casacore
LatticeStatistics.h
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1 //# LatticeStatistics.h: generate statistics from a Lattice
2 //# Copyright (C) 1996,1997,1998,1999,2000,2001,2002,2003
3 //# Associated Universities, Inc. Washington DC, USA.
4 //#
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26 //# $Id$
27 
28 #ifndef LATTICES_LATTICESTATISTICS_H
29 #define LATTICES_LATTICESTATISTICS_H
30 
31 #include <casacore/casa/aips.h>
32 #include <casacore/casa/Arrays/Array.h>
33 #include <casacore/casa/Containers/Block.h>
34 #include <casacore/casa/Arrays/Vector.h>
35 #include <casacore/casa/Containers/Record.h>
36 #include <casacore/lattices/LatticeMath/LatticeStatsBase.h>
37 #include <casacore/lattices/LatticeMath/TiledCollapser.h>
38 #include <casacore/lattices/LatticeMath/TiledCollapser.h>
39 #include <casacore/lattices/LEL/LatticeExprNode.h>
40 #include <casacore/lattices/LatticeMath/LatticeStatsDataProvider.h>
41 #include <casacore/lattices/LatticeMath/MaskedLatticeStatsDataProvider.h>
42 #include <casacore/scimath/Mathematics/NumericTraits.h>
43 #include <casacore/casa/Utilities/DataType.h>
44 #include <casacore/casa/BasicSL/String.h>
45 #include <casacore/casa/Logging/LogIO.h>
46 #include <casacore/scimath/Mathematics/FitToHalfStatisticsData.h>
47 #include <casacore/scimath/Mathematics/StatisticsData.h>
48 #include <casacore/scimath/Mathematics/StatisticsAlgorithm.h>
49 #include <casacore/scimath/Mathematics/StatisticsAlgorithmFactory.h>
50 
51 #include <vector>
52 #include <list>
53 
54 namespace casacore { //# NAMESPACE CASACORE - BEGIN
55 
56 //# Forward Declarations
57 template <class T> class MaskedLattice;
58 template <class T> class TempLattice;
59 class IPosition;
60 
61 #include <casacore/casa/iosstrfwd.h>
62 
63 
64 // <summary>
65 // Compute and display various statistics from a lattice
66 // </summary>
67 // <use visibility=export>
68 // <reviewed reviewer="" date="yyyy/mm/dd" tests="" demos="">
69 // </reviewed>
70 // <prerequisite>
71 // <li> <linkto class=LatticeStatsBase>LatticeStatsBase</linkto>
72 // <li> <linkto class=MaskedLattice>MaskedLattice</linkto>
73 // </prerequisite>
74 
75 // <etymology>
76 // This is a class designed to display and retrieve statistics from lattices
77 // </etymology>
78 
79 // <synopsis>
80 // This class enable you to display and/or retrieve statistics evaluated over
81 // specified regions of a lattice. The dimension of the region is arbitrary, but
82 // the size of each dimension is always the shape of the corresponding lattice axis.
83 // The statistics are displayed as a function of location of the axes not
84 // used to evaluate the statistics over. The axes which you evaluate the statistics
85 // over are called the cursor axes, the others are called the display axes.
86 //
87 // For example, consider a lattice cube (call the axes xyz or [0,1,2]). You could
88 // display statistics from xy planes (cursor axes [0,1]) as a function of z (display
89 // axes [2]). Or you could retrieve statistics from the z axis (cursor axes [2])
90 // for each [x,y] location (display axes [0,1]).
91 //
92 // This class inherits from <linkto class="LatticeStatsBase">LatticeStatsBase</linkto>
93 // This base class provides an <src>enum</src> defining allowed statistics types and a
94 // helper function to convert between a <src>String</src> and a
95 // <src>Vector<Int></src> describing the desired statistics to plot.
96 // An example is shown below.
97 //
98 // This class can list, plot and retrieve statistics. When it lists statistics,
99 // it always lists all the available statistics. When you plot statistics,
100 // you must specify which ones you would like to see.
