import _asap from asap import rcParams from asap import print_log from asap import _n_bools class fitter: """ The fitting class for ASAP. """ def __init__(self): """ Create a fitter object. No state is set. """ self.fitter = _asap.fitter() self.x = None self.y = None self.mask = None self.fitfunc = None self.fitfuncs = None self.fitted = False self.data = None self.components = 0 self._fittedrow = 0 self._p = None self._selection = None self.uselinear = False def set_data(self, xdat, ydat, mask=None): """ Set the absissa and ordinate for the fit. Also set the mask indicationg valid points. This can be used for data vectors retrieved from a scantable. For scantable fitting use 'fitter.set_scan(scan, mask)'. Parameters: xdat: the abcissa values ydat: the ordinate values mask: an optional mask """ self.fitted = False self.x = xdat self.y = ydat if mask == None: self.mask = _n_bools(len(xdat), True) else: self.mask = mask return def set_scan(self, thescan=None, mask=None): """ Set the 'data' (a scantable) of the fitter. Parameters: thescan: a scantable mask: a msk retireved from the scantable """ if not thescan: msg = "Please give a correct scan" if rcParams['verbose']: print msg return else: raise TypeError(msg) self.fitted = False self.data = thescan self.mask = None if mask is None: self.mask = _n_bools(self.data.nchan(), True) else: self.mask = mask return def set_function(self, **kwargs): """ Set the function to be fit. Parameters: poly: use a polynomial of the order given with nonlinear least squares fit lpoly: use polynomial of the order given with linear least squares fit gauss: fit the number of gaussian specified Example: fitter.set_function(gauss=2) # will fit two gaussians fitter.set_function(poly=3) # will fit a 3rd order polynomial via nonlinear method fitter.set_function(lpoly=3) # will fit a 3rd order polynomial via linear method """ #default poly order 0 n=0 if kwargs.has_key('poly'): self.fitfunc = 'poly' n = kwargs.get('poly') self.components = [n] self.uselinear = False elif kwargs.has_key('lpoly'): self.fitfunc = 'poly' n = kwargs.get('lpoly') self.components = [n] self.uselinear = True elif kwargs.has_key('gauss'): n = kwargs.get('gauss') self.fitfunc = 'gauss' self.fitfuncs = [ 'gauss' for i in range(n) ] self.components = [ 3 for i in range(n) ] self.uselinear = False else: msg = "Invalid function type." if rcParams['verbose']: print msg return else: raise TypeError(msg) self.fitter.setexpression(self.fitfunc,n) self.fitted = False return def fit(self, row=0, estimate=False): """ Execute the actual fitting process. All the state has to be set. Parameters: row: specify the row in the scantable estimate: auto-compute an initial parameter set (default False) This can be used to compute estimates even if fit was called before. Example: s = scantable('myscan.asap') s.set_cursor(thepol=1) # select second pol f = fitter() f.set_scan(s) f.set_function(poly=0) f.fit(row=0) # fit first row """ if ((self.x is None or self.y is None) and self.data is None) \ or self.fitfunc is None: msg = "Fitter not yet initialised. Please set data & fit function" if rcParams['verbose']: print msg return else: raise RuntimeError(msg) else: if self.data is not None: self.x = self.data._getabcissa(row) self.y = self.data._getspectrum(row) from asap import asaplog asaplog.push("Fitting:") i = row out = "Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (self.data.getscan(i),self.data.getbeam(i),self.data.getif(i),self.data.getpol(i), self.data.getcycle(i)) asaplog.push(out,False) self.fitter.setdata(self.x, self.y, self.mask) if self.fitfunc == 'gauss': ps = self.fitter.getparameters() if len(ps) == 0 or estimate: self.fitter.estimate() try: fxdpar = list(self.fitter.getfixedparameters()) if len(fxdpar) and fxdpar.count(0) == 0: raise RuntimeError,"No point fitting, if all parameters are fixed." if self.uselinear: converged = self.fitter.lfit() else: converged = self.fitter.fit() if not converged: raise RuntimeError,"Fit didn't converge." except RuntimeError, msg: if rcParams['verbose']: print msg else: raise self._fittedrow = row self.fitted = True print_log() return def store_fit(self, filename=None): """ Save the fit parameters. Parameters: filename: if specified save as an ASCII file, if None (default) store it in the scnatable """ if self.fitted and self.data is not None: pars = list(self.fitter.getparameters()) fixed = list(self.fitter.getfixedparameters()) from asap.asapfit import asapfit fit = asapfit() fit.setparameters(pars) fit.setfixedparameters(fixed) fit.setfunctions(self.fitfuncs) fit.setcomponents(self.components) fit.setframeinfo(self.data._getcoordinfo()) if filename is not None: import os filename = os.path.expandvars(os.path.expanduser(filename)) if os.path.exists(filename): raise IOError("File '%s' exists." % filename) fit.save(filename) else: self.data._addfit(fit,self._fittedrow) #def set_parameters(self, params, fixed=None, component=None): def set_parameters(self,*args,**kwargs): """ Set the parameters to be fitted. Parameters: params: a vector of parameters fixed: a vector of which parameters are to be held fixed (default is none) component: in case of multiple gaussians, the index of the component """ component = None fixed = None params = None if len(args) and isinstance(args[0],dict): kwargs = args[0] if kwargs.has_key("fixed"): fixed = kwargs["fixed"] if kwargs.has_key("params"): params = kwargs["params"] if len(args) == 2 and isinstance(args[1], int): component = args[1] if self.fitfunc is None: msg = "Please specify a fitting function first." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) if self.fitfunc == "gauss" and component is not None: if not self.fitted and sum(self.fitter.getparameters()) == 0: pars = _n_bools(len(self.components)*3, False) fxd = _n_bools(len(pars), False) else: pars = list(self.fitter.getparameters()) fxd = list(self.fitter.getfixedparameters()) i = 3*component pars[i:i+3] = params fxd[i:i+3] = fixed params = pars fixed = fxd self.fitter.setparameters(params) if fixed is not None: self.fitter.setfixedparameters(fixed) print_log() return def set_gauss_parameters(self, peak, centre, fwhm, peakfixed=0, centerfixed=0, fwhmfixed=0, component=0): """ Set the Parameters of a 'Gaussian' component, set with set_function. Parameters: peak, centre, fwhm: The gaussian parameters peakfixed, centerfixed, fwhmfixed: Optional parameters to indicate if the paramters should be held fixed during the fitting process. The default is to keep all parameters flexible. component: The number of the component (Default is the component 0) """ if self.fitfunc != "gauss": msg = "Function only operates on Gaussian components." if rcParams['verbose']: print msg return else: raise ValueError(msg) if 0 <= component < len(self.components): d = {'params':[peak, centre, fwhm], 'fixed':[peakfixed, centerfixed, fwhmfixed]} self.set_parameters(d, component) else: msg = "Please select a valid component." if rcParams['verbose']: print msg return else: raise ValueError(msg) def get_area(self, component=None): """ Return the area under the fitted gaussian component. Parameters: component: the gaussian component selection, default (None) is the sum of all components Note: This will only work for gaussian fits. """ if not self.fitted: return if self.fitfunc == "gauss": pars = list(self.fitter.getparameters()) from math import log,pi,sqrt fac = sqrt(pi/log(16.0)) areas = [] for i in range(len(self.components)): j = i*3 cpars = pars[j:j+3] areas.append(fac * cpars[0] * cpars[2]) else: return None if component is not None: return areas[component] else: return sum(areas) def get_errors(self, component=None): """ Return the errors in the parameters. Parameters: component: get the errors for the specified component only, default is all components """ if not self.fitted: msg = "Not yet fitted." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) errs = list(self.fitter.geterrors()) cerrs = errs if component is not None: if self.fitfunc == "gauss": i = 3*component if i < len(errs): cerrs = errs[i:i+3] return cerrs def get_parameters(self, component=None, errors=False): """ Return the fit paramters. Parameters: component: get the parameters for the specified component only, default is all components """ if not self.fitted: msg = "Not yet fitted." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) pars = list(self.fitter.getparameters()) fixed = list(self.fitter.getfixedparameters()) errs = list(self.fitter.geterrors()) area = [] if component is not None: if self.fitfunc == "gauss": i = 3*component cpars = pars[i:i+3] cfixed = fixed[i:i+3] cerrs = errs[i:i+3] a = self.get_area(component) area = [a for i in range(3)] else: cpars = pars cfixed = fixed cerrs = errs else: cpars = pars cfixed = fixed cerrs = errs if self.fitfunc == "gauss": for c in range(len(self.components)): a = self.get_area(c) area += [a for i in range(3)] fpars = self._format_pars(cpars, cfixed, errors and cerrs, area) if rcParams['verbose']: print fpars return {'params':cpars, 'fixed':cfixed, 'formatted': fpars, 'errors':cerrs} def _format_pars(self, pars, fixed, errors, area): out = '' if self.fitfunc == 'poly': c = 0 for i in range(len(pars)): fix = "" if len(fixed) and fixed[i]: fix = "(fixed)" if errors : out += ' p%d%s= %3.6f (%1.6f),' % (c,fix,pars[i], errors[i]) else: out += ' p%d%s= %3.6f,' % (c,fix,pars[i]) c+=1 out = out[:-1] # remove trailing ',' elif self.fitfunc == 'gauss': i = 0 c = 0 aunit = '' ounit = '' if self.data: aunit = self.data.get_unit() ounit = self.data.get_fluxunit() while i < len(pars): if len(area): out += ' %2d: peak = %3.3f %s , centre = %3.3f %s, FWHM = %3.3f %s\n area = %3.3f %s %s\n' % (c,pars[i],ounit,pars[i+1],aunit,pars[i+2],aunit, area[i],ounit,aunit) else: out += ' %2d: peak = %3.3f %s , centre = %3.3f %s, FWHM = %3.3f %s\n' % (c,pars[i],ounit,pars[i+1],aunit,pars[i+2],aunit,ounit,aunit) c+=1 i+=3 return out def get_estimate(self): """ Return the parameter estimates (for non-linear functions). """ pars = self.fitter.getestimate() fixed = self.fitter.getfixedparameters() if rcParams['verbose']: print self._format_pars(pars,fixed,None) return pars def get_residual(self): """ Return the residual of the fit. """ if not self.fitted: msg = "Not yet fitted." