Source code for pyspeckit.spectrum.fitters

from __future__ import print_function
import matplotlib
import numpy as np
import copy
import re
import warnings

from astropy import log
from astropy import units as u
from six.moves import xrange
from six import string_types

from ..config import mycfg
from ..config import ConfigDescriptor as cfgdec
from . import units
from . import models
from ..specwarnings import warn
from . import interactive
from . import history
from . import widgets

[docs]class Registry(object): """ This class is a simple wrapper to prevent fitter properties from being globals """ def __init__(self): self.npars = {} self.multifitters = {} #to delete self.peakbgfitters = {} self.fitkeys = {} self.associatedkeys = {} self._interactive_help_message_root = """ '?' will print this help message again. The keys denoted by surrounding / / are mnemonics. 1. Left-click or hit 'p' (/p/ick) with the cursor over the plot at both of the two desired X-values to select a fitting range. You can e/x/clude parts of the spectrum by hitting 'x' at two positions. 2. Then /m/iddle-click or hit 'm' twice to select (/m/ark) a peak and width - the first mark should be on the peak of the line, the second should be at the approximate half-max point on the curve. 3. When you're done, right-click or hit 'd' to perform the fit and disconnect the mouse and keyboard (/d/isconnect because you're /d/one). Any time before you're /d/one, you can select a different fitter (see below). To /c/ancel or /c/lear all connections, press 'c' '?' : get help (this message) 'c' : cancel / clear 'p','1' : pick / selection region for fitting 'm','2' : mark / identify a peak 'd','3' : done / do the fit, then disconnect the fitter 'i' : individual components / show each fitted component You can select different fitters to use with the interactive fitting routine. The default is gaussian ('g'), all options are listed below: """ self._make_interactive_help_message() def __copy__(self): # http://stackoverflow.com/questions/1500718/what-is-the-right-way-to-override-the-copy-deepcopy-operations-on-an-object-in-p cls = self.__class__ result = cls.__new__(cls) result.__dict__.update(self.__dict__) return result def __deepcopy__(self, memo): cls = self.__class__ result = cls.__new__(cls) memo[id(self)] = result for k, v in self.__dict__.items(): setattr(result, k, copy.deepcopy(v, memo)) return result
[docs] def add_fitter(self, name, function, npars, override=False, key=None, multisingle=None): ''' Register a fitter function. Parameters ---------- name: string The fit function name. function: function The fitter function. Single-fitters should take npars + 1 input parameters, where the +1 is for a 0th order baseline fit. They should accept an X-axis and data and standard fitting-function inputs (see, e.g., gaussfitter). Multi-fitters should take N * npars, but should also operate on X-axis and data arguments. npars: int How many parameters does the function being fit accept? Other Parameters ---------------- override: True | False Whether to override any existing type if already present. key: char Key to select the fitter in interactive mode ''' if multisingle is not None: warn("The 'multisingle' keyword is no longer required.", DeprecationWarning) if not name in self.peakbgfitters or override: self.peakbgfitters[name] = function if not name in self.multifitters or override: self.multifitters[name] = function if key is not None: self.fitkeys[key] = name self._make_interactive_help_message() self.npars[name] = npars self.associated_keys = dict(zip(self.fitkeys.values(),self.fitkeys.keys()))
def _make_interactive_help_message(self): """ Generate the interactive help message from the fitkeys """ self.interactive_help_message = ( self._interactive_help_message_root + "\n" + "\n".join(["'%s' - select fitter %s" % (key,name) for key,name in self.fitkeys.items()]) + "\n" # trailing \n so that users' input is on a fresh line )
# Declare default registry built in for all spectra default_Registry = Registry() default_Registry.add_fitter('ammonia',models.ammonia_model(),6,key='a') default_Registry.add_fitter('cold_ammonia',models.ammonia.cold_ammonia_model(),6) default_Registry.add_fitter('ammonia_tau',models.ammonia_model_vtau(),6) # not implemented default_Registry.add_fitter(Registry,'ammonia',models.ammonia_model( ),6, ,key='A') default_Registry.add_fitter('formaldehyde',models.formaldehyde_fitter,3,key='F') # CAN'T USE f! reserved for fitting # do'nt override default_Registry.add_fitter('formaldehyde',models.formaldehyde_vheight_fitter,3) default_Registry.add_fitter('gaussian',models.gaussian_fitter(),3,key='g') default_Registry.add_fitter('vheightgaussian',models.gaussian_vheight_fitter(),4) default_Registry.add_fitter('voigt',models.voigt_fitter(),4,key='v') default_Registry.add_fitter('lorentzian',models.lorentzian_fitter(),3,key='L') #default_Registry.add_fitter('hill5',models.hill5infall.hill5_fitter,5) #default_Registry.add_fitter('hcn',models.hcn.hcn_vtau_fitter,4)
[docs]class Specfit(interactive.Interactive): def __init__(self, Spectrum, Registry=None): super(Specfit, self).__init__(Spectrum, interactive_help_message=Registry.interactive_help_message) self.model = None self.parinfo = None self.modelpars = None self.modelerrs = None self.modelplot = [] self.modelcomponents = None self._plotted_components = [] self.npeaks = 0 #self.nclicks_b1 = 0 #self.nclicks_b2 = 0 #self.xmin = 0 #self.xmax = Spectrum.data.shape[0] self.button2action = self.guesspeakwidth self.guesses = [] self.click = 0 self.fitkwargs = {} self.auto = False self.fitleg=None self.residuals=None self.setfitspec() self.fittype = 'gaussian' self.measurements = None self.vheight=False # vheight must be a boolean, can't be none self._component_kwargs = {} self.Registry = Registry self.autoannotate = mycfg['autoannotate'] self.EQW_plots = [] #self.seterrspec() @property def fitter(self): if hasattr(self, '_fitter'): return self._fitter else: raise AttributeError("The 'specfit' object has no 'fitter' yet. " "This means you haven't yet run a fit. The " "fitter is not accessible until after a fit " "has been run.") @fitter.setter def fitter(self, value): self._fitter = value @cfgdec def __call__(self, interactive=False, usemoments=True, fittype=None, clear_all_connections=True, debug=False, guesses='moments', parinfo=None, save=True, annotate=None, show_components=None, use_lmfit=False, verbose=True, clear=True, reset_selection=True, fit_plotted_area=True, use_window_limits=None, vheight=None, exclude=None, **kwargs): """ Fit model functions to a spectrum Parameters ---------- interactive : boolean The plotter window will go into interactive mode. See self.interactive_help_message for details on how to use the interactive fitter. fittype : str [passed to fitting codes; defaults to gaussian] The model to use. Model must be registered in self.Registry. gaussian, lorentzian, and voigt profiles are registered by default guesses : list or 'moments' A list of guesses. Guesses must have length = n*number of parameters in model. Guesses are *required* for multifit fits (there is no automated guessing for most models) EXAMPLE: for single-fit gaussian guesses = [height,amplitude,center,width] for multi-fit gaussian, it is [amplitude, center, width] You can also pass the keyword string 'moments' to have the moments be used to automatically determine the guesses for a *single* peak parinfo : `pyspeckit.spectrum.parinfo.ParinfoList` An alternative way to specify guesses. Supercedes guesses. use_lmfit : boolean If lmfit-py (https://github.com/newville/lmfit-py) is installed, you can use it instead of the pure-python (but slow) mpfit. reset_selection : boolean Override any selections previously made using `fit_plotted_area` or other keywords? fit_plotted_area : boolean If no other limits are specified, the plotter's xmin/xmax will be used to define the fit region. Only respects the x-axis limits, not the y-axis limits. use_window_limits : boolean If ``fit_plotted_area==True`` and no other limits are specified, will use the displayed window area (as set by the zoom tools) as the fitting range. Only respects the x-axis limits, not the y-axis limits. exclude : None or list Passed to selectregion; specifies regions to exclude in xarr units Plotter-related Parameters -------------------------- annotate : None or boolean If None, will use the default stored in self.annotate, otherwise overwrites. Annotations will appear on the plot if a plotter exists. show_components : boolean Show the individual components of a multi-component fit (defaults to blue) clear : boolean Clear previous fitter plots before overplotting the fit? Advanced Parameters ------------------- clear_all_connections : boolean Clear all of the interactive connections from a previous