source: trunk/src/Scantable.h@ 2998

Last change on this file since 2998 was 2969, checked in by Kana Sugimoto, 10 years ago

New Development: No

JIRA Issue: Yes (CAS-6109)

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs: runUnitTest.main(test_sdlist)

Put in Release Notes: No

Module(s): scantable, sdlist

Description: Fixed a bug in time range calculation in scantable.summary (sdlist).

Also enhanced precision of time and direction listed in the method.
Added a parameter, prec, in a private funtion, Scantable::formatDirection to allow setting precision.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 32.9 KB
RevLine 
[824]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
[2]14
15// STL
[2186]16#include <fstream>
17#include <iostream>
18#include <sstream>
[2]19#include <string>
20#include <vector>
21// AIPS++
[455]22#include <casa/aips.h>
[322]23#include <casa/Arrays/MaskedArray.h>
[2186]24#include <casa/Arrays/Vector.h>
[80]25#include <casa/BasicSL/String.h>
[2186]26#include <casa/Containers/Record.h>
27#include <casa/Exceptions/Error.h>
28#include <casa/Quanta/Quantum.h>
[824]29#include <casa/Utilities/CountedPtr.h>
[2186]30#include <coordinates/Coordinates/SpectralCoordinate.h>
[824]31#include <measures/TableMeasures/ScalarMeasColumn.h>
[2186]32#include <scimath/Mathematics/FFTServer.h>
33#include <tables/Tables/ArrayColumn.h>
34#include <tables/Tables/ScalarColumn.h>
35#include <tables/Tables/Table.h>
[1819]36
[2186]37#include "MathUtils.h"
[2767]38#include "STBaselineEnum.h"
[2186]39#include "STFit.h"
40#include "STFitEntry.h"
41#include "STFocus.h"
42#include "STFrequencies.h"
[901]43#include "STHeader.h"
[2186]44#include "STHistory.h"
[824]45#include "STMolecules.h"
[2186]46#include "STPol.h"
[824]47#include "STSelector.h"
[2186]48#include "STTcal.h"
49#include "STWeather.h"
[2]50
[824]51namespace asap {
[2]52
[2666]53class Fitter;
[2773]54class STLineFinder;
55class STBaselineTable;
[2666]56
[824]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*/
[2658]75class Scantable
[824]76{
[902]77
78friend class STMath;
79
[2]80public:
[824]81 /**
82 * Default constructor
83 */
[1350]84 explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
[19]85
[824]86 /**
[2321]87 * Create a Scantable object from an existing table on disk
[824]88 * @param[in] name the name of the existing Scantable
89 */
[2321]90 explicit Scantable(const std::string& name,
91 casa::Table::TableType ttype = casa::Table::Memory);
[2]92
[824]93 /// @fixme this is only sensible for MemoryTables....
