source: trunk/src/Scantable.h@ 2176

Last change on this file since 2176 was 2163, checked in by Malte Marquarding, 13 years ago

Remove various compiler warnings
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 21.9 KB
Line 
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 <string>
17#include <vector>
18#include <iostream>
19#include <fstream>
20// AIPS++
21#include <casa/aips.h>
22#include <casa/Containers/Record.h>
23#include <casa/Arrays/MaskedArray.h>
24#include <casa/BasicSL/String.h>
25#include <casa/Utilities/CountedPtr.h>
26
27#include <tables/Tables/Table.h>
28#include <tables/Tables/ArrayColumn.h>
29#include <tables/Tables/ScalarColumn.h>
30
31#include <measures/TableMeasures/ScalarMeasColumn.h>
32
33#include <coordinates/Coordinates/SpectralCoordinate.h>
34
35#include <casa/Arrays/Vector.h>
36#include <casa/Quanta/Quantum.h>
37
38#include <casa/Exceptions/Error.h>
39
40#include "Logger.h"
41#include "STHeader.h"
42#include "STFrequencies.h"
43#include "STWeather.h"
44#include "STFocus.h"
45#include "STTcal.h"
46#include "STMolecules.h"
47#include "STSelector.h"
48#include "STHistory.h"
49#include "STPol.h"
50#include "STFit.h"
51#include "STFitEntry.h"
52#include "STFitter.h"
53
54namespace asap {
55
56/**
57 * This class contains and wraps a casa::Table, which is used to store
58 * all the information. This can be either a MemoryTable or a
59 * disk based Table.
60 * It provides access functions to the underlying table
61 * It contains n subtables:
62 * @li weather
63 * @li frequencies
64 * @li molecules
65 * @li tcal
66 * @li focus
67 * @li fits
68 *
69 * @brief The main ASAP data container
70 * @author Malte Marquarding
71 * @date
72 * @version
73*/
74class Scantable : private Logger
75{
76
77friend class STMath;
78
79public:
80 /**
81 * Default constructor
82 */
83 explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
84
85 /**
86 * Create a Scantable object form an existing table on disk
87 * @param[in] name the name of the existing Scantable
88 */
89 explicit Scantable(const std::string& name, casa::Table::TableType ttype = casa::Table::Memory);
90
91 /// @fixme this is only sensible for MemoryTables....
92 Scantable(const Scantable& other, bool clear=true);
93
94 /**
95 * Destructor
96 */
97 virtual ~Scantable();
98
99 /**
100 * get a const reference to the underlying casa::Table
101 * @return const \ref casa::Table reference
102 */
103 const casa::Table& table() const;
104
105 /**
106 * get a reference to the underlying casa::Table with the Selection
107 * object applied if set
108 * @return casa::Table reference
109 */
110 casa::Table& table();
111
112
113 /**
114 * Get a handle to the selection object
115 * @return constant STSelector reference
116 */
117 const STSelector& getSelection() const { return selector_; }
118
119 /**
120 * Set the data to be a subset as defined by the STSelector
121 * @param selection a STSelector object
122 */
123 void setSelection(const STSelector& selection);
124
125 /**
126 * unset the selection of the data
127 */
128 void unsetSelection();
129 /**
130 * set the header
131 * @param[in] sth an STHeader object
132 */
133 void setHeader( const STHeader& sth );
134
135 /**
136 * get the header information
137 * @return an STHeader object
138 */
139 STHeader getHeader( ) const;
140
141 /**
142 * Checks if the "other" Scantable is conformant with this,
143 * i.e. if header values are the same.
