source: branches/plotter2/src/Scantable.h@ 2849

Last change on this file since 2849 was 2820, checked in by Malte Marquarding, 11 years ago

Issue #293: added scantbale.drop_history and added extra parameters to scantable.history to allow selection of rows

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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 * @param stype The name of the source
160 */
161 void setSourceName(const std::string& name);
162
163
164 /**
165 * The number of scans in the table
166 * @return number of scans in the table
167 */
168 int nscan() const;
169
170 casa::MEpoch::Types getTimeReference() const;
171
172
173 casa::MEpoch getEpoch(int whichrow) const;
174
175 /**
176 * Get global antenna position
177 * @return casa::MPosition
178 */
179 casa::MPosition getAntennaPosition() const;
180
181 /**
182 * the @ref casa::MDirection for a specific row
183 * @param[in] whichrow the row number
184 * return casa::MDirection
185 */
186 casa::MDirection getDirection( int whichrow ) const;
187
188 /**
189 * get the direction type as a string, e.g. "J2000"
190 * @param[in] whichrow the row number
191 * return the direction string
192 */
193 std::string getDirectionString( int whichrow ) const;
194
195 /**
196 * set the direction type as a string, e.g. "J2000"
197 * @param[in] refstr the direction type
198 */
199 void setDirectionRefString(const std::string& refstr="");
200
201 /**
202 * get the direction reference string
203 * @return a string describing the direction reference
204 */
205 std::string getDirectionRefString() const;
206
207 /**
208 * Return the Flux unit of the data, e.g. "Jy" or "K"
209 * @return string
210 */
211 std::string getFluxUnit() const;
212
213 /**
214 * Set the Flux unit of the data
215 * @param unit a string representing the unit, e.g "Jy" or "K"
216 */
217 void setFluxUnit( const std::string& unit );
218
219 /**
220 * Set the Stokes type of the data
221 * @param feedtype a string representing the type, e.g "circular" or "linear"
222 */
223 void setFeedType( const std::string& feedtype );
224
225 /**
226 *
227 * @param instrument a string representing an insturment. see xxx
228 */
229 void setInstrument( const std::string& instrument );
230
231 /**
232 * (Re)calculate the azimuth and elevationnfor all rows
233 */
234 void calculateAZEL();
235
236 /**
237 * "hard" flag the data, this flags everything selected in setSelection()
238 * param[in] msk a boolean mask of length nchan describing the points to
239 * to be flagged
240 */
241 //void flag( const std::vector<bool>& msk = std::vector<bool>());
242 //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
243
244 void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
245
246 /**
247 * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
248 * param[in] rows list of row numbers to be flagged
249 */
250 void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
251
252 /**
253 * Get flagRow info at the specified row. If true, the whole data
254 * at the row should be flagged.
255 */
256 bool getFlagRow(int whichrow) const
257 { return (flagrowCol_(whichrow) > 0); }
258
259 /**
260 * Flag the data outside a specified range (in a channel-based manner).
261 * (CAS-1807 Wataru Kawasaki)
262 */
263 void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
264
265 /**
266 * Return a list of booleans with the size of nchan for a specified row, to get info
267 * about which channel is clipped.
268 */
269 std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
270 void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
271 casa::Vector<casa::uChar> flgs);
272
273 /**
274 * Return a list of row numbers with respect to the original table.
275 * @return a list of unsigned ints
276 */
277 std::vector<unsigned int> rownumbers() const;
278
279
280 /**
281 * Get the number of beams in the data or a specific scan
282 * @param scanno the scan number to get the number of beams for.
283 * If scanno<0 the number is retrieved from the header.
284 * @return an integer number
285 */
286 int nbeam(int scanno=-1) const;
287 /**
288 * Get the number of IFs in the data or a specific scan
289 * @param scanno the scan number to get the number of IFs for.
290 * If scanno<0 the number is retrieved from the header.
291 * @return an integer number
292 */
293 int nif(int scanno=-1) const;
294 /**
295 * Get the number of polarizations in the data or a specific scan
296 * @param scanno the scan number to get the number of polarizations for.
297 * If scanno<0 the number is retrieved from the header.
298 * @return an integer number
299 */
300 int npol(int scanno=-1) const;
301
302 std::string getPolType() const;
303
304
305 /**
306 * Get the number of integartion cycles
307 * @param scanno the scan number to get the number of rows for.
