Ignore:
Timestamp:
04/01/11 21:43:18 (14 years ago)
Author:
WataruKawasaki
Message:

merged from bug fixes from trunk (r2093)

Location:
branches/casa-prerelease/pre-asap
Files:
14 edited

Legend:

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Added
Removed

  • branches/casa-prerelease/pre-asap

    • Property svn:mergeinfo changed
      /trunkmerged: 2094

  • branches/casa-prerelease/pre-asap/Makefile

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/SConstruct

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/apps

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/external-alma

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/external-alma/atnf/pks/pks_maths.cc

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/getsvnrev.sh

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/python

  • branches/casa-prerelease/pre-asap/python/scantable.py

    r2082 r2095  
    20732073                          clipthresh=None, clipniter=None, plot=None, getresidual=None, outlog=None, blfile=None):
    20742074        """\
    2075         Return a scan which has been baselined (all rows) by sinusoidal functions.
     2075        Return a scan which has been baselined (all rows) with sinusoidal functions.
    20762076        Parameters:
    20772077            insitu:        If False a new scantable is returned.
    … …  
    21662166                               chan_avg_limit=None, plot=None, getresidual=None, outlog=None, blfile=None):
    21672167        """\
    2168         Return a scan which has been baselined (all rows) by cubic spline
    2169         function (piecewise cubic polynomial).
     2168        Return a scan which has been baselined (all rows) with sinusoidal functions.
    21702169        Spectral lines are detected first using linefinder and masked out
    21712170        to avoid them affecting the baseline solution.
    … …  
    23092308
    23102309    @asaplog_post_dec
    2311     def cspline_baseline(self, insitu=None, mask=None, npiece=None, clipthresh=None, clipniter=None, plot=None, outlog=None, blfile=None):
     2310    def cspline_baseline(self, insitu=None, mask=None, npiece=None,
     2311                         clipthresh=None, clipniter=None, plot=None, getresidual=None, outlog=None, blfile=None):
    23122312        """\
    23132313        Return a scan which has been baselined (all rows) by cubic spline function (piecewise cubic polynomial).
    … …  
    23242324                        indivual fit has to be approved, by typing 'y'
    23252325                        or 'n'
     2326            getresidual:if False, returns best-fit values instead of
     2327                        residual. (default is True)
    23262328            outlog:     Output the coefficients of the best-fit
    23272329                        function to logger (default is False)
    … …  
    23502352        nchan = workscan.nchan()
    23512353       
    2352         if mask is None: mask = [True for i in xrange(nchan)]
    2353         if npiece is None: npiece = 2
    2354         if clipthresh is None: clipthresh = 3.0
    2355         if clipniter is None: clipniter = 1
    2356         if plot is None: plot = False
    2357         if outlog is None: outlog = False
    2358         if blfile is None: blfile = ""
     2354        if mask        is None: mask        = [True for i in xrange(nchan)]
     2355        if npiece      is None: npiece      = 2
     2356        if clipthresh  is None: clipthresh  = 3.0
     2357        if clipniter   is None: clipniter   = 1
     2358        if plot        is None: plot        = False
     2359        if getresidual is None: getresidual = True
     2360        if outlog      is None: outlog      = False
     2361        if blfile      is None: blfile      = ""
    23592362
    23602363        outblfile = (blfile != "") and os.path.exists(os.path.expanduser(os.path.expandvars(blfile)))
    … …  
    23622365        try:
    23632366            #CURRENTLY, PLOT=true UNAVAILABLE UNTIL cubic spline fitting is implemented as a fitter method.
    2364             workscan._cspline_baseline(mask, npiece, clipthresh, clipniter, outlog, blfile)
