rapidtide 3.0.7.1__py3-none-any.whl → 3.0.8__py3-none-any.whl

rapidtide/helper_classes.py

@@ -140,342 +140,6 @@ class ProbeRegressor:
         )
 
 
-class SimilarityFunctionator:
-    reftc = None
-    prepreftc = None
-    testtc = None
-    preptesttc = None
-    timeaxis = None
-    similarityfunclen = 0
-    datavalid = False
-    timeaxisvalid = False
-    similarityfuncorigin = 0
-
-    def __init__(
-        self,
-        Fs=0.0,
-        similarityfuncorigin=0,
-        lagmininpts=0,
-        lagmaxinpts=0,
-        ncprefilter=None,
-        negativegradient=False,
-        reftc=None,
-        reftcstart=0.0,
-        detrendorder=1,
-        filterinputdata=True,
-        debug=False,
-    ):
-        self.setFs(Fs)
-        self.similarityfuncorigin = similarityfuncorigin
-        self.lagmininpts = lagmininpts
-        self.lagmaxinpts = lagmaxinpts
-        self.ncprefilter = ncprefilter
-        self.negativegradient = negativegradient
-        self.reftc = reftc
-        self.detrendorder = detrendorder
-        self.filterinputdata = filterinputdata
-        self.debug = debug
-        if self.reftc is not None:
-            self.setreftc(self.reftc)
-            self.reftcstart = reftcstart
-
-    def setFs(self, Fs):
-        self.Fs = Fs
-
-    def preptc(self, thetc, isreftc=False):
-        # prepare timecourse by filtering, normalizing, detrending, and applying a window function
-        if isreftc:
-            thenormtc = tide_math.corrnormalize(
-                self.ncprefilter.apply(self.Fs, thetc),
-                detrendorder=self.detrendorder,
-                windowfunc=self.windowfunc,
-            )
-        else:
-            if self.negativegradient:
-                thenormtc = tide_math.corrnormalize(
-                    -np.gradient(self.ncprefilter.apply(self.Fs, thetc)),
-                    detrendorder=self.detrendorder,
-                    windowfunc=self.windowfunc,
-                )
-            else:
-                if self.filterinputdata:
-                    thenormtc = tide_math.corrnormalize(
-                        self.ncprefilter.apply(self.Fs, thetc),
-                        detrendorder=self.detrendorder,
-                        windowfunc=self.windowfunc,
-                    )
-                else:
-                    thenormtc = tide_math.corrnormalize(
-                        thetc,
-                        detrendorder=self.detrendorder,
-                        windowfunc=self.windowfunc,
-                    )
-
-        return thenormtc
-
-    def trim(self, vector):
-        return vector[
-            self.similarityfuncorigin
-            - self.lagmininpts : self.similarityfuncorigin
-            + self.lagmaxinpts
-        ]
-
-    def getfunction(self, trim=True):
-        if self.datavalid:
-            if trim:
-                return (
-                    self.trim(self.thesimfunc),
-                    self.trim(self.timeaxis),
-                    self.theglobalmax,
-                )
-            else:
-                return self.thesimfunc, self.timeaxis, self.theglobalmax
-        else:
-            if self.timeaxisvalid:
-                if trim:
-                    return None, self.trim(self.timeaxis), None
-                else:
-                    return None, self.timeaxis, None
-            else:
-                print("must calculate similarity function before fetching data")
-                return None, None, None
-
-
-class MutualInformationator(SimilarityFunctionator):
-    def __init__(
-        self,
-        windowfunc="hamming",
-        norm=True,
-        madnorm=False,
-        smoothingtime=-1.0,
-        bins=20,
-        sigma=0.25,
-        *args,
-        **kwargs,
-    ):
-        self.windowfunc = windowfunc
-        self.norm = norm
-        self.madnorm = madnorm
-        self.bins = bins
-        self.sigma = sigma
-        self.smoothingtime = smoothingtime
-        self.smoothingfilter = tide_filt.NoncausalFilter(filtertype="arb")
-        self.mi_norm = 1.0
-        if self.smoothingtime > 0.0:
-            self.smoothingfilter.setfreqs(
-                0.0, 0.0, 1.0 / self.smoothingtime, 1.0 / self.smoothingtime
-            )
-        super(MutualInformationator, self).__init__(*args, **kwargs)
-
-    def setlimits(self, lagmininpts, lagmaxinpts):
-        self.lagmininpts = lagmininpts
-        self.lagmaxinpts = lagmaxinpts
-        origpadtime = self.smoothingfilter.getpadtime()
-        timespan = self.timeaxis[-1] - self.timeaxis[0]
-        newpadtime = np.min([origpadtime, timespan])
-        if newpadtime < origpadtime:
-            print("lowering smoothing filter pad time to", newpadtime)
-            self.smoothingfilter.setpadtime(newpadtime)
-
-    def setbins(self, bins):
-        self.bins = bins
-
-    def setreftc(self, reftc, offset=0.0):
-        self.reftc = reftc + 0.0
-        self.prepreftc = self.preptc(self.reftc, isreftc=True)
-
-        self.timeaxis, self.automi, self.similarityfuncorigin = tide_corr.cross_mutual_info(
-            self.prepreftc,
-            self.prepreftc,
-            Fs=self.Fs,
-            fast=True,
-            negsteps=self.lagmininpts,
-            possteps=self.lagmaxinpts,