94 Scantable(const Scantable& other, bool clear=true);
[161]95
[824]96 /**
97 * Destructor
98 */
99 virtual ~Scantable();
[745]100
[824]101 /**
102 * get a const reference to the underlying casa::Table
[1104]103 * @return const \ref casa::Table reference
[824]104 */
105 const casa::Table& table() const;
[19]106
[824]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();
[21]113
[845]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 */
[824]125 void setSelection(const STSelector& selection);
[845]126
127 /**
128 * unset the selection of the data
129 */
[824]130 void unsetSelection();
131 /**
132 * set the header
[1295]133 * @param[in] sth an STHeader object
[824]134 */
[901]135 void setHeader( const STHeader& sth );
[386]136
[824]137 /**
138 * get the header information
[901]139 * @return an STHeader object
[824]140 */
[901]141 STHeader getHeader( ) const;
[1068]142
[824]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);
[430]150
[824]151 /**
[1068]152 *
153 * @param stype The type of the source, 0 = on, 1 = off
154 */
155 void setSourceType(int stype);
156
[2818]157 /**
158 *
159 * @param stype The name of the source
160 */
161 void setSourceName(const std::string& name);
[1068]162
[2818]163
[1068]164 /**
[1104]165 * The number of scans in the table
[824]166 * @return number of scans in the table
167 */
[845]168 int nscan() const;
[490]169
[915]170 casa::MEpoch::Types getTimeReference() const;
[21]171
[1411]172
173 casa::MEpoch getEpoch(int whichrow) const;
174
[824]175 /**
176 * Get global antenna position
[845]177 * @return casa::MPosition
[824]178 */
179 casa::MPosition getAntennaPosition() const;
[490]180
[1441]181 /**
182 * the @ref casa::MDirection for a specific row
183 * @param[in] whichrow the row number
184 * return casa::MDirection
185 */
[987]186 casa::MDirection getDirection( int whichrow ) const;
[1598]187
[1441]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 */
[1068]193 std::string getDirectionString( int whichrow ) const;
194
[1441]195 /**
196 * set the direction type as a string, e.g. "J2000"
197 * @param[in] refstr the direction type
198 */
[987]199 void setDirectionRefString(const std::string& refstr="");
[1441]200
[1104]201 /**
202 * get the direction reference string
203 * @return a string describing the direction reference
204 */
[1598]205 std::string getDirectionRefString() const;
[987]206
[824]207 /**
[845]208 * Return the Flux unit of the data, e.g. "Jy" or "K"
209 * @return string
[824]210 */
211 std::string getFluxUnit() const;
[472]212
[824]213 /**
[845]214 * Set the Flux unit of the data
215 * @param unit a string representing the unit, e.g "Jy" or "K"
[824]216 */
217 void setFluxUnit( const std::string& unit );
[472]218
[824]219 /**
[1189]220 * Set the Stokes type of the data
[1295]221 * @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]222 */
223 void setFeedType( const std::string& feedtype );
224
225 /**
[824]226 *
[845]227 * @param instrument a string representing an insturment. see xxx
[824]228 */
229 void setInstrument( const std::string& instrument );
[2]230
[845]231 /**
232 * (Re)calculate the azimuth and elevationnfor all rows
233 */
[824]234 void calculateAZEL();
[745]235
[824]236 /**
[845]237 * "hard" flag the data, this flags everything selected in setSelection()
[1104]238 * param[in] msk a boolean mask of length nchan describing the points to
239 * to be flagged
[824]240 */
[1430]241 //void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]242 //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]243
[1994]244 void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
245
[852]246 /**
[1819]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 /**
[852]274 * Return a list of row numbers with respect to the original table.
[902]275 * @return a list of unsigned ints
[852]276 */
277 std::vector<unsigned int> rownumbers() const;
[845]278
[852]279
[845]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 */
[824]286 int nbeam(int scanno=-1) const;
[845]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 */
[824]293 int nif(int scanno=-1) const;
[845]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 */
[824]300 int npol(int scanno=-1) const;
[794]301
[896]302 std::string getPolType() const;
303
[845]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.