     2367            workscan._cspline_baseline(mask, npiece, clipthresh, clipniter, getresidual, outlog, blfile)
    23652368           
    23662369            workscan._add_history("cspline_baseline", varlist)
    … …  
    23832386    def auto_cspline_baseline(self, insitu=None, mask=None, npiece=None, clipthresh=None,
    23842387                              clipniter=None, edge=None, threshold=None,
    2385                               chan_avg_limit=None, plot=None, outlog=None, blfile=None):
     2388                              chan_avg_limit=None, getresidual=None, plot=None, outlog=None, blfile=None):
    23862389        """\
    23872390        Return a scan which has been baselined (all rows) by cubic spline
    … …  
    24232426                        indivual fit has to be approved, by typing 'y'
    24242427                        or 'n'
     2428            getresidual:if False, returns best-fit values instead of
     2429                        residual. (default is True)
    24252430            outlog:     Output the coefficients of the best-fit
    24262431                        function to logger (default is False)
    … …  
    24472452        nchan = workscan.nchan()
    24482453       
    2449         if mask is None: mask = [True for i in xrange(nchan)]
    2450         if npiece is None: npiece = 2
    2451         if clipthresh is None: clipthresh = 3.0
    2452         if clipniter is None: clipniter = 1
    2453         if edge is None: edge = (0, 0)
    2454         if threshold is None: threshold = 3
     2454        if mask           is None: mask          = [True for i in xrange(nchan)]
     2455        if npiece         is None: npiece        = 2
     2456        if clipthresh     is None: clipthresh    = 3.0
     2457        if clipniter      is None: clipniter      = 1
     2458        if edge           is None: edge          = (0, 0)
     2459        if threshold      is None: threshold      = 3
    24552460        if chan_avg_limit is None: chan_avg_limit = 1
    2456         if plot is None: plot = False
    2457         if outlog is None: outlog = False
    2458         if blfile is None: blfile = ""
     2461        if plot           is None: plot           = False
     2462        if getresidual    is None: getresidual    = True
     2463        if outlog         is None: outlog         = False
     2464        if blfile         is None: blfile         = ""
    24592465
    24602466        outblfile = (blfile != "") and os.path.exists(os.path.expanduser(os.path.expandvars(blfile)))
    … …  
    24912497                    curedge += edge[i]
    24922498               
    2493             workscan._auto_cspline_baseline(mask, npiece, clipthresh, clipniter, curedge, threshold, chan_avg_limit, outlog, blfile)
     2499            workscan._auto_cspline_baseline(mask, npiece, clipthresh, clipniter, curedge, threshold, chan_avg_limit, getresidual, outlog, blfile)
    24942500
    24952501            workscan._add_history("auto_cspline_baseline", varlist)
    … …  
    25112517
    25122518    @asaplog_post_dec
    2513     def poly_baseline(self, insitu=None, mask=None, order=None, plot=None, outlog=None, blfile=None):
     2519    def poly_baseline(self, insitu=None, mask=None, order=None, plot=None, getresidual=None, outlog=None, blfile=None):
    25142520        """\
    25152521        Return a scan which has been baselined (all rows) by a polynomial.
    … …  
    25232529                        indivual fit has to be approved, by typing 'y'
    25242530                        or 'n'
     2531            getresidual:if False, returns best-fit values instead of
     2532                        residual. (default is True)
    25252533            outlog:     Output the coefficients of the best-fit
    25262534                        function to logger (default is False)
    … …  
    25452553        nchan = workscan.nchan()
    25462554       
    2547         if mask is None: mask = [True for i in xrange(nchan)]
    2548         if order is None: order = 0
    2549         if plot is None: plot = False
    2550         if outlog is None: outlog = False
    2551         if blfile is None: blfile = ""