-            returnaxis=True,
-        )
-
-        self.timeaxis -= offset
-        self.similarityfunclen = len(self.timeaxis)
-        self.timeaxisvalid = True
-        self.datavalid = False
-        self.mi_norm = np.nan_to_num(1.0 / np.max(self.automi))
-        if self.debug:
-            print(f"MutualInformationator setreftc: {len(self.timeaxis)=}")
-            print(f"MutualInformationator setreftc: {self.timeaxis}")
-            print(f"MutualInformationator setreftc: {self.mi_norm=}")
-
-    def getnormfac(self):
-        return self.mi_norm
-
-    def run(self, thetc, locs=None, trim=True, gettimeaxis=True):
-        if len(thetc) != len(self.reftc):
-            print(
-                "MutualInformationator: timecourses are of different sizes:",
-                len(thetc),
-                "!=",
-                len(self.reftc),
-                "- exiting",
-            )
-            sys.exit()
-
-        self.testtc = thetc
-        self.preptesttc = self.preptc(self.testtc)
-
-        if locs is not None:
-            gettimeaxis = True
-
-        # now calculate the similarity function
-        if trim:
-            retvals = tide_corr.cross_mutual_info(
-                self.preptesttc,
-                self.prepreftc,
-                norm=self.norm,
-                negsteps=self.lagmininpts,
-                possteps=self.lagmaxinpts,
-                locs=locs,
-                madnorm=self.madnorm,
-                returnaxis=gettimeaxis,
-                fast=True,
-                Fs=self.Fs,
-                sigma=self.sigma,
-                bins=self.bins,
-            )
-        else:
-            retvals = tide_corr.cross_mutual_info(
-                self.preptesttc,
-                self.prepreftc,
-                norm=self.norm,
-                negsteps=-1,
-                possteps=-1,
-                locs=locs,
-                madnorm=self.madnorm,
-                returnaxis=gettimeaxis,
-                fast=True,
-                Fs=self.Fs,
-                sigma=self.sigma,
-                bins=self.bins,
-            )
-        if gettimeaxis:
-            self.timeaxis, self.thesimfunc, self.similarityfuncorigin = (
-                retvals[0],
-                retvals[1],
-                retvals[2],
-            )
-            self.timeaxisvalid = True
-        else:
-            self.thesimfunc = retvals[0]
-
-        # normalize
-        self.thesimfunc *= self.mi_norm
-
-        if locs is not None:
-            return self.thesimfunc
-
-        if self.smoothingtime > 0.0:
-            self.thesimfunc = self.smoothingfilter.apply(self.Fs, self.thesimfunc)
-
-        self.similarityfunclen = len(self.thesimfunc)
-        if trim:
-            self.similarityfuncorigin = self.lagmininpts + 1
-        else:
-            self.similarityfuncorigin = self.similarityfunclen // 2 + 1
-
-        # find the global maximum value
-        self.theglobalmax = np.argmax(self.thesimfunc)
-        self.datavalid = True
-
-        # make a dummy filtered baseline
-        self.filteredbaseline = self.thesimfunc * 0.0
-
-        if trim:
-            return (
-                self.trim(self.thesimfunc),
-                self.trim(self.timeaxis),
-                self.theglobalmax,
-            )
-        else:
-            return self.thesimfunc, self.timeaxis, self.theglobalmax
-
-
-class Correlator(SimilarityFunctionator):
-    def __init__(
-        self,
-        windowfunc="hamming",
-        corrweighting="None",
-        corrpadding=0,
-        baselinefilter=None,
-        *args,
-        **kwargs,
-    ):
-        self.windowfunc = windowfunc
-        self.corrweighting = corrweighting
-        self.corrpadding = corrpadding
-        self.baselinefilter = baselinefilter
-        super(Correlator, self).__init__(*args, **kwargs)
-
-    def setlimits(self, lagmininpts, lagmaxinpts):
-        self.lagmininpts = lagmininpts
-        self.lagmaxinpts = lagmaxinpts
-
-    def setreftc(self, reftc, offset=0.0):
-        self.reftc = reftc + 0.0
-        self.prepreftc = self.preptc(self.reftc, isreftc=True)
-        self.similarityfunclen = len(self.reftc) * 2 - 1
-        self.similarityfuncorigin = self.similarityfunclen // 2 + 1
-
-        # make the reference time axis
-        self.timeaxis = (
-            np.arange(0.0, self.similarityfunclen) * (1.0 / self.Fs)
-            - ((self.similarityfunclen - 1) * (1.0 / self.Fs)) / 2.0
-        ) - offset
-        self.timeaxisvalid = True
-        self.datavalid = False
-
-    def run(self, thetc, trim=True):
-        if len(thetc) != len(self.reftc):
-            print(
-                "Correlator: timecourses are of different sizes:",
-                len(thetc),
-                "!=",
-                len(self.reftc),
-                "- exiting",
-            )
-            sys.exit()
-
-        self.testtc = thetc
-        self.preptesttc = self.preptc(self.testtc)
-
-        # now actually do the correlation
-        self.thesimfunc = tide_corr.fastcorrelate(
-            self.preptesttc,
-            self.prepreftc,
-            usefft=True,
-            weighting=self.corrweighting,
-            zeropadding=self.corrpadding,
-            debug=self.debug,
-        )
