source: trunk/src/Scantable.h@ 2286

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

New Development: No (performance tuning)

JIRA Issue: No

Ready for Test: Yes

Interface Changes: Yes

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

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

Put in Release Notes: Yes

Module(s): sdlist, asap.summary

Description:

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

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

I updated scantable.summary so that it flushes the summary string more often to file/logger.
After the modification, scantable.summary could list the data mentioned above in ~ 7 minutes.
The side effect of it is that scantable.summary doesn't return summary string anymore.
(But people may not happy with sub-million lines of string anyway.)
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 23.9 KB
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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 form an existing table on disk
89 * @param[in] name the name of the existing Scantable
90 */
91 explicit Scantable(const std::string& name, casa::Table::TableType ttype = casa::Table::Memory);
92
93 /// @fixme this is only sensible for MemoryTables....
94 Scantable(const Scantable& other, bool clear=true);
95
96 /**
97 * Destructor
98 */
99 virtual ~Scantable();
100
101 /**
102 * get a const reference to the underlying casa::Table
103 * @return const \ref casa::Table reference
104 */
105 const casa::Table& table() const;
106
107 /**
108 * get a reference to the underlying casa::Table with the Selection
109 * object applied if set
110 * @return casa::Table reference
111 */
112 casa::Table& table();
113
114
115 /**
116 * Get a handle to the selection object
117 * @return constant STSelector reference
118 */
119 const STSelector& getSelection() const { return selector_; }
120
121 /**
122 * Set the data to be a subset as defined by the STSelector
123 * @param selection a STSelector object
124 */
125 void setSelection(const STSelector& selection);
126
127 /**
128 * unset the selection of the data
129 */
130 void unsetSelection();
131 /**
132 * set the header
133 * @param[in] sth an STHeader object
134 */
135 void setHeader( const STHeader& sth );
136
137 /**
138 * get the header information
139 * @return an STHeader object
140 */
141 STHeader getHeader( ) const;
142
143 /**
144 * Checks if the "other" Scantable is conformant with this,
145 * i.e. if header values are the same.
146 * @param[in] other another Scantable
147 * @return true or false
148 */
149 bool conformant( const Scantable& other);
150
151 /**
152 *
153 * @param stype The type of the source, 0 = on, 1 = off
154 */
155 void setSourceType(int stype);
156
157
158 /**
159 * The number of scans in the table
160 * @return number of scans in the table
161 */
162 int nscan() const;
163
164 casa::MEpoch::Types getTimeReference() const;
165
166
167 casa::MEpoch getEpoch(int whichrow) const;
168
169 /**
170 * Get global antenna position
171 * @return casa::MPosition
172 */
173 casa::MPosition getAntennaPosition() const;
174
175 /**
176 * the @ref casa::MDirection for a specific row
177 * @param[in] whichrow the row number
178 * return casa::MDirection
179 */
180 casa::MDirection getDirection( int whichrow ) const;
181
182 /**
183 * get the direction type as a string, e.g. "J2000"
184 * @param[in] whichrow the row number
185 * return the direction string
186 */
187 std::string getDirectionString( int whichrow ) const;
188
189 /**
190 * set the direction type as a string, e.g. "J2000"
191 * @param[in] refstr the direction type
192 */
193 void setDirectionRefString(const std::string& refstr="");
194
195 /**
196 * get the direction reference string
197 * @return a string describing the direction reference
198 */
199 std::string getDirectionRefString() const;
200
201 /**
202 * Return the Flux unit of the data, e.g. "Jy" or "K"
203 * @return string
204 */
205 std::string getFluxUnit() const;
206
207 /**
208 * Set the Flux unit of the data
209 * @param unit a string representing the unit, e.g "Jy" or "K"
210 */
211 void setFluxUnit( const std::string& unit );
212
213 /**
214 * Set the Stokes type of the data
215 * @param feedtype a string representing the type, e.g "circular" or "linear"
216 */
217 void setFeedType( const std::string& feedtype );
218
219 /**
220 *
221 * @param instrument a string representing an insturment. see xxx
222 */
223 void setInstrument( const std::string& instrument );
