source: trunk/src/Scantable.h @ 2321

Last change on this file since 2321 was 2321, checked in by Malte Marquarding, 13 years ago

Ticket #249: scantbable schema was changed. This required an update to scantable version 4. I have added a class STUpgrade to handle all schema upgrades. This is handled transparently in the scantable constructor

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[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>
30
[2186]31#include <coordinates/Coordinates/SpectralCoordinate.h>
[322]32
[824]33#include <measures/TableMeasures/ScalarMeasColumn.h>
34
[2186]35#include <scimath/Mathematics/FFTServer.h>
[1598]36
[2186]37#include <tables/Tables/ArrayColumn.h>
38#include <tables/Tables/ScalarColumn.h>
39#include <tables/Tables/Table.h>
[1819]40
[894]41#include "Logger.h"
[2186]42#include "MathUtils.h"
43#include "STFit.h"
44#include "STFitEntry.h"
45#include "STFitter.h"
46#include "STFocus.h"
47#include "STFrequencies.h"
[901]48#include "STHeader.h"
[2186]49#include "STHistory.h"
[824]50#include "STMolecules.h"
[2186]51#include "STPol.h"
[824]52#include "STSelector.h"
[2186]53#include "STTcal.h"
54#include "STWeather.h"
[2]55
[824]56namespace asap {
[2]57
[824]58/**
59  * This class contains and wraps a casa::Table, which is used to store
60  * all the information. This can be either a MemoryTable or a
61  * disk based Table.
62  * It provides access functions to the underlying table
63  * It contains n subtables:
64  * @li weather
65  * @li frequencies
66  * @li molecules
67  * @li tcal
68  * @li focus
69  * @li fits
70  *
71  * @brief The main ASAP data container
72  * @author Malte Marquarding
73  * @date
74  * @version
75*/
[890]76class Scantable : private Logger
[824]77{
[902]78
79friend class STMath;
80
[2]81public:
[824]82  /**
83   * Default constructor
84   */
[1350]85  explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
[19]86
[824]87  /**
[2321]88   * Create a Scantable object from an existing table on disk
[824]89   * @param[in] name the name of the existing Scantable
90   */
[2321]91  explicit Scantable(const std::string& name,
92                     casa::Table::TableType ttype = casa::Table::Memory);
[2]93
[824]94  /// @fixme this is only sensible for MemoryTables....
95  Scantable(const Scantable& other, bool clear=true);
[161]96
[824]97  /**
98   * Destructor
99   */
100  virtual ~Scantable();
[745]101
[824]102  /**
103   * get a const reference to the underlying casa::Table
[1104]104   * @return const \ref casa::Table reference
[824]105   */
106  const casa::Table& table() const;
[19]107
[824]108  /**
109   * get a reference to the underlying casa::Table with the Selection
110   * object applied if set
111   * @return casa::Table reference
112   */
113  casa::Table& table();
[21]114
[845]115
116  /**
117   * Get a handle to the selection object
118   * @return constant STSelector reference
119   */
120  const STSelector& getSelection() const { return selector_; }
121
122  /**
123   * Set the data to be a subset as defined by the STSelector
124   * @param selection a STSelector object
125   */
[824]126  void setSelection(const STSelector& selection);
[845]127
128  /**
129   * unset the selection of the data
130   */
[824]131  void unsetSelection();
132  /**
133   * set the header
[1295]134   * @param[in] sth an STHeader object
[824]135   */
[901]136  void setHeader( const STHeader& sth );
[386]137
[824]138  /**
139   * get the header information
[901]140   * @return an STHeader object
[824]141   */
[901]142  STHeader getHeader( ) const;
[1068]143
[824]144  /**
145   * Checks if the "other" Scantable is conformant with this,
146   * i.e. if  header values are the same.