-        self.similarityfunclen = len(self.thesimfunc)
-        self.similarityfuncorigin = self.similarityfunclen // 2 + 1
-
-        if self.baselinefilter is not None:
-            self.filteredbaseline = self.baselinefilter.apply(self.Fs, self.thesimfunc)
-        else:
-            self.filteredbaseline = self.thesimfunc * 0.0
-
-        # find the global maximum value
-        self.theglobalmax = np.argmax(self.thesimfunc)
-        self.datavalid = True
-
-        if trim:
-            return (
-                self.trim(self.thesimfunc),
-                self.trim(self.timeaxis),
-                self.theglobalmax,
-            )
-        else:
-            return self.thesimfunc, self.timeaxis, self.theglobalmax
-
-
 class Coherer:
     reftc = None
     prepreftc = None
@@ -664,766 +328,3 @@ class Coherer:
             else:
                 self.themax = np.argmax(self.thecoherence)
                 return self.thecoherence, self.freqaxis, self.themax
-
-
-class SimilarityFunctionFitter:
-    corrtimeaxis = None
-    FML_NOERROR = np.uint32(0x0000)
-
-    FML_INITAMPLOW = np.uint32(0x0001)
-    FML_INITAMPHIGH = np.uint32(0x0002)
-    FML_INITWIDTHLOW = np.uint32(0x0004)
-    FML_INITWIDTHHIGH = np.uint32(0x0008)
-    FML_INITLAGLOW = np.uint32(0x0010)
-    FML_INITLAGHIGH = np.uint32(0x0020)
-    FML_INITFAIL = (
-        FML_INITAMPLOW
-        | FML_INITAMPHIGH
-        | FML_INITWIDTHLOW
-        | FML_INITWIDTHHIGH
-        | FML_INITLAGLOW
-        | FML_INITLAGHIGH
-    )
-
-    FML_FITAMPLOW = np.uint32(0x0100)
-    FML_FITAMPHIGH = np.uint32(0x0200)
-    FML_FITWIDTHLOW = np.uint32(0x0400)
-    FML_FITWIDTHHIGH = np.uint32(0x0800)
-    FML_FITLAGLOW = np.uint32(0x1000)
-    FML_FITLAGHIGH = np.uint32(0x2000)
-    FML_FITALGOFAIL = np.uint32(0x0400)
-    FML_FITFAIL = (
-        FML_FITAMPLOW
-        | FML_FITAMPHIGH
-        | FML_FITWIDTHLOW
-        | FML_FITWIDTHHIGH
-        | FML_FITLAGLOW
-        | FML_FITLAGHIGH
-        | FML_FITALGOFAIL
-    )
-
-    def __init__(
-        self,
-        corrtimeaxis=None,
-        lagmin=-30.0,
-        lagmax=30.0,
-        absmaxsigma=1000.0,
-        absminsigma=0.25,
-        hardlimit=True,
-        bipolar=False,
-        lthreshval=0.0,
-        uthreshval=1.0,
-        debug=False,
-        zerooutbadfit=True,
-        maxguess=0.0,
-        useguess=False,
-        searchfrac=0.5,
-        lagmod=1000.0,
-        enforcethresh=True,
-        allowhighfitamps=False,
-        displayplots=False,
-        functype="correlation",
-        peakfittype="gauss",
-    ):
-        r"""
-
-        Parameters
-        ----------
-        corrtimeaxis:  1D float array
-            The time axis of the correlation function
-        lagmin: float
-            The minimum allowed lag time in seconds
-        lagmax: float
-            The maximum allowed lag time in seconds
-        absmaxsigma: float
-            The maximum allowed peak halfwidth in seconds
-        hardlimit
-        bipolar: boolean
-            If true find the correlation peak with the maximum absolute value, regardless of sign
-        threshval
-        uthreshval
-        debug
-        zerooutbadfit
-        maxguess
-        useguess
-        searchfrac
-        lagmod
-        enforcethresh
-        displayplots
-
-        Returns
-        -------
-
-
-        Methods
-        -------
-        fit(corrfunc):
-            Fit the correlation function given in corrfunc and return the location of the peak in seconds, the maximum
-            correlation value, the peak width
-        setrange(lagmin, lagmax):
-            Specify the search range for lag peaks, in seconds
-        """
-        self.setcorrtimeaxis(corrtimeaxis)
-        self.lagmin = lagmin
-        self.lagmax = lagmax
-        self.absmaxsigma = absmaxsigma
-        self.absminsigma = absminsigma
-        self.hardlimit = hardlimit
-        self.bipolar = bipolar
-        self.lthreshval = lthreshval
-        self.uthreshval = uthreshval
-        self.debug = debug
-        if functype == "correlation" or functype == "mutualinfo":
-            self.functype = functype
-        else:
-            print("illegal functype")
-            sys.exit()
-        self.peakfittype = peakfittype
-        self.zerooutbadfit = zerooutbadfit
-        self.maxguess = maxguess
-        self.useguess = useguess
-        self.searchfrac = searchfrac
-        self.lagmod = lagmod
-        self.enforcethresh = enforcethresh
-        self.allowhighfitamps = allowhighfitamps
-        self.displayplots = displayplots
-
-    def _maxindex_noedge(self, corrfunc):
-        """
-
-        Parameters
-        ----------
-        corrfunc
-
-        Returns
-        -------
-
-        """
-        lowerlim = 0
-        upperlim = len(self.corrtimeaxis) - 1
-        done = False
-        while not done:
-            flipfac = 1.0
-            done = True
-            maxindex = (np.argmax(corrfunc[lowerlim:upperlim]) + lowerlim).astype("int32")
-            if self.bipolar:
-                minindex = (np.argmax(-corrfunc[lowerlim:upperlim]) + lowerlim).astype("int32")
-                if np.fabs(corrfunc[minindex]) > np.fabs(corrfunc[maxindex]):
-                    maxindex = minindex
