This class contains and wraps a casa::Table, which is used to store
60 * all the information. This can be either a MemoryTable or a
61 * disk based Table.
62 * It provides access functions to the underlying table
63 * It contains n subtables:
64 * @li weather
65 * @li frequencies
66 * @li molecules
67 * @li tcal
68 * @li focus
69 * @li fits
70 *
71 * @brief The main ASAP data container
72 * @author Malte Marquarding
73 * @date
74 * @version
75*/
76class Scantable : private Logger
77{
78
79friend class STMath;
80
81public:
82 /**
83 * Default constructor
84 */
85 explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
86
87 /**
88 * Create a Scantable object from an existing table on disk
89 * @param[in] name the name of the existing Scantable
90 */
91 explicit Scantable(const std::string& name,
92 casa::Table::TableType ttype = casa::Table::Memory);
93
94 /// @fixme this is only sensible for MemoryTables....
95 Scantable(const Scantable& other, bool clear=true);
96
97 /**
98 * Destructor
99 */
100 virtual ~Scantable();
101
102 /**
103 * get a const reference to the underlying casa::Table
104 * @return const \ref casa::Table reference
105 */
106 const casa::Table& table() const;
107
108 /**
109 * get a reference to the underlying casa::Table with the Selection
110 * object applied if set
111 * @return casa::Table reference
112 */
113 casa::Table& table();
114
115
116 /**
117 * Get a handle to the selection object
118 * @return constant STSelector reference
119 */
120 const STSelector& getSelection() const { return selector_; }
121
122 /**
123 * Set the data to be a subset as defined by the STSelector
124 * @param selection a STSelector object
125 */
126 void setSelection(const STSelector& selection);
127
128 /**
129 * unset the selection of the data
130 */
131 void unsetSelection();
132 /**
133 * set the header
134 * @param[in] sth an STHeader object
135 */
136 void setHeader( const STHeader& sth );
137
138 /**
139 * get the header information
140 * @return an STHeader object
141 */
142 STHeader getHeader( ) const;
143
144 /**
145 * Checks if the "other" Scantable is conformant with this,
146 * i.e. if header values are the same.
147 * @param[in] other another Scantable
148 * @return true or false
149 */
150 bool conformant( const Scantable& other);
151
152 /**
153 *
154 * @param stype The type of the source, 0 = on, 1 = off
155 */
156 void setSourceType(int stype);
157
158
159 /**
160 * The number of scans in the table
161 * @return number of scans in the table
162 */
163 int nscan() const;
164
165 casa::MEpoch::Types getTimeReference() const;
166
167
168 casa::MEpoch getEpoch(int whichrow) const;
169
170 /**
171 * Get global antenna position
172 * @return casa::MPosition
173 */
174 casa::MPosition getAntennaPosition() const;
175
176 /**
177 * the @ref casa::MDirection for a specific row
178 * @param[in] whichrow the row number
179 * return casa::MDirection
180 */
181 casa::MDirection getDirection( int whichrow ) const;
182
183 /**
184 * get the direction type as a string, e.g. "J2000"
185 * @param[in] whichrow the row number
186 * return the direction string
187 */
188 std::string getDirectionString( int whichrow ) const;
189
190 /**
191 * set the direction type as a string, e.g. "J2000"
192 * @param[in] refstr the direction type
193 */
194 void setDirectionRefString(const std::string& refstr="");
195
196 /**
197 * get the direction reference string
198 * @return a string describing the direction reference
199 */
200 std::string getDirectionRefString() const;
201
202 /**
203 * Return the Flux unit of the data, e.g. "Jy" or "K"
204 * @return string
205 */
206 std::string getFluxUnit() const;
207
208 /**
209 * Set the Flux unit of the data
210 * @param unit a string representing the unit, e.g "Jy" or "K"
211 */
212 void setFluxUnit( const std::string& unit );
213
214 /**
215 * Set the Stokes type of the data
216 * @param feedtype a string representing the type, e.g "circular" or "linear"
217 */
218 void setFeedType( const std::string& feedtype );
219
220 /**
221 *
222 * @param instrument a string representing an insturment. see xxx
223 */
224 void setInstrument( const std::string& instrument );
225
226 /**
227 * (Re)calculate the azimuth and elevationnfor all rows
228 */
229 void calculateAZEL();
230
231 /**
232 * "hard" flag the data, this flags everything selected in setSelection()
233 * param[in] msk a boolean mask of length nchan describing the points to
234 * to be flagged
235 */
236 //void flag( const std::vector<bool>& msk = std::vector<bool>());
237 //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
238
239 void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
240
241 /**
242 * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
243 * param[in] rows list of row numbers to be flagged
244 */
245 void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
246
247 /**
248 * Get flagRow info at the specified row. If true, the whole data
249 * at the row should be flagged.