224
225 /**
226 * (Re)calculate the azimuth and elevationnfor all rows
227 */
228 void calculateAZEL();
229
230 /**
231 * "hard" flag the data, this flags everything selected in setSelection()
232 * param[in] msk a boolean mask of length nchan describing the points to
233 * to be flagged
234 */
235 //void flag( const std::vector<bool>& msk = std::vector<bool>());
236 //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
237
238 void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
239
240 /**
241 * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
242 * param[in] rows list of row numbers to be flagged
243 */
244 void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
245
246 /**
247 * Get flagRow info at the specified row. If true, the whole data
248 * at the row should be flagged.
249 */
250 bool getFlagRow(int whichrow) const
251 { return (flagrowCol_(whichrow) > 0); }
252
253 /**
254 * Flag the data outside a specified range (in a channel-based manner).
255 * (CAS-1807 Wataru Kawasaki)
256 */
257 void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
258
259 /**
260 * Return a list of booleans with the size of nchan for a specified row, to get info
261 * about which channel is clipped.
262 */
263 std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
264 void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
265 casa::Vector<casa::uChar> flgs);
266
267 /**
268 * Return a list of row numbers with respect to the original table.
269 * @return a list of unsigned ints
270 */
271 std::vector<unsigned int> rownumbers() const;
272
273
274 /**
275 * Get the number of beams in the data or a specific scan
276 * @param scanno the scan number to get the number of beams for.
277 * If scanno<0 the number is retrieved from the header.
278 * @return an integer number
279 */
280 int nbeam(int scanno=-1) const;
281 /**
282 * Get the number of IFs in the data or a specific scan
283 * @param scanno the scan number to get the number of IFs for.
284 * If scanno<0 the number is retrieved from the header.
285 * @return an integer number
286 */
287 int nif(int scanno=-1) const;
288 /**
289 * Get the number of polarizations in the data or a specific scan
290 * @param scanno the scan number to get the number of polarizations for.
291 * If scanno<0 the number is retrieved from the header.
292 * @return an integer number
293 */
294 int npol(int scanno=-1) const;
295
296 std::string getPolType() const;
297
298
299 /**
300 * Get the number of integartion cycles
301 * @param scanno the scan number to get the number of rows for.
302 * If scanno<0 the number is retrieved from the header.
303 * @return the number of rows (for the specified scanno)
304 */
305 int nrow(int scanno=-1) const;
306
307 int getBeam(int whichrow) const;
308 std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
309
310 int getIF(int whichrow) const;
311 std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
312
313 int getPol(int whichrow) const;
314 std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
315
316 std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
317 int getScan(int whichrow) const { return scanCol_(whichrow); }
318
319 //TT addition
320 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
321
322 /**
323 * Get the number of channels in the data or a specific IF. This currently
324 * varies only with IF number
325 * @param ifno the IF number to get the number of channels for.
326 * If ifno<0 the number is retrieved from the header.
327 * @return an integer number
328 */
329 int nchan(int ifno=-1) const;
330 int getChannels(int whichrow) const;
331
332 int ncycle(int scanno=-1) const;
333 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
334
335 double getInterval(int whichrow) const
336 { return integrCol_(whichrow); }
337
338 float getTsys(int whichrow) const
339 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
340 std::vector<float> getTsysSpectrum(int whichrow) const ;
341 float getElevation(int whichrow) const
342 { return elCol_(whichrow); }
343 float getAzimuth(int whichrow) const
344 { return azCol_(whichrow); }
345 float getParAngle(int whichrow) const
346 { return focus().getParAngle(mfocusidCol_(whichrow)); }
347 int getTcalId(int whichrow) const
348 { return mtcalidCol_(whichrow); }
349
350 std::string getSourceName(int whichrow) const
351 { return srcnCol_(whichrow); }
352
353 std::vector<bool> getMask(int whichrow) const;
354 std::vector<float> getSpectrum(int whichrow,