-                    flipfac = -1.0
-            if upperlim == lowerlim:
-                done = True
-            if maxindex == 0:
-                lowerlim += 1
-                done = False
-            if maxindex == upperlim:
-                upperlim -= 1
-                done = False
-        return maxindex, flipfac
-
-    def setfunctype(self, functype):
-        self.functype = functype
-
-    def setpeakfittype(self, peakfittype):
-        self.peakfittype = peakfittype
-
-    def setrange(self, lagmin, lagmax):
-        self.lagmin = lagmin
-        self.lagmax = lagmax
-
-    def setcorrtimeaxis(self, corrtimeaxis):
-        if corrtimeaxis is not None:
-            self.corrtimeaxis = corrtimeaxis + 0.0
-        else:
-            self.corrtimeaxis = corrtimeaxis
-
-    def setguess(self, useguess, maxguess=0.0):
-        self.useguess = useguess
-        self.maxguess = maxguess
-
-    def setlthresh(self, lthreshval):
-        self.lthreshval = lthreshval
-
-    def setuthresh(self, uthreshval):
-        self.uthreshval = uthreshval
-
-    def diagnosefail(self, failreason):
-        # define error values
-        reasons = []
-        if failreason.astype(np.uint32) & self.FML_INITAMPLOW:
-            reasons.append("Initial amplitude too low")
-        if failreason.astype(np.uint32) & self.FML_INITAMPHIGH:
-            reasons.append("Initial amplitude too high")
-        if failreason.astype(np.uint32) & self.FML_INITWIDTHLOW:
-            reasons.append("Initial width too low")
-        if failreason.astype(np.uint32) & self.FML_INITWIDTHHIGH:
-            reasons.append("Initial width too high")
-        if failreason.astype(np.uint32) & self.FML_INITLAGLOW:
-            reasons.append("Initial Lag too low")
-        if failreason.astype(np.uint32) & self.FML_INITLAGHIGH:
-            reasons.append("Initial Lag too high")
-
-        if failreason.astype(np.uint32) & self.FML_FITAMPLOW:
-            reasons.append("Fit amplitude too low")
-        if failreason.astype(np.uint32) & self.FML_FITAMPHIGH:
-            reasons.append("Fit amplitude too high")
-        if failreason.astype(np.uint32) & self.FML_FITWIDTHLOW:
-            reasons.append("Fit width too low")
-        if failreason.astype(np.uint32) & self.FML_FITWIDTHHIGH:
-            reasons.append("Fit width too high")
-        if failreason.astype(np.uint32) & self.FML_FITLAGLOW:
-            reasons.append("Fit Lag too low")
-        if failreason.astype(np.uint32) & self.FML_FITLAGHIGH:
-            reasons.append("Fit Lag too high")
-        if failreason.astype(np.uint32) & self.FML_FITALGOFAIL:
-            reasons.append("Nonlinear fit failed")
-
-        if len(reasons) > 0:
-            return ", ".join(reasons)
-        else:
-            return "No error"
-
-    def fit(self, incorrfunc):
-        # check to make sure xcorr_x and xcorr_y match
-        if self.corrtimeaxis is None:
-            print("Correlation time axis is not defined - exiting")
-            sys.exit()
-        if len(self.corrtimeaxis) != len(incorrfunc):
-            print(
-                "Correlation time axis and values do not match in length (",
-                len(self.corrtimeaxis),
-                "!=",
-                len(incorrfunc),
-                "- exiting",
-            )
-            sys.exit()
-        # set initial parameters
-        # absmaxsigma is in seconds
-        # maxsigma is in Hz
-        # maxlag is in seconds
-        warnings.filterwarnings("ignore", "Number*")
-        failreason = self.FML_NOERROR
-        maskval = np.uint16(1)  # start out assuming the fit will succeed
-        binwidth = self.corrtimeaxis[1] - self.corrtimeaxis[0]
-
-        # set the search range
-        lowerlim = 0
-        upperlim = len(self.corrtimeaxis) - 1
-        if self.debug:
-            print(
-                "initial search indices are",
-                lowerlim,
-                "to",
-                upperlim,
-                "(",
-                self.corrtimeaxis[lowerlim],
-                self.corrtimeaxis[upperlim],
-                ")",
-            )
-
-        # make an initial guess at the fit parameters for the gaussian
-        # start with finding the maximum value and its location
-        flipfac = 1.0
-        corrfunc = incorrfunc + 0.0
-        if self.useguess:
-            maxindex = tide_util.valtoindex(self.corrtimeaxis, self.maxguess)
-            if (corrfunc[maxindex] < 0.0) and self.bipolar:
-                flipfac = -1.0
-        else:
-            maxindex, flipfac = self._maxindex_noedge(corrfunc)
-        corrfunc *= flipfac
-        maxlag_init = (1.0 * self.corrtimeaxis[maxindex]).astype("float64")
-        maxval_init = corrfunc[maxindex].astype("float64")
-        if self.debug:
-            print(
-                "maxindex, maxlag_init, maxval_init:",
-                maxindex,
-                maxlag_init,
-                maxval_init,
-            )
-
-        # set the baseline and baselinedev levels
-        if (self.functype == "correlation") or (self.functype == "hybrid"):
-            baseline = 0.0
-            baselinedev = 0.0
-        else:
-            # for mutual information, there is a nonzero baseline, so we want the difference from that.