     2555        if mask        is None: mask        = [True for i in xrange(nchan)]
     2556        if order       is None: order       = 0
     2557        if plot        is None: plot        = False
     2558        if getresidual is None: getresidual = True
     2559        if outlog      is None: outlog      = False
     2560        if blfile      is None: blfile      = ""
    25522561
    25532562        outblfile = (blfile != "") and os.path.exists(os.path.expanduser(os.path.expandvars(blfile)))
    … …  
    25792588                    masklist = workscan.get_masklist(f.mask, row=r, silent=True)
    25802589                    #workscan._append_blinfo(blpars, masklist, f.mask)
    2581                     workscan._setspectrum(f.fitter.getresidual(), r)
     2590                    workscan._setspectrum((f.fitter.getresidual() if getresidual else f.fitter.getfit()), r)
    25822591                   
    25832592                    if outblfile:
    … …  
    25912600                if outblfile: blf.close()
    25922601            else:
    2593                 workscan._poly_baseline(mask, order, outlog, blfile)
     2602                workscan._poly_baseline(mask, order, getresidual, outlog, blfile)
    25942603           
    25952604            workscan._add_history("poly_baseline", varlist)
    … …  
    26112620
    26122621    def auto_poly_baseline(self, insitu=None, mask=None, order=None, edge=None, threshold=None,
    2613                            chan_avg_limit=None, plot=None, outlog=None, blfile=None):
     2622                           chan_avg_limit=None, plot=None, getresidual=None, outlog=None, blfile=None):
    26142623        """\
    26152624        Return a scan which has been baselined (all rows) by a polynomial.
    … …  
    26472656                        indivual fit has to be approved, by typing 'y'
    26482657                        or 'n'
     2658            getresidual:if False, returns best-fit values instead of
     2659                        residual. (default is True)
    26492660            outlog:     Output the coefficients of the best-fit
    26502661                        function to logger (default is False)
    … …  
    26672678        nchan = workscan.nchan()
    26682679       
    2669         if mask is None: mask = [True for i in xrange(nchan)]
    2670         if order is None: order = 0
    2671         if edge is None: edge = (0, 0)
    2672         if threshold is None: threshold = 3
     2680        if mask           is None: mask          = [True for i in xrange(nchan)]
     2681        if order          is None: order          = 0
     2682        if edge           is None: edge          = (0, 0)
     2683        if threshold      is None: threshold      = 3
    26732684        if chan_avg_limit is None: chan_avg_limit = 1
    2674         if plot is None: plot = False
    2675         if outlog is None: outlog = False
    2676         if blfile is None: blfile = ""
     2685        if plot           is None: plot           = False
     2686        if getresidual    is None: getresidual    = True
     2687        if outlog         is None: outlog         = False
     2688        if blfile         is None: blfile         = ""
    26772689
    26782690        outblfile = (blfile != "") and os.path.exists(os.path.expanduser(os.path.expandvars(blfile)))
    … …  
    27412753                    masklist = workscan.get_masklist(f.mask, row=r, silent=True)
    27422754                    #workscan._append_blinfo(blpars, masklist, f.mask)
    2743                     workscan._setspectrum(f.fitter.getresidual(), r)
     2755                    workscan._setspectrum((f.fitter.getresidual() if getresidual else f.fitter.getfit()), r)
    27442756
    27452757                    if outblfile:
    … …  
    27592771                        curedge += edge[i]
    27602772               
    2761                 workscan._auto_poly_baseline(mask, order, curedge, threshold, chan_avg_limit, outlog, blfile)
     2773                workscan._auto_poly_baseline(mask, order, curedge, threshold, chan_avg_limit, getresidual, outlog, blfile)
    27622774
    27632775            workscan._add_history("auto_poly_baseline", varlist)