147   * @param[in] other another Scantable
148   * @return true or false
149   */
150  bool conformant( const Scantable& other);
[430]151
[824]152  /**
[1068]153   *
154   * @param stype The type of the source, 0 = on, 1 = off
155   */
156  void setSourceType(int stype);
157
158
159  /**
[1104]160   * The number of scans in the table
[824]161   * @return number of scans in the table
162   */
[845]163  int nscan() const;
[490]164
[915]165  casa::MEpoch::Types getTimeReference() const;
[21]166
[1411]167
168  casa::MEpoch getEpoch(int whichrow) const;
169
[824]170  /**
171   * Get global antenna position
[845]172   * @return casa::MPosition
[824]173   */
174  casa::MPosition getAntennaPosition() const;
[490]175
[1441]176  /**
177   * the @ref casa::MDirection for a specific row
178   * @param[in] whichrow the row number
179   * return casa::MDirection
180   */
[987]181  casa::MDirection getDirection( int whichrow ) const;
[1598]182
[1441]183  /**
184   * get the direction type as a string, e.g. "J2000"
185   * @param[in] whichrow the row number
186   * return the direction string
187   */
[1068]188  std::string getDirectionString( int whichrow ) const;
189
[1441]190  /**
191   * set the direction type as a string, e.g. "J2000"
192   * @param[in] refstr the direction type
193   */
[987]194  void setDirectionRefString(const std::string& refstr="");
[1441]195
[1104]196  /**
197   * get the direction reference string
198   * @return a string describing the direction reference
199   */
[1598]200  std::string getDirectionRefString() const;
[987]201
[824]202  /**
[845]203   *  Return the Flux unit of the data, e.g. "Jy" or "K"
204   * @return string
[824]205   */
206  std::string getFluxUnit() const;
[472]207
[824]208  /**
[845]209   * Set the Flux unit of the data
210   * @param unit a string representing the unit, e.g "Jy" or "K"
[824]211   */
212  void setFluxUnit( const std::string& unit );
[472]213
[824]214  /**
[1189]215   * Set the Stokes type of the data
[1295]216   * @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]217   */
218  void setFeedType( const std::string& feedtype );
219
220  /**
[824]221   *
[845]222   * @param instrument a string representing an insturment. see xxx
[824]223   */
224  void setInstrument( const std::string& instrument );
[2]225
[845]226  /**
227   * (Re)calculate the azimuth and elevationnfor all rows
228   */
[824]229  void calculateAZEL();
[745]230
[824]231  /**
[845]232   * "hard" flag the data, this flags everything selected in setSelection()
[1104]233   * param[in] msk a boolean mask of length nchan describing the points to
234   * to be flagged
[824]235   */
[1430]236  //void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]237  //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]238
[1994]239  void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
240
[852]241  /**
[1819]242   * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
243   * param[in] rows    list of row numbers to be flagged
244   */
245  void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
246
247  /**
248   * Get flagRow info at the specified row. If true, the whole data
249   * at the row should be flagged.
250   */
251  bool getFlagRow(int whichrow) const
252    { return (flagrowCol_(whichrow) > 0); }
253
254  /**
255   * Flag the data outside a specified range (in a channel-based manner).
256   * (CAS-1807 Wataru Kawasaki)
257   */
258  void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
259
260  /**
261   * Return a list of booleans with the size of nchan for a specified row, to get info
262   * about which channel is clipped.
263   */
264  std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
265  void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
266                          casa::Vector<casa::uChar> flgs);
267
268  /**
[852]269   * Return a list of row numbers with respect to the original table.
[902]270   * @return a list of unsigned ints
[852]271   */
272  std::vector<unsigned int> rownumbers() const;
[845]273
[852]274
[845]275  /**
276   * Get the number of beams in the data or a specific scan
277   * @param scanno the scan number to get the number of beams for.
278   * If scanno<0 the number is retrieved from the header.
279   * @return an integer number
280   */
[824]281  int nbeam(int scanno=-1) const;
[845]282  /**
283   * Get the number of IFs in the data or a specific scan
284   * @param scanno the scan number to get the number of IFs for.
285   * If scanno<0 the number is retrieved from the header.
286   * @return an integer number
287   */
[824]288  int nif(int scanno=-1) const;
[845]289  /**
290   * Get the number of polarizations in the data or a specific scan
291   * @param scanno the scan number to get the number of polarizations for.
292   * If scanno<0 the number is retrieved from the header.
293   * @return an integer number
294   */
[824]295  int npol(int scanno=-1) const;
[794]296
[896]297  std::string getPolType() const;
298
[845]299
300  /**
301   * Get the number of integartion cycles
302   * @param scanno the scan number to get the number of rows for.