-            baseline = np.median(corrfunc)
-            baselinedev = mad(corrfunc)
-        if self.debug:
-            print("baseline, baselinedev:", baseline, baselinedev)
-
-        # then calculate the width of the peak
-        if self.peakfittype == "fastquad" or self.peakfittype == "COM":
-            peakstart = np.max([1, maxindex - 2])
-            peakend = np.min([len(self.corrtimeaxis) - 2, maxindex + 2])
-        else:
-            # come here for peakfittype of None, quad, gauss, fastgauss
-            thegrad = np.gradient(corrfunc).astype(
-                "float64"
-            )  # the gradient of the correlation function
-            if (self.functype == "correlation") or (self.functype == "hybrid"):
-                if self.peakfittype == "quad":
-                    peakpoints = np.where(
-                        corrfunc > maxval_init - 0.05, 1, 0
-                    )  # mask for places where correlation exceeds searchfrac*maxval_init
-                else:
-                    peakpoints = np.where(
-                        corrfunc > (baseline + self.searchfrac * (maxval_init - baseline)), 1, 0
-                    )  # mask for places where correlation exceeds searchfrac*maxval_init
-            else:
-                # for mutual information, there is a flattish, nonzero baseline, so we want the difference from that.
-                peakpoints = np.where(
-                    corrfunc > (baseline + self.searchfrac * (maxval_init - baseline)),
-                    1,
-                    0,
-                )
-
-            peakpoints[0] = 0
-            peakpoints[-1] = 0
-            peakstart = np.max([1, maxindex - 1])
-            peakend = np.min([len(self.corrtimeaxis) - 2, maxindex + 1])
-            if self.debug:
-                print("initial peakstart, peakend:", peakstart, peakend)
-            if self.functype == "mutualinfo":
-                while peakpoints[peakend + 1] == 1:
-                    peakend += 1
-                while peakpoints[peakstart - 1] == 1:
-                    peakstart -= 1
-            else:
-                while thegrad[peakend + 1] <= 0.0 and peakpoints[peakend + 1] == 1:
-                    peakend += 1
-                while thegrad[peakstart - 1] >= 0.0 and peakpoints[peakstart - 1] == 1:
-                    peakstart -= 1
-            if self.debug:
-                print("final peakstart, peakend:", peakstart, peakend)
-
-            # deal with flat peak top
-            while (
-                peakend < (len(self.corrtimeaxis) - 3)
-                and corrfunc[peakend] == corrfunc[peakend - 1]
-            ):
-                peakend += 1
-            while peakstart > 2 and corrfunc[peakstart] == corrfunc[peakstart + 1]:
-                peakstart -= 1
-            if self.debug:
-                print("peakstart, peakend after flattop correction:", peakstart, peakend)
-                print("\n")
-                for i in range(peakstart, peakend + 1):
-                    print(self.corrtimeaxis[i], corrfunc[i])
-                print("\n")
-                fig = plt.figure()
-                ax = fig.add_subplot(111)
-                ax.set_title("Peak sent to fitting routine")
-                plt.plot(
-                    self.corrtimeaxis[peakstart : peakend + 1],
-                    corrfunc[peakstart : peakend + 1],
-                    "r",
-                )
-                plt.show()
-
-            # This is calculated from first principles, but it's always big by a factor or ~1.4.