144 * @param[in] other another Scantable
145 * @return true or false
146 */
147 bool conformant( const Scantable& other);
148
149 /**
150 *
151 * @param stype The type of the source, 0 = on, 1 = off
152 */
153 void setSourceType(int stype);
154
155
156 /**
157 * The number of scans in the table
158 * @return number of scans in the table
159 */
160 int nscan() const;
161
162 casa::MEpoch::Types getTimeReference() const;
163
164
165 casa::MEpoch getEpoch(int whichrow) const;
166
167 /**
168 * Get global antenna position
169 * @return casa::MPosition
170 */
171 casa::MPosition getAntennaPosition() const;
172
173 /**
174 * the @ref casa::MDirection for a specific row
175 * @param[in] whichrow the row number
176 * return casa::MDirection
177 */
178 casa::MDirection getDirection( int whichrow ) const;
179
180 /**
181 * get the direction type as a string, e.g. "J2000"
182 * @param[in] whichrow the row number
183 * return the direction string
184 */
185 std::string getDirectionString( int whichrow ) const;
186
187 /**
188 * set the direction type as a string, e.g. "J2000"
189 * @param[in] refstr the direction type
190 */
191 void setDirectionRefString(const std::string& refstr="");
192
193 /**
194 * get the direction reference string
195 * @return a string describing the direction reference
196 */
197 std::string getDirectionRefString() const;
198
199 /**
200 * Return the Flux unit of the data, e.g. "Jy" or "K"
201 * @return string
202 */
203 std::string getFluxUnit() const;
204
205 /**
206 * Set the Flux unit of the data
207 * @param unit a string representing the unit, e.g "Jy" or "K"
208 */
209 void setFluxUnit( const std::string& unit );
210
211 /**
212 * Set the Stokes type of the data
213 * @param feedtype a string representing the type, e.g "circular" or "linear"
214 */
215 void setFeedType( const std::string& feedtype );
216
217 /**
218 *
219 * @param instrument a string representing an insturment. see xxx
220 */
221 void setInstrument( const std::string& instrument );
222
223 /**
224 * (Re)calculate the azimuth and elevationnfor all rows
225 */
226 void calculateAZEL();
227
228 /**
229 * "hard" flag the data, this flags everything selected in setSelection()
230 * param[in] msk a boolean mask of length nchan describing the points to
231 * to be flagged
232 */
233 //void flag( const std::vector<bool>& msk = std::vector<bool>());
234 //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
235
236 void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
237
238 /**
239 * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
240 * param[in] rows list of row numbers to be flagged
241 */
242 void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
243
244 /**
245 * Get flagRow info at the specified row. If true, the whole data
246 * at the row should be flagged.
247 */
248 bool getFlagRow(int whichrow) const
249 { return (flagrowCol_(whichrow) > 0); }
250
251 /**
252 * Flag the data outside a specified range (in a channel-based manner).
253 * (CAS-1807 Wataru Kawasaki)
254 */
255 void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
256
257 /**
258 * Return a list of booleans with the size of nchan for a specified row, to get info
259 * about which channel is clipped.
260 */
261 std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
262 void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
263 casa::Vector<casa::uChar> flgs);
264
265 /**
266 * Return a list of row numbers with respect to the original table.
267 * @return a list of unsigned ints
268 */
269 std::vector<unsigned int> rownumbers() const;
270
271
272 /**
273 * Get the number of beams in the data or a specific scan
274 * @param scanno the scan number to get the number of beams for.
275 * If scanno<0 the number is retrieved from the header.
276 * @return an integer number
277 */
278 int nbeam(int scanno=-1) const;
279 /**
280 * Get the number of IFs in the data or a specific scan
281 * @param scanno the scan number to get the number of IFs for.
282 * If scanno<0 the number is retrieved from the header.
283 * @return an integer number
284 */
285 int nif(int scanno=-1) const;
286 /**
287 * Get the number of polarizations in the data or a specific scan
288 * @param scanno the scan number to get the number of polarizations for.
289 * If scanno<0 the number is retrieved from the header.
290 * @return an integer number
291 */
292 int npol(int scanno=-1) const;
293
294 std::string getPolType() const;
295
296
297 /**
298 * Get the number of integartion cycles
299 * @param scanno the scan number to get the number of rows for.
300 * If scanno<0 the number is retrieved from the header.
301 * @return the number of rows (for the specified scanno)
302 */
303 int nrow(int scanno=-1) const;
304
305 int getBeam(int whichrow) const;
306 std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
307
308 int getIF(int whichrow) const;
309 std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
310
311 int getPol(int whichrow) const;
312 std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
313
314 std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
315 int getScan(int whichrow) const { return scanCol_(whichrow); }
316
317 //TT addition
318 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
319
320 /**
321 * Get the number of channels in the data or a specific IF. This currently
322 * varies only with IF number
323 * @param ifno the IF number to get the number of channels for.