303   * If scanno<0 the number is retrieved from the header.
[1104]304   * @return the number of rows (for the specified scanno)
[845]305   */
[824]306  int nrow(int scanno=-1) const;
[794]307
[1111]308  int getBeam(int whichrow) const;
[1694]309  std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]310
[847]311  int getIF(int whichrow) const;
[1694]312  std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]313
[847]314  int getPol(int whichrow) const;
[1694]315  std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]316
[1694]317  std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]318  int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]319
[1819]320  //TT addition
321  std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
322
[1111]323  /**
324   * Get the number of channels in the data or a specific IF. This currently
325   * varies only with IF number
326   * @param ifno the IF number to get the number of channels for.
327   * If ifno<0 the number is retrieved from the header.
328   * @return an integer number
329   */
330  int nchan(int ifno=-1) const;
[923]331  int getChannels(int whichrow) const;
[206]332
[1111]333  int ncycle(int scanno=-1) const;
334  int getCycle(int whichrow) const { return cycleCol_(whichrow); }
335
[847]336  double getInterval(int whichrow) const
337    { return integrCol_(whichrow); }
[845]338
[865]339  float getTsys(int whichrow) const
340    { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
[2161]341  std::vector<float> getTsysSpectrum(int whichrow) const ;
[847]342  float getElevation(int whichrow) const
343    { return elCol_(whichrow); }
344  float getAzimuth(int whichrow) const
345    { return azCol_(whichrow); }
[865]346  float getParAngle(int whichrow) const
[1819]347    { return focus().getParAngle(mfocusidCol_(whichrow)); }
348  int getTcalId(int whichrow) const
349    { return mtcalidCol_(whichrow); }
[386]350
[865]351  std::string getSourceName(int whichrow) const
352    { return srcnCol_(whichrow); }
353
[847]354  std::vector<bool> getMask(int whichrow) const;
[896]355  std::vector<float> getSpectrum(int whichrow,
[905]356                                 const std::string& poltype = "" ) const;
[847]357
[884]358  void setSpectrum(const std::vector<float>& spec, int whichrow);
359
[902]360  std::string getPolarizationLabel(int index, const std::string& ptype) const
361    { return STPol::getPolLabel(index, ptype ); }
[401]362
[845]363  /**
364   * Write the Scantable to disk
365   * @param filename the output file name
366   */
[824]367  void makePersistent(const std::string& filename);
[745]368
[860]369  std::vector<std::string> getHistory() const
370    { return historyTable_.getHistory(); };
[483]371
[860]372  void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]373
[860]374  void appendToHistoryTable(const STHistory& otherhist)
375    { historyTable_.append(otherhist); }
376
[2163]377  std::string headerSummary();
[2290]378  void summary(const std::string& filename="");
379  std::string oldheaderSummary();
[2286]380  //  std::string summary();
[2290]381  void oldsummary(const std::string& filename="");
382
[1947]383  //std::string getTime(int whichrow=-1, bool showdate=true) const;
384  std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
[1350]385  double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]386
[847]387  // returns unit, conversion frame, doppler, base-frame
[18]388
[847]389  /**
390   * Get the frequency set up
391   * This is forwarded to the STFrequencies subtable
392   * @return unit, frame, doppler
393   */
394  std::vector<std::string> getCoordInfo() const
395    { return freqTable_.getInfo(); };
396
397  void setCoordInfo(std::vector<string> theinfo)
398    { return freqTable_.setInfo(theinfo); };
399
[865]400
401  std::vector<double> getAbcissa(int whichrow) const;
402
[1730]403  std::vector<float> getWeather(int whichrow) const;
404
[847]405  std::string getAbcissaLabel(int whichrow) const;
406  std::vector<double> getRestFrequencies() const
407    { return moleculeTable_.getRestFrequencies(); }
[1819]408  std::vector<double> getRestFrequency(int id) const
409    { return moleculeTable_.getRestFrequency(id); }
[847]410
[1819]411  /**
[1170]412  void setRestFrequencies(double rf, const std::string& name = "",
413                          const std::string& = "Hz");
[1819]414  **/
415  // Modified by Takeshi Nakazato 05/09/2008
416  /***
417  void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
418                          const std::string& = "Hz");
419  ***/
420  void setRestFrequencies(vector<double> rf,
421                          const vector<std::string>& name = vector<std::string>(1,""),
422                          const std::string& = "Hz");
[847]423
[1819]424  //void setRestFrequencies(const std::string& name);
425  void setRestFrequencies(const vector<std::string>& name);
426
[1360]427  void shift(int npix);
428
[1598]429  casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
430
[987]431  void convertDirection(const std::string& newframe);
432
[824]433  STFrequencies& frequencies() { return freqTable_; }