250 */
251 bool getFlagRow(int whichrow) const
252 { return (flagrowCol_(whichrow) > 0); }
253
254 /**
255 * Flag the data outside a specified range (in a channel-based manner).
256 * (CAS-1807 Wataru Kawasaki)
257 */
258 void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
259
260 /**
261 * Return a list of booleans with the size of nchan for a specified row, to get info
262 * about which channel is clipped.
263 */
264 std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
265 void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
266 casa::Vector<casa::uChar> flgs);
267
268 /**
269 * Return a list of row numbers with respect to the original table.
270 * @return a list of unsigned ints
271 */
272 std::vector<unsigned int> rownumbers() const;
273
274
275 /**
276 * Get the number of beams in the data or a specific scan
277 * @param scanno the scan number to get the number of beams for.
278 * If scanno<0 the number is retrieved from the header.
279 * @return an integer number
280 */
281 int nbeam(int scanno=-1) const;
282 /**
283 * Get the number of IFs in the data or a specific scan
284 * @param scanno the scan number to get the number of IFs for.
285 * If scanno<0 the number is retrieved from the header.
286 * @return an integer number
287 */
288 int nif(int scanno=-1) const;
289 /**
290 * Get the number of polarizations in the data or a specific scan
291 * @param scanno the scan number to get the number of polarizations for.
292 * If scanno<0 the number is retrieved from the header.
293 * @return an integer number
294 */
295 int npol(int scanno=-1) const;
296
297 std::string getPolType() const;
298
299
300 /**
301 * Get the number of integartion cycles
302 * @param scanno the scan number to get the number of rows for.
303 * If scanno<0 the number is retrieved from the header.
304 * @return the number of rows (for the specified scanno)
305 */
306 int nrow(int scanno=-1) const;
307
308 int getBeam(int whichrow) const;
309 std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
310
311 int getIF(int whichrow) const;
312 std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
313
314 int getPol(int whichrow) const;
315 std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
316
317 std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
318 int getScan(int whichrow) const { return scanCol_(whichrow); }
319
320 //TT addition
321 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
322
323 /**
324 * Get the number of channels in the data or a specific IF. This currently
325 * varies only with IF number
326 * @param ifno the IF number to get the number of channels for.
327 * If ifno<0 the number is retrieved from the header.
328 * @return an integer number
329 */
330 int nchan(int ifno=-1) const;
331 int getChannels(int whichrow) const;
332
333 int ncycle(int scanno=-1) const;
334 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
335
336 double getInterval(int whichrow) const
337 { return integrCol_(whichrow); }
338
339 float getTsys(int whichrow) const
340 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
341 std::vector<float> getTsysSpectrum(int whichrow) const ;
342 float getElevation(int whichrow) const
343 { return elCol_(whichrow); }
344 float getAzimuth(int whichrow) const
345 { return azCol_(whichrow); }
346 float getParAngle(int whichrow) const
347 { return focus().getParAngle(mfocusidCol_(whichrow)); }
348 int getTcalId(int whichrow) const
349 { return mtcalidCol_(whichrow); }
350
351 std::string getSourceName(int whichrow) const
352 { return srcnCol_(whichrow); }
353
354 std::vector<bool> getMask(int whichrow) const;
355 std::vector<float> getSpectrum(int whichrow,
356 const std::string& poltype = "" ) const;
357
358 void setSpectrum(const std::vector<float>& spec, int whichrow);
359
360 std::string getPolarizationLabel(int index, const std::string& ptype) const
361 { return STPol::getPolLabel(index, ptype ); }
362
363 /**
364 * Write the Scantable to disk
365 * @param filename the output file name
366 */
367 void makePersistent(const std::string& filename);
368
369 std::vector<std::string> getHistory() const
370 { return historyTable_.getHistory(); };
371
372 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
373
374 void appendToHistoryTable(const STHistory& otherhist)
375 { historyTable_.append(otherhist); }
376
377 std::string headerSummary();
378 void summary(const std::string& filename="");
379 std::string oldheaderSummary();
380 // std::string summary();
381 void oldsummary(const std::string& filename="");
382
383 //std::string getTime(int whichrow=-1, bool showdate=true) const;
