source: branches/plotter2/src/STMath.h@ 3037

Last change on this file since 3037 was 2658, checked in by Malte Marquarding, 12 years ago

Ticket #199: Excised Logger::pushLog; now everything is using LogIO
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1//
2// C++ Interface: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12#ifndef ASAPSTMATH_H
13#define ASAPSTMATH_H
14
15#include <map>
16#include <string>
17
18#include <casa/aips.h>
19#include <casa/Arrays/Vector.h>
20#include <casa/BasicSL/String.h>
21#include <casa/Utilities/CountedPtr.h>
22
23#include <scimath/Mathematics/InterpolateArray1D.h>
24
25#include "Scantable.h"
26#include "STDefs.h"
27#include "STPol.h"
28
29namespace asap {
30
31/**
32 * Mathmatical operations on Scantable objects
33 * @author Malte Marquarding
34*/
35class STMath {
36public:
37 // typedef for long method name
38 typedef casa::InterpolateArray1D<casa::Double,
39 casa::Float>::InterpolationMethod imethod;
40
41 // typedef for std::map
42 typedef std::map<std::string, imethod> imap;
43
44/**
45 * whether to operate on the given Scantable or return a new one
46 * @param insitu the toggle for this behaviour
47 */
48 explicit STMath(bool insitu=true);
49
50 virtual ~STMath();
51
52 /**
53 * get the currnt @attr inistu_ state
54 */
55 bool insitu() const { return insitu_;};
56
57 /**
58 * set the currnt @attr inistu state
59 * @param b the new state
60 */
61 void setInsitu(bool b) { insitu_ = b; };
62
63
64 /**
65 * average a vector of Scantables
66 * @param in the vector of Scantables to average
67 * @param mask an optional mask to apply on specific weights
68 * @param weight weighting scheme
69 * @param avmode the mode ov averaging. Per "SCAN" or "ALL".
70 * @return a casa::CountedPtr<Scantable> which either holds a new Scantable
71 * or returns the imput pointer.
72 */
73 casa::CountedPtr<Scantable>
74 average( const std::vector<casa::CountedPtr<Scantable> >& in,
75 const std::vector<bool>& mask = std::vector<bool>(),
76 const std::string& weight = "NONE",
77 const std::string& avmode = "SCAN");
78
79 /**
80 * median average a vector of Scantables. See also STMath::average
81 * @param in the Scantable to average
82 * @param mode the averaging mode. Currently only "MEDIAN"
83 * @param avmode the mode ov averaging. Per "SCAN" or "ALL".
84 * @return a casa::CountedPtr<Scantable> which either holds a new Scantable
85 * or returns the imput pointer.
86 */
87 casa::CountedPtr<Scantable>
88 averageChannel( const casa::CountedPtr<Scantable> & in,
89 const std::string& mode = "MEDIAN",
90 const std::string& avmode = "SCAN");
91
92 /**
93 * Average polarisations together. really only useful if only linears are
94 * available.
95 * @param in the input Scantable
96 * @param mask an optional mask if weight allows one
97 * @param weight weighting scheme
98 * @return
99 */
100 casa::CountedPtr< Scantable >
101 averagePolarisations( const casa::CountedPtr< Scantable > & in,
102 const std::vector<bool>& mask,
103 const std::string& weight );
104
105 /**
106 * Average beams together.