-            #     Which makes me think I dropped a factor if sqrt(2).  So fix that with a final division
-            maxsigma_init = np.float64(
-                ((peakend - peakstart + 1) * binwidth / (2.0 * np.sqrt(-np.log(self.searchfrac))))
-                / np.sqrt(2.0)
-            )
-            if self.debug:
-                print("maxsigma_init:", maxsigma_init)
-
-            # now check the values for errors
-            if self.hardlimit:
-                rangeextension = 0.0
-            else:
-                rangeextension = (self.lagmax - self.lagmin) * 0.75
-            if not (
-                (self.lagmin - rangeextension - binwidth)
-                <= maxlag_init
-                <= (self.lagmax + rangeextension + binwidth)
-            ):
-                if maxlag_init <= (self.lagmin - rangeextension - binwidth):
-                    failreason |= self.FML_INITLAGLOW
-                    maxlag_init = self.lagmin - rangeextension - binwidth
-                else:
-                    failreason |= self.FML_INITLAGHIGH
-                    maxlag_init = self.lagmax + rangeextension + binwidth
-                if self.debug:
-                    print("bad initial")
-            if maxsigma_init > self.absmaxsigma:
-                failreason |= self.FML_INITWIDTHHIGH
-                maxsigma_init = self.absmaxsigma
-                if self.debug:
-                    print("bad initial width - too high")
-            if peakend - peakstart < 2:
-                failreason |= self.FML_INITWIDTHLOW
-                maxsigma_init = np.float64(
-                    ((2 + 1) * binwidth / (2.0 * np.sqrt(-np.log(self.searchfrac)))) / np.sqrt(2.0)
-                )
-                if self.debug:
-                    print("bad initial width - too low")
-            if (self.functype == "correlation") or (self.functype == "hybrid"):
-                if not (self.lthreshval <= maxval_init <= self.uthreshval) and self.enforcethresh:
-                    failreason |= self.FML_INITAMPLOW
-                    if self.debug:
-                        print(
-                            "bad initial amp:",
-                            maxval_init,
-                            "is less than",
-                            self.lthreshval,
-                        )
-                if maxval_init < 0.0:
-                    failreason |= self.FML_INITAMPLOW
-                    maxval_init = 0.0
-                    if self.debug:
-                        print("bad initial amp:", maxval_init, "is less than 0.0")
-                if (maxval_init > 1.0) and self.enforcethresh:
-                    failreason |= self.FML_INITAMPHIGH
-                    maxval_init = 1.0
-                    if self.debug:
-                        print("bad initial amp:", maxval_init, "is greater than 1.0")
-            else:
-                # somewhat different rules for mutual information peaks
-                if ((maxval_init - baseline) < self.lthreshval * baselinedev) or (
-                    maxval_init < baseline
-                ):
-                    failreason |= self.FML_INITAMPLOW
-                    maxval_init = 0.0
-                    if self.debug:
-                        print("bad initial amp:", maxval_init, "is less than 0.0")
-            if (failreason != self.FML_NOERROR) and self.zerooutbadfit:
-                maxval = np.float64(0.0)
-                maxlag = np.float64(0.0)
-                maxsigma = np.float64(0.0)
-            else:
-                maxval = np.float64(maxval_init)
-                maxlag = np.float64(maxlag_init)
-                maxsigma = np.float64(maxsigma_init)
-
-        # refine if necessary
-        if self.peakfittype != "None":
-            if self.peakfittype == "COM":
-                X = self.corrtimeaxis[peakstart : peakend + 1] - baseline
-                data = corrfunc[peakstart : peakend + 1]
-                maxval = maxval_init
-                maxlag = np.sum(X * data) / np.sum(data)
-                maxsigma = 10.0
-            elif self.peakfittype == "gauss":
-                X = self.corrtimeaxis[peakstart : peakend + 1] - baseline
-                data = corrfunc[peakstart : peakend + 1]
-                # do a least squares fit over the top of the peak
-                # p0 = np.array([maxval_init, np.fmod(maxlag_init, lagmod), maxsigma_init], dtype='float64')
-                p0 = np.array([maxval_init, maxlag_init, maxsigma_init], dtype="float64")
-                if self.debug:
-                    print("fit input array:", p0)
-                try:
-                    plsq, dummy = sp.optimize.leastsq(
-                        tide_fit.gaussresiduals, p0, args=(data, X), maxfev=5000
-                    )
-                    maxval = plsq[0] + baseline
-                    maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
-                    maxsigma = plsq[2]
-                except:
-                    failreason |= self.FML_FITALGOFAIL
-                    maxval = np.float64(0.0)
-                    maxlag = np.float64(0.0)
-                    maxsigma = np.float64(0.0)
-                if self.debug:
-                    print("fit output array:", [maxval, maxlag, maxsigma])
-            elif self.peakfittype == "gausscf":
-                X = self.corrtimeaxis[peakstart : peakend + 1] - baseline
-                data = corrfunc[peakstart : peakend + 1]
-                # do a least squares fit over the top of the peak
-                try:
-                    plsq, pcov = curve_fit(
-                        tide_fit.gaussfunc,
-                        X,
-                        data,
-                        p0=[maxval_init, maxlag_init, maxsigma_init],
-                    )
-                    maxval = plsq[0] + baseline
-                    maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
-                    maxsigma = plsq[2]