101 //
102 // This class generates a "storage lattice" into which it writes the accumulated
103 // statistical sums. It is from this storage lattice that the plotting and retrieval
104 // arrays are drawn. The storage lattice is either in core or on disk
105 // depending upon its size (if > 10% of memory given by .aipsrc system.resources.memory
106 // then it goes into a disk-based PagedArray). If on disk, the
107 // storage lattice is deleted when the <src>LatticeStatistics</src> class
108 // object destructs. However, currently, if the process is terminated ungracefully,
109 // the storage lattice will be left over.
110 // </synopsis>
111 //
112 // <note role=tip>
113 // This class has a few virtual functions; they are not part of a nice general
114 // polymorphic interface; rather they have specialized functionality. The idea
115 // of these is that you can derive a class from LatticeStatistics, such as
116 // <linkto class="ImageStatistics">ImageStatistics</linkto> which provides
117 // you with a little more information when displaying/logging the
118 // statistics (such as world coordinates)
119 // The virtual functions are
120 // <ul>
121 // <li> <src>getBeamArea</src> can be used to return the synthesized beam
122 // area so that the FLUX statistic can be computed
123 // <li> <src>listStats</src> is used to list the statistics to the logger
124 // <li> <src>getLabelsM</src> find the X-axis label and the title label
125 // for the plotting.
126 // </ul>
127 // </note>
128 //
129 // <note role=tip>
130 // If you ignore return error statuses from the functions that set the
131 // state of the class, the internal status of the class is set to bad.
132 // This means it will just keep on returning error conditions until you
133 // explicitly recover the situation. A message describing the last
134 // error condition can be recovered with function errorMessage.
135 // </note>
136 
137 
138 // <example>
139 // <srcBlock>
141 //
142 // PagedImage<Float> inImage(inName);
143 //
145 //
146 // LogOrigin or("myClass", "myFunction(...)", WHERE);
147 // LogIO os(or);
148 // LatticeStatistics<Float> stats(SubImage<FLoat>(inImage), os);
149 //
151 //
152 // Vector<Int> cursorAxes(2)
153 // cursorAxes(0) = 1;
154 // cursorAxes(1) = 2;
155 // if (!stats.setAxes(cursorAxes)) return 1;
156 //
158 //
159 // if (!stats.setList(True)) return 1;
160 // String device = "/xs";
161 // Vector<Int> nxy(2);
162 // nxy(0) = 1;
163 // nxy(1) = 1;
164 // Vector<Int> statsToPlot = LatticeStatsBase::toStatisticTypes("mean,rms,sigma");
165 // if (!stats.setPlotting(statsToPlot, device, nxy)) return 1;
166 //
168 //
169 // if (!stats.display ()) return 1;
170 //
172 //
173 // Array<Double> sum;
174 // if (!stats.getStatistic(sum, LatticeStatsBase::SUM)) return 1;
175 //
176 // </srcBlock>
177 // In this example, a <src>PagedImage</src> is constructed (which isA
178 // MaskedLattice) with . We set the cursor axes
179 // to be the y and z axes, we specify to list the statistics if we plot them,
180 // and we ask to plot the mean, standard deviation, and root mean square of each
181 // yz plane as a function of x location on the PGPLOT device "/xs" with
182 // 1 subplot per page (there will be only one in this case). After the
183 // plotting and listing, we also retrieve the sum of the selected pixels
184 // as a function of x location into an array.
185 // </example>
186 
187 // <motivation>
188 // The generation of statistical information from a lattice is a basic
189 // and necessary capability.
190 // </motivation>
191 
192 // <todo asof="1996/11/26">
193 // <li> Implement plotting for complex lattices
194 // <li> Retrieve statistics at specified location of display axes
195 // </todo>
196 
197 
198 template <class T> class LatticeStatistics : public LatticeStatsBase
199 {
200 
201 public:
202 
203 
205 
206  // DEPRECATED. WILL BE REMOVED, USE scimath/Mathematics/StatisticsAlgorithmFactory
207  // instead
208  struct AlgConf {
210  // hinges-fences f factor
212  // fit to have center type
214  // fit to half data portion to use
216  // fit to half center value
217  AccumType cv;
218  // Chauvenet zscore
220  // Chauvenet max iterations
222  };
223 
224 // Constructor takes the lattice and a <src>LogIO</src> object for logging.