107 * @param in the input Scantable
108 * @param mask an optional mask if weight allows one
109 * @param weight weighting scheme
110 * @return
111 */
112 casa::CountedPtr< Scantable >
113 averageBeams( const casa::CountedPtr< Scantable > & in,
114 const std::vector<bool>& mask,
115 const std::string& weight );
116
117 casa::CountedPtr<Scantable>
118 unaryOperate( const casa::CountedPtr<Scantable>& in, float val,
119 const std::string& mode, bool tsys=false );
120
121 // array operation
122 casa::CountedPtr<Scantable>
123 arrayOperate( const casa::CountedPtr<Scantable>& in,
124 const std::vector<float> val,
125 const std::string& mode,
126 const std::string& opmode="channel",
127 bool tsys=false );
128
129 // channel operation
130 casa::CountedPtr<Scantable>
131 arrayOperateChannel( const casa::CountedPtr<Scantable>& in,
132 const std::vector<float> val,
133 const std::string& mode, bool tsys=false );
134
135 // row operation
136 casa::CountedPtr<Scantable>
137 arrayOperateRow( const casa::CountedPtr<Scantable>& in,
138 const std::vector<float> val,
139 const std::string& mode, bool tsys=false );
140
141 // 2d array operation
142 casa::CountedPtr<Scantable>
143 array2dOperate( const casa::CountedPtr<Scantable>& in,
144 const std::vector< std::vector<float> > val,
145 const std::string& mode, bool tsys=false );
146
147 casa::CountedPtr<Scantable>
148 binaryOperate( const casa::CountedPtr<Scantable>& left,
149 const casa::CountedPtr<Scantable>& right,
150 const std::string& mode);
151
152 casa::CountedPtr<Scantable> autoQuotient(const casa::CountedPtr<Scantable>& in,
153 const std::string& mode = "NEAREST",
154 bool preserve = true);
155
156 casa::CountedPtr<Scantable> quotient( const casa::CountedPtr<Scantable>& on,
157 const casa::CountedPtr<Scantable>& off,
158 bool preserve = true );
159
160 /**
161 * Calibrate total power scans (translated from GBTIDL)
162 * @param calon uncalibrated Scantable with CAL noise signal
163 * @param caloff uncalibrated Scantable with no CAL signal
164 * @param tcal optional scalar Tcal, CAL temperature (K)
165 * @return casa::CountedPtr<Scantable> which holds a calibrated Scantable
166 * (spectrum - average of the two CAL on and off spectra;
167 * tsys - mean Tsys = <caloff>*Tcal/<calon-caloff> + Tcal/2)
168 */
169 casa::CountedPtr<Scantable> dototalpower( const casa::CountedPtr<Scantable>& calon,
170 const casa::CountedPtr<Scantable>& caloff,
171 casa::Float tcal=1.0 );
172
173 /**
174 * Combine signal and reference scans (translated from GBTIDL)
175 * @param sig Scantable which contains signal scans
176 * @param ref Scantable which contains reference scans
177 * @param smoothref optional Boxcar smooth width of the reference scans
178 * default: no smoothing (=1)
179 * @param tsysv optional scalar Tsys value at the zenith, required to
180 * set tau, as well
181 * @param tau optional scalar Tau value
182 * @return casa::CountedPtr<Scantable> which holds combined scans
183 * (spectrum = (sig-ref)/ref * Tsys )
184 */
185 casa::CountedPtr<Scantable> dosigref( const casa::CountedPtr<Scantable>& sig,
186 const casa::CountedPtr<Scantable>& ref,
187 int smoothref=1,
188 casa::Float tsysv=0.0,
189 casa::Float tau=0.0 );
190
191 /**
192 * Calibrate GBT Nod scan pairs (translated from GBTIDL)
193 * @param s Scantable which contains Nod scans
194 * @param scans Vector of scan numbers
195 * @param smoothref optional Boxcar smooth width of the reference scans
196 * @param tsysv optional scalar Tsys value at the zenith, required to
197 * set tau, as well
198 * @param tau optional scalar Tau value
199 * @param tcal optional scalar Tcal, CAL temperature (K)
200 * @return casa::CountedPtr<Scantable> which holds calibrated scans
201 */
202 casa::CountedPtr<Scantable> donod( const casa::CountedPtr<Scantable>& s,
203 const std::vector<int>& scans,
204 int smoothref=1,
205 casa::Float tsysv=0.0,
206 casa::Float tau=0.0,
207 casa::Float tcal=0.0 );
208
209 /**
210 * Calibrate frequency switched scans (translated from GBTIDL)
211 * @param s Scantable which contains frequency switched scans
212 * @param scans Vector of scan numbers
213 * @param smoothref optional Boxcar smooth width of the reference scans
214 * @param tsysv optional scalar Tsys value at the zenith, required to
215 * set tau, as well
216 * @param tau optional scalar Tau value
217 * @param tcal optional scalar Tcal, CAL temperature (K)
218 * @return casa::CountedPtr<Scantable> which holds calibrated scans
219 */
220 casa::CountedPtr<Scantable> dofs( const casa::CountedPtr<Scantable>& s,
221 const std::vector<int>& scans,
222 int smoothref=1,
223 casa::Float tsysv=0.0,
224 casa::Float tau=0.0,
225 casa::Float tcal=0.0 );
226
227 /**
228 * Calibrate data with Chopper-Wheel like calibration method
229 * which adopts position switching by antenna motion,
230 * wobbler (nutator) switching and On-The-Fly observation.
231 *
232 * The method is applicable to APEX, and other telescopes other than GBT.
233 *
234 * @param a Scantable which contains ON and OFF scans
235 * @param a string that indicates calibration mode
236 * @param a string that indicates antenna name
237 **/
238 casa::CountedPtr<Scantable> cwcal( const casa::CountedPtr<Scantable>& s,
239 const casa::String calmode,
240 const casa::String antname );
241
242 /**
243 * Calibrate frequency switched scans with Chopper-Wheel like
244 * calibration method.
245 *
246 * The method is applicable to APEX, and other telescopes other than GBT.
