source: branches/alma/src/Scantable.h@ 1674

Last change on this file since 1674 was 1656, checked in by WataruKawasaki, 15 years ago

New Development: Yes

JIRA Issue: Yes (CAS-1433)

Ready to Release: Yes

Interface Changes: Yes

What Interface Changed: functionalities for row-based flagging added

Test Programs:

Put in Release Notes: No

Module(s): sdflag

Description: Added the following functionalities:

sd.scantable._flag_row()

  • to execute row-based flagging

sd.scantable._getflagrow()

  • to get row-based flagging info


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 16.0 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// AIPS++
19#include <casa/aips.h>
20#include <casa/Arrays/MaskedArray.h>
21#include <casa/BasicSL/String.h>
22#include <casa/Utilities/CountedPtr.h>
23
24#include <casa/Exceptions/Error.h>
25
26#include <coordinates/Coordinates/SpectralCoordinate.h>
27
28#include <tables/Tables/Table.h>
29#include <tables/Tables/ArrayColumn.h>
30#include <tables/Tables/ScalarColumn.h>
31
32#include <measures/TableMeasures/ScalarMeasColumn.h>
33
34#include <casa/Arrays/Vector.h>
35#include <casa/Quanta/Quantum.h>
36
37#include "Logger.h"
38#include "STHeader.h"
39#include "STFrequencies.h"
40#include "STWeather.h"
41#include "STFocus.h"
42#include "STTcal.h"
43#include "STMolecules.h"
44#include "STSelector.h"
45#include "STHistory.h"
46#include "STPol.h"
47#include "STFit.h"
48#include "STFitEntry.h"
49
50namespace asap {
51
52/**
53 * This class contains and wraps a casa::Table, which is used to store
54 * all the information. This can be either a MemoryTable or a
55 * disk based Table.
56 * It provides access functions to the underlying table
57 * It contains n subtables:
58 * @li weather
59 * @li frequencies
60 * @li molecules
61 * @li tcal
62 * @li focus
63 * @li fits
64 *
65 * @brief The main ASAP data container
66 * @author Malte Marquarding
67 * @date
68 * @version
69*/
70class Scantable : private Logger
71{
72
73friend class STMath;
74
75public:
76 /**
77 * Default constructor
78 */
79 explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
80
81 /**
82 * Create a Scantable object form an existing table on disk
83 * @param[in] name the name of the existing Scantable
84 */
85 explicit Scantable(const std::string& name, casa::Table::TableType ttype = casa::Table::Memory);
86
87 /// @fixme this is only sensible for MemoryTables....
88 Scantable(const Scantable& other, bool clear=true);
89
90 /**
91 * Destructor
92 */
93 virtual ~Scantable();
94
95 /**
96 * get a const reference to the underlying casa::Table
97 * @return const \ref casa::Table reference
98 */
99 const casa::Table& table() const;
100
101 /**
102 * get a reference to the underlying casa::Table with the Selection
103 * object applied if set
104 * @return casa::Table reference
105 */
106 casa::Table& table();
107
108
109 /**
110 * Get a handle to the selection object
111 * @return constant STSelector reference
112 */
113 const STSelector& getSelection() const { return selector_; }
114
115 /**
116 * Set the data to be a subset as defined by the STSelector
117 * @param selection a STSelector object
118 */
119 void setSelection(const STSelector& selection);
120
121 /**
122 * unset the selection of the data
123 */
124 void unsetSelection();
125 /**
126 * set the header
127 * @param[in] sth an STHeader object
128 */
129 void setHeader( const STHeader& sth );
130
131 /**
132 * get the header information
133 * @return an STHeader object
134 */
135 STHeader getHeader( ) const;
136
137 /**
138 * Checks if the "other" Scantable is conformant with this,
139 * i.e. if header values are the same.
140 * @param[in] other another Scantable
141 * @return true or false
142 */
143 bool conformant( const Scantable& other);
144
145 /**
146 *
147 * @param stype The type of the source, 0 = on, 1 = off
148 */
149 void setSourceType(int stype);
150
151
152 /**
153 * The number of scans in the table
154 * @return number of scans in the table
155 */
156 int nscan() const;
157
158 casa::MEpoch::Types getTimeReference() const;
159
160
161 casa::MEpoch getEpoch(int whichrow) const;
162
163 /**
164 * Get global antenna position
165 * @return casa::MPosition
166 */
167 casa::MPosition getAntennaPosition() const;
168
169 /**
170 * the @ref casa::MDirection for a specific row