355 const std::string& poltype = "" ) const;
356
357 void setSpectrum(const std::vector<float>& spec, int whichrow);
358
359 std::string getPolarizationLabel(int index, const std::string& ptype) const
360 { return STPol::getPolLabel(index, ptype ); }
361
362 /**
363 * Write the Scantable to disk
364 * @param filename the output file name
365 */
366 void makePersistent(const std::string& filename);
367
368 std::vector<std::string> getHistory() const
369 { return historyTable_.getHistory(); };
370
371 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
372
373 void appendToHistoryTable(const STHistory& otherhist)
374 { historyTable_.append(otherhist); }
375
376 std::string headerSummary();
377 // std::string summary();
378 void summary(const std::string& filename="");
379 //std::string getTime(int whichrow=-1, bool showdate=true) const;
380 std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
381 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
382
383 // returns unit, conversion frame, doppler, base-frame
384
385 /**
386 * Get the frequency set up
387 * This is forwarded to the STFrequencies subtable
388 * @return unit, frame, doppler
389 */
390 std::vector<std::string> getCoordInfo() const
391 { return freqTable_.getInfo(); };
392
393 void setCoordInfo(std::vector<string> theinfo)
394 { return freqTable_.setInfo(theinfo); };
395
396
397 std::vector<double> getAbcissa(int whichrow) const;
398
399 std::vector<float> getWeather(int whichrow) const;
400
401 std::string getAbcissaLabel(int whichrow) const;
402 std::vector<double> getRestFrequencies() const
403 { return moleculeTable_.getRestFrequencies(); }
404 std::vector<double> getRestFrequency(int id) const
405 { return moleculeTable_.getRestFrequency(id); }
406
407 /**
408 void setRestFrequencies(double rf, const std::string& name = "",
409 const std::string& = "Hz");
410 **/
411 // Modified by Takeshi Nakazato 05/09/2008
412 /***
413 void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
414 const std::string& = "Hz");
415 ***/
416 void setRestFrequencies(vector<double> rf,
417 const vector<std::string>& name = vector<std::string>(1,""),
418 const std::string& = "Hz");
419
420 //void setRestFrequencies(const std::string& name);
421 void setRestFrequencies(const vector<std::string>& name);
422
423 void shift(int npix);
424
425 casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
426
427 void convertDirection(const std::string& newframe);
428
429 STFrequencies& frequencies() { return freqTable_; }
430 const STFrequencies& frequencies() const { return freqTable_; }
431 STWeather& weather() { return weatherTable_; }
432 const STWeather& weather() const { return weatherTable_; }
433 STFocus& focus() { return focusTable_; }
434 const STFocus& focus() const { return focusTable_; }
435 STTcal& tcal() { return tcalTable_; }
436 const STTcal& tcal() const { return tcalTable_; }
437 STMolecules& molecules() { return moleculeTable_; }
438 const STMolecules& molecules() const { return moleculeTable_; }
439 STHistory& history() { return historyTable_; }
440 const STHistory& history() const { return historyTable_; }
441 STFit& fit() { return fitTable_; }
442 const STFit& fit() const { return fitTable_; }
443
444 std::vector<std::string> columnNames() const;
445
446 void addFit(const STFitEntry& fit, int row);
447 STFitEntry getFit(int row) const
448 { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
449
450 //Added by TT
451 /**
452 * Get the antenna name
453 * @return antenna name string
454 */
455 casa::String getAntennaName() const;
456
457 /**
458 * For GBT MS data only. check a scan list
459 * against the information found in GBT_GO table for
460 * scan number orders to get correct pairs.
461 * @param[in] scan list
462 * @return status
463 */
464 int checkScanInfo(const std::vector<int>& scanlist) const;
465
466 /**
467 * Get the direction as a vector, for a specific row
468 * @param[in] whichrow the row numbyyer
469 * @return the direction in a vector
470 */
471 std::vector<double> getDirectionVector(int whichrow) const;
472
473 /**
474 * Set a flag indicating whether the data was parallactified
475 * @param[in] flag true or false
476 */
477 void parallactify(bool flag)
478 { focus().setParallactify(flag); }
479
480 /**
481 * Reshape spectrum
482 * @param[in] nmin, nmax minimum and maximum channel
483 * @param[in] irow row number
484 *
485 * 30/07/2008 Takeshi Nakazato
486 **/
487 void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
