source: trunk/src/Scantable.h @ 2290

Last change on this file since 2290 was 2290, checked in by Kana Sugimoto, 13 years ago

New Development: Yes

JIRA Issue: Yes (CAS-3219/ASAP-247)

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs: sdlist unit test (reference data to be updated)

Put in Release Notes: Yes

Module(s): scantable.summary, sdlist

Description:

Output format of scantable summary changed.
Less use of TableIterator? for speed up scantable.summary/sdlist now lists a scantable
with 348,000 records (NRO 45m w/ 25beams x 13,920scans) in ~30sec (was ~7 min previously).


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 23.9 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>
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  /**
88   * Create a Scantable object form an existing table on disk
89   * @param[in] name the name of the existing Scantable
90   */
[1385]91  explicit Scantable(const std::string& name, 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
157
158  /**
[1104]159   * The number of scans in the table
[824]160   * @return number of scans in the table
161   */
[845]162  int nscan() const;
[490]163
[915]164  casa::MEpoch::Types getTimeReference() const;
[21]165
[1411]166
167  casa::MEpoch getEpoch(int whichrow) const;
168
[824]169  /**
170   * Get global antenna position
[845]171   * @return casa::MPosition
[824]172   */
173  casa::MPosition getAntennaPosition() const;
[490]174
[1441]175  /**
176   * the @ref casa::MDirection for a specific row
177   * @param[in] whichrow the row number
178   * return casa::MDirection
179   */
[987]180  casa::MDirection getDirection( int whichrow ) const;
[1598]181
[1441]182  /**
183   * get the direction type as a string, e.g. "J2000"
184   * @param[in] whichrow the row number
185   * return the direction string
186   */
[1068]187  std::string getDirectionString( int whichrow ) const;
188
[1441]189  /**
190   * set the direction type as a string, e.g. "J2000"
191   * @param[in] refstr the direction type
192   */
[987]193  void setDirectionRefString(const std::string& refstr="");
[1441]194
[1104]195  /**
196   * get the direction reference string
197   * @return a string describing the direction reference
198   */
[1598]199  std::string getDirectionRefString() const;
[987]200
[824]201  /**
[845]202   *  Return the Flux unit of the data, e.g. "Jy" or "K"
203   * @return string
[824]204   */
205  std::string getFluxUnit() const;
[472]206
[824]207  /**
[845]208   * Set the Flux unit of the data
209   * @param unit a string representing the unit, e.g "Jy" or "K"
[824]210   */
211  void setFluxUnit( const std::string& unit );
[472]212
[824]213  /**
[1189]214   * Set the Stokes type of the data
[1295]215   * @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]216   */
217  void setFeedType( const std::string& feedtype );
218
219  /**
[824]220   *
[845]221   * @param instrument a string representing an insturment. see xxx
[824]222   */
223  void setInstrument( const std::string& instrument );
[2]224
[845]225  /**
226   * (Re)calculate the azimuth and elevationnfor all rows
227   */
[824]228  void calculateAZEL();
[745]229
[824]230  /**
[845]231   * "hard" flag the data, this flags everything selected in setSelection()
[1104]232   * param[in] msk a boolean mask of length nchan describing the points to
233   * to be flagged
[824]234   */
[1430]235  //void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]236  //void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]237
[1994]238  void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
239
[852]240  /**
[1819]241   * Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
242   * param[in] rows    list of row numbers to be flagged
243   */
244  void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
245
246  /**
247   * Get flagRow info at the specified row. If true, the whole data
248   * at the row should be flagged.
249   */
250  bool getFlagRow(int whichrow) const
251    { return (flagrowCol_(whichrow) > 0); }
252
253  /**
254   * Flag the data outside a specified range (in a channel-based manner).
255   * (CAS-1807 Wataru Kawasaki)
256   */
257  void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
258
259  /**
260   * Return a list of booleans with the size of nchan for a specified row, to get info
261   * about which channel is clipped.
262   */
263  std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
264  void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
265                          casa::Vector<casa::uChar> flgs);
266
267  /**
[852]268   * Return a list of row numbers with respect to the original table.
[902]269   * @return a list of unsigned ints
[852]270   */
271  std::vector<unsigned int> rownumbers() const;
[845]272
[852]273
[845]274  /**
275   * Get the number of beams in the data or a specific scan
276   * @param scanno the scan number to get the number of beams for.
277   * If scanno<0 the number is retrieved from the header.
278   * @return an integer number
279   */
[824]280  int nbeam(int scanno=-1) const;
[845]281  /**
282   * Get the number of IFs in the data or a specific scan
283   * @param scanno the scan number to get the number of IFs for.
284   * If scanno<0 the number is retrieved from the header.
285   * @return an integer number