-                except:
-                    failreason |= self.FML_FITALGOFAIL
-                    maxval = np.float64(0.0)
-                    maxlag = np.float64(0.0)
-                    maxsigma = np.float64(0.0)
-                if self.debug:
-                    print("fit output array:", [maxval, maxlag, maxsigma])
-            elif self.peakfittype == "fastgauss":
-                X = self.corrtimeaxis[peakstart : peakend + 1] - baseline
-                data = corrfunc[peakstart : peakend + 1]
-                # do a non-iterative fit over the top of the peak
-                # 6/12/2015  This is just broken.  Gives quantized maxima
-                maxlag = np.float64(1.0 * np.sum(X * data) / np.sum(data))
-                maxsigma = np.float64(
-                    np.sqrt(np.abs(np.sum((X - maxlag) ** 2 * data) / np.sum(data)))
-                )
-                maxval = np.float64(data.max()) + baseline
-            elif self.peakfittype == "fastquad":
-                maxlag, maxval, maxsigma, ismax, badfit = tide_fit.refinepeak_quad(
-                    self.corrtimeaxis, corrfunc, maxindex
-                )
-            elif self.peakfittype == "quad":
-                X = self.corrtimeaxis[peakstart : peakend + 1]
-                data = corrfunc[peakstart : peakend + 1]
-                try:
-                    thecoffs = Polynomial.fit(X, data, 2).convert().coef[::-1]
-                    a = thecoffs[0]
-                    b = thecoffs[1]
-                    c = thecoffs[2]
-                    maxlag = -b / (2.0 * a)
-                    maxval = a * maxlag * maxlag + b * maxlag + c
-                    maxsigma = 1.0 / np.fabs(a)
-                    if self.debug:
-                        print("poly coffs:", a, b, c)
-                        print("maxlag, maxval, maxsigma:", maxlag, maxval, maxsigma)
-                except np.lib.polynomial.RankWarning:
-                    failreason |= self.FML_FITALGOFAIL
-                    maxlag = 0.0
-                    maxval = 0.0
-                    maxsigma = 0.0
-                if self.debug:
-                    print("\n")
-                    for i in range(len(X)):
-                        print(X[i], data[i])
-                    print("\n")
-                    fig = plt.figure()
-                    ax = fig.add_subplot(111)
-                    ax.set_title("Peak and fit")
-                    plt.plot(X, data, "r")
-                    plt.plot(X, c + b * X + a * X * X, "b")
-                    plt.show()
-
-            else:
-                print("illegal peak refinement type")
-
-            # check for errors in fit
-            fitfail = False
-            if self.bipolar:
-                lowestcorrcoeff = -1.0
-            else:
-                lowestcorrcoeff = 0.0
-            if (self.functype == "correlation") or (self.functype == "hybrid"):
-                if maxval < lowestcorrcoeff:
-                    failreason |= self.FML_FITAMPLOW
-                    maxval = lowestcorrcoeff
-                    if self.debug:
-                        print("bad fit amp: maxval is lower than lower limit")
-                    fitfail = True
-                if np.abs(maxval) > 1.0:
-                    if not self.allowhighfitamps:
-                        failreason |= self.FML_FITAMPHIGH
-                        if self.debug:
-                            print(
-                                "bad fit amp: magnitude of",
-                                maxval,
-                                "is greater than 1.0",
-                            )
-                        fitfail = True
-                    maxval = 1.0 * np.sign(maxval)
-            else:
-                # different rules for mutual information peaks
-                if ((maxval - baseline) < self.lthreshval * baselinedev) or (maxval < baseline):
-                    failreason |= self.FML_FITAMPLOW
-                    maxval_init = 0.0
-                    if self.debug:
-                        if (maxval - baseline) < self.lthreshval * baselinedev:
-                            print(
-                                "FITAMPLOW: maxval - baseline:",
-                                maxval - baseline,
-                                " < lthreshval * baselinedev:",
-                                self.lthreshval * baselinedev,
-                            )
-                        if maxval < baseline:
-                            print("FITAMPLOW: maxval < baseline:", maxval, baseline)
-                    if self.debug:
-                        print("bad fit amp: maxval is lower than lower limit")
-            if (self.lagmin > maxlag) or (maxlag > self.lagmax):
-                if self.debug:
-                    print("bad lag after refinement")
-                if self.lagmin > maxlag:
-                    failreason |= self.FML_FITLAGLOW
-                    maxlag = self.lagmin
-                else:
-                    failreason |= self.FML_FITLAGHIGH
-                    maxlag = self.lagmax
-                fitfail = True
-            if maxsigma > self.absmaxsigma:
-                failreason |= self.FML_FITWIDTHHIGH
-                if self.debug:
-                    print("bad width after refinement:", maxsigma, ">", self.absmaxsigma)
-                maxsigma = self.absmaxsigma
-                fitfail = True
-            if maxsigma < self.absminsigma:
-                failreason |= self.FML_FITWIDTHLOW
-                if self.debug:
-                    print("bad width after refinement:", maxsigma, "<", self.absminsigma)
-                maxsigma = self.absminsigma
-                fitfail = True
-            if fitfail:
-                if self.debug:
-                    print("fit fail")
-                if self.zerooutbadfit:
-                    maxval = np.float64(0.0)
-                    maxlag = np.float64(0.0)
