source: trunk/src/Scantable.h@ 2797

Last change on this file since 2797 was 2791, checked in by Malte Marquarding, 12 years ago

Ticket #289: added anility to set Tsys, both for scalar and vector values
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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#include <coordinates/Coordinates/SpectralCoordinate.h>
31#include <measures/TableMeasures/ScalarMeasColumn.h>
32#include <scimath/Mathematics/FFTServer.h>
33#include <tables/Tables/ArrayColumn.h>
34#include <tables/Tables/ScalarColumn.h>
35#include <tables/Tables/Table.h>
36
37#include "MathUtils.h"
38#include "STBaselineEnum.h"
39#include "STFit.h"
40#include "STFitEntry.h"
41#include "STFocus.h"
42#include "STFrequencies.h"
43#include "STHeader.h"
44#include "STHistory.h"
45#include "STMolecules.h"
46#include "STPol.h"
47#include "STSelector.h"
48#include "STTcal.h"
49#include "STWeather.h"
50
51namespace asap {
52
53class Fitter;
54class STLineFinder;
55class STBaselineTable;
56
57/**
58 * This class contains and wraps a casa::Table, which is used to store
59 * all the information. This can be either a MemoryTable or a
60 * disk based Table.
61 * It provides access functions to the underlying table
62 * It contains n subtables:
63 * @li weather
64 * @li frequencies
65 * @li molecules
66 * @li tcal
67 * @li focus
68 * @li fits
69 *
70 * @brief The main ASAP data container
71 * @author Malte Marquarding
72 * @date
73 * @version
74*/
75class Scantable
76{
77
78friend class STMath;
79
80public:
81 /**
82 * Default constructor
83 */
84 explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
85
86 /**
87 * Create a Scantable object from an existing table on disk
88 * @param[in] name the name of the existing Scantable
89 */
90 explicit Scantable(const std::string& name,
91 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 std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
320 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
321
322 //TT addition
323 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
324
325 /**
326 * Get the number of channels in the data or a specific IF. This currently
327 * varies only with IF number
328 * @param ifno the IF number to get the number of channels for.
329 * If ifno<0 the number is retrieved from the header.
330 * @return an integer number
331 */
332 int nchan(int ifno=-1) const;
333 int getChannels(int whichrow) const;
334
335 int ncycle(int scanno=-1) const;
336
337
338 double getInterval(int whichrow) const
339 { return integrCol_(whichrow); }
340
341 float getTsys(int whichrow) const
342 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
343 std::vector<float> getTsysSpectrum(int whichrow) const ;
344
345 void setTsys(const std::vector<float>& newvals, int whichrow);
346
347 float getElevation(int whichrow) const
348 { return elCol_(whichrow); }
349 float getAzimuth(int whichrow) const
350 { return azCol_(whichrow); }
351 float getParAngle(int whichrow) const
352 { return focus().getParAngle(mfocusidCol_(whichrow)); }
353 int getTcalId(int whichrow) const
354 { return mtcalidCol_(whichrow); }
355
356 std::string getSourceName(int whichrow) const
357 { return srcnCol_(whichrow); }
358
359 std::vector<bool> getMask(int whichrow) const;
360 std::vector<float> getSpectrum(int whichrow,
361 const std::string& poltype = "" ) const;
362
363 void setSpectrum(const std::vector<float>& spec, int whichrow);
364
365 std::string getPolarizationLabel(int index, const std::string& ptype) const
366 { return STPol::getPolLabel(index, ptype ); }
367
368 /**
369 * Write the Scantable to disk
370 * @param filename the output file name
371 */
372 void makePersistent(const std::string& filename);
373
374 std::vector<std::string> getHistory() const
375 { return historyTable_.getHistory(); };
376
377 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
378
379 void appendToHistoryTable(const STHistory& otherhist)
380 { historyTable_.append(otherhist); }
381
382 std::string headerSummary();
383 void summary(const std::string& filename="");
384 std::string oldheaderSummary();
385 // std::string summary();
386 void oldsummary(const std::string& filename="");
387
388 //std::string getTime(int whichrow=-1, bool showdate=true) const;
389 std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
390 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
391
392 // returns unit, conversion frame, doppler, base-frame
393
394 /**
395 * Get the frequency set up
396 * This is forwarded to the STFrequencies subtable
397 * @return unit, frame, doppler
398 */
399 std::vector<std::string> getCoordInfo() const
400 { return freqTable_.getInfo(); };
401
402 void setCoordInfo(std::vector<string> theinfo)