286   */
[824]287  int nif(int scanno=-1) const;
[845]288  /**
289   * Get the number of polarizations in the data or a specific scan
290   * @param scanno the scan number to get the number of polarizations for.
291   * If scanno<0 the number is retrieved from the header.
292   * @return an integer number
293   */
[824]294  int npol(int scanno=-1) const;
[794]295
[896]296  std::string getPolType() const;
297
[845]298
299  /**
300   * Get the number of integartion cycles
301   * @param scanno the scan number to get the number of rows for.
302   * If scanno<0 the number is retrieved from the header.
[1104]303   * @return the number of rows (for the specified scanno)
[845]304   */
[824]305  int nrow(int scanno=-1) const;
[794]306
[1111]307  int getBeam(int whichrow) const;
[1694]308  std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]309
[847]310  int getIF(int whichrow) const;
[1694]311  std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]312
[847]313  int getPol(int whichrow) const;
[1694]314  std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]315
[1694]316  std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]317  int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]318
[1819]319  //TT addition
320  std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
321
[1111]322  /**
323   * Get the number of channels in the data or a specific IF. This currently
324   * varies only with IF number
325   * @param ifno the IF number to get the number of channels for.
326   * If ifno<0 the number is retrieved from the header.
327   * @return an integer number
328   */
329  int nchan(int ifno=-1) const;
[923]330  int getChannels(int whichrow) const;
[206]331
[1111]332  int ncycle(int scanno=-1) const;
333  int getCycle(int whichrow) const { return cycleCol_(whichrow); }
334
[847]335  double getInterval(int whichrow) const
336    { return integrCol_(whichrow); }
[845]337
[865]338  float getTsys(int whichrow) const
339    { return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
[2161]340  std::vector<float> getTsysSpectrum(int whichrow) const ;
[847]341  float getElevation(int whichrow) const
342    { return elCol_(whichrow); }
343  float getAzimuth(int whichrow) const
344    { return azCol_(whichrow); }
[865]345  float getParAngle(int whichrow) const
[1819]346    { return focus().getParAngle(mfocusidCol_(whichrow)); }
347  int getTcalId(int whichrow) const
348    { return mtcalidCol_(whichrow); }
[386]349
[865]350  std::string getSourceName(int whichrow) const
351    { return srcnCol_(whichrow); }
352
[847]353  std::vector<bool> getMask(int whichrow) const;
[896]354  std::vector<float> getSpectrum(int whichrow,
[905]355                                 const std::string& poltype = "" ) const;
[847]356
[884]357  void setSpectrum(const std::vector<float>& spec, int whichrow);
358
[902]359  std::string getPolarizationLabel(int index, const std::string& ptype) const
360    { return STPol::getPolLabel(index, ptype ); }
[401]361
[845]362  /**
363   * Write the Scantable to disk
364   * @param filename the output file name
365   */
[824]366  void makePersistent(const std::string& filename);
[745]367
[860]368  std::vector<std::string> getHistory() const
369    { return historyTable_.getHistory(); };
[483]370
[860]371  void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]372
[860]373  void appendToHistoryTable(const STHistory& otherhist)
374    { historyTable_.append(otherhist); }
375
[2163]376  std::string headerSummary();
[2290]377  void summary(const std::string& filename="");
378  std::string oldheaderSummary();
[2286]379  //  std::string summary();
[2290]380  void oldsummary(const std::string& filename="");
381
[1947]382  //std::string getTime(int whichrow=-1, bool showdate=true) const;
383  std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
[1350]384  double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]385
[847]386  // returns unit, conversion frame, doppler, base-frame
[18]387
[847]388  /**
389   * Get the frequency set up
390   * This is forwarded to the STFrequencies subtable
391   * @return unit, frame, doppler
392   */
393  std::vector<std::string> getCoordInfo() const
394    { return freqTable_.getInfo(); };
395
396  void setCoordInfo(std::vector<string> theinfo)
397    { return freqTable_.setInfo(theinfo); };
398
[865]399
400  std::vector<double> getAbcissa(int whichrow) const;
401
[1730]402  std::vector<float> getWeather(int whichrow) const;
403
[847]404  std::string getAbcissaLabel(int whichrow) const;
405  std::vector<double> getRestFrequencies() const
406    { return moleculeTable_.getRestFrequencies(); }
[1819]407  std::vector<double> getRestFrequency(int id) const
408    { return moleculeTable_.getRestFrequency(id); }
[847]409
[1819]410  /**
[1170]411  void setRestFrequencies(double rf, const std::string& name = "",
412                          const std::string& = "Hz");
[1819]413  **/
414  // Modified by Takeshi Nakazato 05/09/2008
415  /***
416  void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
417                          const std::string& = "Hz");
418  ***/
419  void setRestFrequencies(vector<double> rf,
420                          const vector<std::string>& name = vector<std::string>(1,""),
