source: branches/polybatch/src/Scantable.h@ 2233

Last change on this file since 2233 was 1924, checked in by Malte Marquarding, 14 years ago

Ticket #206: use STFitEntry as return objetc instead of pointer wrnagling.

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