interactive session (e.g., a baseline fitting session) before continuing? usemoments : boolean Use the moments of the spectrum as input guesses. Only works for gaussian and gaussian-like models. Only works for single-fit mode (not multifit) DEPRECATED debug : boolean Print debug statements? save : boolean Save best fits in the FITS header as keywords? ONLY IMPLEMENTED FOR GAUSSIANS verbose : boolean Print out extra stuff vheight : None or boolean if None, defaults to self.vheight, otherwise overrides Determines whether a 0th order baseline will be fit along with the line """ if clear: self.clear() if reset_selection: self.selectregion(verbose=verbose, debug=debug, fit_plotted_area=fit_plotted_area, exclude=exclude, use_window_limits=use_window_limits, **kwargs) for arg in ['xmin','xmax','xtype','reset']: if arg in kwargs: kwargs.pop(arg) if fittype is not None: self.fittype = fittype self.fitter = self.Registry.multifitters[self.fittype] if 'multifit' in kwargs: kwargs.pop('multifit') log.warning("The multifit keyword is no longer required. All fits " "allow for multiple components.", DeprecationWarning) if 'guess' in kwargs: if guesses is None: guesses = kwargs.pop('guess') log.warning("The keyword 'guess' is nonstandard; please use 'guesses'") else: raise ValueError("Received keywords 'guess' and 'guesses'. " "Please only use 'guesses'") self.npeaks = 0 self.fitkwargs = kwargs log.debug("Additional keyword arguments passed to fitter are: {0}" .format(kwargs)) if interactive: if self.Spectrum.plotter.axis is None: raise Exception("Interactive fitting requires a plotter.") # reset button count & guesses on every __call__ self.nclicks_b1 = 0 self.nclicks_b2 = 0 self.guesses = [] self.start_interactive(clear_all_connections=clear_all_connections, reset_selection=True, debug=debug, **kwargs) elif (self.fittype in self.Registry.multifitters or guesses is not None or parinfo is not None): if guesses is None and parinfo is None: raise ValueError("You must input guesses when using multifit." " Also, baseline (continuum fit) first!") elif parinfo is not None: self.guesses = parinfo.values self.parinfo = parinfo self.multifit(show_components=show_components, verbose=verbose, debug=debug, use_lmfit=use_lmfit, annotate=annotate, parinfo=parinfo, guesses=None, **kwargs) elif guesses is not None: if isinstance(guesses, tuple): guesses = list(guesses) self.guesses = guesses self.multifit(show_components=show_components, verbose=verbose, debug=debug, use_lmfit=use_lmfit, fittype=fittype, guesses=guesses, annotate=annotate, **kwargs) else: raise ValueError("Guess and parinfo were somehow invalid.") else: raise ValueError("Can't fit with given fittype {0}:" " it is not Registered as a fitter.".format(self.fittype)) if save: self.savefit()
[docs] def EQW(self, plot=False, plotcolor='g', fitted=True, continuum=None, components=False, annotate=False, alpha=0.5, loc='lower left', xmin=None, xmax=None, xunits=None, continuum_as_baseline=False, xunit='pixel', midpt_location='plot-center'): """ Returns the equivalent width (integral of "baseline" or "continuum" minus the spectrum) over the selected range (the selected range defaults to self.xmin:self.xmax, so it may include multiple lines!) Parameters ---------- plot : bool Plots a box indicating the EQW if plot==True (i.e., it will have a width equal to the equivalent width, and a height equal to the measured continuum) fitted : bool Use the fitted model? If false, uses the data continuum : None or float Can specify a fixed continuum with this keyword, otherwise will use the fitted baseline. WARNING: continuum=0 will still "work", but will give numerically invalid results. Similarly, a negative continuum will work, but will yield results with questionable physical meaning. continuum_as_baseline : bool Replace the baseline with the specified continuum when computing the absorption depth of the line components : bool If your fit is multi-component, will attempt to acquire centroids for each component and print out individual EQWs xmin : float xmax : float The range over which to compute the EQW xunit : str The units of xmin/xmax midpt_location : 'fitted', 'plot-center' If 'plot' is set, this determines where the EQW will be drawn. It can be the fitted centroid or the plot-center, i.e. (xmin+xmax)/2 Returns ------- Equivalent Width, or widths if components=True """ if continuum is not None: # if continuum is specified, don't bother with checks if np.median(self.Spectrum.baseline.basespec) == 0: raise ValueError("Baseline / continuum is zero: equivalent width is undefined.") elif np.median(self.Spectrum.baseline.basespec) < 0: if mycfg.WARN: warn( "WARNING: Baseline / continuum is negative: equivalent width is poorly defined." ) if xunits is not None and xunit=='pixel': # todo: deprecation warning xunit = xunits # determine range to use if xmin is None: xmin = self.xmin #self.Spectrum.xarr.x_to_pix(self.xmin) else: xmin = self.Spectrum.xarr.x_to_pix(xmin, xval_units=xunit) if xmax is None: xmax = self.xmax #self.Spectrum.xarr.x_to_pix(self.xmax) else: xmax = self.Spectrum.xarr.x_to_pix(xmax, xval_units=xunit) dx = np.abs(self.Spectrum.xarr[xmin:xmax].cdelt(approx=True).value) log.debug("xmin={0} xmax={1} dx={2} continuum={3}" .format(xmin, xmax, dx, continuum)) if components: centroids = self.fitter.analytic_centroids() integrals = self.fitter.component_integrals(self.Spectrum.xarr[xmin:xmax],dx=dx) eqw = [] for cen,integ in zip(centroids,integrals): center_pix = self.Spectrum.xarr.x_to_pix(cen) if continuum is None: continuum = self.Spectrum.baseline.basespec[center_pix] elif continuum_as_baseline: integrals[-1] += -(self.Spectrum.baseline.basespec[xmin:xmax] - continuum).sum() * dx eqw.append(-integ / continuum) if plot: plot = False if mycfg.WARN: warn("Cannot plot multiple Equivalent Widths") elif fitted: model = self.get_model(self.Spectrum.xarr[xmin:xmax], add_baseline=False) # EQW is positive for absorption lines # fitted components are assume to be continuum-subtracted integral = (-model).sum() * dx if continuum is None: # centroid in data units # (may fail if model has pos + neg values) center = (model*self.Spectrum.xarr[xmin:xmax]).sum()/model.sum() center_pix = self.Spectrum.xarr.x_to_pix(center) continuum = self.Spectrum.baseline.basespec[center_pix] elif continuum_as_baseline: integral += -(self.Spectrum.baseline.basespec[xmin:xmax] - continuum).sum() * dx eqw = integral / continuum else: if continuum_as_baseline: diffspec = (continuum - self.Spectrum.data) elif self.Spectrum.baseline.subtracted is False: diffspec = (self.Spectrum.baseline.basespec - self.Spectrum.data) else: diffspec = -self.Spectrum.data sumofspec = diffspec[xmin:xmax].sum() * dx if continuum is None: continuum = np.median(self.Spectrum.baseline.basespec) eqw = sumofspec / continuum if plot and self.Spectrum.plotter.axis: if midpt_location == 'plot-center': midpt_pixel = int(np.round((xmin+xmax)/2.0)) midpt = self.Spectrum.xarr[midpt_pixel].value elif midpt_location == 'fitted': try: shifts = np.array([self.Spectrum.specfit.parinfo[x].value for x in self.Spectrum.specfit.parinfo.keys() if 'SHIFT' in x]) except AttributeError: raise AttributeError("Can only specify midpt_location=" "fitted if there is a SHIFT parameter" "for the fitted model") # We choose to display the eqw fit at the center of the fitted # line set, closest to the passed window. # Note that this has the potential to show a eqw "rectangle" # centered on a fitted line other than the one measured for the # eqw call, if there are more than one fitted lines within the # window. midpt_pixel = int((xmin+xmax)/2) midval = self.Spectrum.xarr[midpt_pixel].value midpt_index = np.argmin(np.abs(shifts-midval)) midpt = shifts[midpt_index] midpt_pixel = self.Spectrum.xarr.x_to_pix(midpt) else: raise ValueError("midpt_location must be 'plot-center' or " "fitted") if continuum_as_baseline: midpt_level = continuum else: midpt_level = self.Spectrum.baseline.basespec[midpt_pixel] log.debug("EQW plotting: midpt={0}, midpt_pixel={1}, " "midpt_level={2}, eqw={3}".format(midpt, midpt_pixel, midpt_level, eqw)) self.EQW_plots.append(self.Spectrum.plotter.axis.fill_between( [midpt-eqw/2.0,midpt+eqw/2.0], [0,0], [midpt_level,midpt_level], color=plotcolor, alpha=alpha, label='EQW: %0.3g' % eqw)) if annotate: self.Spectrum.plotter.axis.legend( [(matplotlib.collections.CircleCollection([0],facecolors=[plotcolor],edgecolors=[plotcolor]))], [('EQW: %0.3g' % eqw)], markerscale=0.01, borderpad=0.1, handlelength=0.1, handletextpad=0.1, loc=loc) if self.Spectrum.plotter.autorefresh: self.Spectrum.plotter.refresh() if hasattr(self.Spectrum,'header'): history.write_history(self.Spectrum.header, "EQW for %s: %s" % (self.fittype,eqw)) return eqw
[docs] def register_fitter(self,*args,**kwargs): """ Register a model fitter """ self.Registry.add_fitter(*args,**kwargs)