[1375]434  const STFrequencies& frequencies() const { return freqTable_; }
[824]435  STWeather& weather() { return weatherTable_; }
[1375]436  const STWeather& weather() const { return weatherTable_; }
[824]437  STFocus& focus() { return focusTable_; }
[1375]438  const STFocus& focus() const { return focusTable_; }
[824]439  STTcal& tcal() { return tcalTable_; }
[1375]440  const STTcal& tcal() const { return tcalTable_; }
[824]441  STMolecules& molecules() { return moleculeTable_; }
[1375]442  const STMolecules& molecules() const { return moleculeTable_; }
[860]443  STHistory& history() { return historyTable_; }
[1375]444  const STHistory& history() const { return historyTable_; }
[972]445  STFit& fit() { return fitTable_; }
[1375]446  const STFit& fit() const { return fitTable_; }
[2]447
[902]448  std::vector<std::string> columnNames() const;
[896]449
[972]450  void addFit(const STFitEntry& fit, int row);
451  STFitEntry getFit(int row) const
452    { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
453
[1391]454  //Added by TT
455  /**
456   * Get the antenna name
457   * @return antenna name string
458   */
[1819]459  casa::String getAntennaName() const;
[1391]460
461  /**
462   * For GBT MS data only. check a scan list
463   * against the information found in GBT_GO table for
464   * scan number orders to get correct pairs.
465   * @param[in] scan list
466   * @return status
467   */
468  int checkScanInfo(const std::vector<int>& scanlist) const;
469
470  /**
471   * Get the direction as a vector, for a specific row
472   * @param[in] whichrow the row numbyyer
473   * @return the direction in a vector
474   */
475  std::vector<double> getDirectionVector(int whichrow) const;
476
[1586]477  /**
478   * Set a flag indicating whether the data was parallactified
479   * @param[in] flag true or false
480   */
[1598]481  void parallactify(bool flag)
[1727]482    { focus().setParallactify(flag); }
483
[1819]484  /**
485   * Reshape spectrum
486   * @param[in] nmin, nmax minimum and maximum channel
487   * @param[in] irow       row number
488   *
489   * 30/07/2008 Takeshi Nakazato
490   **/
491  void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
492  void reshapeSpectrum( int nmin, int nmax, int irow ) ;
493
494  /**
495   * Change channel number under fixed bandwidth
496   * @param[in] nchan, dnu new channel number and spectral resolution
497   * @param[in] irow       row number
498   *
499   * 27/08/2008 Takeshi Nakazato
500   **/
501  void regridChannel( int nchan, double dnu ) ;
502  void regridChannel( int nchan, double dnu, int irow ) ;
503
[2047]504  bool getFlagtraFast(casa::uInt whichrow);
[1819]505
[2012]506  void polyBaseline(const std::vector<bool>& mask,
507                    int order,
[2094]508                    bool getResidual=true,
[2189]509                    const std::string& progressInfo="true,1000",
510                    const bool outLogger=false,
[2012]511                    const std::string& blfile="");
512  void autoPolyBaseline(const std::vector<bool>& mask,
513                        int order,
514                        const std::vector<int>& edge,
515                        float threshold=3.0,
516                        int chanAvgLimit=1,
[2094]517                        bool getResidual=true,
[2189]518                        const std::string& progressInfo="true,1000",
519                        const bool outLogger=false,
[2012]520                        const std::string& blfile="");
521  void cubicSplineBaseline(const std::vector<bool>& mask,
522                           int nPiece,
523                           float thresClip,
524                           int nIterClip,
[2094]525                           bool getResidual=true,
[2189]526                           const std::string& progressInfo="true,1000",
527                           const bool outLogger=false,
[2012]528                           const std::string& blfile="");
529  void autoCubicSplineBaseline(const std::vector<bool>& mask,
530                               int nPiece,
531                               float thresClip,
532                               int nIterClip,
533                               const std::vector<int>& edge,
534                               float threshold=3.0,
535                               int chanAvgLimit=1,
[2094]536                               bool getResidual=true,
[2189]537                               const std::string& progressInfo="true,1000",
538                               const bool outLogger=false,
[2012]539                               const std::string& blfile="");
[2047]540  void sinusoidBaseline(const std::vector<bool>& mask,
[2186]541                        const bool applyFFT,
542                        const std::string& fftMethod,
543                        const std::string& fftThresh,
544                        const std::vector<int>& addNWaves,
545                        const std::vector<int>& rejectNWaves,
[2047]546                        float thresClip,
547                        int nIterClip,
[2081]548                        bool getResidual=true,