225 // You can specify whether you want to see progress meters or not.
226 // You can force the storage lattice to be disk based, otherwise
227 // the decision for core or disk is taken for you.
228 // If <src>clone</src> is True, the input lattice will be cloned, so the caller
229 // can make changes to the input lattice, but the statistics will reflect the
230 // lattice as it was at construction. If False, a reference to the input lattice
231 // is used, and so the caller shouldn't make changes to the input lattice between
232 // construction and calling statistics computation methods, unless it calls setNewLattice()
233 // to update the changed lattice. Obviously, cloning the lattice impacts performance
234 // and memory usage.
235  LatticeStatistics (const MaskedLattice<T>& lattice,
236  LogIO& os,
237  Bool showProgress=True,
238  Bool forceDisk=False,
239  Bool clone=True);
240 
241 // Constructor takes the lattice only. In the absence of a logger you get no messages.
242 // This includes error messages and potential listing of the statistics.
243 // You can specify whether you want to see progress meters or not.
244 // You can force the storage lattice to be disk based, otherwise
245 // the decision for core or disk is taken for you.
246  LatticeStatistics (const MaskedLattice<T>& lattice,
247  Bool showProgress=True,
248  Bool forceDisk=False,
249  Bool clone=True);
250 
251 // Copy constructor. Copy semantics are followed. Therefore any storage lattice
252 // that has already been created for <src>other</src> is copied to <src>*this</src>
254 
255 // Destructor
256  virtual ~LatticeStatistics ();
257 
258 // Assignment operator. Deletes any storage lattice associated with
259 // the object being assigned to and copies any storage lattice that has
260 // already been created for "other".
262 
263 // Set the cursor axes (0 relative). A return value of <src>False</src>
264 // indicates you have asked for an invalid axis. The default state of the class
265 // is to set the cursor axes to all axes in the lattice.
266  Bool setAxes (const Vector<Int>& cursorAxes);
267 
268 // You may specify a pixel intensity range as either one for which
269 // all pixels in that range are included or one for which all pixels
270 // in that range are excluded. One or the other of <src>include</src>
271 // and <src>exclude</src> must therefore be a zero length vector if you
272 // call this function. If you are setting an <src>include</src>
273 // range, then if you set <src>setMinMaxToInclude=True</src>, the
274 // minimum and maximum values that this class returns will always be
275 // the minimum and maximum of the <src>include</src> range, respectively.
276 // A return value of <src>False</src> indicates that
277 // you have given both an <src>include</src> and an <src>exclude</src>
278 // range. A vector of length 1 for <src>include</src> and/or <src>exclude</src>
279 // means that the range will be set to (say for <src>include</src>)
280 // <src>-abs(include(0))</src> to <src>abs(include(0))</src>. A return value
281 // of <src>False</src> indicates that both an inclusion and exclusion
282 // range were given or that the internal state of the class is bad. If you don't
283 // call this function, the default state of the class is to include all pixels.
284  Bool setInExCludeRange(const Vector<T>& include,
285  const Vector<T>& exclude,
286  Bool setMinMaxToInclude=False);
287 
288 // This function allows you to control whether the statistics are written to
289 // the output stream if you are also making a plot. A return value of
290 // <src>False</src> indicates that the internal state of the class is bad.
291 // If you have created the <src>LatticeStatistics</src> object without
292 // a <src>LogIO</src> object, you won't see any listings, but no error
293 // conditions will be generated. The default state of the class is to
294 // not list the output when making a plot.
295  Bool setList(const Bool& doList);
296 
297 // Display the statistics by listing and/or plotting them. If you don't call
298 // this function then you won't see anything ! A return value of <src>False</src>
299 // indicates an invalid plotting device, or that the internal state of the class is bad.