[1104]309 * @return the number of rows (for the specified scanno)
[845]310 */
[824]311 int nrow(int scanno=-1) const;
[794]312
[1111]313 int getBeam(int whichrow) const;
[1694]314 std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]315
[847]316 int getIF(int whichrow) const;
[1694]317 std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]318
[847]319 int getPol(int whichrow) const;
[1694]320 std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]321
[1694]322 std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]323 int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]324
[2667]325 std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
326 int getCycle(int whichrow) const { return cycleCol_(whichrow); }
327
[1819]328 //TT addition
329 std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
330
[1111]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;
[923]339 int getChannels(int whichrow) const;
[206]340
[1111]341 int ncycle(int scanno=-1) const;
342
[2667]343
[847]344 double getInterval(int whichrow) const
345 { return integrCol_(whichrow); }
[845]346
[865]347 float getTsys(int whichrow) const
348 { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
[2161]349 std::vector<float> getTsysSpectrum(int whichrow) const ;
[2791]350
351 void setTsys(const std::vector<float>& newvals, int whichrow);
352
[847]353 float getElevation(int whichrow) const
354 { return elCol_(whichrow); }
355 float getAzimuth(int whichrow) const
356 { return azCol_(whichrow); }
[865]357 float getParAngle(int whichrow) const
[1819]358 { return focus().getParAngle(mfocusidCol_(whichrow)); }
359 int getTcalId(int whichrow) const
360 { return mtcalidCol_(whichrow); }
[386]361
[865]362 std::string getSourceName(int whichrow) const
363 { return srcnCol_(whichrow); }
364
[847]365 std::vector<bool> getMask(int whichrow) const;
[896]366 std::vector<float> getSpectrum(int whichrow,
[905]367 const std::string& poltype = "" ) const;
[847]368
[884]369 void setSpectrum(const std::vector<float>& spec, int whichrow);
370
[902]371 std::string getPolarizationLabel(int index, const std::string& ptype) const
372 { return STPol::getPolLabel(index, ptype ); }
[401]373
[845]374 /**
375 * Write the Scantable to disk
376 * @param filename the output file name
377 */
[824]378 void makePersistent(const std::string& filename);
[745]379
[2820]380 std::vector<std::string> getHistory(int nrow=-1, int start=0) const
381 { return historyTable_.getHistory(nrow, start); }
[483]382
[2820]383 uint historyLength()
384 { return historyTable_.nrow(); }
385
386 void dropHistory() { historyTable_.drop(); }
387
[860]388 void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]389
[860]390 void appendToHistoryTable(const STHistory& otherhist)
391 { historyTable_.append(otherhist); }
392
[2163]393 std::string headerSummary();
[2290]394 void summary(const std::string& filename="");
395 std::string oldheaderSummary();
[2286]396 // std::string summary();
[2290]397 void oldsummary(const std::string& filename="");
398
[1947]399 //std::string getTime(int whichrow=-1, bool showdate=true) const;
[2818]400 std::string getTime(int whichrow=-1, bool showdate=true,
401 casa::uInt prec=0) const;
[1350]402 double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]403
[847]404 // returns unit, conversion frame, doppler, base-frame
[18]405
[847]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
[865]417
418 std::vector<double> getAbcissa(int whichrow) const;
419
[1730]420 std::vector<float> getWeather(int whichrow) const;
421
[847]422 std::string getAbcissaLabel(int whichrow) const;
423 std::vector<double> getRestFrequencies() const
424 { return moleculeTable_.getRestFrequencies(); }
[1819]425 std::vector<double> getRestFrequency(int id) const
426 { return moleculeTable_.getRestFrequency(id); }
[847]427
[1819]428 /**
[1170]429 void setRestFrequencies(double rf, const std::string& name = "",
430 const std::string& = "Hz");
[1819]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");
[847]440
[1819]441 //void setRestFrequencies(const std::string& name);
442 void setRestFrequencies(const vector<std::string>& name);
443
[1360]444 void shift(int npix);
445
[1598]446 casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
447
[987]448 void convertDirection(const std::string& newframe);
449
[824]450 STFrequencies& frequencies() { return freqTable_; }