register_fitter.__doc__ += Registry.add_fitter.__doc__
[docs] def seterrspec(self, usestd=None, useresiduals=True): """ Simple wrapper function to set the error spectrum; will either use the input spectrum or determine the error using the RMS of the residuals, depending on whether the residuals exist. """ if (self.Spectrum.error is not None) and not usestd: if (self.Spectrum.error == 0).all(): if self.residuals is not None and useresiduals: residuals_std = self.residuals.std() if residuals_std == 0: self.errspec = np.ones(self.spectofit.shape[0]) warnings.warn("Residuals have 0 standard deviation. " "That's probably too good to be true.") else: self.errspec = np.ones(self.spectofit.shape[0]) * residuals_std elif type(self.Spectrum.error) is np.ma.masked_array: # force errspec to be a non-masked array of ones self.errspec = self.Spectrum.error.data + 1 else: self.errspec = self.Spectrum.error + 1 else: # this is the default behavior if spectrum.error is set self.errspec = self.Spectrum.error.copy() elif self.residuals is not None and useresiduals: self.errspec = np.ones(self.spectofit.shape[0]) * self.residuals.std() else: self.errspec = np.ones(self.spectofit.shape[0]) * self.spectofit.std()
[docs] def setfitspec(self): """ Set the spectrum that will be fit. This is primarily to remove NANs from consideration: if you simply remove the data from both the X-axis and the Y-axis, it will not be considered for the fit, and a linear X-axis is not needed for fitting. However, it may be possible to do this using masked arrays instead of setting errors to be 1e10.... """ if self.Spectrum.data.sum() is np.ma.masked: self.spectofit = np.zeros_like(self.Spectrum.data) self.errspec = np.zeros_like(self.Spectrum.data) self._valid = False return # see https://github.com/numpy/numpy/issues/3474 self.spectofit = np.ma.copy(self.Spectrum.data) if hasattr(self.Spectrum.data, 'mask') and hasattr(self.spectofit, 'mask'): assert np.all(self.Spectrum.data.mask == self.spectofit.mask) self._valid = True if hasattr(self.Spectrum,'baseline'): if ((not self.Spectrum.baseline.subtracted and self.Spectrum.baseline.basespec is not None and len(self.spectofit) == len(self.Spectrum.baseline.basespec))): self.spectofit -= self.Spectrum.baseline.basespec OKmask = np.isfinite(self.spectofit) with warnings.catch_warnings(): # catch a specific np1.7 futurewarning relating to masks warnings.simplefilter("ignore") self.spectofit[~OKmask] = 0 self.seterrspec() # the "OK" mask is just checking that the values are finite self.errspec[~OKmask] = 1e10 # if an includemask is set *and* there are some included values, "mask out" the rest # otherwise, if *all* data are excluded, we should assume that means the includemask # simply hasn't been initialized if self.includemask is not None and (self.includemask.shape == self.errspec.shape) and any(self.includemask): self.errspec[~self.includemask] = 1e10*self.errspec.max()
@property def mask(self): """ Mask: True means "exclude" """ if ((hasattr(self.spectofit, 'mask') and self.spectofit.shape==self.spectofit.mask.shape)): mask = self.spectofit.mask else: mask = np.zeros_like(self.spectofit, dtype='bool') return mask @property def dof(self): """ degrees of freedom in fit """ if not hasattr(self, 'npix_fitted'): raise AttributeError('No fit has been run, so npix_fitted is not ' 'defined and dof cannot be computed.') return (self.npix_fitted - self.vheight - self.npeaks * self.Registry.npars[self.fittype] + np.sum(self.parinfo.fixed) + np.sum([x != '' for x in self.parinfo.tied])) #self.dof = self.includemask.sum()-self.npeaks*self.Registry.npars[self.fittype]-vheight+np.sum(self.parinfo.fixed) @property def mask_sliced(self): """ Sliced (subset) Mask: True means "exclude" """ return self.mask[self.xmin:self.xmax]
[docs] def multifit(self, fittype=None, renormalize='auto', annotate=None, show_components=None, verbose=True, color=None, guesses=None, parinfo=None, reset_fitspec=True, use_window_limits=None, use_lmfit=False, plot=True, **kwargs): """ Fit multiple gaussians (or other profiles) Parameters ---------- fittype : str What function will be fit? fittype must have been Registryed in the peakbgfitters dict. Uses default ('gaussian') if not specified renormalize : 'auto' or bool if 'auto' or True, will attempt to rescale small data (<1e-9) to be closer to 1 (scales by the median) so that the fit converges better parinfo : `~parinfo` structure Guess structure; supercedes ``guesses`` guesses : list or 'moments' Either a list of guesses matching the number of parameters * the number of peaks for the model, or 'moments' to fit a single spectrum with the moments as guesses """ if reset_fitspec: self.setfitspec() if not self._valid: raise ValueError("Data are invalid; cannot be fit.") #if self.fitkwargs.has_key('negamp'): self.fitkwargs.pop('negamp') # We now do this in gaussfitter.py if fittype is not None: self.fittype = fittype bad_kws = ['fittype','plot'] for kw in bad_kws: if kw in self.fitkwargs: del self.fitkwargs[kw] if guesses is not None and parinfo is not None: raise ValueError("Both guesses and parinfo were specified, " "but only one of these is allowed.") if guesses is None: if parinfo is not None: guesses = list(parinfo.values) else: guesses = list(self.guesses) elif isinstance(guesses, string_types) and guesses in ('moment', 'moments'): guesses = self.moments(vheight=False, **kwargs) else: guesses = list(guesses) # needs to be mutable, but needs to be a copy!! if len(guesses) < self.Registry.npars[self.fittype]: raise ValueError("Too few parameters input. Need at least %i for %s models" % (self.Registry.npars[self.fittype],self.fittype)) self.npeaks = len(guesses)/self.Registry.npars[self.fittype] self.fitter = self.Registry.multifitters[self.fittype] self.vheight = False if self.fitter.vheight: # Need to reset the parinfo if vheight has previously been set, # otherwise npars will disagree, which causes problems if # renormalization happens self.fitter.vheight = False self.fitter.npeaks = self.npeaks self.fitter._make_parinfo(npeaks=self.npeaks) # add kwargs to fitkwargs self.fitkwargs.update(kwargs) if 'renormalize' in self.fitkwargs: del self.fitkwargs['renormalize'] # if parinfo was specified, we use it and ignore guesses otherwise, we # make a parinfo so we can test 'scaleable' below if parinfo is not None: pinf_for_scaling = parinfo else: pinf_for_scaling, _ = self.fitter._make_parinfo(parvalues=guesses, npeaks=self.npeaks, **self.fitkwargs) scalefactor = 1.0 if renormalize in ('auto',True): datarange = np.nanmax(self.spectofit[self.xmin:self.xmax]) - np.nanmin(self.spectofit[self.xmin:self.xmax]) if abs(datarange) < 1e-9: scalefactor = np.nanmedian(np.abs(self.spectofit)) if not np.isfinite(scalefactor): raise ValueError("non-finite scalefactor = {0} encountered.".format(scalefactor)) elif scalefactor == 0: raise ValueError("scalefactor = {0} encountered, which will result " "in divide-by-zero errors".format(scalefactor)) log.info("Renormalizing data by factor %e to improve fitting procedure" % scalefactor) self.spectofit /= scalefactor self.errspec /= scalefactor # this error should be unreachable, but is included as a sanity check if self.fitter.npeaks * self.fitter.npars != len(pinf_for_scaling): raise ValueError("Length of parinfo doesn't agree with " " npeaks * npars = {0}" .format(self.fitter.npeaks * self.fitter.npars)) if len(guesses) != len(pinf_for_scaling): raise ValueError("Length of parinfo doens't match length of guesses") # zip guesses with parinfo: truncates parinfo if len(parinfo) > len(guesses) # actually not sure how/when/if this should happen; this might be a bad hack # revisit with tests!! for jj,(guess,par) in enumerate(zip(guesses,pinf_for_scaling)): if par.scaleable: guesses[jj] /= scalefactor # if parinfo was passed in, this will change it # if it was not, it will change only the placeholder # (becuase we are passing by reference above) par.value /= scalefactor par.limits = [lim / scalefactor for lim in par.limits] log.debug("Rescaled guesses to {0}".format(guesses)) # all fit data must be float64, otherwise the optimizers may take steps # less than the precision of the data and get stuck xtofit = self.Spectrum.xarr[self.xmin:self.xmax][~self.mask_sliced].astype('float64') spectofit = self.spectofit[self.xmin:self.xmax][~self.mask_sliced].astype('float64') err = self.errspec[self.xmin:self.xmax][~self.mask_sliced].astype('float64') if np.all(err == 0): raise ValueError("Errors are all zero. This should not occur and " "is a bug. (if you set the errors to all zero, " "they should be overridden and set to 1)") if parinfo is not None: self._validate_parinfo(parinfo, mode='fix') else: pinf, _ = self.fitter._make_parinfo(parvalues=guesses, npeaks=self.npeaks, **self.fitkwargs) new_guesses = self._validate_parinfo(pinf, 'guesses') if any((x!