247 *
248 * @param a Scantable which contains ON and OFF scans
249 * @param a string that indicates antenna name
250 **/
251 casa::CountedPtr<Scantable> cwcalfs( const casa::CountedPtr<Scantable>& s,
252 const casa::String antname );
253
254
255 /**
256 * Folding frequency-switch data
257 * @param sig
258 * @param ref
259 * @param choffset
260 **/
261 casa::CountedPtr<Scantable> dofold( const casa::CountedPtr<Scantable> &sig,
262 const casa::CountedPtr<Scantable> &ref,
263 casa::Double choffset,
264 casa::Double choffset2 = 0.0 );
265
266 /**
267 * ALMA calibration
268 **/
269 casa::CountedPtr<Scantable> almacal( const casa::CountedPtr<Scantable>& s,
270 const casa::String calmode ) ;
271 casa::CountedPtr<Scantable> almacalfs( const casa::CountedPtr<Scantable>& s ) ;
272
273 casa::CountedPtr<Scantable>
274 freqSwitch( const casa::CountedPtr<Scantable>& in );
275
276 std::vector<float> statistic(const casa::CountedPtr<Scantable>& in,
277 const std::vector<bool>& mask,
278 const std::string& which);
279
280 std::vector<float> statisticRow(const casa::CountedPtr<Scantable>& in,
281 const std::vector<bool>& mask,
282 const std::string& which,
283 int row);
284
285 std::vector< int > minMaxChan(const casa::CountedPtr<Scantable>& in,
286 const std::vector<bool>& mask,
287 const std::string& which);
288
289 casa::CountedPtr<Scantable> bin( const casa::CountedPtr<Scantable>& in,
290 int width=5);
291 casa::CountedPtr<Scantable>
292 resample(const casa::CountedPtr<Scantable>& in,
293 const std::string& method, float width);
294
295 casa::CountedPtr<Scantable>
296 smooth(const casa::CountedPtr<Scantable>& in, const std::string& kernel,
297 float width, int order=2);
298
299 casa::CountedPtr<Scantable>
300 gainElevation(const casa::CountedPtr<Scantable>& in,
301 const std::vector<float>& coeff,
302 const std::string& fileName,
303 const std::string& method);
304 casa::CountedPtr<Scantable>
305 convertFlux(const casa::CountedPtr<Scantable>& in, float d,
306 float etaap, float jyperk);
307
308 casa::CountedPtr<Scantable> opacity(const casa::CountedPtr<Scantable>& in,
309 const std::vector<float>& tau);
310
311 casa::CountedPtr<Scantable>
312 merge(const std::vector<casa::CountedPtr<Scantable> >& in);
313
314 casa::CountedPtr<Scantable>
315 invertPhase( const casa::CountedPtr<Scantable>& in);
316
317 casa::CountedPtr<Scantable>
318 rotateXYPhase( const casa::CountedPtr<Scantable>& in, float phase);
319
320 casa::CountedPtr<Scantable>
321 rotateLinPolPhase( const casa::CountedPtr<Scantable>& in, float phase);
322
323 casa::CountedPtr<Scantable>
324 swapPolarisations(const casa::CountedPtr<Scantable>& in);
325
326 casa::CountedPtr<Scantable>
327 frequencyAlign( const casa::CountedPtr<Scantable>& in,
328 const std::string& refTime = "",
329 const std::string& method = "cubic" );
330
331 casa::CountedPtr<Scantable>
332 convertPolarisation( const casa::CountedPtr<Scantable>& in,
333 const std::string& newtype);
334
335 casa::CountedPtr<Scantable>
336 mxExtract( const casa::CountedPtr<Scantable>& in,
337 const std::string& srctype = "on");
338
339 /**
340 * "hard" flag the data, this flags everything selected in setSelection()
341 * @param frequency the frequency to remove
342 * @param width the number of lags to flag left to the side of the frequency
343 */
344 casa::CountedPtr<Scantable>
345 lagFlag( const casa::CountedPtr<Scantable>& in, double start,
346 double end, const std::string& mode="frequency");
347
348 std::vector<float>
349 fft( const casa::CountedPtr<Scantable>& in,
350 const std::vector<int>& whichrow,
351 bool getRealImag=false );
352
353 // test for average spectra with different channel/resolution
354 casa::CountedPtr<Scantable>
355 new_average( const std::vector<casa::CountedPtr<Scantable> >& in,
356 const bool& compel,
357 const std::vector<bool>& mask = std::vector<bool>(),
358 const std::string& weight = "NONE",
359 const std::string& avmode = "SCAN" )
360 throw (casa::AipsError) ;