421                          const std::string& = "Hz");
[847]422
[1819]423  //void setRestFrequencies(const std::string& name);
424  void setRestFrequencies(const vector<std::string>& name);
425
[1360]426  void shift(int npix);
427
[1598]428  casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
429
[987]430  void convertDirection(const std::string& newframe);
431
[824]432  STFrequencies& frequencies() { return freqTable_; }
[1375]433  const STFrequencies& frequencies() const { return freqTable_; }
[824]434  STWeather& weather() { return weatherTable_; }
[1375]435  const STWeather& weather() const { return weatherTable_; }
[824]436  STFocus& focus() { return focusTable_; }
[1375]437  const STFocus& focus() const { return focusTable_; }
[824]438  STTcal& tcal() { return tcalTable_; }
[1375]439  const STTcal& tcal() const { return tcalTable_; }
[824]440  STMolecules& molecules() { return moleculeTable_; }
[1375]441  const STMolecules& molecules() const { return moleculeTable_; }
[860]442  STHistory& history() { return historyTable_; }
[1375]443  const STHistory& history() const { return historyTable_; }
[972]444  STFit& fit() { return fitTable_; }
[1375]445  const STFit& fit() const { return fitTable_; }
[2]446
[902]447  std::vector<std::string> columnNames() const;
[896]448
[972]449  void addFit(const STFitEntry& fit, int row);
450  STFitEntry getFit(int row) const
451    { STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
452
[1391]453  //Added by TT
454  /**
455   * Get the antenna name
456   * @return antenna name string
457   */
[1819]458  casa::String getAntennaName() const;
[1391]459
460  /**
461   * For GBT MS data only. check a scan list
462   * against the information found in GBT_GO table for
463   * scan number orders to get correct pairs.
464   * @param[in] scan list
465   * @return status
466   */
467  int checkScanInfo(const std::vector<int>& scanlist) const;
468
469  /**
470   * Get the direction as a vector, for a specific row
471   * @param[in] whichrow the row numbyyer
472   * @return the direction in a vector
473   */
474  std::vector<double> getDirectionVector(int whichrow) const;
475
[1586]476  /**
477   * Set a flag indicating whether the data was parallactified
478   * @param[in] flag true or false
479   */
[1598]480  void parallactify(bool flag)
[1727]481    { focus().setParallactify(flag); }
482
[1819]483  /**
484   * Reshape spectrum
485   * @param[in] nmin, nmax minimum and maximum channel
486   * @param[in] irow       row number
487   *
488   * 30/07/2008 Takeshi Nakazato
489   **/
490  void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
491  void reshapeSpectrum( int nmin, int nmax, int irow ) ;
492
493  /**
494   * Change channel number under fixed bandwidth
495   * @param[in] nchan, dnu new channel number and spectral resolution
496   * @param[in] irow       row number
497   *
498   * 27/08/2008 Takeshi Nakazato
499   **/
500  void regridChannel( int nchan, double dnu ) ;
501  void regridChannel( int nchan, double dnu, int irow ) ;
502
[2047]503  bool getFlagtraFast(casa::uInt whichrow);
[1819]504
[2012]505  void polyBaseline(const std::vector<bool>& mask,
506                    int order,
[2094]507                    bool getResidual=true,
[2189]508                    const std::string& progressInfo="true,1000",
509                    const bool outLogger=false,
[2012]510                    const std::string& blfile="");
511  void autoPolyBaseline(const std::vector<bool>& mask,
512                        int order,
513                        const std::vector<int>& edge,
514                        float threshold=3.0,
515                        int chanAvgLimit=1,
[2094]516                        bool getResidual=true,
[2189]517                        const std::string& progressInfo="true,1000",
518                        const bool outLogger=false,
[2012]519                        const std::string& blfile="");
520  void cubicSplineBaseline(const std::vector<bool>& mask,
521                           int nPiece,
522                           float thresClip,
523                           int nIterClip,
[2094]524                           bool getResidual=true,
[2189]525                           const std::string& progressInfo="true,1000",
526                           const bool outLogger=false,
[2012]527                           const std::string& blfile="");
528  void autoCubicSplineBaseline(const std::vector<bool>& mask,
529                               int nPiece,
530                               float thresClip,
531                               int nIterClip,
532                               const std::vector<int>& edge,
533                               float threshold=3.0,
534                               int chanAvgLimit=1,
[2094]535                               bool getResidual=true,
[2189]536                               const std::string& progressInfo="true,1000",
537                               const bool outLogger=false,
[2012]538                               const std::string& blfile="");
[2047]539  void sinusoidBaseline(const std::vector<bool>& mask,
[2186]540                        const bool applyFFT,
541                        const std::string& fftMethod,
542                        const std::string& fftThresh,