308 * If scanno<0 the number is retrieved from the header.
309 * @return the number of rows (for the specified scanno)
310 */
311 int nrow(int scanno=-1) const;
312
313 int getBeam(int whichrow) const;
314 std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
315
316 int getIF(int whichrow) const;
317 std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
318
319 int getPol(int whichrow) const;
320 std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
321
322 std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
323 int getScan(int whichrow) const { return scanCol_(whichrow); }
324
325 std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
326 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
327
328 //TT addition
329 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
330
331 /**
332 * Get the number of channels in the data or a specific IF. This currently
333 * varies only with IF number
334 * @param ifno the IF number to get the number of channels for.
335 * If ifno<0 the number is retrieved from the header.
336 * @return an integer number
337 */
338 int nchan(int ifno=-1) const;
339 int getChannels(int whichrow) const;
340
341 int ncycle(int scanno=-1) const;
342
343
344 double getInterval(int whichrow) const
345 { return integrCol_(whichrow); }
346
347 float getTsys(int whichrow) const
348 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
349 std::vector<float> getTsysSpectrum(int whichrow) const ;
350
351 void setTsys(const std::vector<float>& newvals, int whichrow);
352
353 float getElevation(int whichrow) const
354 { return elCol_(whichrow); }
355 float getAzimuth(int whichrow) const
356 { return azCol_(whichrow); }
357 float getParAngle(int whichrow) const
358 { return focus().getParAngle(mfocusidCol_(whichrow)); }
359 int getTcalId(int whichrow) const
360 { return mtcalidCol_(whichrow); }
361
362 std::string getSourceName(int whichrow) const
363 { return srcnCol_(whichrow); }
364
365 std::vector<bool> getMask(int whichrow) const;
366 std::vector<float> getSpectrum(int whichrow,
367 const std::string& poltype = "" ) const;
368
369 void setSpectrum(const std::vector<float>& spec, int whichrow);
370
371 std::string getPolarizationLabel(int index, const std::string& ptype) const
372 { return STPol::getPolLabel(index, ptype ); }
373
374 /**
375 * Write the Scantable to disk
376 * @param filename the output file name
377 */
378 void makePersistent(const std::string& filename);
379
380 std::vector<std::string> getHistory(int nrow=-1, int start=0) const
381 { return historyTable_.getHistory(nrow, start); }
382
383 uint historyLength()
384 { return historyTable_.nrow(); }
385
386 void dropHistory() { historyTable_.drop(); }
387
388 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
389
390 void appendToHistoryTable(const STHistory& otherhist)
391 { historyTable_.append(otherhist); }
392
393 std::string headerSummary();
394 void summary(const std::string& filename="");
395 std::string oldheaderSummary();
396 // std::string summary();
397 void oldsummary(const std::string& filename="");
398
399 //std::string getTime(int whichrow=-1, bool showdate=true) const;
400 std::string getTime(int whichrow=-1, bool showdate=true,
401 casa::uInt prec=0) const;
402 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
403
404 // returns unit, conversion frame, doppler, base-frame
405
406 /**
407 * Get the frequency set up
408 * This is forwarded to the STFrequencies subtable
409 * @return unit, frame, doppler
410 */
411 std::vector<std::string> getCoordInfo() const
412 { return freqTable_.getInfo(); };
413
414 void setCoordInfo(std::vector<string> theinfo)
415 { return freqTable_.setInfo(theinfo); };
416
417
418 std::vector<double> getAbcissa(int whichrow) const;
419
420 std::vector<float> getWeather(int whichrow) const;
421
422 std::string getAbcissaLabel(int whichrow) const;
423 std::vector<double> getRestFrequencies() const
424 { return moleculeTable_.getRestFrequencies(); }
425 std::vector<double> getRestFrequency(int id) const
426 { return moleculeTable_.getRestFrequency(id); }
427
428 /**
429 void setRestFrequencies(double rf, const std::string& name = "",
430 const std::string& = "Hz");
431 **/
432 // Modified by Takeshi Nakazato 05/09/2008
433 /***
434 void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
435 const std::string& = "Hz");
436 ***/
437 void setRestFrequencies(vector<double> rf,
438 const vector<std::string>& name = vector<std::string>(1,""),
439 const std::string& = "Hz");