384 std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
385 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
386
387 // returns unit, conversion frame, doppler, base-frame
388
389 /**
390 * Get the frequency set up
391 * This is forwarded to the STFrequencies subtable
392 * @return unit, frame, doppler
393 */
394 std::vector<std::string> getCoordInfo() const
395 { return freqTable_.getInfo(); };
396
397 void setCoordInfo(std::vector<string> theinfo)
398 { return freqTable_.setInfo(theinfo); };
399
400
401 std::vector<double> getAbcissa(int whichrow) const;
402
403 std::vector<float> getWeather(int whichrow) const;
404
405 std::string getAbcissaLabel(int whichrow) const;
406 std::vector<double> getRestFrequencies() const
407 { return moleculeTable_.getRestFrequencies(); }
408 std::vector<double> getRestFrequency(int id) const
409 { return moleculeTable_.getRestFrequency(id); }
410
411 /**
412 void setRestFrequencies(double rf, const std::string& name = "",
413 const std::string& = "Hz");
414 **/
415 // Modified by Takeshi Nakazato 05/09/2008
416 /***
417 void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
418 const std::string& = "Hz");
419 ***/
420 void setRestFrequencies(vector<double> rf,
421 const vector<std::string>& name = vector<std::string>(1,""),
422 const std::string& = "Hz");
423
424 //void setRestFrequencies(const std::string& name);
425 void setRestFrequencies(const vector<std::string>& name);
426
427 void shift(int npix);
428
429 casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
430
431 void convertDirection(const std::string& newframe);
432
433 STFrequencies& frequencies() { return freqTable_; }
434 const STFrequencies& frequencies() const { return freqTable_; }
435 STWeather& weather() { return weatherTable_; }
436 const STWeather& weather() const { return weatherTable_; }
437 STFocus& focus() { return focusTable_; }
438 const STFocus& focus() const { return focusTable_; }
439 STTcal& tcal() { return tcalTable_; }
440 const STTcal& tcal() const { return tcalTable_; }
441 STMolecules& molecules() { return moleculeTable_; }
442 const STMolecules& molecules() const { return moleculeTable_; }
443 STHistory& history() { return historyTable_; }
444 const STHistory& history() const { return historyTable_; }
445 STFit& fit() { return fitTable_; }
446 const STFit& fit() const { return fitTable_; }
447
448 std::vector<std::string> columnNames() const;
449
450 void addFit(const STFitEntry& fit, int row);
451 STFitEntry getFit(int row) const
452 { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
453
454 //Added by TT
455 /**
456 * Get the antenna name
457 * @return antenna name string
458 */
459 casa::String getAntennaName() const;
460
461 /**
462 * For GBT MS data only. check a scan list
463 * against the information found in GBT_GO table for
464 * scan number orders to get correct pairs.
465 * @param[in] scan list
466 * @return status
467 */
468 int checkScanInfo(const std::vector<int>& scanlist) const;
469
470 /**
471 * Get the direction as a vector, for a specific row
472 * @param[in] whichrow the row numbyyer
473 * @return the direction in a vector
474 */
475 std::vector<double> getDirectionVector(int whichrow) const;
476
477 /**
478 * Set a flag indicating whether the data was parallactified
479 * @param[in] flag true or false
480 */
481 void parallactify(bool flag)
482 { focusTable_.setParallactify(flag); }
483
484 /**
485 * Reshape spectrum
486 * @param[in] nmin, nmax minimum and maximum channel
487 * @param[in] irow row number
488 *
489 * 30/07/2008 Takeshi Nakazato
490 **/
491 void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
492 void reshapeSpectrum( int nmin, int nmax, int irow ) ;
493
494 /**
495 * Change channel number under fixed bandwidth
496 * @param[in] nchan, dnu new channel number and spectral resolution
497 * @param[in] irow row number
498 *
499 * 27/08/2008 Takeshi Nakazato
500 **/
501 void regridChannel( int nchan, double dnu ) ;
502 void regridChannel( int nchan, double dnu, int irow ) ;
503 void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
504
505 void regridSpecChannel( double dnu, int nchan=-1 ) ;
506
507 bool getFlagtraFast(casa::uInt whichrow);
508
509 void polyBaseline(const std::vector<bool>& mask,
510 int order,
511 bool getResidual=true,
512 const std::string& progressInfo="true,1000",
513 const bool outLogger=false,
514 const std::string& blfile="");
515 void autoPolyBaseline(const std::vector<bool>& mask,
516 int order,
517 const std::vector<int>& edge,
518 float threshold=3.0,
519 int chanAvgLimit=1,
520 bool getResidual=true,