300 
301  Bool display();
302 
303  Bool getLayerStats(String& stats, Double area,
304  Int zAxis=-1, Int zLayer=-1,
305  Int hAxis=-1, Int hLayer=-1);
306 
307  typedef std::pair<String,String> stat_element;
308  typedef std::list<stat_element> stat_list;
309  Bool getLayerStats( stat_list &stats, Double area,
310  Int zAxis=-1, Int zLayer=-1,
311  Int hAxis=-1, Int hLayer=-1);
312 
313 // Return the display axes. The returned vector will be valid only if <src>setAxes</src>
314 // has been called, or if one of the active "display" or "get*" methods has been called.
316 
317 // Recover the desired Statistic into an array. If you choose to use
318 // the T version, be aware that the values in the AccumType version of the
319 // Array may not be representable in the T version (e.g. large values for
320 // SumSq). The shape of the
321 // array is the shape of the display axes (e.g. if the shape of the lattice is
322 // [nx,ny,nz] and you ask for the mean of the y axis the shape of the returned
323 // array would be [nx,nz]. A returned array of zero shape indicates that there
324 // were no good values. A return value of <src>False</src>
325 // indicates that the internal state of the class is bad.
326 // <group>
329 // </group>
330 
331 // Recover position of min and max. Only works if there are no
332 // display axes (i.e. statistics found over entire image), otherwise,
333 // the returned values are resized to 0 shape. A return
334 // value of <src>False</src> indicates that the internal state of
335 // the class is bad.
336  Bool getMinMaxPos(IPosition& minPos, IPosition& maxPos);
337 
338 // This function gets a vector containing all the statistics
339 // for a given location. If <src>posInLattice=True</src> then
340 // the location is a location in the input lattice. Any
341 // positions on the display axes are ignored. Otherwise, you
342 // should just give locations for the display axes only.
343 // Use can use the enum in class LatticeStatsBase to find out
344 // which locations in the vector contain which statistics.
345 // A returned vector of zero shape indicates that there
346 // were no good values. A return value of <src>False</src>
347 // indicates that the internal state of the class is bad.
349  const IPosition& pos,
350  const Bool posInLattice=False);
351 
352 // Reset argument error condition. If you specify invalid arguments to
353 // one of the above <src>set</src> functions, an internal flag will be set which will
354 // prevent the work functions from doing anything (should you have chosen
355 // to ignore the Boolean return values of the <src>set</src> functions).
356 // This function allows you to reset that internal state to good.
358 
359 // Get full lattice min and max only. Returns False if no unmasked data, else returns True.
360 // Honours any include or exclude range if set.
361  Bool getFullMinMax (T& dataMin, T& dataMax);
362 
363 // Recover last error message
364  String errorMessage() const {return error_p;};
365 
366 // Set a new MaskedLattice object. A return value of <src>False</src> indicates the
367 // lattice had an invalid type or that the internal state of the class is bad.
368 // If <src>clone</src> is True, the input lattice will be cloned, so the caller
369 // can make changes to the input lattice, but the statistics will reflect the
370 // lattice as it was at construction. If False, a reference to the input lattice
371 // is used, and so the caller shouldn't make changes to the input lattice between
372 // construction and calling statistics computation methods, unless it calls setNewLattice()
373 // to update the changed lattice. Obviously, cloning the lattice impacts performance
374 // and memory usage.
375  Bool setNewLattice(const MaskedLattice<T>& lattice, Bool clone=True);
376 
377 // Did we construct with a logger ?
378  Bool hasLogger () const {return haveLogger_p;};
379 
380  // configure object to use Classical Statistics
381  // The time, t_x, it takes to compute classical statistics using algorithm x, can
382  // be modeled by
383  // t_x = n_sets*(a_x + b_x*n_el)
384  // where n_sets is the number of independent sets of data to compute stats on,
385  // each containing n_el number of elements. a_x is the time it takes to compute
386  // stats a a single set of data, and b_x is the time it takes to accumulate
387  // a single point.
388  // The old algorithm was developed in the early history of the project, I'm guessing
389  // by Neil Kileen, while the new algorithm was developed in 2015 by Dave Mehringer
390  // as part of the stats framework project. The old algorithm is faster in the regime
391  // of large n_sets and small n_el, while the new algorithm is faster in the
392  // regime of small n_sets and large n_el.