403 { return freqTable_.setInfo(theinfo); };
404
405
406 std::vector<double> getAbcissa(int whichrow) const;
407
408 std::vector<float> getWeather(int whichrow) const;
409
410 std::string getAbcissaLabel(int whichrow) const;
411 std::vector<double> getRestFrequencies() const
412 { return moleculeTable_.getRestFrequencies(); }
413 std::vector<double> getRestFrequency(int id) const
414 { return moleculeTable_.getRestFrequency(id); }
415
416 /**
417 void setRestFrequencies(double rf, const std::string& name = "",
418 const std::string& = "Hz");
419 **/
420 // Modified by Takeshi Nakazato 05/09/2008
421 /***
422 void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
423 const std::string& = "Hz");
424 ***/
425 void setRestFrequencies(vector<double> rf,
426 const vector<std::string>& name = vector<std::string>(1,""),
427 const std::string& = "Hz");
428
429 //void setRestFrequencies(const std::string& name);
430 void setRestFrequencies(const vector<std::string>& name);
431
432 void shift(int npix);
433
434 casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
435
436 void convertDirection(const std::string& newframe);
437
438 STFrequencies& frequencies() { return freqTable_; }
439 const STFrequencies& frequencies() const { return freqTable_; }
440 STWeather& weather() { return weatherTable_; }
441 const STWeather& weather() const { return weatherTable_; }
442 STFocus& focus() { return focusTable_; }
443 const STFocus& focus() const { return focusTable_; }
444 STTcal& tcal() { return tcalTable_; }
445 const STTcal& tcal() const { return tcalTable_; }
446 STMolecules& molecules() { return moleculeTable_; }
447 const STMolecules& molecules() const { return moleculeTable_; }
448 STHistory& history() { return historyTable_; }
449 const STHistory& history() const { return historyTable_; }
450 STFit& fit() { return fitTable_; }
451 const STFit& fit() const { return fitTable_; }
452
453 std::vector<std::string> columnNames() const;
454
455 void addFit(const STFitEntry& fit, int row);
456 STFitEntry getFit(int row) const
457 { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
458
459 //Added by TT
460 /**
461 * Get the antenna name
462 * @return antenna name string
463 */
464 casa::String getAntennaName() const;
465
466 /**
467 * For GBT MS data only. check a scan list
468 * against the information found in GBT_GO table for
469 * scan number orders to get correct pairs.
470 * @param[in] scan list
471 * @return status
472 */
473 int checkScanInfo(const std::vector<int>& scanlist) const;
474
475 /**
476 * Get the direction as a vector, for a specific row
477 * @param[in] whichrow the row numbyyer
478 * @return the direction in a vector
479 */
480 std::vector<double> getDirectionVector(int whichrow) const;
481
482 /**
483 * Set a flag indicating whether the data was parallactified
484 * @param[in] flag true or false
485 */
486 void parallactify(bool flag)
487 { focusTable_.setParallactify(flag); }
488
489 /**
490 * Reshape spectrum
491 * @param[in] nmin, nmax minimum and maximum channel
492 * @param[in] irow row number
493 *
494 * 30/07/2008 Takeshi Nakazato
495 **/
496 void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
497 void reshapeSpectrum( int nmin, int nmax, int irow ) ;
498
499 /**
500 * Change channel number under fixed bandwidth
501 * @param[in] nchan, dnu new channel number and spectral resolution
502 * @param[in] irow row number
503 *
504 * 27/08/2008 Takeshi Nakazato
505 **/
506 void regridChannel( int nchan, double dnu ) ;
507 void regridChannel( int nchan, double dnu, int irow ) ;
508 void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
509 void regridSpecChannel( double dnu, int nchan=-1 ) ;
510
511 bool getFlagtraFast(casa::uInt whichrow);
512
513 std::vector<std::string> applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
514 std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
515 void polyBaseline(const std::vector<bool>& mask,
516 int order,
517 float thresClip,
518 int nIterClip,
519 bool getResidual=true,
520 const std::string& progressInfo="true,1000",
521 const bool outLogger=false,
522 const std::string& blfile="",
523 const std::string& bltable="");
524 void autoPolyBaseline(const std::vector<bool>& mask,
525 int order,
526 float thresClip,
527 int nIterClip,
528 const std::vector<int>& edge,
529 float threshold=3.0,
530 int chanAvgLimit=1,
531 bool getResidual=true,
532 const std::string& progressInfo="true,1000",
533 const bool outLogger=false,
534 const std::string& blfile="",
535 const std::string& bltable="");
536 void chebyshevBaseline(const std::vector<bool>& mask,
537 int order,
538 float thresClip,
539 int nIterClip,
540 bool getResidual=true,