521 const std::string& progressInfo="true,1000",
522 const bool outLogger=false,
523 const std::string& blfile="");
524 void chebyshevBaseline(const std::vector<bool>& mask,
525 int order,
526 float thresClip,
527 int nIterClip,
528 bool getResidual=true,
529 const std::string& progressInfo="true,1000",
530 const bool outLogger=false,
531 const std::string& blfile="");
532 void autoChebyshevBaseline(const std::vector<bool>& mask,
533 int order,
534 float thresClip,
535 int nIterClip,
536 const std::vector<int>& edge,
537 float threshold=3.0,
538 int chanAvgLimit=1,
539 bool getResidual=true,
540 const std::string& progressInfo="true,1000",
541 const bool outLogger=false,
542 const std::string& blfile="");
543 void cubicSplineBaseline(const std::vector<bool>& mask,
544 int nPiece,
545 float thresClip,
546 int nIterClip,
547 bool getResidual=true,
548 const std::string& progressInfo="true,1000",
549 const bool outLogger=false,
550 const std::string& blfile="");
551 void autoCubicSplineBaseline(const std::vector<bool>& mask,
552 int nPiece,
553 float thresClip,
554 int nIterClip,
555 const std::vector<int>& edge,
556 float threshold=3.0,
557 int chanAvgLimit=1,
558 bool getResidual=true,
559 const std::string& progressInfo="true,1000",
560 const bool outLogger=false,
561 const std::string& blfile="");
562 void sinusoidBaseline(const std::vector<bool>& mask,
563 const bool applyFFT,
564 const std::string& fftMethod,
565 const std::string& fftThresh,
566 const std::vector<int>& addNWaves,
567 const std::vector<int>& rejectNWaves,
568 float thresClip,
569 int nIterClip,
570 bool getResidual=true,
571 const std::string& progressInfo="true,1000",
572 const bool outLogger=false,
573 const std::string& blfile="");
574 void autoSinusoidBaseline(const std::vector<bool>& mask,
575 const bool applyFFT,
576 const std::string& fftMethod,
577 const std::string& fftThresh,
578 const std::vector<int>& addNWaves,
579 const std::vector<int>& rejectNWaves,
580 float thresClip,
581 int nIterClip,
582 const std::vector<int>& edge,
583 float threshold=3.0,
584 int chanAvgLimit=1,
585 bool getResidual=true,
586 const std::string& progressInfo="true,1000",
587 const bool outLogger=false,
588 const std::string& blfile="");
589 std::vector<float> execFFT(const int whichrow,
590 const std::vector<bool>& inMask,
591 bool getRealImag=false,
592 bool getAmplitudeOnly=false);
593 float getRms(const std::vector<bool>& mask, int whichrow);
594 std::string formatBaselineParams(const std::vector<float>& params,
595 const std::vector<bool>& fixed,
596 float rms,
597 int nClipped,
598 const std::string& masklist,
599 int whichrow,
600 bool verbose=false,
601 bool csvformat=false,
602 int start=-1,
603 int count=-1,
604 bool resetparamid=false) const;
605 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
606 const std::vector<float>& params,
607 const std::vector<bool>& fixed,
608 float rms,
609 int nClipped,
610 const std::string& masklist,
611 int whichrow,
612 bool verbose=false,
613 bool csvformat=false) const;
614 std::vector<uint> getMoleculeIdColumnData() const;
615 void setMoleculeIdColumnData(const std::vector<uint>& molids);
616
617
618private:
619
620 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
621
622 /**
623 * Turns a time value into a formatted string
624 * @param x
625 * @return
626 */
627 std::string formatSec(casa::Double x) const;
628
629 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
630 std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
631
632 /**
633 * Turns a casa::MDirection into a nicely formatted string
634 * @param md an casa::MDirection
635 * @return
636 */
637 std::string formatDirection(const casa::MDirection& md) const;
638
639 /**
640 * Create a unique file name for the paged (temporary) table
641 * @return just the name
642 */
643 static casa::String generateName();
644
645 /**
646 * attach to cached columns
647 */
648 void attach();
649
650 /**
651 * Set up the main casa::Table
652 */
653 void setupMainTable();
654
655 void attachSubtables();
656 void copySubtables(const Scantable& other);
657
658 /**
659 * Convert an "old" asap1 style row index into a new index
660 * @param[in] therow
661 * @return and index into @table_
662 */
663 int rowToScanIndex(int therow);
664
665 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
666
667 static const casa::uInt version_ = 4;
668
669 STSelector selector_;
670
671 casa::Table::TableType type_;
672
673 // the actual data
674 casa::Table table_;
675 casa::Table originalTable_;
676
677 STTcal tcalTable_;
678 STFrequencies freqTable_;
679 STWeather weatherTable_;
