### Navigation

- index
- modules |
- modules |
- homepage|
- search|
- documentation »
- Module code »

# Source code for spacepy.seapy

    #!/usr/bin/python
    # -*- coding: utf-8 -*-

    """SeaPy -- Superposed Epoch in Python.

    This module contains superposed epoch class types and a variety of functions
    for using on superposed epoch objects.
    Each instance must be initialized with (assuming import seapy as se):

    >>> obj = se.Sea(data, times, epochs)

    To perform a superposed epoch analysis

    >>> obj.sea()

    To plot

    >>> obj.plot()

    If multiple SeaPy objects exist, these can be combined into a single object

    >>> objdict = seadict([obj1, obj2],['obj1name','obj2name'])

    and then used to create a multipanel plot

    >>> multisea(objdict)

    For two-dimensional superposed epoch analyses, initialize an Sea2d() instance

    >>> obj = se.Sea2d(data, times, epochs, y=[4., 12.])

    All object methods are the same as for the 1D object. Also, the multisea()
    function should accept both 1D and 2D objects, even mixed together. Currently,
    the plot() method is recommended for 2D SEA.

    --++-- By Steve Morley --++--

    smorley@lanl.gov
    Los Alamos National Laboratory

    Copyright 2010 Los Alamos National Security, LLC.
    """
    from __future__ import division

    import warnings

    import numpy as np
    import numpy.ma as ma
    import numbers
    import datetime as dt
    import spacepy.toolbox as tb
    from spacepy import help
    import spacepy.time as spt
    import matplotlib.pyplot as plt
    from matplotlib.dates import date2num, num2date

    __contact__ = 'Steve Morley, smorley@lanl.gov'

    class SeaBase(object):
        """SeaPy Superposed epoch analysis base class

        Do not use directly -- subclass it!

        """
        def __init__(self, data, times, epochs, **kwargs):
            self.data = np.asarray(data, dtype=float)
            if isinstance(times, spt.Ticktock):
                self.times=times.UTC
            else:
                self.times = times
            if isinstance(epochs, spt.Ticktock):
                self.epochs = epochs.UTC
            else:
                self.epochs = epochs
            self.verbose = kwargs['verbose']
            if type(kwargs['delta']) == dt.timedelta:
                t_delt = kwargs['delta'].days + kwargs['delta'].seconds/86400
                self.delta = t_delt
            else:
                self.delta = kwargs['delta']
            if type(kwargs['window']) == dt.timedelta:
                self.window = kwargs['window'].days + kwargs['window'].seconds/86400
            else:
                self.window = kwargs['window']
            self.window = np.ceil(float(self.window)/float(self.delta))
            if kwargs['window'] != self.window:
                warnings.warn(
                    'Window size changed to {0} (points) to fit resolution ({1})'.format(
                    self.window, self.delta))
            self.bound_type = None

        def __str__(self):
            """Define String Representation of Sea object"""

            strhead = 'Superposed Epoch Object:'
            strtail = 'Data array - {0}; #Epochs - {1}'.format(self.data.shape, len(self.epochs))
            return ' '.join((strhead, strtail))

        __repr__ = __str__

        def __len__(self):
            """Calling len(obj) will return the number of epochs."""

            return len(self.epochs)

        def restoreepochs(self):
            """Replaces epoch times stored in obj.badepochs in the epochs attribute

            """
            try:
                dum = self.badepochs
            except AttributeError:
                raise AttributeError('No bad epochs to restore')

            self.epochs = np.union1d(self.badepochs,self.epochs)
            if self.verbose: print('Bad epochs restored to epochs attribute')

            return None

        def _timeepoch(self, delt):
            #check type of time input and throw error message
            el1,ep1 = self.times[0], self.epochs[0]
            el1num = isinstance(el1, numbers.Number) or (type(el1)==np.float64)
            ep1num = isinstance(ep1, numbers.Number) or (type(ep1)==np.float64)
            if isinstance(el1, dt.datetime) and (type(el1) == type(self.epochs[0])):
                #both time and epochs are datetime objects
                #convert to serial time
                if self.verbose:
                    print('converting to serial time')
                dum = date2num(self.epochs)
                t_epoch = np.array(dum)
                dum = date2num(self.times)
                time = np.array(dum)
                ser_flag=False
            elif el1num and ep1num:
                #time is serial, do nothing
                if self.verbose:
                    print('time is serial')
                t_epoch = np.array(self.epochs, dtype=float)
                time = np.array(self.times, dtype=float)
                ser_flag=True
            else:
                raise ValueError('Time and Epochs must be consistently typed (numeric/datetime)')