=y) for x,y in zip(guesses, new_guesses)): warn("Guesses have been changed from {0} to {1}" .format(guesses, new_guesses)) guesses = new_guesses mpp,model,mpperr,chi2 = self.fitter(xtofit, spectofit, err=err, npeaks=self.npeaks, parinfo=parinfo, # the user MUST be allowed to override parinfo. params=guesses, use_lmfit=use_lmfit, **self.fitkwargs) any_out_of_range = self._validate_parinfo(self.fitter.parinfo, mode='check') if any(any_out_of_range): warn("The fitter returned values that are outside the " "parameter limits. DEBUG INFO: {0}".format(any_out_of_range)) self.spectofit *= scalefactor self.errspec *= scalefactor if hasattr(self.fitter.mp,'status'): self.mpfit_status = models.mpfit_messages[self.fitter.mp.status] if model is None: raise ValueError("Model was not set by fitter. Examine your fitter.") self.chi2 = chi2 self.model = model * scalefactor self.parinfo = self.fitter.parinfo # rescale any scaleable parameters for par in self.parinfo: if par.scaleable: par.value *= scalefactor if par.error is not None: par.error *= scalefactor if par.limits is not None: par.limits = [lim*scalefactor for lim in par.limits] self.modelpars = self.parinfo.values self.modelerrs = self.parinfo.errors self.residuals = spectofit - self.model if self.Spectrum.plotter.axis is not None and plot: if color is not None: kwargs.update({'composite_fit_color':color}) self.plot_fit(annotate=annotate, show_components=show_components, use_window_limits=use_window_limits, **kwargs) # Re-organize modelerrs so that any parameters that are tied to others inherit the errors of the params they are tied to if 'tied' in self.fitkwargs: for ii, element in enumerate(self.fitkwargs['tied']): if not element.strip(): continue if '[' in element and ']' in element: i1 = element.index('[') + 1 i2 = element.index(']') loc = int(element[i1:i2]) else: # assume lmfit version varnames = re.compile('([a-zA-Z][a-zA-Z_0-9]*)').search(element).groups() if not varnames: continue elif len(varnames) > 1: warn("The 'tied' parameter {0} is not simple enough for error propagation".format(element)) continue else: varname = varnames[0] loc = self.parinfo.names.index(varname) self.modelerrs[ii] = self.modelerrs[loc] # make sure the full model is populated self._full_model() # calculate the number of pixels included in the fit. This should # *only* be done when fitting, not when selecting data. # (see self.dof) self.npix_fitted = self.includemask.sum() - self.mask.sum() self.history_fitpars()
[docs] def refit(self, use_lmfit=False): """ Redo a fit using the current parinfo as input """ return self.multifit(parinfo=self.parinfo, use_lmfit=use_lmfit, reset_fitspec=False)
[docs] def history_fitpars(self): if hasattr(self.Spectrum,'header'): history.write_history(self.Spectrum.header, "SPECFIT: Fitted " "profile of type %s" % (self.fittype)) history.write_history(self.Spectrum.header, "Chi^2: %g DOF: %i" % (self.chi2, self.dof)) for par in self.parinfo: history.write_history(self.Spectrum.header, str(par))
[docs] def peakbgfit(self, usemoments=True, annotate=None, vheight=True, height=0, negamp=None, fittype=None, renormalize='auto', color=None, use_lmfit=False, show_components=None, debug=False, use_window_limits=True, guesses=None, nsigcut_moments=None, plot=True, parinfo=None, **kwargs): """ Fit a single peak (plus a background) Parameters ---------- usemoments : bool The initial guess will be set by the fitter's 'moments' function (this overrides 'guesses') annotate : bool Make a legend? vheight : bool Fit a (constant) background as well as a peak? height : float initial guess for background negamp : bool If True, assumes amplitude is negative. If False, assumes positive. If None, can be either. fittype : bool What function will be fit? fittype must have been Registryed in the peakbgfitters dict renormalize : 'auto' or bool if 'auto' or True, will attempt to rescale small data (<1e-9) to be closer to 1 (scales by the median) so that the fit converges better nsigcut_moments : bool pass to moment guesser; can do a sigma cut for moment guessing """ self.npeaks = 1 self.auto = True self.setfitspec() if fittype is not None: self.fittype=fittype NP = self.Registry.peakbgfitters[self.fittype].default_npars if guesses is not None: log.debug("Using user-specified guesses.") self.guesses = guesses if len(guesses) != NP + vheight: raise ValueError("Invalid guesses specified for single-fitter." "Expected {0}, got {1}. Perhaps you should " "use the multifitter (multifit=True)?" .format(NP+vheight, len(guesses))) elif usemoments: # this can be done within gaussfit but I want to save them # use this INDEPENDENT of fittype for now (voigt and gauss get same guesses) log.debug("Using moment-based guesses.") moments_f = self.Registry.peakbgfitters[self.fittype].moments self.guesses = moments_f(self.Spectrum.xarr[self.xmin:self.xmax], self.spectofit[self.xmin:self.xmax], vheight=vheight, negamp=negamp, nsigcut=nsigcut_moments, **kwargs) else: if negamp: self.guesses = [height,-1,0,1] else: self.guesses = [height,1,0,1] # If we're fitting anything but a simple Gaussian, we need the length # of guesses to be right so we pad with appended zeros # BUT, if the guesses from the moments have the right number of # parameters, we don't need to do this. if NP > len(self.guesses): for ii in xrange(len(self.guesses),NP): self.guesses += [0.0] self.fitter = self.Registry.peakbgfitters[self.fittype] log.debug("n(guesses): %s Guesses: %s vheight: %s " % (len(self.guesses),self.guesses,vheight)) scalefactor = 1.0 if renormalize in ('auto',True): datarange = self.spectofit[self.xmin:self.xmax].max() - self.spectofit[self.xmin:self.xmax].min() if abs(datarange) < 1e-9: scalefactor = np.median(np.abs(self.spectofit)) log.info("Renormalizing data by factor %e to improve fitting procedure" % scalefactor) self.spectofit /= scalefactor self.errspec /= scalefactor self.guesses[0] /= scalefactor if vheight: self.guesses[1] /= scalefactor log.debug("Guesses before fit: {0}".format(self.guesses)) if 'debug' in self.fitkwargs: debug = self.fitkwargs['debug'] del self.fitkwargs['debug'] mpp,model,mpperr,chi2 = self.fitter( self.Spectrum.xarr[self.xmin:self.xmax], self.spectofit[self.xmin:self.xmax], err=self.errspec[self.xmin:self.xmax], vheight=vheight, params=self.guesses, parinfo=parinfo, debug=debug, use_lmfit=use_lmfit, **self.fitkwargs) log.debug("1. Guesses, fits after: {0}, {1}".format(self.guesses, mpp)) self.spectofit *= scalefactor self.errspec *= scalefactor if hasattr(self.fitter.mp,'status'): self.mpfit_status = models.mpfit_messages[self.fitter.mp.status] self.parinfo = self.fitter.parinfo if model is None: raise ValueError("Model was not set by fitter. Examine your fitter.") self.chi2 = chi2 self.vheight=vheight if vheight: self.Spectrum.baseline.order = 0 self.Spectrum.baseline.baselinepars = [mpp[0]*scalefactor] # first item in list form self.Spectrum.baseline.basespec = self.Spectrum.data*0 + mpp[0]*scalefactor self.model = model*scalefactor - mpp[0]*scalefactor # I removed this recently for some reason, but more code depends on it being in place # Need to figure out *WHY* anything would want an extra parameter if len(mpp) == self.fitter.npars+1: mpp = mpp[1:] else: self.model = model*scalefactor self.residuals = self.spectofit[self.xmin:self.xmax] - self.model*scalefactor self.modelpars = mpp self.modelerrs = mpperr # rescale any scaleable parameters for par in self.parinfo: if par.scaleable: par.value = par.value * scalefactor if par.error is not None: par.error = par.error * scalefactor if self.Spectrum.plotter.axis is not None and plot: if color is not None: kwargs.update({'composite_fit_color':color}) self.plot_fit(annotate=annotate, use_window_limits=use_window_limits, show_components=show_components, **kwargs) # make sure the full model is populated self._full_model(debug=debug) self.npix_fitted = self.includemask.sum() - self.mask.sum() log.debug("2. Guesses, fits after vheight removal: {0},{1}" .format(self.guesses, mpp)) self.history_fitpars()
def _full_model(self, debug=False, **kwargs): """ Compute the model for the whole spectrum """ self.fullmodel = self.get_full_model(debug=debug,**kwargs) self.fullresiduals = self.Spectrum.data - self.fullmodel
[docs] def get_full_model(self, debug=False,**kwargs): """ compute the model over the full axis """ return self.get_model(self.Spectrum.xarr, debug=debug,**kwargs)
[docs] def get_model(self, xarr, pars=None, debug=False, add_baseline=None): """ Compute the model over a given axis """ if pars is None: return self.get_model_frompars(xarr=xarr, pars=self.parinfo, add_baseline=add_baseline, debug=debug) else: return self.get_model_frompars(xarr=xarr, pars=pars, add_baseline=add_baseline, debug=debug)