440
441 //void setRestFrequencies(const std::string& name);
442 void setRestFrequencies(const vector<std::string>& name);
443
444 void shift(int npix);
445
446 casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
447
448 void convertDirection(const std::string& newframe);
449
450 STFrequencies& frequencies() { return freqTable_; }
451 const STFrequencies& frequencies() const { return freqTable_; }
452 STWeather& weather() { return weatherTable_; }
453 const STWeather& weather() const { return weatherTable_; }
454 STFocus& focus() { return focusTable_; }
455 const STFocus& focus() const { return focusTable_; }
456 STTcal& tcal() { return tcalTable_; }
457 const STTcal& tcal() const { return tcalTable_; }
458 STMolecules& molecules() { return moleculeTable_; }
459 const STMolecules& molecules() const { return moleculeTable_; }
460 STHistory& history() { return historyTable_; }
461 const STHistory& history() const { return historyTable_; }
462 STFit& fit() { return fitTable_; }
463 const STFit& fit() const { return fitTable_; }
464
465 std::vector<std::string> columnNames() const;
466
467 void addFit(const STFitEntry& fit, int row);
468 STFitEntry getFit(int row) const
469 { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
470
471 //Added by TT
472 /**
473 * Get the antenna name
474 * @return antenna name string
475 */
476 casa::String getAntennaName() const;
477
478 /**
479 * For GBT MS data only. check a scan list
480 * against the information found in GBT_GO table for
481 * scan number orders to get correct pairs.
482 * @param[in] scan list
483 * @return status
484 */
485 int checkScanInfo(const std::vector<int>& scanlist) const;
486
487 /**
488 * Get the direction as a vector, for a specific row
489 * @param[in] whichrow the row numbyyer
490 * @return the direction in a vector
491 */
492 std::vector<double> getDirectionVector(int whichrow) const;
493
494 /**
495 * Set a flag indicating whether the data was parallactified
496 * @param[in] flag true or false
497 */
498 void parallactify(bool flag)
499 { focusTable_.setParallactify(flag); }
500
501 /**
502 * Reshape spectrum
503 * @param[in] nmin, nmax minimum and maximum channel
504 * @param[in] irow row number
505 *
506 * 30/07/2008 Takeshi Nakazato
507 **/
508 void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
509 void reshapeSpectrum( int nmin, int nmax, int irow ) ;
510
511 /**
512 * Change channel number under fixed bandwidth
513 * @param[in] nchan, dnu new channel number and spectral resolution
514 * @param[in] irow row number
515 *
516 * 27/08/2008 Takeshi Nakazato
517 **/
518 void regridChannel( int nchan, double dnu ) ;
519 void regridChannel( int nchan, double dnu, int irow ) ;
520 void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
521 void regridSpecChannel( double dnu, int nchan=-1 ) ;
522
523 bool getFlagtraFast(casa::uInt whichrow);
524
525 std::vector<std::string> applyBaselineTable(const std::string& bltable,
526 const bool returnfitresult,
527 const std::string& outbltable,
528 const bool outbltableexists,
529 const bool overwrite);
530 std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList,
531 const bool returnfitresult,
532 const std::string& outbltable,
533 const bool outbltableexists,
534 const bool overwrite);
535 void polyBaseline(const std::vector<bool>& mask,
536 int order,
537 float thresClip,
538 int nIterClip,
539 bool getResidual=true,
540 const std::string& progressInfo="true,1000",
541 const bool outLogger=false,
542 const std::string& blfile="",
543 const std::string& bltable="");
544 void autoPolyBaseline(const std::vector<bool>& mask,
545 int order,
546 float thresClip,
547 int nIterClip,
548 const std::vector<int>& edge,
549 float threshold=3.0,
550 int chanAvgLimit=1,
551 bool getResidual=true,
552 const std::string& progressInfo="true,1000",
553 const bool outLogger=false,
554 const std::string& blfile="",
555 const std::string& bltable="");
556 void chebyshevBaseline(const std::vector<bool>& mask,
557 int order,
558 float thresClip,
559 int nIterClip,
560 bool getResidual=true,
561 const std::string& progressInfo="true,1000",
562 const bool outLogger=false,
563 const std::string& blfile="",
564 const std::string& bltable="");
565 void autoChebyshevBaseline(const std::vector<bool>& mask,
566 int order,
567 float thresClip,
568 int nIterClip,
569 const std::vector<int>& edge,
570 float threshold=3.0,
571 int chanAvgLimit=1,
572 bool getResidual=true,
573 const std::string& progressInfo="true,1000",