393  // If one always wants to use one of these algorithms, that algorithm's coefficients
394  // should be set to 0, while setting the other algorithm's coefficients to positive
395  // values. Note that it's the relative, not the absolute, values of these
396  // coeffecients that is important
397  // The version that takes no parameters uses the default values of the coefficients;
398  // <group>
399  void configureClassical();
400 
401  void configureClassical(Double aOld, Double bOld, Double aNew, Double bNew);
402  // </group>
403 
404  // configure to use fit to half algorithm.
405  void configureFitToHalf(
408  AccumType centerValue=0
409  );
410 
411  // configure to use hinges-fences algorithm
413 
414  // configure to use Chauvenet's criterion
415  void configureChauvenet(
416  Double zscore=-1, Int maxIterations=-1
417  );
418 
419  // get number of iterations associated with Chauvenet criterion algorithm
420  std::map<String, uInt> getChauvenetNiter() const { return _chauvIters; }
421 
422 protected:
423 
428 
429 // doRobust means that when the storage lattice is generated, the
430 // robust statistics are generated as well
431 
436 //
437 // Virtual Functions. See implementation to figure it all out !
438 
439  // FIXME The indirect dependence of this class on ImageInterface related
440  // issues (eg flux density) breaks encapsulation. All the ImageInterface related code should be
441  // encapsulated in ImageStatistics. Unfortunately, that requires significantly
442  // more time than I have atm. A return value of False means that the object in
443  // question cannot compute flux density values. The default implementation returns False.
444  virtual Bool _canDoFlux() const { return False; }
445 
446  virtual Quantum<AccumType> _flux(Bool&, AccumType, Double) const {
447  ThrowCc("Logic Error: This object cannot compute flux density");
448  }
449 
450  virtual void listMinMax (ostringstream& osMin,
451  ostringstream& osMax,
452  Int oWidth, DataType type);
453 
454  //
455 
456 // List the statistics to the logger. The implementation here
457 // is adequate for all lattices. See ImageStatistics for an
458 // example of where extra information is provided. hasBeam is
459 // the return value of getBeamArea. If it is true, that means
460 // that the FLUX statistics will be available in the storage
461 // lattice. dPos is the location of the start of the cursor in the
462 // storage image for this row. stats(j,i) is the statistics matrix.
463 // for the jth point and the ith statistic.
464 // The return value is False if something goes wrong !
465 // Have a look at the implementation to see what you really
466 // have to do.
467  virtual Bool listStats (Bool hasBeam, const IPosition& dPos,
468  const Matrix<AccumType>& ord);
469  virtual Bool listLayerStats (
470  const Matrix<AccumType>& ord,
471  ostringstream& rslt, Int zLayer);
472 /*
473 // Gets labels for higher order axes and x axis.
474 // dPos is the location of the start of the cursor in the
475 // storage image for this row.
476  virtual void getLabels(String& higherOrderLabel, String& xAxisLabel,
477  const IPosition& dPos) const;
478 */
479 // Given a location in the storage lattice, convert those locations on the
480 // non-statistics axis (the last one) and optionally account for the
481 // lattice subsectioning
482  IPosition locInLattice (const IPosition& storagePosition,
483  Bool relativeToParent=True) const;
484 
485 // Non-virtual functions
486 //
487 // set stream manipulators
488  void setStream (ostream& os, Int oPrec);
489 
490  // get the storage lattice shape
491  inline IPosition _storageLatticeShape() const { return pStoreLattice_p->shape(); }
492 
493  virtual Bool _computeFlux(
494  Array<AccumType>& flux, const Array<AccumType>& npts, const Array<AccumType>& sum
495  );
496 
497  virtual Bool _computeFlux(
498  Quantum<AccumType>& flux, AccumType sum, const IPosition& pos,
499  Bool posInLattice
500  );
501 
502  // convert a position in the input lattice to the corresponding
503  // position in the stats storage lattice. The number of elements
504  // in storagePos will not be changed and only the first N elements
505  // will be modified where N = the number of elements in latticePos.