  • branches/casa-prerelease/pre-asap/src

  • branches/casa-prerelease/pre-asap/src/SConscript

    • Property svn:mergeinfo changed (with no actual effect on merging)

  • branches/casa-prerelease/pre-asap/src/Scantable.cpp

    r2082 r2095  
    17611761}
    17621762
    1763 void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool outLogger, const std::string& blfile)
     1763void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, bool outLogger, const std::string& blfile)
    17641764{
    17651765  ofstream ofs;
    … …  
    17891789    chanMask = getCompositeChanMask(whichrow, mask);
    17901790    fitBaseline(chanMask, whichrow, fitter);
    1791     setSpectrum(fitter.getResidual(), whichrow);
     1791    setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
    17921792    outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
    17931793  }
    … …  
    17961796}
    17971797
    1798 void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile)
     1798void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, bool outLogger, const std::string& blfile)
    17991799{
    18001800  ofstream ofs;
    … …  
    18501850
    18511851    fitBaseline(chanMask, whichrow, fitter);
    1852     setSpectrum(fitter.getResidual(), whichrow);
     1852    setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
    18531853
    18541854    outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
    … …  
    18581858}
    18591859
    1860 void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool outLogger, const std::string& blfile)
     1860void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, bool outLogger, const std::string& blfile)
    18611861{
    18621862  ofstream ofs;
    … …  
    18861886    chanMask = getCompositeChanMask(whichrow, mask);
    18871887    //fitBaseline(chanMask, whichrow, fitter);
    1888     //setSpectrum(fitter.getResidual(), whichrow);
     1888    //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
    18891889    std::vector<int> pieceEdges;
    18901890    std::vector<float> params;
    1891     std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, thresClip, nIterClip, true);
     1891    std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, thresClip, nIterClip, getResidual);
    18921892    setSpectrum(res, whichrow);
    18931893    //
    … …  
    18991899}
    19001900
    1901 void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile)
     1901void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, bool outLogger, const std::string& blfile)
    19021902{
    19031903  ofstream ofs;
    … …  
    19541954
    19551955    //fitBaseline(chanMask, whichrow, fitter);
    1956     //setSpectrum(fitter.getResidual(), whichrow);
     1956    //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
    19571957    std::vector<int> pieceEdges;
    19581958    std::vector<float> params;
    1959     std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, thresClip, nIterClip, true);
     1959    std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, thresClip, nIterClip, getResidual);
    19601960    setSpectrum(res, whichrow);
    19611961    //
    … …  
    19731973  }
    19741974  if (nPiece < 1) {
    1975     throw(AipsError("wrong number of the sections for fitting"));
     1975    throw(AipsError("number of the sections must be one or more"));
    19761976  }
    19771977
    … …  
    22152215    chanMask = getCompositeChanMask(whichrow, mask);
    22162216    //fitBaseline(chanMask, whichrow, fitter);
    2217     //setSpectrum(fitter.getResidual(), whichrow);
     2217    //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
    22182218    std::vector<float> params;
    2219     //std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, thresClip, nIterClip, true);
    22202219    std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, maxWaveLength, params, thresClip, nIterClip, getResidual);
    22212220    setSpectrum(res, whichrow);
    … …  
    22832282
    22842283    //fitBaseline(chanMask, whichrow, fitter);
    2285     //setSpectrum(fitter.getResidual(), whichrow);
     2284    //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
    22862285    std::vector<float> params;
    22872286    std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, maxWaveLength, params, thresClip, nIterClip, getResidual);
    … …  
    23352334
    23362335  const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
    2337   double baseXFactor = 2.0*PI/(double)maxWaveLength/(double)(nChan-1);  //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter.
     2336  double baseXFactor = 2.0*PI/(double)maxWaveLength/(double)(nChan-1);  //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK)
    23382337
    23392338  // xArray : contains elemental values for computing the least-square matrix.
    … …  
    26352634
    26362635  if (verbose) {
    2637     for (int i = 0; i < 60; ++i) {
    2638       oss << "-";
    2639     }
    2640     oss << endl;
    26412636    oss <<  " Scan[" << getScan(whichrow)  << "]";
    26422637    oss <<  " Beam[" << getBeam(whichrow)  << "]";
    … …  
    26592654    oss << "Results of baseline fit" << endl;
    26602655    oss << "  rms = " << setprecision(6) << rms << endl;
     2656    for (int i = 0; i < 60; ++i) {
     2657      oss << "-";
     2658    }
     2659    oss << flush;
    26612660  }
    26622661