[1375]451 const STFrequencies& frequencies() const { return freqTable_; }
[824]452 STWeather& weather() { return weatherTable_; }
[1375]453 const STWeather& weather() const { return weatherTable_; }
[824]454 STFocus& focus() { return focusTable_; }
[1375]455 const STFocus& focus() const { return focusTable_; }
[824]456 STTcal& tcal() { return tcalTable_; }
[1375]457 const STTcal& tcal() const { return tcalTable_; }
[824]458 STMolecules& molecules() { return moleculeTable_; }
[1375]459 const STMolecules& molecules() const { return moleculeTable_; }
[860]460 STHistory& history() { return historyTable_; }
[1375]461 const STHistory& history() const { return historyTable_; }
[972]462 STFit& fit() { return fitTable_; }
[1375]463 const STFit& fit() const { return fitTable_; }
[2]464
[902]465 std::vector<std::string> columnNames() const;
[896]466
[972]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
[1391]471 //Added by TT
472 /**
473 * Get the antenna name
474 * @return antenna name string
475 */
[1819]476 casa::String getAntennaName() const;
[1391]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
[1586]494 /**
495 * Set a flag indicating whether the data was parallactified
496 * @param[in] flag true or false
497 */
[1598]498 void parallactify(bool flag)
[2357]499 { focusTable_.setParallactify(flag); }
[1727]500
[1819]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 ) ;
[2595]520 void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
[2435]521 void regridSpecChannel( double dnu, int nchan=-1 ) ;
522
[2831]523 bool isAllChannelsFlagged(casa::uInt whichrow);
[1819]524
[2811]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);
[2767]535 void polyBaseline(const std::vector<bool>& mask,
536 int order,
537 float thresClip,
538 int nIterClip,
[2094]539 bool getResidual=true,
[2189]540 const std::string& progressInfo="true,1000",
[2767]541 const bool outLogger=false,
542 const std::string& blfile="",
543 const std::string& bltable="");
[2012]544 void autoPolyBaseline(const std::vector<bool>& mask,
[2767]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="");
[2645]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,
[2767]563 const std::string& blfile="",
564 const std::string& bltable="");
[2645]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,
[2767]575 const std::string& blfile="",
576 const std::string& bltable="");
[2012]577 void cubicSplineBaseline(const std::vector<bool>& mask,
578 int nPiece,
579 float thresClip,
580 int nIterClip,
[2094]581 bool getResidual=true,
[2189]582 const std::string& progressInfo="true,1000",
583 const bool outLogger=false,
[2767]584 const std::string& blfile="",
585 const std::string& bltable="");
[2012]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,
[2094]593 bool getResidual=true,
[2189]594 const std::string& progressInfo="true,1000",
595 const bool outLogger=false,
[2767]596 const std::string& blfile="",
597 const std::string& bltable="");
[2047]598 void sinusoidBaseline(const std::vector<bool>& mask,
[2767]599 const std::string& fftInfo,
[2186]600 const std::vector<int>& addNWaves,
601 const std::vector<int>& rejectNWaves,
[2047]602 float thresClip,
603 int nIterClip,
[2081]604 bool getResidual=true,
[2189]605 const std::string& progressInfo="true,1000",
606 const bool outLogger=false,
[2767]607 const std::string& blfile="",
608 const std::string& bltable="");
[2047]609 void autoSinusoidBaseline(const std::vector<bool>& mask,
[2767]610 const std::string& fftInfo,
[2186]611 const std::vector<int>& addNWaves,
612 const std::vector<int>& rejectNWaves,
[2047]613 float thresClip,
614 int nIterClip,
615 const std::vector<int>& edge,
616 float threshold=3.0,
617 int chanAvgLimit=1,
[2081]618 bool getResidual=true,
[2189]619 const std::string& progressInfo="true,1000",
620 const bool outLogger=false,
[2767]621 const std::string& blfile="",
622 const std::string& bltable="");
[2186]623 std::vector<float> execFFT(const int whichrow,
624 const std::vector<bool>& inMask,
625 bool getRealImag=false,
626 bool getAmplitudeOnly=false);
[2012]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,
[2193]631 int nClipped,
[2012]632 const std::string& masklist,
633 int whichrow,
[2064]634 bool verbose=false,
[2641]635 bool csvformat=false,
[2064]636 int start=-1,
637 int count=-1,
638 bool resetparamid=false) const;
[2012]639 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