171 * @param[in] whichrow the row number
172 * return casa::MDirection
173 */
174 casa::MDirection getDirection( int whichrow ) const;
175
176 /**
177 * get the direction type as a string, e.g. "J2000"
178 * @param[in] whichrow the row number
179 * return the direction string
180 */
181 std::string getDirectionString( int whichrow ) const;
182
183 /**
184 * set the direction type as a string, e.g. "J2000"
185 * @param[in] refstr the direction type
186 */
187 void setDirectionRefString(const std::string& refstr="");
188
189 /**
190 * get the direction reference string
191 * @return a string describing the direction reference
192 */
193 std::string getDirectionRefString() const;
194
195 /**
196 * Return the Flux unit of the data, e.g. "Jy" or "K"
197 * @return string
198 */
199 std::string getFluxUnit() const;
200
201 /**
202 * Set the Flux unit of the data
203 * @param unit a string representing the unit, e.g "Jy" or "K"
204 */
205 void setFluxUnit( const std::string& unit );
206
207 /**
208 * Set the Stokes type of the data
209 * @param feedtype a string representing the type, e.g "circular" or "linear"
210 */
211 void setFeedType( const std::string& feedtype );
212
213 /**
214 *
215 * @param instrument a string representing an insturment. see xxx
216 */
217 void setInstrument( const std::string& instrument );
218
219 /**
220 * (Re)calculate the azimuth and elevationnfor all rows
221 */
222 void calculateAZEL();
223
224 /**
225 * "hard" flag the data, this flags everything selected in setSelection()
226 * param[in] msk a boolean mask of length nchan describing the points to
227 * to be flagged
228 */
229 //void flag( const std::vector<bool>& msk = std::vector<bool>());
230 void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
231
232 /**
233 * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
234 * param[in] rows list of row numbers to be flagged
235 */
236 void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
237
238 /**
239 * Get flagRow info at the specified row. If true, the whole data
240 * at the row should be flagged.
241 */
242 bool getFlagRow(int whichrow) const
243 { return (flagrowCol_(whichrow) > 0); }
244
245 /**
246 * Return a list of row numbers with respect to the original table.
247 * @return a list of unsigned ints
248 */
249 std::vector<unsigned int> rownumbers() const;
250
251
252 /**
253 * Get the number of beams in the data or a specific scan
254 * @param scanno the scan number to get the number of beams for.
255 * If scanno<0 the number is retrieved from the header.
256 * @return an integer number
257 */
258 int nbeam(int scanno=-1) const;
259 /**
260 * Get the number of IFs in the data or a specific scan
261 * @param scanno the scan number to get the number of IFs for.
262 * If scanno<0 the number is retrieved from the header.
263 * @return an integer number
264 */
265 int nif(int scanno=-1) const;
266 /**
267 * Get the number of polarizations in the data or a specific scan
268 * @param scanno the scan number to get the number of polarizations for.
269 * If scanno<0 the number is retrieved from the header.
270 * @return an integer number
271 */
272 int npol(int scanno=-1) const;
273
274 std::string getPolType() const;
275
276
277 /**
278 * Get the number of integartion cycles
279 * @param scanno the scan number to get the number of rows for.
280 * If scanno<0 the number is retrieved from the header.
281 * @return the number of rows (for the specified scanno)
282 */
283 int nrow(int scanno=-1) const;
284
285 int getBeam(int whichrow) const;
286 std::vector<uint> getBeamNos() { return getNumbers(beamCol_); }
287
288 int getIF(int whichrow) const;
289 std::vector<uint> getIFNos() { return getNumbers(ifCol_); }
290
291 int getPol(int whichrow) const;
292 std::vector<uint> getPolNos() { return getNumbers(polCol_); }
293
294 std::vector<uint> getScanNos() { return getNumbers(scanCol_); }
295 int getScan(int whichrow) const { return scanCol_(whichrow); }
296
297 //TT addition
298 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
299
300 /**
301 * Get the number of channels in the data or a specific IF. This currently
302 * varies only with IF number
303 * @param ifno the IF number to get the number of channels for.
304 * If ifno<0 the number is retrieved from the header.
305 * @return an integer number
306 */