541 const std::string& progressInfo="true,1000",
542 const bool outLogger=false,
543 const std::string& blfile="",
544 const std::string& bltable="");
545 void autoChebyshevBaseline(const std::vector<bool>& mask,
546 int order,
547 float thresClip,
548 int nIterClip,
549 const std::vector<int>& edge,
550 float threshold=3.0,
551 int chanAvgLimit=1,
552 bool getResidual=true,
553 const std::string& progressInfo="true,1000",
554 const bool outLogger=false,
555 const std::string& blfile="",
556 const std::string& bltable="");
557 void cubicSplineBaseline(const std::vector<bool>& mask,
558 int nPiece,
559 float thresClip,
560 int nIterClip,
561 bool getResidual=true,
562 const std::string& progressInfo="true,1000",
563 const bool outLogger=false,
564 const std::string& blfile="",
565 const std::string& bltable="");
566 void autoCubicSplineBaseline(const std::vector<bool>& mask,
567 int nPiece,
568 float thresClip,
569 int nIterClip,
570 const std::vector<int>& edge,
571 float threshold=3.0,
572 int chanAvgLimit=1,
573 bool getResidual=true,
574 const std::string& progressInfo="true,1000",
575 const bool outLogger=false,
576 const std::string& blfile="",
577 const std::string& bltable="");
578 void sinusoidBaseline(const std::vector<bool>& mask,
579 const std::string& fftInfo,
580 const std::vector<int>& addNWaves,
581 const std::vector<int>& rejectNWaves,
582 float thresClip,
583 int nIterClip,
584 bool getResidual=true,
585 const std::string& progressInfo="true,1000",
586 const bool outLogger=false,
587 const std::string& blfile="",
588 const std::string& bltable="");
589 void autoSinusoidBaseline(const std::vector<bool>& mask,
590 const std::string& fftInfo,
591 const std::vector<int>& addNWaves,
592 const std::vector<int>& rejectNWaves,
593 float thresClip,
594 int nIterClip,
595 const std::vector<int>& edge,
596 float threshold=3.0,
597 int chanAvgLimit=1,
598 bool getResidual=true,
599 const std::string& progressInfo="true,1000",
600 const bool outLogger=false,
601 const std::string& blfile="",
602 const std::string& bltable="");
603 std::vector<float> execFFT(const int whichrow,
604 const std::vector<bool>& inMask,
605 bool getRealImag=false,
606 bool getAmplitudeOnly=false);
607 float getRms(const std::vector<bool>& mask, int whichrow);
608 std::string formatBaselineParams(const std::vector<float>& params,
609 const std::vector<bool>& fixed,
610 float rms,
611 int nClipped,
612 const std::string& masklist,
613 int whichrow,
614 bool verbose=false,
615 bool csvformat=false,
616 int start=-1,
617 int count=-1,
618 bool resetparamid=false) const;
619 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
620 const std::vector<float>& params,
621 const std::vector<bool>& fixed,
622 float rms,
623 int nClipped,
624 const std::string& masklist,
625 int whichrow,
626 bool verbose=false,
627 bool csvformat=false) const;
628 std::vector<uint> getMoleculeIdColumnData() const;
629 void setMoleculeIdColumnData(const std::vector<uint>& molids);
630 double calculateModelSelectionCriteria(const std::string& valname,
631 const std::string& blfunc,
632 int order,
633 const std::vector<bool>& inMask,
634 int whichrow,
635 bool useLineFinder,
636 const std::vector<int>& edge,
637 float threshold,
638 int chanAvgLimit);
639 static std::vector<bool> getMaskFromMaskList(const int nchan,
640 const std::vector<int>& masklist);
641 static casa::Vector<casa::uInt> getMaskListFromMask(
642 const std::vector<bool>& mask);
643 static std::vector<int> splitToIntList(const std::string& str,
644 const char delim);
645 static std::vector<string> splitToStringList(const std::string& str,
646 const char delim);
647
648 void dropXPol();
649
650private:
651
652 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
653
654 /**
655 * Turns a time value into a formatted string
656 * @param x
657 * @return
658 */
659 std::string formatSec(casa::Double x) const;
660
661 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
662 std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
663
664 /**
665 * Turns a casa::MDirection into a nicely formatted string
666 * @param md an casa::MDirection
667 * @return
668 */
669 std::string formatDirection(const casa::MDirection& md) const;
670
671 /**
672 * Create a unique file name for the paged (temporary) table
673 * @return just the name
674 */
675 static casa::String generateName();
676
677 /**
678 * attach to cached columns
679 */
680 void attach();
681
682 /**
683 * Set up the main casa::Table
684 */
685 void setupMainTable();
686
687 void attachSubtables();
688 void copySubtables(const Scantable& other);
689
690 /**
691 * Convert an "old" asap1 style row index into a new index
692 * @param[in] therow
693 * @return and index into @table_