640 const std::vector<float>& params,
641 const std::vector<bool>& fixed,
642 float rms,
[2193]643 int nClipped,
[2012]644 const std::string& masklist,
645 int whichrow,
[2641]646 bool verbose=false,
647 bool csvformat=false) const;
[2591]648 std::vector<uint> getMoleculeIdColumnData() const;
649 void setMoleculeIdColumnData(const std::vector<uint>& molids);
[2888]650
651 /**
652 * Get row idx of root table
653 **/
654 std::vector<uint> getRootTableRowNumbers() const;
655
[2713]656 double calculateModelSelectionCriteria(const std::string& valname,
657 const std::string& blfunc,
658 int order,
659 const std::vector<bool>& inMask,
660 int whichrow,
661 bool useLineFinder,
662 const std::vector<int>& edge,
663 float threshold,
664 int chanAvgLimit);
[2767]665 static std::vector<bool> getMaskFromMaskList(const int nchan,
[2789]666 const std::vector<int>& masklist);
667 static casa::Vector<casa::uInt> getMaskListFromMask(
668 const std::vector<bool>& mask);
669 static std::vector<int> splitToIntList(const std::string& str,
670 const char delim);
671 static std::vector<string> splitToStringList(const std::string& str,
672 const char delim);
[1907]673
[2789]674 void dropXPol();
[2012]675
[824]676private:
[896]677
678 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
679
[824]680 /**
[2005]681 * Turns a time value into a formatted string
[824]682 * @param x
683 * @return
684 */
685 std::string formatSec(casa::Double x) const;
[18]686
[824]687 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[2818]688 std::string formatTime(const casa::MEpoch& me, bool showdate,
689 casa::uInt prec)const;
[22]690
[824]691 /**
692 * Turns a casa::MDirection into a nicely formatted string
693 * @param md an casa::MDirection
[2969]694 * @param prec output precision of direction
[824]695 * @return
696 */
[2969]697 std::string formatDirection(const casa::MDirection& md, casa::Int prec=7) const;
[19]698
[824]699 /**
700 * Create a unique file name for the paged (temporary) table
701 * @return just the name
702 */
703 static casa::String generateName();
[286]704
[824]705 /**
706 * attach to cached columns
707 */
708 void attach();
[50]709
[824]710 /**
711 * Set up the main casa::Table
712 */
713 void setupMainTable();
[88]714
[859]715 void attachSubtables();
[865]716 void copySubtables(const Scantable& other);
717
[824]718 /**
719 * Convert an "old" asap1 style row index into a new index
720 * @param[in] therow
721 * @return and index into @table_
722 */
723 int rowToScanIndex(int therow);
[212]724
[1694]725 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]726
[2321]727 static const casa::uInt version_ = 4;
[286]728
[824]729 STSelector selector_;
[236]730
[824]731 casa::Table::TableType type_;
[465]732
[824]733 // the actual data
734 casa::Table table_;
735 casa::Table originalTable_;
[745]736
[824]737 STTcal tcalTable_;
738 STFrequencies freqTable_;
739 STWeather weatherTable_;
740 STFocus focusTable_;
741 STMolecules moleculeTable_;
[860]742 STHistory historyTable_;
[960]743 STFit fitTable_;
[860]744
[824]745 // Cached Columns to avoid reconstructing them for each row get/put
[847]746 casa::ScalarColumn<casa::Double> integrCol_;
[824]747 casa::MDirection::ScalarColumn dirCol_;
[847]748 casa::MEpoch::ScalarColumn timeCol_;
[923]749 casa::ScalarColumn<casa::Float> azCol_;
750 casa::ScalarColumn<casa::Float> elCol_;
[824]751 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]752 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]753 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]754 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]755 casa::ArrayColumn<casa::uChar> flagsCol_;
[430]756
[824]757 // id in frequencies table
758 casa::ScalarColumn<casa::uInt> mfreqidCol_;
759 // id in tcal table
760 casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]761
[824]762 casa::ArrayColumn<casa::String> histitemCol_;
[972]763 casa::ScalarColumn<casa::Int> mfitidCol_;
[824]764 casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]765
[824]766 casa::ScalarColumn<casa::uInt> mfocusidCol_;
767
768 casa::ScalarColumn<casa::uInt> mmolidCol_;
769
[896]770 static std::map<std::string, STPol::STPolFactory *> factories_;
771 void initFactories();
772
[1819]773 /**
774 * Add an auxiliary column to the main table and attach it to a
775 * cached column. Use for adding new columns that the original asap2
776 * tables do not have.