[docs] def get_model_frompars(self, xarr, pars, debug=False, add_baseline=None): """ Compute the model over a given axis """ if ((add_baseline is None and (self.Spectrum.baseline.subtracted or self.vheight)) or add_baseline is False): return self.fitter.n_modelfunc(pars,**self.fitter.modelfunc_kwargs)(xarr) else: return (self.fitter.n_modelfunc(pars, **self.fitter.modelfunc_kwargs)(xarr) + self.Spectrum.baseline.get_model(np.arange(xarr.size)))
[docs] def plot_model(self, pars, offset=0.0, annotate=False, clear=False, **kwargs): """ Plot a model from specified input parameters (see plot_fit for kwarg specification) annotate is set to "false" because arbitrary annotations are not yet implemented """ # really, plot_fit should be thin on top of plot_model, but that's # not how I wrote it, so it will have to wait for a refactor if clear: self.clear() return self.plot_fit(pars=pars, offset=offset, annotate=False, **kwargs)
#def assess_npeaks(self): # """ # Attempt to determine whether any of the peaks are unnecessary # """ # if self.npeaks <= 1: # return # npars = self.fitter.npars # perpeakpars = [self.parinfo.values[ii*npars:(ii+1)*npars] for ii in # range(self.npeaks)] # parsets = [((x[0][0],x[1][0]),x[0][1]+x[1][1]) for x in # itertools.combinations(perpeakpars, self.npeaks-1)] # parsets = [x # for y in itertools.combinations(perpeakpars, self.npeaks-1) # for x in y] # chi2_without = [(self.spectofit[self.xmin:self.xmax] - # self.get_model_frompars(self.xarr, self.pars[ii*npars:
[docs] def plot_fit(self, xarr=None, annotate=None, show_components=None, composite_fit_color='red', lw=0.5, composite_lw=0.75, pars=None, offset=None, use_window_limits=None, show_hyperfine_components=None, plotkwargs={}, **kwargs): """ Plot the fit. Must have fitted something before calling this! It will be automatically called whenever a spectrum is fit (assuming an axis for plotting exists) kwargs are passed to the fitter's components attribute Parameters ---------- xarr : None If none, will use the spectrum's xarr. Otherwise, plot the specified xarr. This is useful if you want to plot a well-sampled model when the input spectrum is undersampled annotate : None or bool Annotate the plot? If not specified, defaults to self.autoannotate show_components : None or bool show_hyperfine_components : None or bool Show the individual gaussian components overlaid on the composite fit use_window_limits : None or bool If False, will reset the window to include the whole spectrum. If True, leaves the window as is. Defaults to self.use_window_limits if None. pars : parinfo A parinfo structure or list of model parameters. If none, uses best-fit offset : None or float Y-offset. If none, uses the default self.Spectrum.plotter offset, otherwise, uses the specified float. """ #if self.Spectrum.baseline.subtracted is False and self.Spectrum.baseline.basespec is not None: # # don't display baseline if it's included in the fit # plot_offset = self.Spectrum.plotter.offset+(self.Spectrum.baseline.basespec * (~self.vheight)) #else: if offset is None: plot_offset = self.Spectrum.plotter.offset else: plot_offset = offset if xarr is None: xarr = self.Spectrum.xarr if pars is not None: model = self.get_model_frompars(xarr, pars) else: self._full_model() model = self.fullmodel self.modelplot += self.Spectrum.plotter.axis.plot(xarr, model + plot_offset, color=composite_fit_color, linewidth=lw, **plotkwargs) # Plot components if show_components or show_hyperfine_components: self.plot_components(xarr=xarr, show_hyperfine_components=show_hyperfine_components, pars=pars, plotkwargs=plotkwargs) uwl = use_window_limits if use_window_limits is not None else self.use_window_limits # plotter kwargs are kwargs for the Spectrum.plotter, # whereas plotkwargs are for the matplotlib plot command plotterkwargs = {} plotterkwargs.update(self.Spectrum.plotter.plotkwargs) plotterkwargs['use_window_limits'] = uwl self.Spectrum.plotter.reset_limits(**plotterkwargs) if self.Spectrum.plotter.autorefresh: self.Spectrum.plotter.refresh() if annotate or ((annotate is None) and self.autoannotate): self.annotate() if self.vheight: self.Spectrum.baseline.annotate()
[docs] def plot_components(self, xarr=None, show_hyperfine_components=None, component_yoffset=0.0, component_lw=0.75, pars=None, component_fit_color='blue', component_kwargs={}, add_baseline=False, plotkwargs={}, **kwargs): """ Overplot the individual components of a fit Parameters ---------- xarr : None If none, will use the spectrum's xarr. Otherwise, plot the specified xarr. This is useful if you want to plot a well-sampled model when the input spectrum is undersampled show_hyperfine_components : None | bool Keyword argument to pass to component codes; determines whether to return individual (e.g., hyperfine) components of a composite model component_yoffset : float Vertical (y-direction) offset to add to the components when plotting component_lw : float Line width of component lines component_fitcolor : color Color of component lines component_kwargs : dict Keyword arguments to pass to the fitter.components method add_baseline : bool Add the fit to the components before plotting. Makes sense to use if self.Spectrum.baseline.subtracted == False pars : parinfo A parinfo structure or list of model parameters. If none, uses best-fit """ plot_offset = self.Spectrum.plotter.offset if xarr is None: xarr = self.Spectrum.xarr if show_hyperfine_components is not None: component_kwargs['return_hyperfine_components'] = show_hyperfine_components self._component_kwargs = component_kwargs if pars is None: pars = self.modelpars self.modelcomponents = self.fitter.components(xarr=xarr, pars=pars, **component_kwargs) yoffset = plot_offset + component_yoffset if add_baseline: yoffset += self.Spectrum.baseline.basespec for data in self.modelcomponents: # can have multidimensional components if len(data.shape) > 1: for d in data: self._plotted_components += self.Spectrum.plotter.axis.plot(xarr, d + yoffset, color=component_fit_color, linewidth=component_lw, **plotkwargs) else: self._plotted_components += self.Spectrum.plotter.axis.plot(xarr, data + yoffset, color=component_fit_color, linewidth=component_lw, **plotkwargs)
[docs] def fullsizemodel(self): """ If the model was fit to a sub-region of the spectrum, expand it (with zeros wherever the model was not defined) to fill the spectrum. Examples -------- >>> noise = np.random.randn(100) >>> xarr = np.linspace(-50,50,100) >>> signal = np.exp(-(xarr-5)**2/(2*3.**2)) >>> sp = pyspeckit.Spectrum(data=noise + signal, xarr=xarr, xarrkwargs={'units':'km/s'}) >>> sp.specfit(xmin=-25,xmax=25) >>> sp.specfit.model.shape (48,) >>> sp.specfit.fullsizemodel() >>> sp.specfit.model.shape (100,) """ if self.model.shape != self.Spectrum.data.shape: temp = np.zeros(self.Spectrum.data.shape) temp[self.xmin:self.xmax] = self.model self.model = temp self.residuals = self.spectofit - self.model self.selectregion(reset=True)
[docs] def plotresiduals(self, fig=2, axis=None, clear=True, color='k', linewidth=0.5, drawstyle='steps-mid', yoffset=0.0, label=True, pars=None, zeroline=None, set_limits=True, **kwargs): """ Plot residuals of the fit. Specify a figure or axis; defaults to figure(2). Parameters ---------- fig : int Figure number. Overridden by axis axis : axis The axis to plot on pars : None or parlist If set, the residuals will be computed for the input parameters zeroline : bool or None Plot the "zero" line through the center of the residuals. If None, defaults to "True if yoffset!=0, False otherwise" kwargs are passed to matplotlib plot """ self._full_model(pars=pars) if axis is None: if isinstance(fig,int): fig=matplotlib.pyplot.figure(fig) self.residualaxis = matplotlib.pyplot.gca() if clear: self.residualaxis.clear() else: self.residualaxis = axis if clear: self.residualaxis.clear() self.residualplot = self.residualaxis.plot(self.Spectrum.xarr, self.fullresiduals+yoffset, drawstyle=drawstyle, linewidth=linewidth, color=color, **kwargs) if zeroline or (zeroline is None and yoffset != 0): self.residualplot += self.residualaxis.plot(self.Spectrum.xarr, (np.zeros_like(self.Spectrum.xarr.value)+yoffset), linestyle='--', color='k', alpha=0.5) if set_limits: if ((self.Spectrum.plotter.xmin is not None) and (self.Spectrum.plotter.xmax is not None)): self.residualaxis.set_xlim(self.Spectrum.plotter.xmin.value, self.Spectrum.plotter.xmax.value) if ((self.Spectrum.plotter.ymin is not None) and (self.Spectrum.plotter.ymax is not None)): self.residualaxis.set_ylim(self.Spectrum.plotter.ymin, self.Spectrum.plotter.ymax) if label: self.residualaxis.set_xlabel(self.Spectrum.plotter.xlabel) self.residualaxis.set_ylabel(self.Spectrum.plotter.ylabel) self.residualaxis.set_title("Residuals") if self.Spectrum.plotter.autorefresh: self.residualaxis.figure.canvas.draw()