680 STFocus focusTable_;
681 STMolecules moleculeTable_;
682 STHistory historyTable_;
683 STFit fitTable_;
684
685 // Cached Columns to avoid reconstructing them for each row get/put
686 casa::ScalarColumn<casa::Double> integrCol_;
687 casa::MDirection::ScalarColumn dirCol_;
688 casa::MEpoch::ScalarColumn timeCol_;
689 casa::ScalarColumn<casa::Float> azCol_;
690 casa::ScalarColumn<casa::Float> elCol_;
691 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
692 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
693 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
694 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
695 casa::ArrayColumn<casa::uChar> flagsCol_;
696
697 // id in frequencies table
698 casa::ScalarColumn<casa::uInt> mfreqidCol_;
699 // id in tcal table
700 casa::ScalarColumn<casa::uInt> mtcalidCol_;
701
702 casa::ArrayColumn<casa::String> histitemCol_;
703 casa::ScalarColumn<casa::Int> mfitidCol_;
704 casa::ScalarColumn<casa::uInt> mweatheridCol_;
705
706 casa::ScalarColumn<casa::uInt> mfocusidCol_;
707
708 casa::ScalarColumn<casa::uInt> mmolidCol_;
709
710 static std::map<std::string, STPol::STPolFactory *> factories_;
711 void initFactories();
712
713 /**
714 * Add an auxiliary column to the main table and attach it to a
715 * cached column. Use for adding new columns that the original asap2
716 * tables do not have.
717 * @param[in] col reference to the cached column to be attached
718 * @param[in] colName column name in asap table
719 * @param[in] defValue default value to fill in the column
720 *
721 * 25/10/2009 Wataru Kawasaki
722 */
723 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
724 const casa::String&,
725 const T2&);
726 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
727 const casa::String&,
728 const casa::Array<T2>&);
729
730 void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
731 double getChebyshevPolynomial(int n, double x);
732 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
733 const std::vector<bool>& mask,
734 int order,
735 std::vector<float>& params,
736 int& nClipped,
737 float thresClip=3.0,
738 int nIterClip=1,
739 bool getResidual=true);
740 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
741 const std::vector<bool>& mask,
742 int nPiece,
743 std::vector<int>& idxEdge,
744 std::vector<float>& params,
745 int& nClipped,
746 float thresClip=3.0,
747 int nIterClip=1,
748 bool getResidual=true);
749 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
750 const std::vector<bool>& mask,
751 const std::vector<int>& waveNumbers,
752 std::vector<float>& params,
753 int& nClipped,
754 float thresClip=3.0,
755 int nIterClip=1,
756 bool getResidual=true);
757 void selectWaveNumbers(const int whichrow,
758 const std::vector<bool>& chanMask,
759 const bool applyFFT,
760 const std::string& fftMethod,
761 const std::string& fftThresh,
762 const std::vector<int>& addNWaves,
763 const std::vector<int>& rejectNWaves,
764 std::vector<int>& nWaves);
765 void parseThresholdExpression(const std::string& fftThresh,
766 std::string& fftThAttr,
767 float& fftThSigma,
768 int& fftThTop);
769 void doSelectWaveNumbers(const int whichrow,
770 const std::vector<bool>& chanMask,
771 const std::string& fftMethod,
772 const float fftThSigma,
773 const int fftThTop,
774 const std::string& fftThAttr,
775 std::vector<int>& nWaves);
776 void addAuxWaveNumbers(const int whichrow,
777 const std::vector<int>& addNWaves,
778 const std::vector<int>& rejectNWaves,
779 std::vector<int>& nWaves);
780 void setWaveNumberListUptoNyquistFreq(const int whichrow,
781 std::vector<int>& nWaves);
782 bool hasSameNchanOverIFs();
783 std::string getMaskRangeList(const std::vector<bool>& mask,
784 int whichrow,
785 const casa::String& coordInfo,
786 bool hasSameNchan,
787 bool verbose=false);
788 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
789 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
790 std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
791 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
792 //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
793 void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, Fitter& fitter);
794 void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped);
795 void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped);
796 void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
797 void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
798
799 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
800
801};
802
803} // namespace
804
805#endif
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