574 const bool outLogger=false,
575 const std::string& blfile="",
576 const std::string& bltable="");
577 void cubicSplineBaseline(const std::vector<bool>& mask,
578 int nPiece,
579 float thresClip,
580 int nIterClip,
581 bool getResidual=true,
582 const std::string& progressInfo="true,1000",
583 const bool outLogger=false,
584 const std::string& blfile="",
585 const std::string& bltable="");
586 void autoCubicSplineBaseline(const std::vector<bool>& mask,
587 int nPiece,
588 float thresClip,
589 int nIterClip,
590 const std::vector<int>& edge,
591 float threshold=3.0,
592 int chanAvgLimit=1,
593 bool getResidual=true,
594 const std::string& progressInfo="true,1000",
595 const bool outLogger=false,
596 const std::string& blfile="",
597 const std::string& bltable="");
598 void sinusoidBaseline(const std::vector<bool>& mask,
599 const std::string& fftInfo,
600 const std::vector<int>& addNWaves,
601 const std::vector<int>& rejectNWaves,
602 float thresClip,
603 int nIterClip,
604 bool getResidual=true,
605 const std::string& progressInfo="true,1000",
606 const bool outLogger=false,
607 const std::string& blfile="",
608 const std::string& bltable="");
609 void autoSinusoidBaseline(const std::vector<bool>& mask,
610 const std::string& fftInfo,
611 const std::vector<int>& addNWaves,
612 const std::vector<int>& rejectNWaves,
613 float thresClip,
614 int nIterClip,
615 const std::vector<int>& edge,
616 float threshold=3.0,
617 int chanAvgLimit=1,
618 bool getResidual=true,
619 const std::string& progressInfo="true,1000",
620 const bool outLogger=false,
621 const std::string& blfile="",
622 const std::string& bltable="");
623 std::vector<float> execFFT(const int whichrow,
624 const std::vector<bool>& inMask,
625 bool getRealImag=false,
626 bool getAmplitudeOnly=false);
627 float getRms(const std::vector<bool>& mask, int whichrow);
628 std::string formatBaselineParams(const std::vector<float>& params,
629 const std::vector<bool>& fixed,
630 float rms,
631 int nClipped,
632 const std::string& masklist,
633 int whichrow,
634 bool verbose=false,
635 bool csvformat=false,
636 int start=-1,
637 int count=-1,
638 bool resetparamid=false) const;
639 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
640 const std::vector<float>& params,
641 const std::vector<bool>& fixed,
642 float rms,
643 int nClipped,
644 const std::string& masklist,
645 int whichrow,
646 bool verbose=false,
647 bool csvformat=false) const;
648 std::vector<uint> getMoleculeIdColumnData() const;
649 void setMoleculeIdColumnData(const std::vector<uint>& molids);
650 double calculateModelSelectionCriteria(const std::string& valname,
651 const std::string& blfunc,
652 int order,
653 const std::vector<bool>& inMask,
654 int whichrow,
655 bool useLineFinder,
656 const std::vector<int>& edge,
657 float threshold,
658 int chanAvgLimit);
659 static std::vector<bool> getMaskFromMaskList(const int nchan,
660 const std::vector<int>& masklist);
661 static casa::Vector<casa::uInt> getMaskListFromMask(
662 const std::vector<bool>& mask);
663 static std::vector<int> splitToIntList(const std::string& str,
664 const char delim);
665 static std::vector<string> splitToStringList(const std::string& str,
666 const char delim);
667
668 void dropXPol();
669
670private:
671
672 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
673
674 /**
675 * Turns a time value into a formatted string
676 * @param x
677 * @return
678 */
679 std::string formatSec(casa::Double x) const;
680
681 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
682 std::string formatTime(const casa::MEpoch& me, bool showdate,
683 casa::uInt prec)const;
684
685 /**
686 * Turns a casa::MDirection into a nicely formatted string
687 * @param md an casa::MDirection
688 * @return
689 */
690 std::string formatDirection(const casa::MDirection& md) const;
691
692 /**
693 * Create a unique file name for the paged (temporary) table
694 * @return just the name
695 */
696 static casa::String generateName();
697
698 /**
699 * attach to cached columns
700 */
701 void attach();
702
703 /**
704 * Set up the main casa::Table
705 */
706 void setupMainTable();
707
708 void attachSubtables();
709 void copySubtables(const Scantable& other);
710
711 /**
712 * Convert an "old" asap1 style row index into a new index
713 * @param[in] therow
714 * @return and index into @table_
715 */
716 int rowToScanIndex(int therow);
717
718 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
719
720 static const casa::uInt version_ = 4;
721