[docs] def annotate(self,loc='upper right',labelspacing=0.25, markerscale=0.01, borderpad=0.1, handlelength=0.1, handletextpad=0.1, fontsize=10, frameon=False, chi2=None, optimal_chi2_kwargs={}, **kwargs): """ Add a legend to the plot showing the fitted parameters _clearlegend() will remove the legend chi2 : {True or 'reduced' or 'optimal' or 'allthree'} kwargs passed to legend """ self._clearlegend() pl = matplotlib.collections.CircleCollection([0],edgecolors=['k']) if hasattr(self.fitter,'annotations'): self._annotation_labels = self.fitter.annotations() else: raise Exception("Fitter %s has no annotations." % self.fitter) #xtypename = units.unit_type_dict[self.Spectrum.xarr.xtype] xcharconv = units.SmartCaseNoSpaceDict({u.Hz.physical_type:'\\nu', u.m.physical_type:'\\lambda', (u.km/u.s).physical_type:'v', 'pixels':'x', u.dimensionless_unscaled:'x', 'dimensionless':'x', }) try: xchar = xcharconv[self.Spectrum.xarr.unit.physical_type] except AttributeError: unit_key = self.Spectrum.xarr.unit xchar = xcharconv[u.Unit(unit_key).physical_type] self._annotation_labels = [L.replace('x',xchar) if L[1]=='x' else L for L in self._annotation_labels] if chi2 is not None: chi2n_label = '$\\chi^2/\\nu = %0.2g$' % (self.chi2/self.dof) chi2opt_label = '$\\chi^2_o/\\nu = %0.2g$' % self.optimal_chi2(**optimal_chi2_kwargs) chi2_label = '$\\chi^2 = %0.2g$' % self.chi2 if chi2 == 'allthree': self._annotation_labels.append("\n".join([chi2n_label, chi2_label, chi2opt_label])) elif chi2 == 'reduced': self._annotation_labels.append(chi2n_label) elif chi2 == 'optimal': self._annotation_labels.append(chi2opt_label) else: self._annotation_labels.append(chi2_label) if self.Spectrum.plotter.axis: try: self.fitleg = self.Spectrum.plotter.axis.legend( tuple([pl]*len(self._annotation_labels)), self._annotation_labels, loc=loc, markerscale=markerscale, borderpad=borderpad, handlelength=handlelength, handletextpad=handletextpad, labelspacing=labelspacing, frameon=frameon, fontsize=fontsize, **kwargs) self.Spectrum.plotter.axis.add_artist(self.fitleg) except TypeError as ex: print("Error {0} was raised, which may indicate an outdated mpl version".format(ex)) try: self.fitleg.set_draggable(True) except AttributeError: # wrong version and/or non-interactive backend pass if self.Spectrum.plotter.autorefresh: self.Spectrum.plotter.refresh()
[docs] def print_fit(self, print_baseline=True, **kwargs): """ Print the best-fit parameters to the command line """ if self.Spectrum.baseline.baselinepars is not None and print_baseline: print("Baseline: " + " + ".join(["%12g x^%i" % (x,i) for i,x in enumerate(self.Spectrum.baseline.baselinepars[::-1])])) for i,p in enumerate(self.parinfo): print("%15s: %12g +/- %12g" % (p['parname'],p['value'],p['error']))
[docs] def clear(self, legend=True, components=True): """ Remove the fitted model from the plot Also removes the legend by default """ if self.Spectrum.plotter.axis is not None: for p in self.modelplot: p.set_visible(False) if legend: self._clearlegend() if components: self._clearcomponents() if self.Spectrum.plotter.autorefresh: self.Spectrum.plotter.refresh() # Empty the modelplot array to free memory self.modelplot = [] # remove residuals from self if they're there. if hasattr(self,'residualplot'): for L in self.residualplot: if L in self.Spectrum.plotter.axis.lines: self.Spectrum.plotter.axis.lines.remove(L)
def _clearcomponents(self): for pc in self._plotted_components: pc.set_visible(False) if pc in self.Spectrum.plotter.axis.lines: self.Spectrum.plotter.axis.lines.remove(pc) if self.Spectrum.plotter.autorefresh: self.Spectrum.plotter.refresh() # Empty the plotted components array to free memory self._plotted_components = [] def _clearlegend(self): """ Remove the legend from the plot window """ axis = self.Spectrum.plotter.axis if axis and axis.legend_ == self.fitleg: axis.legend_ = None if axis and self.fitleg is not None: # don't remove fitleg unless it's in the current axis # self.fitleg.set_visible(False) if self.fitleg in axis.artists: axis.artists.remove(self.fitleg) if self.Spectrum.plotter.autorefresh: self.Spectrum.plotter.refresh()
[docs] def savefit(self): """ Save the fit parameters from a Gaussian fit to the FITS header .. todo:: THESE SHOULD BE WRITTEN FOR EACH TYPE OF MODEL TO BE FIT """ if self.modelpars is not None and hasattr(self.Spectrum,'header'): for ii,p in enumerate(self.modelpars): try: if ii % 3 == 0: self.Spectrum.header['AMP%1i' % (ii/3)] = (p,"Gaussian best fit amplitude #%i" % (ii/3)) elif ii % 3 == 1: self.Spectrum.header['CEN%1i' % (ii/3)] = (p,"Gaussian best fit center #%i" % (ii/3)) elif ii % 3 == 2: self.Spectrum.header['WID%1i' % (ii/3)] = (p,"Gaussian best fit width #%i" % (ii/3)) except ValueError as ex: log.info("Failed to save fit to header: {0}".format(ex))
[docs] def downsample(self,factor): """ Downsample the model spectrum (and the spectofit spectra) This should only be done when Spectrum.smooth is called """ if self.model is not None: self.model = self.model[::factor] if self.residuals is not None: self.residuals = self.residuals[::factor] self.spectofit = self.spectofit[::factor] self.errspec = self.errspec[::factor] self.includemask = self.includemask[::factor]
[docs] def crop(self,x1pix,x2pix): """ When spectrum.crop is called, this must be too """ if self.model is not None: self.model = self.model[x1pix:x2pix] if hasattr(self,'fullmodel'): self.fullmodel = self.fullmodel[x1pix:x2pix] self.includemask = self.includemask[x1pix:x2pix] self.setfitspec()
[docs] def integral(self, analytic=False, direct=False, threshold='auto', integration_limits=None, integration_limit_units='pixels', return_error=False, **kwargs): """ Return the integral of the fitted spectrum Parameters ---------- analytic : bool Return the analytic integral of the fitted function? .. WARNING:: This approach is only implemented for some models .. todo:: Implement error propagation for this approach direct : bool Return the integral of the *spectrum* (as opposed to the *fit*) over a range defined by the `integration_limits` if specified or `threshold` otherwise threshold : 'auto' or 'error' or float Determines what data to be included in the integral based off of where the model is greater than this number If 'auto', the threshold will be set to peak_fraction * the peak model value. If 'error', uses the error spectrum as the threshold See `self.get_model_xlimits` for details integration_limits : None or 2-tuple Manually specify the limits in `integration_limit_units` units return_error : bool Return the error on the integral if set. The error computed by sigma = sqrt(sum(sigma_i^2)) * dx kwargs : passed to `self.fitter.integral` if ``not(direct)`` Returns ------- np.scalar or np.ndarray with the integral or integral & error """ if analytic: return self.fitter.analytic_integral(modelpars=self.parinfo.values) xmin,xmax = self.get_model_xlimits(units='pixels', threshold=threshold) if integration_limits is None: integration_limits = [xmin,xmax] integration_limits = [ self.Spectrum.xarr.x_to_pix(x,xval_units=integration_limit_units) for x in integration_limits] if xmax - xmin > 1: # can only get cdelt if there's more than 1 pixel dx = self.Spectrum.xarr[xmin:xmax].cdelt().value else: dx = None if dx is None: #dx = np.abs(np.concatenate([np.diff(self.Spectrum.xarr),[0]])) #warn("Irregular X-axis. The last pixel is ignored.") self.Spectrum.xarr.make_dxarr() dx = self.Spectrum.xarr.dxarr.value else: # shouldn't shape be a 'property'? dx = np.repeat(np.abs(dx), self.Spectrum.shape) if direct: integrand = self.Spectrum.data[xmin:xmax] if not self.Spectrum.baseline.subtracted: integrand -= self.Spectrum.baseline.basespec[xmin:xmax] integ = (integrand * dx[xmin:xmax]).sum() if return_error: # compute error assuming a "known mean" (not a sample mean). If sample mean, multiply # by sqrt(len(dx)/(len(dx)-1)) (which should be very near 1) error = np.sqrt((dx[xmin:xmax] * self.Spectrum.error[xmin:xmax]**2).sum() / dx[xmin:xmax].sum()) return np.array([integ,error]) else: return integ #OK = np.abs( fullmodel ) > threshold #integ = (self.spectofit[OK] * dx[OK]).sum() #error = np.sqrt((self.errspec[OK]**2 * dx[OK]).sum()/dx[OK].sum()) else: if not hasattr(self.fitter,'integral'): raise AttributeError("The fitter %s does not have an integral implemented" % self.fittype) # the model considered here must NOT include the baseline! # if it does, you'll get the integral of the continuum #fullmodel = self.get_full_model(add_baseline=False) if self.Spectrum.xarr.cdelt() is not None: dx = np.median(dx) integ = self.fitter.integral(self.modelpars, dx=dx, **kwargs) if return_error: if mycfg.WARN: warn("WARNING: The computation of the error " "on the integral is not obviously " "correct or robust... it's just a guess.") OK = self.model_mask(threshold=threshold, add_baseline=False) error = np.sqrt((self.errspec[OK]**2).sum()) * dx #raise NotImplementedError("We haven't written up correct error estimation for integrals of fits") else: integ = 0 error = 0 warn("An analytic integal could not be computed because the X-axis is irregular. Try direct=True when integrating, or find a way to linearize the X-axis") if return_error: return integ,error else: return integ