694 */
695 int rowToScanIndex(int therow);
696
697 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
698
699 static const casa::uInt version_ = 4;
700
701 STSelector selector_;
702
703 casa::Table::TableType type_;
704
705 // the actual data
706 casa::Table table_;
707 casa::Table originalTable_;
708
709 STTcal tcalTable_;
710 STFrequencies freqTable_;
711 STWeather weatherTable_;
712 STFocus focusTable_;
713 STMolecules moleculeTable_;
714 STHistory historyTable_;
715 STFit fitTable_;
716
717 // Cached Columns to avoid reconstructing them for each row get/put
718 casa::ScalarColumn<casa::Double> integrCol_;
719 casa::MDirection::ScalarColumn dirCol_;
720 casa::MEpoch::ScalarColumn timeCol_;
721 casa::ScalarColumn<casa::Float> azCol_;
722 casa::ScalarColumn<casa::Float> elCol_;
723 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
724 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
725 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
726 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
727 casa::ArrayColumn<casa::uChar> flagsCol_;
728
729 // id in frequencies table
730 casa::ScalarColumn<casa::uInt> mfreqidCol_;
731 // id in tcal table
732 casa::ScalarColumn<casa::uInt> mtcalidCol_;
733
734 casa::ArrayColumn<casa::String> histitemCol_;
735 casa::ScalarColumn<casa::Int> mfitidCol_;
736 casa::ScalarColumn<casa::uInt> mweatheridCol_;
737
738 casa::ScalarColumn<casa::uInt> mfocusidCol_;
739
740 casa::ScalarColumn<casa::uInt> mmolidCol_;
741
742 static std::map<std::string, STPol::STPolFactory *> factories_;
743 void initFactories();
744
745 /**
746 * Add an auxiliary column to the main table and attach it to a
747 * cached column. Use for adding new columns that the original asap2
748 * tables do not have.
749 * @param[in] col reference to the cached column to be attached
750 * @param[in] colName column name in asap table
751 * @param[in] defValue default value to fill in the column
752 *
753 * 25/10/2009 Wataru Kawasaki
754 */
755 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
756 const casa::String&,
757 const T2&);
758 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
759 const casa::String&,
760 const casa::Array<T2>&);
761
762 double getNormalPolynomial(int n, double x);
763 double getChebyshevPolynomial(int n, double x);
764 std::vector<std::vector<double> > getPolynomialModel(int order,
765 int nchan,
766 double (Scantable::*pfunc)(int, double));
767 std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
768 double (Scantable::*pfunc)(int, double),
769 std::vector<int>& nChanNos);
770 std::vector<float> doPolynomialFitting(const std::vector<float>& data,
771 const std::vector<bool>& mask,
772 int order,
773 std::vector<float>& params,
774 float& rms,
775 std::vector<bool>& finalMask,
776 float clipth,
777 int clipn);
778 std::vector<float> doPolynomialFitting(const std::vector<float>& data,
779 const std::vector<bool>& mask,
780 int order,
781 std::vector<float>& params,
782 float& rms,
783 std::vector<bool>& finalMask,
784 int& nClipped,
785 float thresClip=3.0,
786 int nIterClip=0,
787 bool getResidual=true);
788 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
789 const std::vector<bool>& mask,
790 int order,
791 std::vector<float>& params,
792 float& rms,
793 std::vector<bool>& finalMask,
794 float clipth,
795 int clipn);
796 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
797 const std::vector<bool>& mask,
798 int order,
799 std::vector<float>& params,
800 float& rms,
801 std::vector<bool>& finalMask,
802 int& nClipped,
803 float thresClip=3.0,
804 int nIterClip=0,
805 bool getResidual=true);
806 std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
807 const std::vector<bool>& mask,
808 const std::vector<std::vector<double> >& model,
809 std::vector<float>& params,
810 float& rms,
811 std::vector<bool>& finalMask,
812 int& nClipped,
813 float thresClip=3.0,
814 int nIterClip=0,
815 bool getResidual=true);
816 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
817 const std::vector<bool>& mask,
818 std::vector<int>& idxEdge,
819 std::vector<float>& params,
820 float& rms,
821 std::vector<bool>& finalMask,
822 float clipth,
823 int clipn);
824 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
825 const std::vector<bool>& mask,
826 int nPiece,
827 std::vector<int>& idxEdge,
828 std::vector<float>& params,
829 float& rms,
830 std::vector<bool>& finalMask,
831 float clipth,
832 int clipn);
833 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
834 const std::vector<bool>& mask,
835 int nPiece,
836 bool useGivenPieceBoundary,
837 std::vector<int>& idxEdge,
838 std::vector<float>& params,
839 float& rms,
840 std::vector<bool>& finalMask,
841 int& nClipped,