324 * If ifno<0 the number is retrieved from the header.
325 * @return an integer number
326 */
327 int nchan(int ifno=-1) const;
328 int getChannels(int whichrow) const;
329
330 int ncycle(int scanno=-1) const;
331 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
332
333 double getInterval(int whichrow) const
334 { return integrCol_(whichrow); }
335
336 float getTsys(int whichrow) const
337 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
338 std::vector<float> getTsysSpectrum(int whichrow) const ;
339 float getElevation(int whichrow) const
340 { return elCol_(whichrow); }
341 float getAzimuth(int whichrow) const
342 { return azCol_(whichrow); }
343 float getParAngle(int whichrow) const
344 { return focus().getParAngle(mfocusidCol_(whichrow)); }
345 int getTcalId(int whichrow) const
346 { return mtcalidCol_(whichrow); }
347
348 std::string getSourceName(int whichrow) const
349 { return srcnCol_(whichrow); }
350
351 std::vector<bool> getMask(int whichrow) const;
352 std::vector<float> getSpectrum(int whichrow,
353 const std::string& poltype = "" ) const;
354
355 void setSpectrum(const std::vector<float>& spec, int whichrow);
356
357 std::string getPolarizationLabel(int index, const std::string& ptype) const
358 { return STPol::getPolLabel(index, ptype ); }
359
360 /**
361 * Write the Scantable to disk
362 * @param filename the output file name
363 */
364 void makePersistent(const std::string& filename);
365
366 std::vector<std::string> getHistory() const
367 { return historyTable_.getHistory(); };
368
369 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
370
371 void appendToHistoryTable(const STHistory& otherhist)
372 { historyTable_.append(otherhist); }
373
374 std::string headerSummary();
375 std::string summary();
376 //std::string getTime(int whichrow=-1, bool showdate=true) const;
377 std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
378 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
379
380 // returns unit, conversion frame, doppler, base-frame
381
382 /**
383 * Get the frequency set up
384 * This is forwarded to the STFrequencies subtable
385 * @return unit, frame, doppler
386 */
387 std::vector<std::string> getCoordInfo() const
388 { return freqTable_.getInfo(); };
389
390 void setCoordInfo(std::vector<string> theinfo)
391 { return freqTable_.setInfo(theinfo); };
392
393
394 std::vector<double> getAbcissa(int whichrow) const;
395
396 std::vector<float> getWeather(int whichrow) const;
397
398 std::string getAbcissaLabel(int whichrow) const;
399 std::vector<double> getRestFrequencies() const
400 { return moleculeTable_.getRestFrequencies(); }
401 std::vector<double> getRestFrequency(int id) const
402 { return moleculeTable_.getRestFrequency(id); }
403
404 /**
405 void setRestFrequencies(double rf, const std::string& name = "",
406 const std::string& = "Hz");
407 **/
408 // Modified by Takeshi Nakazato 05/09/2008
409 /***
410 void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
411 const std::string& = "Hz");
412 ***/
413 void setRestFrequencies(vector<double> rf,
414 const vector<std::string>& name = vector<std::string>(1,""),
415 const std::string& = "Hz");
416
417 //void setRestFrequencies(const std::string& name);
418 void setRestFrequencies(const vector<std::string>& name);
419
420 void shift(int npix);
421
422 casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
423
424 void convertDirection(const std::string& newframe);
425
426 STFrequencies& frequencies() { return freqTable_; }
427 const STFrequencies& frequencies() const { return freqTable_; }
428 STWeather& weather() { return weatherTable_; }
429 const STWeather& weather() const { return weatherTable_; }
430 STFocus& focus() { return focusTable_; }
431 const STFocus& focus() const { return focusTable_; }
432 STTcal& tcal() { return tcalTable_; }
433 const STTcal& tcal() const { return tcalTable_; }
434 STMolecules& molecules() { return moleculeTable_; }
435 const STMolecules& molecules() const { return moleculeTable_; }
436 STHistory& history() { return historyTable_; }
437 const STHistory& history() const { return historyTable_; }
438 STFit& fit() { return fitTable_; }
439 const STFit& fit() const { return fitTable_; }
440
441 std::vector<std::string> columnNames() const;
442
443 void addFit(const STFitEntry& fit, int row);
444 STFitEntry getFit(int row) const
445 { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
446
447 //Added by TT
448 /**
449 * Get the antenna name
450 * @return antenna name string
451 */
452 casa::String getAntennaName() const;
453
454 /**
455 * For GBT MS data only. check a scan list
456 * against the information found in GBT_GO table for
457 * scan number orders to get correct pairs.