  • branches/casa-prerelease/pre-asap/src/Scantable.h

    r2082 r2095  
    497497  void polyBaseline(const std::vector<bool>& mask,
    498498                    int order,
     499                    bool getResidual=true,
    499500                    bool outLogger=false,
    500501                    const std::string& blfile="");
    … …  
    504505                        float threshold=3.0,
    505506                        int chanAvgLimit=1,
     507                        bool getResidual=true,
    506508                        bool outLogger=false,
    507509                        const std::string& blfile="");
    … …  
    510512                           float thresClip,
    511513                           int nIterClip,
     514                           bool getResidual=true,
    512515                           bool outLogger=false,
    513516                           const std::string& blfile="");
    … …  
    519522                               float threshold=3.0,
    520523                               int chanAvgLimit=1,
     524                               bool getResidual=true,
    521525                               bool outLogger=false,
    522526                               const std::string& blfile="");
    … …  
    679683                                          float thresClip=3.0,
    680684                                          int nIterClip=1,
    681                                           bool getResidual=false);
     685                                          bool getResidual=true);
    682686  std::vector<float> doSinusoidFitting(const std::vector<float>& data,
    683687                                       const std::vector<bool>& mask,
    … …  
    687691                                       float thresClip=3.0,
    688692                                       int nIterClip=1,
    689                                        bool getResidual=false);
     693                                       bool getResidual=true);
    690694  bool hasSameNchanOverIFs();
    691695  std::string getMaskRangeList(const std::vector<bool>& mask,

  • branches/casa-prerelease/pre-asap/src/ScantableWrapper.h

    r2082 r2095  
    257257  { table_->reshapeSpectrum( nmin, nmax ); }
    258258
    259   void polyBaseline(const std::vector<bool>& mask, int order, bool outlog=false, const std::string& blfile="")
    260   { table_->polyBaseline(mask, order, outlog, blfile); }
    261 
    262   void autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold=5.0, int chan_avg_limit=1, bool outlog=false, const std::string& blfile="")
    263   { table_->autoPolyBaseline(mask, order, edge, threshold, chan_avg_limit, outlog, blfile); }
    264 
    265   void cubicSplineBaseline(const std::vector<bool>& mask, int npiece, float clipthresh, int clipniter, bool outlog=false, const std::string& blfile="")
    266   { table_->cubicSplineBaseline(mask, npiece, clipthresh, clipniter, outlog, blfile); }
    267 
    268   void autoCubicSplineBaseline(const std::vector<bool>& mask, int npiece, float clipthresh, int clipniter, const std::vector<int>& edge, float threshold=5.0, int chan_avg_limit=1, bool outlog=false, const std::string& blfile="")
    269   { table_->autoCubicSplineBaseline(mask, npiece, clipthresh, clipniter, edge, threshold, chan_avg_limit, outlog, blfile); }
     259  void polyBaseline(const std::vector<bool>& mask, int order, bool getresidual=true, bool outlog=false, const std::string& blfile="")
     260  { table_->polyBaseline(mask, order, getresidual, outlog, blfile); }
     261
     262  void autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold=5.0, int chan_avg_limit=1, bool getresidual=true, bool outlog=false, const std::string& blfile="")
     263  { table_->autoPolyBaseline(mask, order, edge, threshold, chan_avg_limit, getresidual, outlog, blfile); }
     264
     265  void cubicSplineBaseline(const std::vector<bool>& mask, int npiece, float clipthresh, int clipniter, bool getresidual=true, bool outlog=false, const std::string& blfile="")
     266  { table_->cubicSplineBaseline(mask, npiece, clipthresh, clipniter, getresidual, outlog, blfile); }
     267
     268  void autoCubicSplineBaseline(const std::vector<bool>& mask, int npiece, float clipthresh, int clipniter, const std::vector<int>& edge, float threshold=5.0, int chan_avg_limit=1, bool getresidual=true, bool outlog=false, const std::string& blfile="")
     269  { table_->autoCubicSplineBaseline(mask, npiece, clipthresh, clipniter, edge, threshold, chan_avg_limit, getresidual, outlog, blfile); }
    270270
    271271  void sinusoidBaseline(const std::vector<bool>& mask, const std::vector<int>& nwave, float maxwavelength, float clipthresh, int clipniter, bool getresidual=true, bool outlog=false, const std::string& blfile="")
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