506  // <src>storagePos</src> must therefore have at least as many elements
507  // as <src>latticePos</src>. Returns False if
508  //<src>latticePos</src> is inconsistent with the input lattice.
510  IPosition& storagePos, const IPosition& latticePos
511  );
512 
513 private:
514 
516  SHARED_PTR<const MaskedLattice<T> > _inLatPtrMgr;
517 
522 
525 
528 
530  std::map<String, uInt> _chauvIters;
531 
533 
535  // coefficients from timings run on PagedImages on
536  // etacarinae.cv.nrao.edu (dmehring's development
537  // machine)
538  _aOld = 4.7e-7;
539  _bOld = 2.3e-8;
540  _aNew = 1.6e-5;
541  _bNew = 1.5e-8;
542  }
543 
544 // Summarize the statistics found over the entire lattice
545  virtual void summStats();
546 
547  virtual void displayStats(
548  AccumType nPts, AccumType sum, AccumType median,
549  AccumType medAbsDevMed, AccumType quartile, AccumType sumSq, AccumType mean,
550  AccumType var, AccumType rms, AccumType sigma, AccumType dMin, AccumType dMax,
551  AccumType q1, AccumType q3
552  );
553 
554 // Calculate statistic from storage lattice and return in an array
557  Bool dropDeg);
558 
559 // Find the median per cursorAxes chunk
560  void generateRobust ();
561 
562 // Create a new storage lattice
564 
565 // Given a location in the lattice and a statistic type, work
566 // out where to put it in the storage lattice
567  IPosition locInStorageLattice(const IPosition& latticePosition,
569 
570 // Find min and max of good data in arrays specified by pointers
571  void minMax (Bool& none, AccumType& dMin, AccumType& dMax,
572  const Vector<AccumType>& d,
573  const Vector<AccumType>& n) const;
574 
575 // Retrieve a statistic from the storage lattice and return in an array
578  const Bool dropDeg);
579 
580 // Retrieve a statistic from the storage lattice at the specified
581 // location and return in an array
583  const IPosition& pos,
584  const Bool posInLattice);
585 
586 // Find the shape of slice from the statistics lattice at one
587 // spatial pixel
588  IPosition statsSliceShape () const;
589 
590 // See if there were some valid points found in the storage lattice
591  Bool someGoodPoints ();
592 
593 // Stretch min and max by 5%
594  void stretchMinMax (AccumType& dMin, AccumType& dMax) const;
595 
599  ) const;
600 
601  void _doStatsLoop(uInt nsets, CountedPtr<LattStatsProgress> progressMeter);
602 
603  inline static AccumType _mean(const AccumType& sum, const AccumType& npts) {
604  return npts <= 0 ? 0 : sum/npts;
605  }
606 
607  inline static AccumType _rms(const AccumType& sumsq, const AccumType& npts) {
608  return npts <= 0 ? 0 : sqrt(sumsq/npts);
609  }
610 
611 };
612 
613 //# Declare extern templates for often used types.
614 #ifdef AIPS_CXX11
615  extern template class LatticeStatistics<Float>;
616 #endif
617 
618 
619 } //# NAMESPACE CASA - END
620 
621 #ifndef CASACORE_NO_AUTO_TEMPLATES
622 #include <casacore/lattices/LatticeMath/LatticeStatistics.tcc>
623 #endif //# CASACORE_NO_AUTO_TEMPLATES
624 #endif
A Vector of integers, for indexing into Array<T> objects.
Definition: IPosition.h:119
virtual Bool listLayerStats(const Matrix< AccumType > &ord, ostringstream &rslt, Int zLayer)
A Lattice that can be used for temporary storage.
int Int
Definition: aipstype.h:50
void configureClassical()
configure object to use Classical Statistics The time, t_x, it takes to compute classical statistics ...
Vector< Int > displayAxes() const
Return the display axes.