[docs] def model_mask(self, **kwargs): """ Get a mask (boolean array) of the region where the fitted model is significant Parameters ---------- threshold : 'auto' or 'error' or float The threshold to compare the model values to for selecting the mask region. * auto: uses `peak_fraction` times the model peak * error: use the spectrum error * float: any floating point number as an absolute threshold peak_fraction : float Parameter used if ``threshold=='auto'`` to determine fraction of model peak to set threshold at add_baseline : bool Add the fitted baseline to the model before comparing to threshold? Returns ------- mask : `~numpy.ndarray` A boolean mask array with the same size as the spectrum, set to ``True`` where the fitted model has values above a specified threshold """ return self._compare_to_threshold(**kwargs)
def _compare_to_threshold(self, threshold='auto', peak_fraction=0.01, add_baseline=False): """ Identify pixels that are above some threshold """ model = self.get_full_model(add_baseline=add_baseline) # auto-set threshold from some fraction of the model peak if threshold=='auto': threshold = peak_fraction * np.abs(model).max() elif threshold=='error': threshold = self.errspec OK = np.abs(model) > threshold return OK
[docs] def get_model_xlimits(self, threshold='auto', peak_fraction=0.01, add_baseline=False, unit='pixels', units=None): """ Return the x positions of the first and last points at which the model is above some threshold Parameters ---------- threshold : 'auto' or 'error' or float If 'auto', the threshold will be set to peak_fraction * the peak model value. If 'error', uses the error spectrum as the threshold peak_fraction : float ignored unless threshold == 'auto' add_baseline : bool Include the baseline when computing whether the model is above the threshold? default FALSE. Passed to get_full_model. units : str A valid unit type, e.g. 'pixels' or 'angstroms' """ OK = self._compare_to_threshold(threshold=threshold, peak_fraction=peak_fraction, add_baseline=add_baseline) # find the first & last "True" values xpixmin = OK.argmax() xpixmax = len(OK) - OK[::-1].argmax() - 1 if units is not None and unit =='pixels': # todo: deprecate unit = units if unit == 'pixels': return [xpixmin,xpixmax] else: return self.Spectrum.xarr[[xpixmin,xpixmax]].as_unit(units)
[docs] def shift_pars(self, frame=None): """ Shift the velocity / wavelength / frequency of the fitted parameters into a different frame Right now this only takes care of redshift and only if redshift is defined. It should be extended to do other things later """ for ii,pi in enumerate(self.parinfo): for partype in ('shift','offset','velo'): if partype in str.lower(pi['parname']): if frame is not None: self.modelpars[ii] = self.Spectrum.xarr.x_in_frame(self.modelpars[ii], frame)
[docs] def moments(self, fittype=None, **kwargs): """ Return the moments see the :mod:`~pyspeckit.spectrum.moments` module Parameters ---------- fittype : None or str The registered fit type to use for moment computation """ if fittype is None: fittype = self.fittype return list(self.Registry.multifitters[fittype].moments( self.Spectrum.xarr[self.xmin:self.xmax], self.spectofit[self.xmin:self.xmax], **kwargs))
[docs] def button3action(self, event, debug=False, nwidths=1): """ Disconnect the interactiveness Perform the fit (or die trying) Hide the guesses """ if self.nclicks_b1 == 0: # there has been no selection # therefore, we assume *everything* is selected self.includemask[:] = True self.Spectrum.plotter.figure.canvas.mpl_disconnect(self.click) self.Spectrum.plotter.figure.canvas.mpl_disconnect(self.keyclick) if self.npeaks > 0: if hasattr(self, 'fitter'): self.guesses = self.fitter.parse_3par_guesses(self.guesses) else: # default fitter is a Gaussian, which has 3 parameters if len(self.guesses) % 3 != 0: log.error("Default fitter is Gaussian, and there were " "{0} guess parameters, which is not a " "multiple of 3.".format(len(self.guesses))) log.info("{0} Guesses : {1} X channel range: {2}-{3}" .format(len(self.guesses), self.guesses, self.xmin, self.xmax)) self.multifit(use_window_limits=True) for p in self.button2plot + self.button1plot: p.set_visible(False) # disconnect interactive window (and more importantly, reconnect to # original interactive cmds) self.clear_all_connections()
[docs] def copy(self, parent=None, registry=None): """ Create a copy of the spectral fit - includes copies of the _full_model, the registry, the fitter, parinfo, modelpars, modelerrs, model, npeaks Parameters ---------- parent : `pyspeckit.classes.Spectrum` A `~Spectrum` instance that is the parent of the specfit instance. This needs to be specified at some point, but defaults to None to prevent overwriting a previous plot. """ if registry is None: if hasattr(parent, 'Registry'): registry = parent.Registry else: # only make a copy if we're not already given a specific registry # to inherit copy.deepcopy(self.Registry) newspecfit = Specfit(parent, Registry=registry) newspecfit.parinfo = copy.deepcopy(self.parinfo) if newspecfit.parinfo is None: newspecfit.modelpars = None newspecfit.modelerrs = None else: newspecfit.modelpars = newspecfit.parinfo.values newspecfit.modelerrs = newspecfit.parinfo.errors newspecfit.includemask = self.includemask.copy() newspecfit.model = copy.copy(self.model) newspecfit.npeaks = self.npeaks if hasattr(self,'fitter'): newspecfit.fitter = copy.deepcopy(self.fitter) newspecfit.fitter.parinfo = newspecfit.parinfo if hasattr(self,'fullmodel'): newspecfit._full_model() # this is ridiculous, absurd, and infuriating... newspecfit.button2action = newspecfit.guesspeakwidth if parent is not None: newspecfit.Spectrum.plotter = parent.plotter else: newspecfit.Spectrum.plotter = None return newspecfit
def __copy__(self): return self.copy(parent=self.Spectrum)
[docs] def add_sliders(self, parlimitdict=None, **kwargs): """ Add a Sliders window in a new figure appropriately titled Parameters ---------- parlimitdict: dict Each parameter needs to have displayed limits; these are set in min-max pairs. If this is left empty, the widget will try to guess at reasonable limits, but the guessing is not very sophisticated yet. .. todo:: Add a button in the navbar that makes this window pop up http://stackoverflow.com/questions/4740988/add-new-navigate-modes-in-matplotlib """ if parlimitdict is None: # try to create a reasonable parlimit dict parlimitdict = {} for param in self.parinfo: if not param.parname in parlimitdict: if any( (x in param['parname'].lower() for x in ('shift','xoff')) ): lower, upper = (self.Spectrum.xarr[self.includemask].min().value, self.Spectrum.xarr[self.includemask].max().value) elif any( (x in param['parname'].lower() for x in ('width','fwhm')) ): xvalrange = (self.Spectrum.xarr[self.includemask].max().value - self.Spectrum.xarr[self.includemask].min().value) lower,upper = (0,xvalrange) elif any( (x in param['parname'].lower() for x in ('amp','peak','height')) ): datarange = self.spectofit.max() - self.spectofit.min() lower,upper = (param['value']-datarange, param['value']+datarange) else: lower = param['value'] * 0.1 upper = param['value'] * 10 # override guesses with limits if param.limited[0]: # nextafter -> next representable float lower = np.nextafter(param.limits[0], param.limits[0]+1) if param.limited[1]: upper = np.nextafter(param.limits[1], param.limits[1]-1) parlimitdict[param.parname] = (lower,upper) if hasattr(self,'fitter'): self.SliderWidget = widgets.FitterSliders(self, self.Spectrum.plotter.figure, npars=self.fitter.npars, parlimitdict=parlimitdict, **kwargs) else: log.error("Must have a fitter instantiated before creating sliders")
[docs] def optimal_chi2(self, reduced=True, threshold='error', **kwargs): """ Compute an "optimal" :math:`\\chi^2` statistic, i.e. one in which only pixels in which the model is statistically significant are included Parameters ---------- reduced : bool Return the reduced :math:`\\chi^2` threshold : 'auto' or 'error' or float If 'auto', the threshold will be set to peak_fraction * the peak model value, where peak_fraction is a kwarg passed to get_model_xlimits reflecting the fraction of the model peak to consider significant If 'error', uses the error spectrum as the threshold kwargs : dict passed to :meth:`get_model_xlimits` Returns ------- chi2 : float :math:`\\chi^2` statistic or reduced :math:`\\chi^2` statistic (:math:`\\chi^2/n`) .. math:: \\chi^2 = \\sum( (d_i - m_i)^2 / e_i^2 ) """ modelmask = self._compare_to_threshold(threshold=threshold, **kwargs) chi2 = np.sum((self.fullresiduals[modelmask]/self.errspec[modelmask])**2) if reduced: # vheight included here or not? assuming it should be... return chi2/self.dof else: return chi2