458 * @param[in] scan list
459 * @return status
460 */
461 int checkScanInfo(const std::vector<int>& scanlist) const;
462
463 /**
464 * Get the direction as a vector, for a specific row
465 * @param[in] whichrow the row numbyyer
466 * @return the direction in a vector
467 */
468 std::vector<double> getDirectionVector(int whichrow) const;
469
470 /**
471 * Set a flag indicating whether the data was parallactified
472 * @param[in] flag true or false
473 */
474 void parallactify(bool flag)
475 { focus().setParallactify(flag); }
476
477 /**
478 * Reshape spectrum
479 * @param[in] nmin, nmax minimum and maximum channel
480 * @param[in] irow row number
481 *
482 * 30/07/2008 Takeshi Nakazato
483 **/
484 void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
485 void reshapeSpectrum( int nmin, int nmax, int irow ) ;
486
487 /**
488 * Change channel number under fixed bandwidth
489 * @param[in] nchan, dnu new channel number and spectral resolution
490 * @param[in] irow row number
491 *
492 * 27/08/2008 Takeshi Nakazato
493 **/
494 void regridChannel( int nchan, double dnu ) ;
495 void regridChannel( int nchan, double dnu, int irow ) ;
496
497 bool getFlagtraFast(casa::uInt whichrow);
498
499 void polyBaseline(const std::vector<bool>& mask,
500 int order,
501 bool getResidual=true,
502 bool outLogger=false,
503 const std::string& blfile="");
504 void autoPolyBaseline(const std::vector<bool>& mask,
505 int order,
506 const std::vector<int>& edge,
507 float threshold=3.0,
508 int chanAvgLimit=1,
509 bool getResidual=true,
510 bool outLogger=false,
511 const std::string& blfile="");
512 void cubicSplineBaseline(const std::vector<bool>& mask,
513 int nPiece,
514 float thresClip,
515 int nIterClip,
516 bool getResidual=true,
517 bool outLogger=false,
518 const std::string& blfile="");
519 void autoCubicSplineBaseline(const std::vector<bool>& mask,
520 int nPiece,
521 float thresClip,
522 int nIterClip,
523 const std::vector<int>& edge,
524 float threshold=3.0,
525 int chanAvgLimit=1,
526 bool getResidual=true,
527 bool outLogger=false,
528 const std::string& blfile="");
529 void sinusoidBaseline(const std::vector<bool>& mask,
530 const std::vector<int>& nWaves,
531 float maxWaveLength,
532 float thresClip,
533 int nIterClip,
534 bool getResidual=true,
535 bool outLogger=false,
536 const std::string& blfile="");
537 void autoSinusoidBaseline(const std::vector<bool>& mask,
538 const std::vector<int>& nWaves,
539 float maxWaveLength,
540 float thresClip,
541 int nIterClip,
542 const std::vector<int>& edge,
543 float threshold=3.0,
544 int chanAvgLimit=1,
545 bool getResidual=true,
546 bool outLogger=false,
547 const std::string& blfile="");
548 float getRms(const std::vector<bool>& mask, int whichrow);
549 std::string formatBaselineParams(const std::vector<float>& params,
550 const std::vector<bool>& fixed,
551 float rms,
552 const std::string& masklist,
553 int whichrow,
554 bool verbose=false,
555 int start=-1,
556 int count=-1,
557 bool resetparamid=false) const;
558 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
559 const std::vector<float>& params,
560 const std::vector<bool>& fixed,
561 float rms,
562 const std::string& masklist,
563 int whichrow,
564 bool verbose=false) const;
565
566
567private:
568
569 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
570
571 /**
572 * Turns a time value into a formatted string
573 * @param x
574 * @return
575 */
576 std::string formatSec(casa::Double x) const;
577
578 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
579 std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
580
581 /**
582 * Turns a casa::MDirection into a nicely formatted string
583 * @param md an casa::MDirection
584 * @return
585 */
586 std::string formatDirection(const casa::MDirection& md) const;
587
588 /**
589 * Create a unique file name for the paged (temporary) table
590 * @return just the name
591 */
592 static casa::String generateName();
593
594 /**