722 STSelector selector_;
723
724 casa::Table::TableType type_;
725
726 // the actual data
727 casa::Table table_;
728 casa::Table originalTable_;
729
730 STTcal tcalTable_;
731 STFrequencies freqTable_;
732 STWeather weatherTable_;
733 STFocus focusTable_;
734 STMolecules moleculeTable_;
735 STHistory historyTable_;
736 STFit fitTable_;
737
738 // Cached Columns to avoid reconstructing them for each row get/put
739 casa::ScalarColumn<casa::Double> integrCol_;
740 casa::MDirection::ScalarColumn dirCol_;
741 casa::MEpoch::ScalarColumn timeCol_;
742 casa::ScalarColumn<casa::Float> azCol_;
743 casa::ScalarColumn<casa::Float> elCol_;
744 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
745 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
746 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
747 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
748 casa::ArrayColumn<casa::uChar> flagsCol_;
749
750 // id in frequencies table
751 casa::ScalarColumn<casa::uInt> mfreqidCol_;
752 // id in tcal table
753 casa::ScalarColumn<casa::uInt> mtcalidCol_;
754
755 casa::ArrayColumn<casa::String> histitemCol_;
756 casa::ScalarColumn<casa::Int> mfitidCol_;
757 casa::ScalarColumn<casa::uInt> mweatheridCol_;
758
759 casa::ScalarColumn<casa::uInt> mfocusidCol_;
760
761 casa::ScalarColumn<casa::uInt> mmolidCol_;
762
763 static std::map<std::string, STPol::STPolFactory *> factories_;
764 void initFactories();
765
766 /**
767 * Add an auxiliary column to the main table and attach it to a
768 * cached column. Use for adding new columns that the original asap2
769 * tables do not have.
770 * @param[in] col reference to the cached column to be attached
771 * @param[in] colName column name in asap table
772 * @param[in] defValue default value to fill in the column
773 *
774 * 25/10/2009 Wataru Kawasaki
775 */
776 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
777 const casa::String&,
778 const T2&);
779 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
780 const casa::String&,
781 const casa::Array<T2>&);
782
783 double getNormalPolynomial(int n, double x);
784 double getChebyshevPolynomial(int n, double x);
785 std::vector<std::vector<double> > getPolynomialModel(int order,
786 int nchan,
787 double (Scantable::*pfunc)(int, double));
788 std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
789 double (Scantable::*pfunc)(int, double),
790 std::vector<int>& nChanNos);
791 std::vector<float> doPolynomialFitting(const std::vector<float>& data,
792 const std::vector<bool>& mask,
793 int order,
794 std::vector<float>& params,
795 float& rms,
796 std::vector<bool>& finalMask,
797 float clipth,
798 int clipn);
799 std::vector<float> doPolynomialFitting(const std::vector<float>& data,
800 const std::vector<bool>& mask,
801 int order,
802 std::vector<float>& params,
803 float& rms,
804 std::vector<bool>& finalMask,
805 int& nClipped,
806 float thresClip=3.0,
807 int nIterClip=0,
808 bool getResidual=true);
809 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
810 const std::vector<bool>& mask,
811 int order,
812 std::vector<float>& params,
813 float& rms,
814 std::vector<bool>& finalMask,
815 float clipth,
816 int clipn);
817 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
818 const std::vector<bool>& mask,
819 int order,
820 std::vector<float>& params,
821 float& rms,
822 std::vector<bool>& finalMask,
823 int& nClipped,
824 float thresClip=3.0,
825 int nIterClip=0,
826 bool getResidual=true);
827 std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
828 const std::vector<bool>& mask,
829 const std::vector<std::vector<double> >& model,
830 std::vector<float>& params,
831 float& rms,
832 std::vector<bool>& finalMask,
833 int& nClipped,
834 float thresClip=3.0,
835 int nIterClip=0,
836 bool getResidual=true);
837 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
838 const std::vector<bool>& mask,
839 std::vector<int>& idxEdge,
840 std::vector<float>& params,
841 float& rms,
842 std::vector<bool>& finalMask,
843 float clipth,
844 int clipn);
845 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
846 const std::vector<bool>& mask,
847 int nPiece,
848 std::vector<int>& idxEdge,
849 std::vector<float>& params,
850 float& rms,
851 std::vector<bool>& finalMask,
852 float clipth,
853 int clipn);
854 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
855 const std::vector<bool>& mask,
856 int nPiece,
857 bool useGivenPieceBoundary,
858 std::vector<int>& idxEdge,
859 std::vector<float>& params,
860 float& rms,