842 float thresClip=3.0,
843 int nIterClip=0,
844 bool getResidual=true);
845 std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
846 const std::vector<bool>& mask,
847 const std::vector<std::vector<double> >& model,
848 int nPiece,
849 bool useGivenPieceBoundary,
850 std::vector<int>& idxEdge,
851 std::vector<float>& params,
852 float& rms,
853 std::vector<bool>& finalMask,
854 int& nClipped,
855 float thresClip=3.0,
856 int nIterClip=0,
857 bool getResidual=true);
858 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
859 const std::vector<bool>& mask,
860 const std::vector<int>& waveNumbers,
861 std::vector<float>& params,
862 float& rms,
863 std::vector<bool>& finalMask,
864 float clipth,
865 int clipn);
866 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
867 const std::vector<bool>& mask,
868 const std::vector<int>& waveNumbers,
869 std::vector<float>& params,
870 float& rms,
871 std::vector<bool>& finalMask,
872 int& nClipped,
873 float thresClip=3.0,
874 int nIterClip=0,
875 bool getResidual=true);
876 std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
877 std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
878 std::vector<int>& nChanNos);
879 std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
880 const std::vector<int>& rejectNWaves);
881 std::vector<int> selectWaveNumbers(const int whichrow,
882 const std::vector<bool>& chanMask,
883 //const std::string& fftInfo,
884 const bool applyFFT,
885 const std::string& fftMethod,
886 const std::string& fftThresh,
887 const std::vector<int>& addNWaves,
888 const std::vector<int>& rejectNWaves);
889 int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
890 void parseFFTInfo(const std::string& fftInfo,
891 bool& applyFFT,
892 std::string& fftMethod,
893 std::string& fftThresh);
894 void parseFFTThresholdInfo(const std::string& fftThresh,
895 std::string& fftThAttr,
896 float& fftThSigma,
897 int& fftThTop);
898 void doSelectWaveNumbers(const int whichrow,
899 const std::vector<bool>& chanMask,
900 const std::string& fftMethod,
901 const float fftThSigma,
902 const int fftThTop,
903 const std::string& fftThAttr,
904 std::vector<int>& nWaves);
905 void addAuxWaveNumbers(const int whichrow,
906 const std::vector<int>& addNWaves,
907 const std::vector<int>& rejectNWaves,
908 std::vector<int>& nWaves);
909 void setWaveNumberListUptoNyquistFreq(const int whichrow,
910 std::vector<int>& nWaves);
911 void initialiseBaselining(const std::string& blfile,
912 std::ofstream& ofs,
913 const bool outLogger,
914 bool& outTextFile,
915 bool& csvFormat,
916 casa::String& coordInfo,
917 bool& hasSameNchan,
918 const std::string& progressInfo,
919 bool& showProgress,
920 int& minNRow,
921 casa::Vector<casa::Double>& timeSecCol);
922 void finaliseBaselining(const bool outBaselineTable,
923 STBaselineTable* pbt,
924 const string& bltable,
925 const bool outTextFile,
926 std::ofstream& ofs);
927 void initLineFinder(const std::vector<int>& edge,
928 const float threshold,
929 const int chanAvgLimit,
930 STLineFinder& lineFinder);
931 bool hasSameNchanOverIFs();
932 std::string getMaskRangeList(const std::vector<bool>& mask,
933 int whichrow,
934 const casa::String& coordInfo,
935 bool hasSameNchan,
936 bool verbose=false);
937 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
938 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
939 std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
940 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
941 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
942 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);
943 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);
944 void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
945 void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
946
947 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
948
949 double doCalculateModelSelectionCriteria(const std::string& valname,
950 const std::vector<float>& spec,
951 const std::vector<bool>& mask,
952 const std::string& blfunc,
953 int order);
954 double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
955 std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
956 void parseBlInfo(const std::string& blInfo, int& whichrow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF);
957 std::vector<float> doApplyBaselineTable(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms);
958 std::vector<float> doSubtractBaseline(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, std::vector<bool>& finalmask, float clipth, int clipn, bool uself, int irow, float lfth, std::vector<int>& lfedge, int lfavg);
959
960};
961} // namespace
962
963#endif
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