307 int nchan(int ifno=-1) const;
308 int getChannels(int whichrow) const;
309
310 int ncycle(int scanno=-1) const;
311 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
312
313 double getInterval(int whichrow) const
314 { return integrCol_(whichrow); }
315
316 float getTsys(int whichrow) const
317 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
318 float getElevation(int whichrow) const
319 { return elCol_(whichrow); }
320 float getAzimuth(int whichrow) const
321 { return azCol_(whichrow); }
322 float getParAngle(int whichrow) const
323 { return paraCol_(whichrow); }
324 int getTcalId(int whichrow) const
325 { return mtcalidCol_(whichrow); }
326
327 std::string getSourceName(int whichrow) const
328 { return srcnCol_(whichrow); }
329
330 std::vector<bool> getMask(int whichrow) const;
331 std::vector<float> getSpectrum(int whichrow,
332 const std::string& poltype = "" ) const;
333
334 void setSpectrum(const std::vector<float>& spec, int whichrow);
335
336 std::string getPolarizationLabel(int index, const std::string& ptype) const
337 { return STPol::getPolLabel(index, ptype ); }
338
339 /**
340 * Write the Scantable to disk
341 * @param filename the output file name
342 */
343 void makePersistent(const std::string& filename);
344
345 std::vector<std::string> getHistory() const
346 { return historyTable_.getHistory(); };
347
348 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
349
350 void appendToHistoryTable(const STHistory& otherhist)
351 { historyTable_.append(otherhist); }
352
353 std::string summary(bool verbose=false);
354 std::string getTime(int whichrow=-1, bool showdate=true) const;
355 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
356
357 // returns unit, conversion frame, doppler, base-frame
358
359 /**
360 * Get the frequency set up
361 * This is forwarded to the STFrequencies subtable
362 * @return unit, frame, doppler
363 */
364 std::vector<std::string> getCoordInfo() const
365 { return freqTable_.getInfo(); };
366
367 void setCoordInfo(std::vector<string> theinfo)
368 { return freqTable_.setInfo(theinfo); };
369
370
371 std::vector<double> getAbcissa(int whichrow) const;
372
373 std::string getAbcissaLabel(int whichrow) const;
374 std::vector<double> getRestFrequencies() const
375 { return moleculeTable_.getRestFrequencies(); }
376 std::vector<double> getRestFrequency(int id) const
377 { return moleculeTable_.getRestFrequency(id); }
378
379 /**
380 void setRestFrequencies(double rf, const std::string& name = "",
381 const std::string& = "Hz");
382 **/
383 // Modified by Takeshi Nakazato 05/09/2008
384 /***
385 void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
386 const std::string& = "Hz");
387 ***/
388 void setRestFrequencies(vector<double> rf,
389 const vector<std::string>& name = vector<std::string>(1,""),
390 const std::string& = "Hz");
391
392 //void setRestFrequencies(const std::string& name);
393 void setRestFrequencies(const vector<std::string>& name);
394
395 void shift(int npix);
396
397 void convertDirection(const std::string& newframe);
398
399 STFrequencies& frequencies() { return freqTable_; }
400 const STFrequencies& frequencies() const { return freqTable_; }
401 STWeather& weather() { return weatherTable_; }
402 const STWeather& weather() const { return weatherTable_; }
403 STFocus& focus() { return focusTable_; }
404 const STFocus& focus() const { return focusTable_; }
405 STTcal& tcal() { return tcalTable_; }
406 const STTcal& tcal() const { return tcalTable_; }
407 STMolecules& molecules() { return moleculeTable_; }
408 const STMolecules& molecules() const { return moleculeTable_; }
409 STHistory& history() { return historyTable_; }
410 const STHistory& history() const { return historyTable_; }
411 STFit& fit() { return fitTable_; }
412 const STFit& fit() const { return fitTable_; }
413
414 std::vector<std::string> columnNames() const;
415
416 void addFit(const STFitEntry& fit, int row);
417 STFitEntry getFit(int row) const
418 { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
419
420 //Added by TT
421 /**
422 * Get the antenna name
423 * @return antenna name string
424 */
425 std::string getAntennaName() const;
426
427 /**
428 * For GBT MS data only. check a scan list
429 * against the information found in GBT_GO table for
430 * scan number orders to get correct pairs.