361
362private:
363 casa::CountedPtr<Scantable> applyToPol( const casa::CountedPtr<Scantable>& in,
364 STPol::polOperation fptr,
365 casa::Float phase);
366
367 static imethod stringToIMethod(const std::string& in);
368 static WeightType stringToWeight(const std::string& in);
369
370 void scaleByVector(casa::Table& in,
371 const casa::Vector<casa::Float>& factor,
372 bool dotsys);
373
374 void scaleFromAsciiTable(casa::Table& in, const std::string& filename,
375 const std::string& method,
376 const casa::Vector<casa::Float>& xout,
377 bool dotsys);
378
379 void scaleFromTable(casa::Table& in, const casa::Table& table,
380 const std::string& method,
381 const casa::Vector<casa::Float>& xout, bool dotsys);
382
383 void convertBrightnessUnits(casa::CountedPtr<Scantable>& in,
384 bool tokelvin, float cfac);
385
386 casa::CountedPtr< Scantable >
387 smoothOther( const casa::CountedPtr< Scantable >& in,
388 const std::string& kernel,
389 float width, int order=2 );
390
391 casa::CountedPtr< Scantable >
392 getScantable(const casa::CountedPtr< Scantable >& in, bool droprows);
393
394 casa::MaskedArray<casa::Float>
395 maskedArray( const casa::Vector<casa::Float>& s,
396 const casa::Vector<casa::uChar>& f );
397 casa::MaskedArray<casa::Double>
398 maskedArray( const casa::Vector<casa::Double>& s,
399 const casa::Vector<casa::uChar>& f );
400 casa::Vector<casa::uChar>
401 flagsFromMA(const casa::MaskedArray<casa::Float>& ma);
402
403 casa::Vector<casa::Float> getSpectrumFromTime( double reftime, const casa::Vector<casa::Double> &v, const vector<int> &idx, const casa::Matrix<casa::Float>& sp, string mode = "before" ) ;
404 casa::Vector<casa::Float> getTcalFromTime( double reftime, const casa::Vector<casa::Double> &v, const vector<int> &idx, const casa::CountedPtr<Scantable>& s, string mode="before" ) ;
405 casa::Vector<casa::Float> getTsysFromTime( double reftime, const casa::Vector<casa::Double> &v, const vector<int> &idx, const casa::CountedPtr<Scantable>& s, string mode="before" ) ;
406 vector<int> getRowIdFromTime( double reftime, const casa::Vector<casa::Double>& t ) ;
407
408 // Chopper-Wheel type calibration
409 void calibrateCW( casa::CountedPtr<Scantable> &out,
410 const casa::CountedPtr<Scantable> &on,
411 const casa::CountedPtr<Scantable> &off,
412 const casa::CountedPtr<Scantable> &sky,
413 const casa::CountedPtr<Scantable> &hot,
414 const casa::CountedPtr<Scantable> &cold,
415 const casa::Vector<casa::uInt> &rows,
416 const casa::String &antname ) ;
417
418 // Tsys * (ON-OFF)/OFF
419 void calibrateALMA( casa::CountedPtr<Scantable>& out,
420 const casa::CountedPtr<Scantable>& on,
421 const casa::CountedPtr<Scantable>& off,
422 const casa::Vector<casa::uInt>& rows ) ;
423
424 // Frequency switching
425 void calibrateFS( casa::CountedPtr<Scantable> &sig,
426 casa::CountedPtr<Scantable> &ref,
427 const casa::CountedPtr<Scantable> &rsig,
428 const casa::CountedPtr<Scantable> &rref,
429 const casa::CountedPtr<Scantable> &sky,
430 const casa::CountedPtr<Scantable> &hot,
431 const casa::CountedPtr<Scantable> &cold,
432 const casa::Vector<casa::uInt> &rows ) ;
433 void calibrateAPEXFS( casa::CountedPtr<Scantable> &sig,
434 casa::CountedPtr<Scantable> &ref,
435 const vector< casa::CountedPtr<Scantable> > &on,
436 const vector< casa::CountedPtr<Scantable> > &sky,
437 const vector< casa::CountedPtr<Scantable> > &hot,
438 const vector< casa::CountedPtr<Scantable> > &cold,
439 const casa::Vector<casa::uInt> &rows ) ;
440 void copyRows( casa::Table &out,
441 const casa::Table &in,
442 casa::uInt startout,
443 casa::uInt startin,
444 casa::uInt nrow,
445 casa::Bool copySpectra=true,
446 casa::Bool copyFlagtra=true,
447 casa::Bool copyTsys=true ) ;
448 casa::CountedPtr<Scantable> averageWithinSession( casa::CountedPtr<Scantable> &s,
449 vector<bool> &mask,
450 string weight ) ;
451
452 bool insitu_;
453};
454
455}
456#endif
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