488 void reshapeSpectrum( int nmin, int nmax, int irow ) ;
489
490 /**
491 * Change channel number under fixed bandwidth
492 * @param[in] nchan, dnu new channel number and spectral resolution
493 * @param[in] irow row number
494 *
495 * 27/08/2008 Takeshi Nakazato
496 **/
497 void regridChannel( int nchan, double dnu ) ;
498 void regridChannel( int nchan, double dnu, int irow ) ;
499
500 bool getFlagtraFast(casa::uInt whichrow);
501
502 void polyBaseline(const std::vector<bool>& mask,
503 int order,
504 bool getResidual=true,
505 const std::string& progressInfo="true,1000",
506 const bool outLogger=false,
507 const std::string& blfile="");
508 void autoPolyBaseline(const std::vector<bool>& mask,
509 int order,
510 const std::vector<int>& edge,
511 float threshold=3.0,
512 int chanAvgLimit=1,
513 bool getResidual=true,
514 const std::string& progressInfo="true,1000",
515 const bool outLogger=false,
516 const std::string& blfile="");
517 void cubicSplineBaseline(const std::vector<bool>& mask,
518 int nPiece,
519 float thresClip,
520 int nIterClip,
521 bool getResidual=true,
522 const std::string& progressInfo="true,1000",
523 const bool outLogger=false,
524 const std::string& blfile="");
525 void autoCubicSplineBaseline(const std::vector<bool>& mask,
526 int nPiece,
527 float thresClip,
528 int nIterClip,
529 const std::vector<int>& edge,
530 float threshold=3.0,
531 int chanAvgLimit=1,
532 bool getResidual=true,
533 const std::string& progressInfo="true,1000",
534 const bool outLogger=false,
535 const std::string& blfile="");
536 void sinusoidBaseline(const std::vector<bool>& mask,
537 const bool applyFFT,
538 const std::string& fftMethod,
539 const std::string& fftThresh,
540 const std::vector<int>& addNWaves,
541 const std::vector<int>& rejectNWaves,
542 float thresClip,
543 int nIterClip,
544 bool getResidual=true,
545 const std::string& progressInfo="true,1000",
546 const bool outLogger=false,
547 const std::string& blfile="");
548 void autoSinusoidBaseline(const std::vector<bool>& mask,
549 const bool applyFFT,
550 const std::string& fftMethod,
551 const std::string& fftThresh,
552 const std::vector<int>& addNWaves,
553 const std::vector<int>& rejectNWaves,
554 float thresClip,
555 int nIterClip,
556 const std::vector<int>& edge,
557 float threshold=3.0,
558 int chanAvgLimit=1,
559 bool getResidual=true,
560 const std::string& progressInfo="true,1000",
561 const bool outLogger=false,
562 const std::string& blfile="");
563 std::vector<float> execFFT(const int whichrow,
564 const std::vector<bool>& inMask,
565 bool getRealImag=false,
566 bool getAmplitudeOnly=false);
567 float getRms(const std::vector<bool>& mask, int whichrow);
568 std::string formatBaselineParams(const std::vector<float>& params,
569 const std::vector<bool>& fixed,
570 float rms,
571 int nClipped,
572 const std::string& masklist,
573 int whichrow,
574 bool verbose=false,
575 int start=-1,
576 int count=-1,
577 bool resetparamid=false) const;
578 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
579 const std::vector<float>& params,
580 const std::vector<bool>& fixed,
581 float rms,
582 int nClipped,
583 const std::string& masklist,
584 int whichrow,
585 bool verbose=false) const;
586
587
588private:
589
590 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
591
592 /**
593 * Turns a time value into a formatted string
594 * @param x
595 * @return
596 */
597 std::string formatSec(casa::Double x) const;
598
599 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
600 std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
601
602 /**
603 * Turns a casa::MDirection into a nicely formatted string
604 * @param md an casa::MDirection
605 * @return
606 */
607 std::string formatDirection(const casa::MDirection& md) const;
608
609 /**
610 * Create a unique file name for the paged (temporary) table
611 * @return just the name
612 */
613 static casa::String generateName();
614
615 /**
616 * attach to cached columns
617 */
618 void attach();
619
620 /**
621 * Set up the main casa::Table
622 */
623 void setupMainTable();
624
625 void attachSubtables();
626 void copySubtables(const Scantable& other);
627
628 /**
629 * Convert an "old" asap1 style row index into a new index
630 * @param[in] therow
631 * @return and index into @table_
632 */
633 int rowToScanIndex(int therow);
634
635 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
636
637 static const casa::uInt version_ = 3;
638
639 STSelector selector_;
640
641 casa::Table::TableType type_;