431 * @param[in] scan list
432 * @return status
433 */
434 int checkScanInfo(const std::vector<int>& scanlist) const;
435
436 /**
437 * Get the direction as a vector, for a specific row
438 * @param[in] whichrow the row numbyyer
439 * @return the direction in a vector
440 */
441 std::vector<double> getDirectionVector(int whichrow) const;
442
443 /**
444 * Reshape spectrum
445 * @param[in] nmin, nmax minimum and maximum channel
446 * @param[in] irow row number
447 *
448 * 30/07/2008 Takeshi Nakazato
449 **/
450 void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
451 void reshapeSpectrum( int nmin, int nmax, int irow ) ;
452
453 /**
454 * Change channel number under fixed bandwidth
455 * @param[in] nchan, dnu new channel number and spectral resolution
456 * @param[in] irow row number
457 *
458 * 27/08/2008 Takeshi Nakazato
459 **/
460 void regridChannel( int nchan, double dnu ) ;
461 void regridChannel( int nchan, double dnu, int irow ) ;
462
463
464private:
465
466 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
467
468 /**
469 * Turns a time vale into a formatted string
470 * @param x
471 * @return
472 */
473 std::string formatSec(casa::Double x) const;
474
475 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
476
477 /**
478 * Turns a casa::MDirection into a nicely formatted string
479 * @param md an casa::MDirection
480 * @return
481 */
482 std::string formatDirection(const casa::MDirection& md) const;
483
484
485 /**
486 * Create a unique file name for the paged (temporary) table
487 * @return just the name
488 */
489 static casa::String generateName();
490
491 /**
492 * attach to cached columns
493 */
494 void attach();
495
496 /**
497 * Set up the main casa::Table
498 */
499 void setupMainTable();
500
501 void attachSubtables();
502 void copySubtables(const Scantable& other);
503
504 /**
505 * Convert an "old" asap1 style row index into a new index
506 * @param[in] therow
507 * @return and index into @table_
508 */
509 int rowToScanIndex(int therow);
510
511 std::vector<uint> getNumbers(casa::ScalarColumn<casa::uInt>& col);
512
513 static const casa::uInt version_ = 2;
514
515 STSelector selector_;
516
517 casa::Table::TableType type_;
518
519 // the actual data
520 casa::Table table_;
521 casa::Table originalTable_;
522
523 STTcal tcalTable_;
524 STFrequencies freqTable_;
525 STWeather weatherTable_;
526 STFocus focusTable_;
527 STMolecules moleculeTable_;
528 STHistory historyTable_;
529 STFit fitTable_;
530
531 // Cached Columns to avoid reconstructing them for each row get/put
532 casa::ScalarColumn<casa::Double> integrCol_;
533 casa::MDirection::ScalarColumn dirCol_;
534 casa::MEpoch::ScalarColumn timeCol_;
535 casa::ScalarColumn<casa::Float> azCol_;
536 casa::ScalarColumn<casa::Float> elCol_;
537 casa::ScalarColumn<casa::Float> paraCol_;
538 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
539 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
540 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
541 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
542 casa::ArrayColumn<casa::uChar> flagsCol_;
543
544 // id in frequencies table
545 casa::ScalarColumn<casa::uInt> mfreqidCol_;
546 // id in tcal table
547 casa::ScalarColumn<casa::uInt> mtcalidCol_;
548
549 casa::ArrayColumn<casa::String> histitemCol_;
550 casa::ScalarColumn<casa::Int> mfitidCol_;
551 casa::ScalarColumn<casa::uInt> mweatheridCol_;
552
553 casa::ScalarColumn<casa::uInt> mfocusidCol_;
554
555 casa::ScalarColumn<casa::uInt> mmolidCol_;
556
557 static std::map<std::string, STPol::STPolFactory *> factories_;
558 void initFactories();
559
560 /**
561 * Add an auxiliary column to the main table and attach it to a
562 * cached column. Use for adding new columns that the original asap2
563 * tables do not have.
564 * @param[in] col reference to the cached column to be attached
565 * @param[in] colName column name in asap table
566 * @param[in] defValue default value to fill in the column
567 *
568 * 25/10/2009 Wataru Kawasaki
569 */
570 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
571 const casa::String&,
572 const T2&);
573 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
574 const casa::String&,
575 const casa::Array<T2>&);
576};
577
578
579} // namespace
580
581#endif
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