777 * @param[in] col reference to the cached column to be attached
778 * @param[in] colName column name in asap table
779 * @param[in] defValue default value to fill in the column
780 *
781 * 25/10/2009 Wataru Kawasaki
782 */
783 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
784 const casa::String&,
785 const T2&);
786 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
787 const casa::String&,
788 const casa::Array<T2>&);
[1907]789
[2767]790 double getNormalPolynomial(int n, double x);
[2645]791 double getChebyshevPolynomial(int n, double x);
[2773]792 std::vector<std::vector<double> > getPolynomialModel(int order,
793 int nchan,
794 double (Scantable::*pfunc)(int, double));
795 std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
796 double (Scantable::*pfunc)(int, double),
797 std::vector<int>& nChanNos);
[2767]798 std::vector<float> doPolynomialFitting(const std::vector<float>& data,
799 const std::vector<bool>& mask,
800 int order,
801 std::vector<float>& params,
802 float& rms,
803 std::vector<bool>& finalMask,
804 float clipth,
805 int clipn);
806 std::vector<float> doPolynomialFitting(const std::vector<float>& data,
807 const std::vector<bool>& mask,
808 int order,
809 std::vector<float>& params,
810 float& rms,
811 std::vector<bool>& finalMask,
812 int& nClipped,
813 float thresClip=3.0,
814 int nIterClip=0,
815 bool getResidual=true);
[2645]816 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
[2767]817 const std::vector<bool>& mask,
818 int order,
819 std::vector<float>& params,
820 float& rms,
821 std::vector<bool>& finalMask,
822 float clipth,
823 int clipn);
824 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
825 const std::vector<bool>& mask,
826 int order,
827 std::vector<float>& params,
828 float& rms,
829 std::vector<bool>& finalMask,
830 int& nClipped,
831 float thresClip=3.0,
832 int nIterClip=0,
833 bool getResidual=true);
834 std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
835 const std::vector<bool>& mask,
[2773]836 const std::vector<std::vector<double> >& model,
[2767]837 std::vector<float>& params,
838 float& rms,
839 std::vector<bool>& finalMask,
840 int& nClipped,
841 float thresClip=3.0,
842 int nIterClip=0,
843 bool getResidual=true);
844 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
[2645]845 const std::vector<bool>& mask,
[2767]846 std::vector<int>& idxEdge,
[2645]847 std::vector<float>& params,
[2767]848 float& rms,
[2737]849 std::vector<bool>& finalMask,
[2767]850 float clipth,
851 int clipn);
852 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
853 const std::vector<bool>& mask,
854 int nPiece,
855 std::vector<int>& idxEdge,
856 std::vector<float>& params,
[2737]857 float& rms,
[2767]858 std::vector<bool>& finalMask,
859 float clipth,
860 int clipn);
[2012]861 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
862 const std::vector<bool>& mask,
[2081]863 int nPiece,
[2767]864 bool useGivenPieceBoundary,
[2064]865 std::vector<int>& idxEdge,
[2012]866 std::vector<float>& params,
[2767]867 float& rms,
868 std::vector<bool>& finalMask,
[2193]869 int& nClipped,
[2012]870 float thresClip=3.0,
[2767]871 int nIterClip=0,
[2094]872 bool getResidual=true);
[2773]873 std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
874 const std::vector<bool>& mask,
875 const std::vector<std::vector<double> >& model,
876 int nPiece,
877 bool useGivenPieceBoundary,
878 std::vector<int>& idxEdge,
879 std::vector<float>& params,
880 float& rms,
881 std::vector<bool>& finalMask,
882 int& nClipped,
883 float thresClip=3.0,
884 int nIterClip=0,
885 bool getResidual=true);
[2047]886 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
887 const std::vector<bool>& mask,
[2081]888 const std::vector<int>& waveNumbers,
[2047]889 std::vector<float>& params,
[2767]890 float& rms,
891 std::vector<bool>& finalMask,
892 float clipth,