[docs] def get_pymc(self, **kwargs): """ Create a pymc MCMC sampler from the current fitter. Defaults to 'uninformative' priors `kwargs` are passed to the fitter's get_pymc method, with parameters defined below. Parameters ---------- data : np.ndarray error : np.ndarray use_fitted_values : bool Each parameter with a measured error will have a prior defined by the Normal distribution with sigma = par.error and mean = par.value Examples -------- >>> x = pyspeckit.units.SpectroscopicAxis(np.linspace(-10,10,50), unit='km/s') >>> e = np.random.randn(50) >>> d = np.exp(-np.asarray(x)**2/2.)*5 + e >>> sp = pyspeckit.Spectrum(data=d, xarr=x, error=np.ones(50)*e.std()) >>> sp.specfit(fittype='gaussian') >>> MCuninformed = sp.specfit.get_pymc() >>> MCwithpriors = sp.specfit.get_pymc(use_fitted_values=True) >>> MCuninformed.sample(1000) >>> MCuninformed.stats()['AMPLITUDE0'] >>> # WARNING: This will fail because width cannot be set <0, but it may randomly reach that... >>> # How do you define a likelihood distribution with a lower limit?! >>> MCwithpriors.sample(1000) >>> MCwithpriors.stats()['AMPLITUDE0'] """ if hasattr(self.fitter,'get_pymc'): return self.fitter.get_pymc(self.Spectrum.xarr, self.spectofit, self.errspec, **kwargs) else: raise AttributeError("Fitter %r does not have pymc implemented." % self.fitter)
[docs] def get_emcee(self, nwalkers=None, **kwargs): """ Get an emcee walker ensemble for the data & model using the current model type Parameters ---------- data : np.ndarray error : np.ndarray nwalkers : int Number of walkers to use. Defaults to 2 * self.fitters.npars Examples -------- >>> import pyspeckit >>> x = pyspeckit.units.SpectroscopicAxis(np.linspace(-10,10,50), unit='km/s') >>> e = np.random.randn(50) >>> d = np.exp(-np.asarray(x)**2/2.)*5 + e >>> sp = pyspeckit.Spectrum(data=d, xarr=x, error=np.ones(50)*e.std()) >>> sp.specfit(fittype='gaussian') >>> emcee_ensemble = sp.specfit.get_emcee() >>> p0 = emcee_ensemble.p0 * (np.random.randn(*emcee_ensemble.p0.shape) / 10. + 1.0) >>> pos,logprob,state = emcee_ensemble.run_mcmc(p0,100) """ import emcee if hasattr(self.fitter,'get_emcee_ensemblesampler'): nwalkers = (self.fitter.npars * self.fitter.npeaks + self.fitter.vheight) * 2 emc = self.fitter.get_emcee_ensemblesampler(self.Spectrum.xarr, self.spectofit, self.errspec, nwalkers) emc.nwalkers = nwalkers emc.p0 = np.array([self.parinfo.values] * emc.nwalkers) return emc
[docs] def get_components(self, **kwargs): """ If a model has been fitted, return the components of the model Parameters ---------- kwargs are passed to self.fitter.components """ if self.modelpars is not None: self.modelcomponents = self.fitter.components(self.Spectrum.xarr, self.modelpars, **kwargs) return self.modelcomponents
[docs] def measure_approximate_fwhm(self, threshold='error', emission=True, interpolate_factor=1, plot=False, grow_threshold=2, **kwargs): """ Measure the FWHM of a fitted line This procedure is designed for multi-component *blended* lines; if the true FWHM is known (i.e., the line is well-represented by a single gauss/voigt/lorentz profile), use that instead. Do not use this for multiple independently peaked profiles. This MUST be run AFTER a fit has been performed! Parameters ---------- threshold : 'error' | float The threshold above which the spectrum will be interpreted as part of the line. This threshold is applied to the *model*. If it is 'noise', self.error will be used. emission : bool Is the line absorption or emission? interpolate_factor : integer Magnification factor for determining sub-pixel FWHM. If used, "zooms-in" by using linear interpolation within the line region plot : bool Overplot a line at the FWHM indicating the FWHM. kwargs are passed to matplotlib.plot grow_threshold : int Minimum number of valid points. If the total # of points above the threshold is <= to this number, it will be grown by 1 pixel on each side Returns ------- The approximated FWHM, if it can be computed If there are <= 2 valid pixels, a fwhm cannot be computed """ if threshold == 'error': threshold = self.Spectrum.error if np.all(self.Spectrum.error==0): threshold = 1e-3*self.Spectrum.data.max() if self.Spectrum.baseline.subtracted is False: data = self.Spectrum.data - self.Spectrum.baseline.basespec else: data = self.Spectrum.data * 1 model = self.get_full_model(add_baseline=False) if np.count_nonzero(model) == 0: raise ValueError("The model is all zeros. No FWHM can be " "computed.") # can modify inplace because data is a copy of self.Spectrum.data if not emission: data *= -1 model *= -1 line_region = model > threshold if line_region.sum() == 0: raise ValueError("No valid data included in FWHM computation") if line_region.sum() <= grow_threshold: line_region[line_region.argmax()-1:line_region.argmax()+1] = True reverse_argmax = len(line_region) - line_region.argmax() - 1 line_region[reverse_argmax-1:reverse_argmax+1] = True log.warning("Fewer than {0} pixels were identified as part of the fit." " To enable statistical measurements, the range has been" " expanded by 2 pixels including some regions below the" " threshold.".format(grow_threshold)) # determine peak (because data is neg if absorption, always use max) peak = data[line_region].max() xarr = self.Spectrum.xarr[line_region] xarr.make_dxarr() cd = xarr.dxarr.min() if interpolate_factor > 1: newxarr = units.SpectroscopicAxis(np.arange(xarr.min().value-cd.value, xarr.max().value+cd.value, cd.value / float(interpolate_factor) ), unit=xarr.unit, equivalencies=xarr.equivalencies ) # load the metadata from xarr # newxarr._update_from(xarr) data = np.interp(newxarr,xarr,data[line_region]) xarr = newxarr else: data = data[line_region] # need the peak location so we can find left/right half-max locations peakloc = data.argmax() hm_left = np.argmin(np.abs(data[:peakloc]-peak/2.)) hm_right = np.argmin(np.abs(data[peakloc:]-peak/2.)) + peakloc deltax = xarr[hm_right]-xarr[hm_left] if plot: # for plotting, use a negative if absorption sign = 1 if emission else -1 # shift with baseline if baseline is plotted if not self.Spectrum.baseline.subtracted: basespec = self.Spectrum.baseline.get_model(xarr) yoffleft = self.Spectrum.plotter.offset + basespec[hm_left] yoffright = self.Spectrum.plotter.offset + basespec[hm_right] else: yoffleft = yoffright = self.Spectrum.plotter.offset log.debug("peak={2} yoffleft={0} yoffright={1}".format(yoffleft, yoffright, peak)) log.debug("hm_left={0} hm_right={1} xarr[hm_left]={2} xarr[hm_right]={3}".format(hm_left, hm_right, xarr[hm_left], xarr[hm_right])) self.Spectrum.plotter.axis.plot([xarr[hm_right].value, xarr[hm_left].value], np.array([sign*peak/2.+yoffleft, sign*peak/2.+yoffright]), **kwargs) self.Spectrum.plotter.refresh() # debug print hm_left,hm_right,"FWHM: ",deltax # debug self.Spectrum.plotter.axis.plot(xarr,data,color='magenta') # debug self.Spectrum.plotter.refresh() # debug raise TheDead return deltax
def _validate_parinfo(self, parinfo, mode='fix'): assert mode in ('fix','raise','check','guesses') any_out_of_range = [] for param in parinfo: if (param.limited[0] and (param.value < param.limits[0])): if (np.allclose(param.value, param.limits[0])): # nextafter -> next representable float if mode in ('fix', 'guesses'): warn("{0} is less than the lower limit {1}, but very close." " Converting to {1}+ULP".format(param.value, param.limits[0])) param.value = np.nextafter(param.limits[0], param.limits[0]+1) elif mode == 'raise': raise ValueError("{0} is less than the lower limit {1}, but very close." .format(param.value, param.limits[1])) elif mode == 'check': any_out_of_range.append("lt:close",) else: raise ValueError("{0} is less than the lower limit {1}" .format(param.value, param.limits[0])) elif mode == 'check': any_out_of_range.append(False) if (param.limited[1] and (param.value > param.limits[1])): if (np.allclose(param.value, param.limits[1])): if mode in ('fix', 'guesses'): param.value = np.nextafter(param.limits[1], param.limits[1]-1) warn("{0} is greater than the upper limit {1}, but very close." " Converting to {1}-ULP".format(param.value, param.limits[1])) elif mode == 'raise': raise ValueError("{0} is greater than the upper limit {1}, but very close." .format(param.value, param.limits[1])) elif mode == 'check': any_out_of_range.append("gt:close") else: raise ValueError("{0} is greater than the upper limit {1}" .format(param.value, param.limits[1])) elif mode == 'check': any_out_of_range.append(False) if mode == 'guesses': return parinfo.values return any_out_of_range