543                        const std::vector<int>& addNWaves,
544                        const std::vector<int>& rejectNWaves,
[2047]545                        float thresClip,
546                        int nIterClip,
[2081]547                        bool getResidual=true,
[2189]548                        const std::string& progressInfo="true,1000",
549                        const bool outLogger=false,
[2047]550                        const std::string& blfile="");
551  void autoSinusoidBaseline(const std::vector<bool>& mask,
[2186]552                            const bool applyFFT,
553                            const std::string& fftMethod,
554                            const std::string& fftThresh,
555                            const std::vector<int>& addNWaves,
556                            const std::vector<int>& rejectNWaves,
[2047]557                            float thresClip,
558                            int nIterClip,
559                            const std::vector<int>& edge,
560                            float threshold=3.0,
561                            int chanAvgLimit=1,
[2081]562                            bool getResidual=true,
[2189]563                            const std::string& progressInfo="true,1000",
564                            const bool outLogger=false,
[2047]565                            const std::string& blfile="");
[2186]566  std::vector<float> execFFT(const int whichrow,
567                             const std::vector<bool>& inMask,
568                             bool getRealImag=false,
569                             bool getAmplitudeOnly=false);
[2012]570  float getRms(const std::vector<bool>& mask, int whichrow);
571  std::string formatBaselineParams(const std::vector<float>& params,
572                                   const std::vector<bool>& fixed,
573                                   float rms,
[2193]574                                   int nClipped,
[2012]575                                   const std::string& masklist,
576                                   int whichrow,
[2064]577                                   bool verbose=false,
578                                   int start=-1,
579                                   int count=-1,
580                                   bool resetparamid=false) const;
[2012]581  std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
582                                            const std::vector<float>& params,
583                                            const std::vector<bool>& fixed,
584                                            float rms,
[2193]585                                            int nClipped,
[2012]586                                            const std::string& masklist,
587                                            int whichrow,
588                                            bool verbose=false) const;
[1907]589
[2012]590
[824]591private:
[896]592
593  casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
594
[824]595  /**
[2005]596   * Turns a time value into a formatted string
[824]597   * @param x
598   * @return
599   */
600  std::string formatSec(casa::Double x) const;
[18]601
[824]602  std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]603  std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]604
[824]605  /**
606   *  Turns a casa::MDirection into a nicely formatted string
607   * @param md an casa::MDirection
608   * @return
609   */
610  std::string formatDirection(const casa::MDirection& md) const;
[19]611
[824]612  /**
613   * Create a unique file name for the paged (temporary) table
614   * @return just the name
615   */
616  static casa::String generateName();
[286]617
[824]618  /**
619   * attach to cached columns
620   */
621  void attach();
[50]622
[824]623  /**
624   * Set up the main casa::Table
625   */
626  void setupMainTable();
[88]627
[859]628  void attachSubtables();
[865]629  void copySubtables(const Scantable& other);
630
[824]631  /**
632   * Convert an "old" asap1 style row index into a new index
633   * @param[in] therow
634   * @return and index into @table_
635   */
636  int rowToScanIndex(int therow);
[212]637
[1694]638  std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]639
[1586]640  static const casa::uInt version_ = 3;
[286]641
[824]642  STSelector selector_;
[236]643
[824]644  casa::Table::TableType type_;
[465]645
[824]646  // the actual data
647  casa::Table table_;
648  casa::Table originalTable_;
[745]649
[824]650  STTcal tcalTable_;
651  STFrequencies freqTable_;
652  STWeather weatherTable_;
653  STFocus focusTable_;
654  STMolecules moleculeTable_;
[860]655  STHistory historyTable_;
[960]656  STFit fitTable_;
[860]657
[824]658  // Cached Columns to avoid reconstructing them for each row get/put
[847]659  casa::ScalarColumn<casa::Double> integrCol_;
[824]660  casa::MDirection::ScalarColumn dirCol_;
[847]661  casa::MEpoch::ScalarColumn timeCol_;
[923]662  casa::ScalarColumn<casa::Float> azCol_;
663  casa::ScalarColumn<casa::Float> elCol_;
[824]664  casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]665  casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]666  casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]667  casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]668  casa::ArrayColumn<casa::uChar> flagsCol_;
