source: trunk/src/Scantable.h@ 1603

Last change on this file since 1603 was 1598, checked in by Malte Marquarding, 15 years ago

Ticket #170: added scantable.get_coordinate(row). Note that this in the specified reference frame NOT in the basese frame, e.g. usually LSRK/BARY not TOPO. That means that coord.to_frequency(coord.get_rerencepixel()) != coord.get_reference_value(). You need to run {{{freq_align to rectify this

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