642
643 // the actual data
644 casa::Table table_;
645 casa::Table originalTable_;
646
647 STTcal tcalTable_;
648 STFrequencies freqTable_;
649 STWeather weatherTable_;
650 STFocus focusTable_;
651 STMolecules moleculeTable_;
652 STHistory historyTable_;
653 STFit fitTable_;
654
655 // Cached Columns to avoid reconstructing them for each row get/put
656 casa::ScalarColumn<casa::Double> integrCol_;
657 casa::MDirection::ScalarColumn dirCol_;
658 casa::MEpoch::ScalarColumn timeCol_;
659 casa::ScalarColumn<casa::Float> azCol_;
660 casa::ScalarColumn<casa::Float> elCol_;
661 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
662 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
663 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
664 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
665 casa::ArrayColumn<casa::uChar> flagsCol_;
666
667 // id in frequencies table
668 casa::ScalarColumn<casa::uInt> mfreqidCol_;
669 // id in tcal table
670 casa::ScalarColumn<casa::uInt> mtcalidCol_;
671
672 casa::ArrayColumn<casa::String> histitemCol_;
673 casa::ScalarColumn<casa::Int> mfitidCol_;
674 casa::ScalarColumn<casa::uInt> mweatheridCol_;
675
676 casa::ScalarColumn<casa::uInt> mfocusidCol_;
677
678 casa::ScalarColumn<casa::uInt> mmolidCol_;
679
680 static std::map<std::string, STPol::STPolFactory *> factories_;
681 void initFactories();
682
683 /**
684 * Add an auxiliary column to the main table and attach it to a
685 * cached column. Use for adding new columns that the original asap2
686 * tables do not have.
687 * @param[in] col reference to the cached column to be attached
688 * @param[in] colName column name in asap table
689 * @param[in] defValue default value to fill in the column
690 *
691 * 25/10/2009 Wataru Kawasaki
692 */
693 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
694 const casa::String&,
695 const T2&);
696 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
697 const casa::String&,
698 const casa::Array<T2>&);
699
700 void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
701 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
702 const std::vector<bool>& mask,
703 int nPiece,
704 std::vector<int>& idxEdge,
705 std::vector<float>& params,
706 int& nClipped,
707 float thresClip=3.0,
708 int nIterClip=1,
709 bool getResidual=true);
710 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
711 const std::vector<bool>& mask,
712 const std::vector<int>& waveNumbers,
713 std::vector<float>& params,
714 int& nClipped,
715 float thresClip=3.0,
716 int nIterClip=1,
717 bool getResidual=true);
718 void selectWaveNumbers(const int whichrow,
719 const std::vector<bool>& chanMask,
720 const bool applyFFT,
721 const std::string& fftMethod,
722 const std::string& fftThresh,
723 const std::vector<int>& addNWaves,
724 const std::vector<int>& rejectNWaves,
725 std::vector<int>& nWaves);
726 void parseThresholdExpression(const std::string& fftThresh,
727 std::string& fftThAttr,
728 float& fftThSigma,
729 int& fftThTop);
730 void doSelectWaveNumbers(const int whichrow,
731 const std::vector<bool>& chanMask,
732 const std::string& fftMethod,
733 const float fftThSigma,
734 const int fftThTop,
735 const std::string& fftThAttr,
736 std::vector<int>& nWaves);
737 void addAuxWaveNumbers(const std::vector<int>& addNWaves,
738 const std::vector<int>& rejectNWaves,
739 std::vector<int>& nWaves);
740 bool hasSameNchanOverIFs();
741 std::string getMaskRangeList(const std::vector<bool>& mask,
742 int whichrow,
743 const casa::String& coordInfo,
744 bool hasSameNchan,
745 bool verbose=false);
746 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
747 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const;
748 std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const;
749 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
750 //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
751 void outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, Fitter& fitter);
752 void outputFittingResult(bool outLogger, bool outTextFile, 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);
753 void outputFittingResult(bool outLogger, bool outTextFile, 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);
754 void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
755 void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
756
757 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
758
759
760};
761
762} // namespace
763
764#endif
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