[2189]549                        const std::string& progressInfo="true,1000",
550                        const bool outLogger=false,
[2047]551                        const std::string& blfile="");
552  void autoSinusoidBaseline(const std::vector<bool>& mask,
[2186]553                            const bool applyFFT,
554                            const std::string& fftMethod,
555                            const std::string& fftThresh,
556                            const std::vector<int>& addNWaves,
557                            const std::vector<int>& rejectNWaves,
[2047]558                            float thresClip,
559                            int nIterClip,
560                            const std::vector<int>& edge,
561                            float threshold=3.0,
562                            int chanAvgLimit=1,
[2081]563                            bool getResidual=true,
[2189]564                            const std::string& progressInfo="true,1000",
565                            const bool outLogger=false,
[2047]566                            const std::string& blfile="");
[2186]567  std::vector<float> execFFT(const int whichrow,
568                             const std::vector<bool>& inMask,
569                             bool getRealImag=false,
570                             bool getAmplitudeOnly=false);
[2012]571  float getRms(const std::vector<bool>& mask, int whichrow);
572  std::string formatBaselineParams(const std::vector<float>& params,
573                                   const std::vector<bool>& fixed,
574                                   float rms,
[2193]575                                   int nClipped,
[2012]576                                   const std::string& masklist,
577                                   int whichrow,
[2064]578                                   bool verbose=false,
579                                   int start=-1,
580                                   int count=-1,
581                                   bool resetparamid=false) const;
[2012]582  std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
583                                            const std::vector<float>& params,
584                                            const std::vector<bool>& fixed,
585                                            float rms,
[2193]586                                            int nClipped,
[2012]587                                            const std::string& masklist,
588                                            int whichrow,
589                                            bool verbose=false) const;
[1907]590
[2012]591
[824]592private:
[896]593
594  casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
595
[824]596  /**
[2005]597   * Turns a time value into a formatted string
[824]598   * @param x
599   * @return
600   */
601  std::string formatSec(casa::Double x) const;
[18]602
[824]603  std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]604  std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]605
[824]606  /**
607   *  Turns a casa::MDirection into a nicely formatted string
608   * @param md an casa::MDirection
609   * @return
610   */
611  std::string formatDirection(const casa::MDirection& md) const;
[19]612
[824]613  /**
614   * Create a unique file name for the paged (temporary) table
615   * @return just the name
616   */
617  static casa::String generateName();
[286]618
[824]619  /**
620   * attach to cached columns
621   */
622  void attach();
[50]623
[824]624  /**
625   * Set up the main casa::Table
626   */
627  void setupMainTable();
[88]628
[859]629  void attachSubtables();
[865]630  void copySubtables(const Scantable& other);
631
[824]632  /**
633   * Convert an "old" asap1 style row index into a new index
634   * @param[in] therow
635   * @return and index into @table_
636   */
637  int rowToScanIndex(int therow);
[212]638
[1694]639  std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]640
[2321]641  static const casa::uInt version_ = 4;
[286]642
[824]643  STSelector selector_;
[236]644
[824]645  casa::Table::TableType type_;
[465]646
[824]647  // the actual data
648  casa::Table table_;
649  casa::Table originalTable_;
[745]650
[824]651  STTcal tcalTable_;
652  STFrequencies freqTable_;
653  STWeather weatherTable_;
654  STFocus focusTable_;
655  STMolecules moleculeTable_;
[860]656  STHistory historyTable_;
[960]657  STFit fitTable_;
[860]658
[824]659  // Cached Columns to avoid reconstructing them for each row get/put
[847]660  casa::ScalarColumn<casa::Double> integrCol_;
[824]661  casa::MDirection::ScalarColumn dirCol_;
[847]662  casa::MEpoch::ScalarColumn timeCol_;
[923]663  casa::ScalarColumn<casa::Float> azCol_;
664  casa::ScalarColumn<casa::Float> elCol_;
[824]665  casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]666  casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]667  casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]668  casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]669  casa::ArrayColumn<casa::uChar> flagsCol_;
[430]670
[824]671  // id in frequencies table
672  casa::ScalarColumn<casa::uInt> mfreqidCol_;
673  // id in tcal table