[430]669
[824]670  // id in frequencies table
671  casa::ScalarColumn<casa::uInt> mfreqidCol_;
672  // id in tcal table
673  casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]674
[824]675  casa::ArrayColumn<casa::String> histitemCol_;
[972]676  casa::ScalarColumn<casa::Int> mfitidCol_;
[824]677  casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]678
[824]679  casa::ScalarColumn<casa::uInt> mfocusidCol_;
680
681  casa::ScalarColumn<casa::uInt> mmolidCol_;
682
[896]683  static std::map<std::string, STPol::STPolFactory *> factories_;
684  void initFactories();
685
[1819]686  /**
687   * Add an auxiliary column to the main table and attach it to a
688   * cached column. Use for adding new columns that the original asap2
689   * tables do not have.
690   * @param[in] col      reference to the cached column to be attached
691   * @param[in] colName  column name in asap table
692   * @param[in] defValue default value to fill in the column
693   *
694   * 25/10/2009 Wataru Kawasaki
695   */
696  template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
697                                                       const casa::String&,
698                                                       const T2&);
699  template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
700                                                      const casa::String&,
701                                                      const casa::Array<T2>&);
[1907]702
[2012]703  void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
704  std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
705                                          const std::vector<bool>& mask,
[2081]706                                          int nPiece,
[2064]707                                          std::vector<int>& idxEdge,
[2012]708                                          std::vector<float>& params,
[2193]709                                          int& nClipped,
[2012]710                                          float thresClip=3.0,
[2058]711                                          int nIterClip=1,
[2094]712                                          bool getResidual=true);
[2047]713  std::vector<float> doSinusoidFitting(const std::vector<float>& data,
714                                       const std::vector<bool>& mask,
[2081]715                                       const std::vector<int>& waveNumbers,
[2047]716                                       std::vector<float>& params,
[2193]717                                       int& nClipped,
[2047]718                                       float thresClip=3.0,
[2058]719                                       int nIterClip=1,
[2094]720                                       bool getResidual=true);
[2186]721  void selectWaveNumbers(const int whichrow,
722                         const std::vector<bool>& chanMask,
723                         const bool applyFFT,
724                         const std::string& fftMethod,
725                         const std::string& fftThresh,
726                         const std::vector<int>& addNWaves,
727                         const std::vector<int>& rejectNWaves,
728                         std::vector<int>& nWaves);
729  void parseThresholdExpression(const std::string& fftThresh,
730                                std::string& fftThAttr,
731                                float& fftThSigma,
732                                int& fftThTop);
733  void doSelectWaveNumbers(const int whichrow,
734                           const std::vector<bool>& chanMask,
735                           const std::string& fftMethod,
736                           const float fftThSigma,
737                           const int fftThTop,
738                           const std::string& fftThAttr,
739                           std::vector<int>& nWaves);
740  void addAuxWaveNumbers(const std::vector<int>& addNWaves,
741                         const std::vector<int>& rejectNWaves,
742                         std::vector<int>& nWaves);
[2012]743  bool hasSameNchanOverIFs();
744  std::string getMaskRangeList(const std::vector<bool>& mask,
745                                int whichrow,
746                                const casa::String& coordInfo,
[2047]747                                bool hasSameNchan,
748                                bool verbose=false);
749  std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2012]750  std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const;
[2193]751  std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const;
[2012]752  std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
753  //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
[2047]754  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]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, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped);
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<float>& params, const int nClipped);
[2189]757  void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
758  void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]759
760  void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
761
762
[2]763};
764
[824]765} // namespace
766
[2]767#endif
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