595 * attach to cached columns
596 */
597 void attach();
598
599 /**
600 * Set up the main casa::Table
601 */
602 void setupMainTable();
603
604 void attachSubtables();
605 void copySubtables(const Scantable& other);
606
607 /**
608 * Convert an "old" asap1 style row index into a new index
609 * @param[in] therow
610 * @return and index into @table_
611 */
612 int rowToScanIndex(int therow);
613
614 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
615
616 static const casa::uInt version_ = 3;
617
618 STSelector selector_;
619
620 casa::Table::TableType type_;
621
622 // the actual data
623 casa::Table table_;
624 casa::Table originalTable_;
625
626 STTcal tcalTable_;
627 STFrequencies freqTable_;
628 STWeather weatherTable_;
629 STFocus focusTable_;
630 STMolecules moleculeTable_;
631 STHistory historyTable_;
632 STFit fitTable_;
633
634 // Cached Columns to avoid reconstructing them for each row get/put
635 casa::ScalarColumn<casa::Double> integrCol_;
636 casa::MDirection::ScalarColumn dirCol_;
637 casa::MEpoch::ScalarColumn timeCol_;
638 casa::ScalarColumn<casa::Float> azCol_;
639 casa::ScalarColumn<casa::Float> elCol_;
640 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
641 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
642 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
643 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
644 casa::ArrayColumn<casa::uChar> flagsCol_;
645
646 // id in frequencies table
647 casa::ScalarColumn<casa::uInt> mfreqidCol_;
648 // id in tcal table
649 casa::ScalarColumn<casa::uInt> mtcalidCol_;
650
651 casa::ArrayColumn<casa::String> histitemCol_;
652 casa::ScalarColumn<casa::Int> mfitidCol_;
653 casa::ScalarColumn<casa::uInt> mweatheridCol_;
654
655 casa::ScalarColumn<casa::uInt> mfocusidCol_;
656
657 casa::ScalarColumn<casa::uInt> mmolidCol_;
658
659 static std::map<std::string, STPol::STPolFactory *> factories_;
660 void initFactories();
661
662 /**
663 * Add an auxiliary column to the main table and attach it to a
664 * cached column. Use for adding new columns that the original asap2
665 * tables do not have.
666 * @param[in] col reference to the cached column to be attached
667 * @param[in] colName column name in asap table
668 * @param[in] defValue default value to fill in the column
669 *
670 * 25/10/2009 Wataru Kawasaki
671 */
672 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
673 const casa::String&,
674 const T2&);
675 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
676 const casa::String&,
677 const casa::Array<T2>&);
678
679 void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
680 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
681 const std::vector<bool>& mask,
682 int nPiece,
683 std::vector<int>& idxEdge,
684 std::vector<float>& params,
685 float thresClip=3.0,
686 int nIterClip=1,
687 bool getResidual=true);
688 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
689 const std::vector<bool>& mask,
690 const std::vector<int>& waveNumbers,
691 float maxWaveLength,
692 std::vector<float>& params,
693 float thresClip=3.0,
694 int nIterClip=1,
695 bool getResidual=true);
696 bool hasSameNchanOverIFs();
697 std::string getMaskRangeList(const std::vector<bool>& mask,
698 int whichrow,
699 const casa::String& coordInfo,
700 bool hasSameNchan,
701 bool verbose=false);
702 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
703 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const;
704 std::string formatBaselineParamsFooter(float rms, bool verbose) const;
705 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
706 //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
707 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);
708 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);
709 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);
710
711 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
712
713
714};
715
716} // namespace
717
718#endif
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