674  casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]675
[824]676  casa::ArrayColumn<casa::String> histitemCol_;
[972]677  casa::ScalarColumn<casa::Int> mfitidCol_;
[824]678  casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]679
[824]680  casa::ScalarColumn<casa::uInt> mfocusidCol_;
681
682  casa::ScalarColumn<casa::uInt> mmolidCol_;
683
[896]684  static std::map<std::string, STPol::STPolFactory *> factories_;
685  void initFactories();
686
[1819]687  /**
688   * Add an auxiliary column to the main table and attach it to a
689   * cached column. Use for adding new columns that the original asap2
690   * tables do not have.
691   * @param[in] col      reference to the cached column to be attached
692   * @param[in] colName  column name in asap table
693   * @param[in] defValue default value to fill in the column
694   *
695   * 25/10/2009 Wataru Kawasaki
696   */
697  template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
698                                                       const casa::String&,
699                                                       const T2&);
700  template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
701                                                      const casa::String&,
702                                                      const casa::Array<T2>&);
[1907]703
[2012]704  void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
705  std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
706                                          const std::vector<bool>& mask,
[2081]707                                          int nPiece,
[2064]708                                          std::vector<int>& idxEdge,
[2012]709                                          std::vector<float>& params,
[2193]710                                          int& nClipped,
[2012]711                                          float thresClip=3.0,
[2058]712                                          int nIterClip=1,
[2094]713                                          bool getResidual=true);
[2047]714  std::vector<float> doSinusoidFitting(const std::vector<float>& data,
715                                       const std::vector<bool>& mask,
[2081]716                                       const std::vector<int>& waveNumbers,
[2047]717                                       std::vector<float>& params,
[2193]718                                       int& nClipped,
[2047]719                                       float thresClip=3.0,
[2058]720                                       int nIterClip=1,
[2094]721                                       bool getResidual=true);
[2186]722  void selectWaveNumbers(const int whichrow,
723                         const std::vector<bool>& chanMask,
724                         const bool applyFFT,
725                         const std::string& fftMethod,
726                         const std::string& fftThresh,
727                         const std::vector<int>& addNWaves,
728                         const std::vector<int>& rejectNWaves,
729                         std::vector<int>& nWaves);
730  void parseThresholdExpression(const std::string& fftThresh,
731                                std::string& fftThAttr,
732                                float& fftThSigma,
733                                int& fftThTop);
734  void doSelectWaveNumbers(const int whichrow,
735                           const std::vector<bool>& chanMask,
736                           const std::string& fftMethod,
737                           const float fftThSigma,
738                           const int fftThTop,
739                           const std::string& fftThAttr,
740                           std::vector<int>& nWaves);
741  void addAuxWaveNumbers(const std::vector<int>& addNWaves,
742                         const std::vector<int>& rejectNWaves,
743                         std::vector<int>& nWaves);
[2012]744  bool hasSameNchanOverIFs();
745  std::string getMaskRangeList(const std::vector<bool>& mask,
746                                int whichrow,
747                                const casa::String& coordInfo,
[2047]748                                bool hasSameNchan,
749                                bool verbose=false);
750  std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2012]751  std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const;
[2193]752  std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const;
[2012]753  std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
754  //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
[2047]755  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);
[2193]756  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, const int nClipped);
757  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, const int nClipped);
[2189]758  void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
759  void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]760
761  void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
762
763
[2]764};
765
[824]766} // namespace
767
[2]768#endif
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