latools/latools.py
def despike(self, expdecay_despiker=False, exponent=None,
                noise_despiker=True, win=3, nlim=12., exponentplot=False,
                maxiter=4, autorange_kwargs={}, focus_stage='rawdata'):
        """
        Despikes data with exponential decay and noise filters.

        Parameters
        ----------
        expdecay_despiker : bool
            Whether or not to apply the exponential decay filter.
        exponent : None or float
            The exponent for the exponential decay filter. If None,
            it is determined automatically using `find_expocoef`.
        tstep : None or float
            The timeinterval between measurements. If None, it is
            determined automatically from the Time variable.
        noise_despiker : bool
            Whether or not to apply the standard deviation spike filter.
        win : int
            The rolling window over which the spike filter calculates
            the trace statistics.
        nlim : float
            The number of standard deviations above the rolling mean
            that data are excluded.
        exponentplot : bool
            Whether or not to show a plot of the automatically determined
            exponential decay exponent.
        maxiter : int
            The max number of times that the fitler is applied.
        focus_stage : str
            Which stage of analysis to apply processing to. 
            Defaults to 'rawdata'. Can be one of:
            * 'rawdata': raw data, loaded from csv file.
            * 'despiked': despiked data.
            * 'signal'/'background': isolated signal and background data.
              Created by self.separate, after signal and background
              regions have been identified by self.autorange.
            * 'bkgsub': background subtracted data, created by 
              self.bkg_correct
            * 'ratios': element ratio data, created by self.ratio.
            * 'calibrated': ratio data calibrated to standards, created by self.calibrate.

        Returns
        -------
        None
        """
        if focus_stage != self.focus_stage:
            self.set_focus(focus_stage)

        if expdecay_despiker and exponent is None:
            if not hasattr(self, 'expdecay_coef'):
                self.find_expcoef(plot=exponentplot,
                                  autorange_kwargs=autorange_kwargs)
            exponent = self.expdecay_coef
            time.sleep(0.1)

        with self.pbar.set(total=len(self.data), desc='Despiking') as prog:
            for d in self.data.values():
                d.despike(expdecay_despiker, exponent,
                        noise_despiker, win, nlim, maxiter)
                prog.update()

        self.stages_complete.update(['despiked'])
        self.focus_stage = 'despiked'
        return
def despike(self, expdecay_despiker=False, exponent=None,
                noise_despiker=True, win=3, nlim=12., exponentplot=False,
                maxiter=4, autorange_kwargs={}, focus_stage='rawdata'):
        """
        Despikes data with exponential decay and noise filters.

        Parameters
        ----------
        expdecay_despiker : bool
            Whether or not to apply the exponential decay filter.
        exponent : None or float
            The exponent for the exponential decay filter. If None,
            it is determined automatically using `find_expocoef`.
        tstep : None or float
            The timeinterval between measurements. If None, it is
            determined automatically from the Time variable.
        noise_despiker : bool
            Whether or not to apply the standard deviation spike filter.
        win : int
            The rolling window over which the spike filter calculates
            the trace statistics.
        nlim : float
            The number of standard deviations above the rolling mean
            that data are excluded.
        exponentplot : bool
            Whether or not to show a plot of the automatically determined
            exponential decay exponent.
        maxiter : int
            The max number of times that the fitler is applied.
        focus_stage : str
            Which stage of analysis to apply processing to. 
            Defaults to 'rawdata'. Can be one of:
            * 'rawdata': raw data, loaded from csv file.
            * 'despiked': despiked data.
            * 'signal'/'background': isolated signal and background data.
              Created by self.separate, after signal and background
              regions have been identified by self.autorange.
            * 'bkgsub': background subtracted data, created by 
              self.bkg_correct
            * 'ratios': element ratio data, created by self.ratio.
            * 'calibrated': ratio data calibrated to standards, created by self.calibrate.

        Returns
        -------
        None
        """
        if focus_stage != self.focus_stage:
            self.set_focus(focus_stage)

        if expdecay_despiker and exponent is None:
            if not hasattr(self, 'expdecay_coef'):
                self.find_expcoef(plot=exponentplot,
                                  autorange_kwargs=autorange_kwargs)
            exponent = self.expdecay_coef
            time.sleep(0.1)

        with self.pbar.set(total=len(self.data), desc='Despiking') as prog:
            for d in self.data.values():
                d.despike(expdecay_despiker, exponent,
                        noise_despiker, win, nlim, maxiter)
                prog.update()

        self.stages_complete.update(['despiked'])
        self.focus_stage = 'despiked'
        return
Despikes data with exponential decay and noise filters.

        Parameters
        ----------
        expdecay_despiker : bool
            Whether or not to apply the exponential decay filter.
        exponent : None or float
            The exponent for the exponential decay filter. If None,
            it is determined automatically using `find_expocoef`.
        tstep : None or float
            The timeinterval between measurements. If None, it is
            determined automatically from the Time variable.
        noise_despiker : bool
            Whether or not to apply the standard deviation spike filter.
        win : int
            The rolling window over which the spike filter calculates
            the trace statistics.
        nlim : float
            The number of standard deviations above the rolling mean
            that data are excluded.
        exponentplot : bool
            Whether or not to show a plot of the automatically determined
            exponential decay exponent.
        maxiter : int
            The max number of times that the fitler is applied.
        focus_stage : str
            Which stage of analysis to apply processing to. 
            Defaults to 'rawdata'. Can be one of:
            * 'rawdata': raw data, loaded from csv file.
            * 'despiked': despiked data.
            * 'signal'/'background': isolated signal and background data.
              Created by self.separate, after signal and background
              regions have been identified by self.autorange.
            * 'bkgsub': background subtracted data, created by 
              self.bkg_correct
            * 'ratios': element ratio data, created by self.ratio.
            * 'calibrated': ratio data calibrated to standards, created by self.calibrate.

        Returns
        -------
        None