893 int clipn);
894 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
895 const std::vector<bool>& mask,
896 const std::vector<int>& waveNumbers,
897 std::vector<float>& params,
898 float& rms,
899 std::vector<bool>& finalMask,
[2193]900 int& nClipped,
[2047]901 float thresClip=3.0,
[2767]902 int nIterClip=0,
[2094]903 bool getResidual=true);
[2773]904 std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
905 std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
906 std::vector<int>& nChanNos);
907 std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
908 const std::vector<int>& rejectNWaves);
909 std::vector<int> selectWaveNumbers(const int whichrow,
910 const std::vector<bool>& chanMask,
911 //const std::string& fftInfo,
912 const bool applyFFT,
913 const std::string& fftMethod,
914 const std::string& fftThresh,
915 const std::vector<int>& addNWaves,
916 const std::vector<int>& rejectNWaves);
917 int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
[2767]918 void parseFFTInfo(const std::string& fftInfo,
919 bool& applyFFT,
920 std::string& fftMethod,
921 std::string& fftThresh);
[2773]922 void parseFFTThresholdInfo(const std::string& fftThresh,
923 std::string& fftThAttr,
924 float& fftThSigma,
925 int& fftThTop);
[2186]926 void doSelectWaveNumbers(const int whichrow,
927 const std::vector<bool>& chanMask,
928 const std::string& fftMethod,
929 const float fftThSigma,
930 const int fftThTop,
931 const std::string& fftThAttr,
932 std::vector<int>& nWaves);
[2411]933 void addAuxWaveNumbers(const int whichrow,
934 const std::vector<int>& addNWaves,
[2186]935 const std::vector<int>& rejectNWaves,
936 std::vector<int>& nWaves);
[2411]937 void setWaveNumberListUptoNyquistFreq(const int whichrow,
938 std::vector<int>& nWaves);
[2773]939 void initialiseBaselining(const std::string& blfile,
940 std::ofstream& ofs,
941 const bool outLogger,
942 bool& outTextFile,
943 bool& csvFormat,
944 casa::String& coordInfo,
945 bool& hasSameNchan,
946 const std::string& progressInfo,
947 bool& showProgress,
948 int& minNRow,
949 casa::Vector<casa::Double>& timeSecCol);
950 void finaliseBaselining(const bool outBaselineTable,
951 STBaselineTable* pbt,
952 const string& bltable,
953 const bool outTextFile,
954 std::ofstream& ofs);
955 void initLineFinder(const std::vector<int>& edge,
956 const float threshold,
957 const int chanAvgLimit,
958 STLineFinder& lineFinder);
[2012]959 bool hasSameNchanOverIFs();
960 std::string getMaskRangeList(const std::vector<bool>& mask,
961 int whichrow,
962 const casa::String& coordInfo,
[2047]963 bool hasSameNchan,
964 bool verbose=false);
965 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]966 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
967 std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]968 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
[2773]969 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
[2641]970 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);
971 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);
[2189]972 void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
973 void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]974
975 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
976
[2713]977 double doCalculateModelSelectionCriteria(const std::string& valname,
978 const std::vector<float>& spec,
979 const std::vector<bool>& mask,
980 const std::string& blfunc,
981 int order);
[2737]982 double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
[2767]983 std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
984 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);
985 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);
986 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);
[2713]987
[2]988};
[824]989} // namespace
990
[2]991#endif
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