LatticeExprNode median(const LatticeExprNode &expr)
Bool retrieveStorageStatistic(Array< AccumType > &slice, const LatticeStatsBase::StatisticsTypes type, const Bool dropDeg)
Retrieve a statistic from the storage lattice and return in an array.
Int mi
Chauvenet max iterations.
std::map< String, uInt > _chauvIters
Bool getMinMaxPos(IPosition &minPos, IPosition &maxPos)
Recover position of min and max.
const MaskedLattice< T > * pInLattice_p
LatticeExprNode sum(const LatticeExprNode &expr)
void configureChauvenet(Double zscore=-1, Int maxIterations=-1)
configure to use Chauvenet&#39;s criterion
void configureFitToHalf(FitToHalfStatisticsData::CENTER centerType=FitToHalfStatisticsData::CMEAN, FitToHalfStatisticsData::USE_DATA useData=FitToHalfStatisticsData::LE_CENTER, AccumType centerValue=0)
configure to use fit to half algorithm.
void configureHingesFences(Double f)
configure to use hinges-fences algorithm
Base class for LatticeStatistics class.
Double hf
hinges-fences f factor
Bool someGoodPoints()
See if there were some valid points found in the storage lattice.
A templated, abstract base class for array-like objects with masks.
Definition: ImageConcat.h:46
Bool setList(const Bool &doList)
This function allows you to control whether the statistics are written to the output stream if you ar...
Data provider which allows stats framework to iterate through an unmasked lattice.
virtual ~LatticeStatistics()
Destructor.
A 2-D Specialization of the Array class.
Definition: Array.h:53
ostream-like interface to creating log messages.
Definition: LogIO.h:167
Bool getStatistic(Array< AccumType > &stat, LatticeStatsBase::StatisticsTypes type, Bool dropDeg=True)
Recover the desired Statistic into an array.
std::list< stat_element > stat_list
USE_DATA
which section of data to use, greater than or less than the center value
void _doStatsLoop(uInt nsets, CountedPtr< LattStatsProgress > progressMeter)
std::pair< String, String > stat_element
Bool hasLogger() const
Did we construct with a logger ?
Bool calculateStatistic(Array< AccumType > &slice, LatticeStatsBase::StatisticsTypes type, Bool dropDeg)
Calculate statistic from storage lattice and return in an array.
Bool doRobust_p
doRobust means that when the storage lattice is generated, the robust statistics are generated as wel...
LatticeStatistics< T > & operator=(const LatticeStatistics< T > &other)
Assignment operator.
Bool display()
Display the statistics by listing and/or plotting them.
ALGORITHM
implemented algorithms
Bool getFullMinMax(T &dataMin, T &dataMax)
Get full lattice min and max only.
Bool setNewLattice(const MaskedLattice< T > &lattice, Bool clone=True)
Set a new MaskedLattice object.
virtual Bool _canDoFlux() const
Virtual Functions.
void generateRobust()
Find the median per cursorAxes chunk.
std::map< String, uInt > getChauvenetNiter() const
get number of iterations associated with Chauvenet criterion algorithm
IPosition statsSliceShape() const
Find the shape of slice from the statistics lattice at one spatial pixel.
virtual void summStats()
Summarize the statistics found over the entire lattice.
CENTER
choice of center point based on the corresponding statistics from the entire distribution of data...
Bool getLayerStats(String &stats, Double area, Int zAxis=-1, Int zLayer=-1, Int hAxis=-1, Int hLayer=-1)
Char PrecisionType
Higher precision type (Float->Double)
Data provider which allows stats framework to iterate through a masked lattice.
IPosition _storageLatticeShape() const
get the storage lattice shape
Referenced counted pointer for constant data.
Definition: CountedPtr.h:86
LatticeStatistics(const MaskedLattice< T > &lattice, LogIO &os, Bool showProgress=True, Bool forceDisk=False, Bool clone=True)
Constructor takes the lattice and a LogIO object for logging.
virtual Quantum< AccumType > _flux(Bool &, AccumType, Double) const
void minMax(Bool &none, AccumType &dMin, AccumType &dMax, const Vector< AccumType > &d, const Vector< AccumType > &n) const
Find min and max of good data in arrays specified by pointers.
double Double
Definition: aipstype.h:55
AccumType cv
fit to half center value
Compute and display various statistics from a lattice.