-                    maxsigma = np.float64(0.0)
-                maskval = np.uint16(0)
-            # print(maxlag_init, maxlag, maxval_init, maxval, maxsigma_init, maxsigma, maskval, failreason, fitfail)
-        else:
-            maxval = np.float64(maxval_init)
-            maxlag = np.float64(np.fmod(maxlag_init, self.lagmod))
-            maxsigma = np.float64(maxsigma_init)
-            if failreason != self.FML_NOERROR:
-                maskval = np.uint16(0)
-            else:
-                maskval = np.uint16(1)
-
-        if self.debug or self.displayplots:
-            print(
-                "init to final: maxval",
-                maxval_init,
-                maxval,
-                ", maxlag:",
-                maxlag_init,
-                maxlag,
-                ", width:",
-                maxsigma_init,
-                maxsigma,
-            )
-        if self.displayplots and (self.peakfittype != "None") and (maskval != 0.0):
-            fig = plt.figure()
-            ax = fig.add_subplot(111)
-            ax.set_title("Data and fit")
-            hiresx = np.arange(X[0], X[-1], (X[1] - X[0]) / 10.0)
-            plt.plot(
-                X,
-                data,
-                "ro",
-                hiresx,
-                tide_fit.gauss_eval(hiresx, np.array([maxval, maxlag, maxsigma])),
-                "b-",
-            )
-            plt.show()
-        return (
-            maxindex,
-            maxlag,
-            flipfac * maxval,
-            maxsigma,
-            maskval,
-            failreason,
-            peakstart,
-            peakend,
-        )
-
-
-class FrequencyTracker:
-    freqs = None
-    times = None
-
-    def __init__(self, lowerlim=0.1, upperlim=0.6, nperseg=32, Q=10.0, debug=False):
-        self.lowerlim = lowerlim
-        self.upperlim = upperlim
-        self.nperseg = nperseg
-        self.Q = Q
-        self.debug = debug
-        self.nfft = self.nperseg
-
-    def track(self, x, fs):
-        self.freqs, self.times, thespectrogram = sp.signal.spectrogram(
-            np.concatenate(
-                [np.zeros(int(self.nperseg // 2)), x, np.zeros(int(self.nperseg // 2))],
-                axis=0,
-            ),
-            fs=fs,
-            detrend="constant",
-            scaling="spectrum",
-            nfft=None,
-            window=np.hamming(self.nfft),
-            noverlap=(self.nperseg - 1),
-        )
-        lowerliminpts = tide_util.valtoindex(self.freqs, self.lowerlim)
-        upperliminpts = tide_util.valtoindex(self.freqs, self.upperlim)
-
-        if self.debug:
-            print(self.times.shape, self.freqs.shape, thespectrogram.shape)
-            print(self.times)
-
-        # initialize the peak fitter
-        thefitter = SimilarityFunctionFitter(
-            corrtimeaxis=self.freqs,
-            lagmin=self.lowerlim,
-            lagmax=self.upperlim,
-            absmaxsigma=10.0,
-            absminsigma=0.1,
-            debug=self.debug,
-            peakfittype="fastquad",
-            zerooutbadfit=False,
-            useguess=False,
-        )
-
-        peakfreqs = np.zeros((thespectrogram.shape[1] - 1), dtype=float)
-        for i in range(0, thespectrogram.shape[1] - 1):
-            (
-                maxindex,
-                peakfreqs[i],
-                maxval,
-                maxsigma,
-                maskval,
-                failreason,
-                peakstart,
-                peakend,
-            ) = thefitter.fit(thespectrogram[:, i])
-            if not (lowerliminpts <= maxindex <= upperliminpts):
-                peakfreqs[i] = -1.0
-
-        return self.times[:-1], peakfreqs
-
-    def clean(self, x, fs, times, peakfreqs, numharmonics=2):
-        nyquistfreq = 0.5 * fs
-        y = x * 0.0
-        halfwidth = int(self.nperseg // 2)
-        padx = np.concatenate([np.zeros(halfwidth), x, np.zeros(halfwidth)], axis=0)
-        pady = np.concatenate([np.zeros(halfwidth), y, np.zeros(halfwidth)], axis=0)
-        padweight = padx * 0.0
-        if self.debug:
-            print(fs, len(times), len(peakfreqs))
-        for i in range(0, len(times)):
-            centerindex = int(times[i] * fs)
-            xstart = centerindex - halfwidth
-            xend = centerindex + halfwidth
-            if peakfreqs[i] > 0.0:
-                filtsignal = padx[xstart:xend]
-                numharmonics = np.min([numharmonics, int((nyquistfreq // peakfreqs[i]) - 1)])
-                if self.debug:
-                    print("numharmonics:", numharmonics, nyquistfreq // peakfreqs[i])
-                for j in range(numharmonics + 1):
-                    workingfreq = (j + 1) * peakfreqs[i]
-                    if self.debug:
-                        print("workingfreq:", workingfreq)
-                    ws = [workingfreq * 0.95, workingfreq * 1.05]
-                    wp = [workingfreq * 0.9, workingfreq * 1.1]
-                    gpass = 1.0
-                    gstop = 40.0
-                    b, a = sp.signal.iirdesign(wp, ws, gpass, gstop, ftype="cheby2", fs=fs)
-                    if self.debug:
-                        print(
-                            i,
-                            j,
-                            times[i],
-                            centerindex,
-                            halfwidth,
-                            xstart,
-                            xend,
-                            xend - xstart,
-                            wp,
-                            ws,
-                            len(a),
-                            len(b),
-                        )
-                    filtsignal = sp.signal.filtfilt(b, a, sp.signal.filtfilt(b, a, filtsignal))
-                pady[xstart:xend] += filtsignal
-            else:
-                pady[xstart:xend] += padx[xstart:xend]
-            padweight[xstart:xend] += 1.0
-        return (pady / padweight)[halfwidth:-halfwidth]