861 std::vector<bool>& finalMask,
862 int& nClipped,
863 float thresClip=3.0,
864 int nIterClip=0,
865 bool getResidual=true);
866 std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
867 const std::vector<bool>& mask,
868 const std::vector<std::vector<double> >& model,
869 int nPiece,
870 bool useGivenPieceBoundary,
871 std::vector<int>& idxEdge,
872 std::vector<float>& params,
873 float& rms,
874 std::vector<bool>& finalMask,
875 int& nClipped,
876 float thresClip=3.0,
877 int nIterClip=0,
878 bool getResidual=true);
879 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
880 const std::vector<bool>& mask,
881 const std::vector<int>& waveNumbers,
882 std::vector<float>& params,
883 float& rms,
884 std::vector<bool>& finalMask,
885 float clipth,
886 int clipn);
887 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
888 const std::vector<bool>& mask,
889 const std::vector<int>& waveNumbers,
890 std::vector<float>& params,
891 float& rms,
892 std::vector<bool>& finalMask,
893 int& nClipped,
894 float thresClip=3.0,
895 int nIterClip=0,
896 bool getResidual=true);
897 std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
898 std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
899 std::vector<int>& nChanNos);
900 std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
901 const std::vector<int>& rejectNWaves);
902 std::vector<int> selectWaveNumbers(const int whichrow,
903 const std::vector<bool>& chanMask,
904 //const std::string& fftInfo,
905 const bool applyFFT,
906 const std::string& fftMethod,
907 const std::string& fftThresh,
908 const std::vector<int>& addNWaves,
909 const std::vector<int>& rejectNWaves);
910 int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
911 void parseFFTInfo(const std::string& fftInfo,
912 bool& applyFFT,
913 std::string& fftMethod,
914 std::string& fftThresh);
915 void parseFFTThresholdInfo(const std::string& fftThresh,
916 std::string& fftThAttr,
917 float& fftThSigma,
918 int& fftThTop);
919 void doSelectWaveNumbers(const int whichrow,
920 const std::vector<bool>& chanMask,
921 const std::string& fftMethod,
922 const float fftThSigma,
923 const int fftThTop,
924 const std::string& fftThAttr,
925 std::vector<int>& nWaves);
926 void addAuxWaveNumbers(const int whichrow,
927 const std::vector<int>& addNWaves,
928 const std::vector<int>& rejectNWaves,
929 std::vector<int>& nWaves);
930 void setWaveNumberListUptoNyquistFreq(const int whichrow,
931 std::vector<int>& nWaves);
932 void initialiseBaselining(const std::string& blfile,
933 std::ofstream& ofs,
934 const bool outLogger,
935 bool& outTextFile,
936 bool& csvFormat,
937 casa::String& coordInfo,
938 bool& hasSameNchan,
939 const std::string& progressInfo,
940 bool& showProgress,
941 int& minNRow,
942 casa::Vector<casa::Double>& timeSecCol);
943 void finaliseBaselining(const bool outBaselineTable,
944 STBaselineTable* pbt,
945 const string& bltable,
946 const bool outTextFile,
947 std::ofstream& ofs);
948 void initLineFinder(const std::vector<int>& edge,
949 const float threshold,
950 const int chanAvgLimit,
951 STLineFinder& lineFinder);
952 bool hasSameNchanOverIFs();
953 std::string getMaskRangeList(const std::vector<bool>& mask,
954 int whichrow,
955 const casa::String& coordInfo,
956 bool hasSameNchan,
957 bool verbose=false);
958 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
959 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
960 std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
961 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
962 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
963 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);
964 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);
965 void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
966 void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
967
968 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
969
970 double doCalculateModelSelectionCriteria(const std::string& valname,
971 const std::vector<float>& spec,
972 const std::vector<bool>& mask,
973 const std::string& blfunc,
974 int order);
975 double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
976 std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
977 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);
978 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);
979 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);
980
981};
982} // namespace
983
984#endif
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