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) return self.fitter.getresidual() def get_chi2(self): """ Return chi^2. """ if not self.fitted: msg = "Not yet fitted." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) ch2 = self.fitter.getchi2() if rcParams['verbose']: print 'Chi^2 = %3.3f' % (ch2) return ch2 def get_fit(self): """ Return the fitted ordinate values. """ if not self.fitted: msg = "Not yet fitted." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) return self.fitter.getfit() def commit(self): """ Return a new scan where the fits have been commited (subtracted) """ if not self.fitted: msg = "Not yet fitted." if rcParams['verbose']: print msg return else: raise RuntimeError(msg) from asap import scantable if not isinstance(self.data, scantable): msg = "Not a scantable" if rcParams['verbose']: print msg return else: raise TypeError(msg) scan = self.data.copy() scan._setspectrum(self.fitter.getresidual()) print_log() return scan def plot(self, residual=False, components=None, plotparms=False, filename=None): """ Plot the last fit. Parameters: residual: an optional parameter indicating if the residual should be plotted (default 'False') components: a list of components to plot, e.g [0,1], -1 plots the total fit. Default is to only plot the total fit. plotparms: Inidicates if the parameter values should be present on the plot """ if not self.fitted: return if not self._p or self._p.is_dead: if rcParams['plotter.gui']: from asap.asaplotgui import asaplotgui as asaplot else: from asap.asaplot import asaplot self._p = asaplot() self._p.hold() self._p.clear() self._p.set_panels() self._p.palette(0) tlab = 'Spectrum' xlab = 'Abcissa' ylab = 'Ordinate' from matplotlib.numerix import ma,logical_not,logical_and,array m = self.mask if self.data: tlab = self.data._getsourcename(self._fittedrow) xlab = self.data._getabcissalabel(self._fittedrow) m = logical_and(self.mask, array(self.data._getmask(self._fittedrow), copy=False)) ylab = self.data._get_ordinate_label() colours = ["#777777","#dddddd","red","orange","purple","green","magenta", "cyan"] self._p.palette(0,colours) self._p.set_line(label='Spectrum') y = ma.masked_array(self.y,mask=logical_not(m)) self._p.plot(self.x, y) if residual: self._p.palette(1) self._p.set_line(label='Residual') y = ma.masked_array(self.get_residual(), mask=logical_not(m)) self._p.plot(self.x, y) self._p.palette(2) if components is not None: cs = components if isinstance(components,int): cs = [components] if plotparms: self._p.text(0.15,0.15,str(self.get_parameters()['formatted']),size=8) n = len(self.components) self._p.palette(3) for c in cs: if 0 <= c < n: lab = self.fitfuncs[c]+str(c) self._p.set_line(label=lab) y = ma.masked_array(self.fitter.evaluate(c), mask=logical_not(m)) self._p.plot(self.x, y) elif c == -1: self._p.palette(2) self._p.set_line(label="Total Fit") y = ma.masked_array(self.fitter.getfit(), mask=logical_not(m)) self._p.plot(self.x, y) else: self._p.palette(2) self._p.set_line(label='Fit') y = ma.masked_array(self.fitter.getfit(), mask=logical_not(m)) self._p.plot(self.x, y) xlim=[min(self.x),max(self.x)] self._p.axes.set_xlim(xlim) self._p.set_axes('xlabel',xlab) self._p.set_axes('ylabel',ylab) self._p.set_axes('title',tlab) self._p.release() if (not rcParams['plotter.gui']): self._p.save(filename) print_log() def auto_fit(self, insitu=None, plot=False): """ Return a scan where the function is applied to all rows for all Beams/IFs/Pols. """ from asap import scantable if not isinstance(self.data, scantable) : msg = "Data is not a scantable" if rcParams['verbose']: print msg return else: raise TypeError(msg) if insitu is None: insitu = rcParams['insitu'] if not insitu: scan = self.data.copy() else: scan = self.data rows = xrange(scan.nrow()) # Save parameters of baseline fits as a class attribute. # NOTICE: This does not reflect changes in scantable! if len(rows) > 0: self.blpars=[] from asap import asaplog asaplog.push("Fitting:") for r in rows: out = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (scan.getscan(r),scan.getbeam(r),scan.getif(r),scan.getpol(r), scan.getcycle(r)) asaplog.push(out, False) self.x = scan._getabcissa(r) self.y = scan._getspectrum(r) self.data = None self.fit() fpar = self.get_parameters() if plot: self.plot(residual=True) x = raw_input("Accept fit ([y]/n): ") if x.upper() == 'N': self.blpars.append(None) continue scan._setspectrum(self.fitter.getresidual(), r) self.blpars.append(fpar) if plot: self._p.unmap() self._p = None print_log() return scan