source: trunk/src/Scantable.h@ 2659

Last change on this file since 2659 was 2658, checked in by Malte Marquarding, 12 years ago

Ticket #199: Excised Logger::pushLog; now everything is using LogIO
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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
[2658]41
[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*/
[2658]76class Scantable
[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)
[2357]482 { focusTable_.setParallactify(flag); }
[1727]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 ) ;
[2595]503 void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
[1819]504
[2435]505 void regridSpecChannel( double dnu, int nchan=-1 ) ;
506
[2047]507 bool getFlagtraFast(casa::uInt whichrow);
[1819]508
[2012]509 void polyBaseline(const std::vector<bool>& mask,
510 int order,
[2094]511 bool getResidual=true,
[2189]512 const std::string& progressInfo="true,1000",
513 const bool outLogger=false,
[2012]514 const std::string& blfile="");
515 void autoPolyBaseline(const std::vector<bool>& mask,
516 int order,
517 const std::vector<int>& edge,
518 float threshold=3.0,
519 int chanAvgLimit=1,
[2094]520 bool getResidual=true,
[2189]521 const std::string& progressInfo="true,1000",
522 const bool outLogger=false,
[2012]523 const std::string& blfile="");
[2645]524 void chebyshevBaseline(const std::vector<bool>& mask,
525 int order,
526 float thresClip,
527 int nIterClip,
528 bool getResidual=true,
529 const std::string& progressInfo="true,1000",
530 const bool outLogger=false,
531 const std::string& blfile="");
532 void autoChebyshevBaseline(const std::vector<bool>& mask,
533 int order,
534 float thresClip,
535 int nIterClip,
536 const std::vector<int>& edge,
537 float threshold=3.0,
538 int chanAvgLimit=1,
539 bool getResidual=true,
540 const std::string& progressInfo="true,1000",
541 const bool outLogger=false,
542 const std::string& blfile="");
[2012]543 void cubicSplineBaseline(const std::vector<bool>& mask,
544 int nPiece,
545 float thresClip,
546 int nIterClip,
[2094]547 bool getResidual=true,
[2189]548 const std::string& progressInfo="true,1000",
549 const bool outLogger=false,
[2012]550 const std::string& blfile="");
551 void autoCubicSplineBaseline(const std::vector<bool>& mask,
552 int nPiece,
553 float thresClip,
554 int nIterClip,
555 const std::vector<int>& edge,
556 float threshold=3.0,
557 int chanAvgLimit=1,
[2094]558 bool getResidual=true,
[2189]559 const std::string& progressInfo="true,1000",
560 const bool outLogger=false,
[2012]561 const std::string& blfile="");
[2047]562 void sinusoidBaseline(const std::vector<bool>& mask,
[2186]563 const bool applyFFT,
564 const std::string& fftMethod,
565 const std::string& fftThresh,
566 const std::vector<int>& addNWaves,
567 const std::vector<int>& rejectNWaves,
[2047]568 float thresClip,
569 int nIterClip,
[2081]570 bool getResidual=true,
[2189]571 const std::string& progressInfo="true,1000",
572 const bool outLogger=false,
[2047]573 const std::string& blfile="");
574 void autoSinusoidBaseline(const std::vector<bool>& mask,
[2186]575 const bool applyFFT,
576 const std::string& fftMethod,
577 const std::string& fftThresh,
578 const std::vector<int>& addNWaves,
579 const std::vector<int>& rejectNWaves,
[2047]580 float thresClip,
581 int nIterClip,
582 const std::vector<int>& edge,
583 float threshold=3.0,
584 int chanAvgLimit=1,
[2081]585 bool getResidual=true,
[2189]586 const std::string& progressInfo="true,1000",
587 const bool outLogger=false,
[2047]588 const std::string& blfile="");
[2186]589 std::vector<float> execFFT(const int whichrow,
590 const std::vector<bool>& inMask,
591 bool getRealImag=false,
592 bool getAmplitudeOnly=false);
[2012]593 float getRms(const std::vector<bool>& mask, int whichrow);
594 std::string formatBaselineParams(const std::vector<float>& params,
595 const std::vector<bool>& fixed,
596 float rms,
[2193]597 int nClipped,
[2012]598 const std::string& masklist,
599 int whichrow,
[2064]600 bool verbose=false,
[2641]601 bool csvformat=false,
[2064]602 int start=-1,
603 int count=-1,
604 bool resetparamid=false) const;
[2012]605 std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
606 const std::vector<float>& params,
607 const std::vector<bool>& fixed,
608 float rms,
[2193]609 int nClipped,
[2012]610 const std::string& masklist,
611 int whichrow,
[2641]612 bool verbose=false,
613 bool csvformat=false) const;
[2591]614 std::vector<uint> getMoleculeIdColumnData() const;
615 void setMoleculeIdColumnData(const std::vector<uint>& molids);
[1907]616
[2012]617
[824]618private:
[896]619
620 casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
621
[824]622 /**
[2005]623 * Turns a time value into a formatted string
[824]624 * @param x
625 * @return
626 */
627 std::string formatSec(casa::Double x) const;
[18]628
[824]629 std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]630 std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]631
[824]632 /**
633 * Turns a casa::MDirection into a nicely formatted string
634 * @param md an casa::MDirection
635 * @return
636 */
637 std::string formatDirection(const casa::MDirection& md) const;
[19]638
[824]639 /**
640 * Create a unique file name for the paged (temporary) table
641 * @return just the name
642 */
643 static casa::String generateName();
[286]644
[824]645 /**
646 * attach to cached columns
647 */
648 void attach();
[50]649
[824]650 /**
651 * Set up the main casa::Table
652 */
653 void setupMainTable();
[88]654
[859]655 void attachSubtables();