FitToHalfStatisticsData::CENTER ct
fit to have center type
LatticeExprNode sqrt(const LatticeExprNode &expr)
virtual Bool _computeFlux(Array< AccumType > &flux, const Array< AccumType > &npts, const Array< AccumType > &sum)
Bool getConvertedStatistic(Array< T > &stat, LatticeStatsBase::StatisticsTypes type, Bool dropDeg=True)
bool Bool
Define the standard types used by Casacore.
Definition: aipstype.h:42
void setStream(ostream &os, Int oPrec)
Non-virtual functions.
void _latticePosToStoragePos(IPosition &storagePos, const IPosition &latticePos)
convert a position in the input lattice to the corresponding position in the stats storage lattice...
Allows a common way for configuring and creating stats algorithm objects.
StatisticsTypes
This enum StatisticTypes is provided for use with the LatticeStatistics<T>::setPlotting function...
Bool setInExCludeRange(const Vector< T > &include, const Vector< T > &exclude, Bool setMinMaxToInclude=False)
You may specify a pixel intensity range as either one for which all pixels in that range are included...
void stretchMinMax(AccumType &dMin, AccumType &dMax) const
Stretch min and max by 5%.
IPosition locInStorageLattice(const IPosition &latticePosition, LatticeStatsBase::StatisticsTypes type) const
Given a location in the lattice and a statistic type, work out where to put it in the storage lattice...
Quantities (i.e. dimensioned values)
Definition: MeasValue.h:40
Bool setAxes(const Vector< Int > &cursorAxes)
Set the cursor axes (0 relative).
virtual void listMinMax(ostringstream &osMin, ostringstream &osMax, Int oWidth, DataType type)
const Bool False
Definition: aipstype.h:44
template <class T, class U> class vector;
Definition: Array.h:169
Bool getStats(Vector< AccumType > &, const IPosition &pos, const Bool posInLattice=False)
This function gets a vector containing all the statistics for a given location.
*IPosition locInLattice(const IPosition &storagePosition, Bool relativeToParent=True) const
Given a location in the storage lattice, convert those locations on the non-statistics axis (the last...
Bool generateStorageLattice()
Create a new storage lattice.
String errorMessage() const
Recover last error message.
SHARED_PTR< const MaskedLattice< T > > _inLatPtrMgr
FitToHalfStatisticsData::USE_DATA ud
fit to half data portion to use
LatticeExprNode mean(const LatticeExprNode &expr)
CountedPtr< TempLattice< AccumType > > pStoreLattice_p
TableExprNode rms(const TableExprNode &array)
Definition: ExprNode.h:1844
String: the storage and methods of handling collections of characters.
Definition: String.h:223
virtual Bool listStats(Bool hasBeam, const IPosition &dPos, const Matrix< AccumType > &ord)
List the statistics to the logger.
StatisticsData::ALGORITHM algorithm
#define ThrowCc(m)
Definition: Error.h:86
NumericTraits< T >::PrecisionType AccumType
virtual void displayStats(AccumType nPts, AccumType sum, AccumType median, AccumType medAbsDevMed, AccumType quartile, AccumType sumSq, AccumType mean, AccumType var, AccumType rms, AccumType sigma, AccumType dMin, AccumType dMax, AccumType q1, AccumType q3)
const Bool True
Definition: aipstype.h:43
void _configureDataProviders(LatticeStatsDataProvider< T > &lattDP, MaskedLatticeStatsDataProvider< T > &maskedLattDP) const
this file contains all the compiler specific defines
Definition: mainpage.dox:28
static AccumType _rms(const AccumType &sumsq, const AccumType &npts)
void resetError()
Reset argument error condition.
static AccumType _mean(const AccumType &sum, const AccumType &npts)
unsigned int uInt
Definition: aipstype.h:51
StatisticsAlgorithmFactory< AccumType, const T *, const Bool * > _saf