[865]656 void copySubtables(const Scantable& other);
657
[824]658 /**
659 * Convert an "old" asap1 style row index into a new index
660 * @param[in] therow
661 * @return and index into @table_
662 */
663 int rowToScanIndex(int therow);
[212]664
[1694]665 std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]666
[2321]667 static const casa::uInt version_ = 4;
[286]668
[824]669 STSelector selector_;
[236]670
[824]671 casa::Table::TableType type_;
[465]672
[824]673 // the actual data
674 casa::Table table_;
675 casa::Table originalTable_;
[745]676
[824]677 STTcal tcalTable_;
678 STFrequencies freqTable_;
679 STWeather weatherTable_;
680 STFocus focusTable_;
681 STMolecules moleculeTable_;
[860]682 STHistory historyTable_;
[960]683 STFit fitTable_;
[860]684
[824]685 // Cached Columns to avoid reconstructing them for each row get/put
[847]686 casa::ScalarColumn<casa::Double> integrCol_;
[824]687 casa::MDirection::ScalarColumn dirCol_;
[847]688 casa::MEpoch::ScalarColumn timeCol_;
[923]689 casa::ScalarColumn<casa::Float> azCol_;
690 casa::ScalarColumn<casa::Float> elCol_;
[824]691 casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]692 casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]693 casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]694 casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]695 casa::ArrayColumn<casa::uChar> flagsCol_;
[430]696
[824]697 // id in frequencies table
698 casa::ScalarColumn<casa::uInt> mfreqidCol_;
699 // id in tcal table
700 casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]701
[824]702 casa::ArrayColumn<casa::String> histitemCol_;
[972]703 casa::ScalarColumn<casa::Int> mfitidCol_;
[824]704 casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]705
[824]706 casa::ScalarColumn<casa::uInt> mfocusidCol_;
707
708 casa::ScalarColumn<casa::uInt> mmolidCol_;
709
[896]710 static std::map<std::string, STPol::STPolFactory *> factories_;
711 void initFactories();
712
[1819]713 /**
714 * Add an auxiliary column to the main table and attach it to a
715 * cached column. Use for adding new columns that the original asap2
716 * tables do not have.
717 * @param[in] col reference to the cached column to be attached
718 * @param[in] colName column name in asap table
719 * @param[in] defValue default value to fill in the column
720 *
721 * 25/10/2009 Wataru Kawasaki
722 */
723 template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
724 const casa::String&,
725 const T2&);
726 template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
727 const casa::String&,
728 const casa::Array<T2>&);
[1907]729
[2012]730 void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
[2645]731 double getChebyshevPolynomial(int n, double x);
732 std::vector<float> doChebyshevFitting(const std::vector<float>& data,
733 const std::vector<bool>& mask,
734 int order,
735 std::vector<float>& params,
736 int& nClipped,
737 float thresClip=3.0,
738 int nIterClip=1,
739 bool getResidual=true);
[2012]740 std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
741 const std::vector<bool>& mask,
[2081]742 int nPiece,
[2064]743 std::vector<int>& idxEdge,
[2012]744 std::vector<float>& params,
[2193]745 int& nClipped,
[2012]746 float thresClip=3.0,
[2058]747 int nIterClip=1,
[2094]748 bool getResidual=true);
[2047]749 std::vector<float> doSinusoidFitting(const std::vector<float>& data,
750 const std::vector<bool>& mask,
[2081]751 const std::vector<int>& waveNumbers,
[2047]752 std::vector<float>& params,
[2193]753 int& nClipped,
[2047]754 float thresClip=3.0,
[2058]755 int nIterClip=1,
[2094]756 bool getResidual=true);
[2186]757 void selectWaveNumbers(const int whichrow,
758 const std::vector<bool>& chanMask,
759 const bool applyFFT,
760 const std::string& fftMethod,
761 const std::string& fftThresh,
762 const std::vector<int>& addNWaves,
763 const std::vector<int>& rejectNWaves,
764 std::vector<int>& nWaves);
765 void parseThresholdExpression(const std::string& fftThresh,
766 std::string& fftThAttr,
767 float& fftThSigma,
768 int& fftThTop);
769 void doSelectWaveNumbers(const int whichrow,
770 const std::vector<bool>& chanMask,
771 const std::string& fftMethod,
772 const float fftThSigma,
773 const int fftThTop,
774 const std::string& fftThAttr,
775 std::vector<int>& nWaves);
[2411]776 void addAuxWaveNumbers(const int whichrow,
777 const std::vector<int>& addNWaves,
[2186]778 const std::vector<int>& rejectNWaves,
779 std::vector<int>& nWaves);
[2411]780 void setWaveNumberListUptoNyquistFreq(const int whichrow,
781 std::vector<int>& nWaves);
[2012]782 bool hasSameNchanOverIFs();
783 std::string getMaskRangeList(const std::vector<bool>& mask,
784 int whichrow,
785 const casa::String& coordInfo,
[2047]786 bool hasSameNchan,
787 bool verbose=false);
788 std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]789 std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
790 std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]791 std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
792 //std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
[2641]793 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, Fitter& fitter);
794 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);
795 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]796 void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
797 void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]798
799 void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
800
[2]801};
802
[824]803} // namespace
804
[2]805#endif
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