            lose0 = np.where(t_epoch > time[-1]-(self.window*self.delta))
            lose1 = np.where(t_epoch < time[0]+(self.window*self.delta))
            if len(lose0)>0 and len(lose1)>0:
                linds = np.union1d(lose0[0],lose1[0])
                if len(linds)>0:
                    if self.verbose: print('sea(): %s out-of-range epochs moved to badepochs attribute'\
                    % len(linds))
                if ser_flag:
                    self.badepochs = t_epoch[linds]
                else:
                    self.badepochs = num2date(t_epoch[linds])
                ##TODO: replace following two lines with calls to tOverlapHalf
                keep0 = np.where(t_epoch <= time[-1]-(self.window*self.delta))
                keep1 = np.where(t_epoch >= time[0]+(self.window*self.delta))
                kinds = np.intersect1d(keep0[0],keep1[0])

                self.epochs = t_epoch[kinds]
                t_epoch = t_epoch[kinds]
                if len(self.epochs)==0:
                    raise RuntimeError('No valid epochs for data supplied')
            return time, t_epoch

    class Sea(SeaBase):
        """SeaPy Superposed epoch analysis object

        Initialize object with data, times, epochs, window (half-width) and delta (optional).
        'times' and epochs should be in some useful format
        Includes method to perform superposed epoch analysis of input data series

        Parameters
        ==========
        data : array_like
            list or array of data
        times : array_like
            list of datetime objects (or list of serial times)
        epochs : array_like
            list of datetime objects (or serial times) for zero epochs in SEA
        window : datetime.timedelta
            size of the half-window for the SEA (can also be given as serial time)
        delta : datetime.timedelta
            resolution of the input data series, which must be uniform (can also be
            given as serial time)

        Notes
        =====
        Output can be nicely plotted with :py:meth:`plot`, or for multiple objects
        use the :py:func:`multisea` function

        .. currentmodule:: spacepy.seapy
        .. autosummary::
            ~Sea.sea
            ~Sea.plot
        .. automethod:: sea
        .. automethod:: plot
        """
        def __init__(self, data, times, epochs, window=3., delta=1., verbose=True):
            super(Sea, self).__init__(data, times, epochs, \
                  window=window, delta=delta, verbose=verbose)

        def sea(self, **kwargs):
            """Method called to perform superposed epoch analysis on data in object.

            Uses object attributes obj.data, obj.times, obj.epochs, obj.delta,
            obj.window, all of which must be available on instantiation.

    	Other Parameters
            ================
            storedata : boolean
    	    saves matrix of epoch windows as obj.datacube (default = False)
    	quartiles : list
    	    calculates the quartiles as the upper and lower bounds (and is default);
            ci : float
    	    will find the bootstrapped confidence intervals (and requires ci_quan to be set);
            mad : float
    	    will use +/- the median absolute deviation for the bounds;
            ci_quan : string
    	    can be set to 'median' or 'mean'

            Notes
            =====
            A basic plot can be raised with :meth:`plot`
            """
            #check this hasn't already been done
            #TODO: find out why doing two .sea() calls back-to-back fails 2nd time
            if hasattr(self, 'semedian') or hasattr(self, 'semean'):
                return None

            #check defaults
            defaults = {'storedata': True, 'quartiles': True, 'ci': False,
                        'mad': False, 'ci_quan': 'median'}
            for default in defaults:
                if default not in kwargs:
                    kwargs[default] = defaults[default]

            #ensure all input is np array
            delt = float(self.delta)
            if isinstance(self.data, np.ndarray):
                y = self.data
            else:
                y = np.asarray(self.data, dtype=float)

            if kwargs['ci']:
                kwargs['quartiles'], kwargs['mad'] = False, False
            if kwargs['mad']:
                kwargs['quartiles'], kwargs['ci'] = False, False

            time, t_epoch = self._timeepoch(delt)

            #build SEA matrix and perform analysis
            wind = int(self.window)
            m = int(2*wind + 1)
            n = len(t_epoch)
            y_sea = np.zeros((n,m), dtype=float)
            blankslice = np.zeros([m], dtype=float)
            for i in range(n):
                dif = np.abs(time-t_epoch[i])
                j = np.where(dif == np.min(dif))
                stpt = j[0][0]-wind
                enpt = j[0][0]+wind+1
                sea_slice = blankslice.copy()
                if stpt < 0: #fix for bad epochs not correctly moved to badepochs attr #TODO: make badepochs robust or do all checking here
                    sea_slice[0:abs(stpt)] = np.NaN
                    sea_slice[abs(stpt):] = y[0:enpt]
                elif enpt >= len(y):
                    tmpslice = y[stpt:]
                    sea_slice[:len(tmpslice)] = tmpslice
                    sea_slice[len(tmpslice):] = np.NaN
                else:
                    sea_slice = y[stpt:enpt]

                y_sea[i,0:] = sea_slice

            #find SEA mean, median and percentiles - exclude NaNs (or badval)
            try:
                badval = kwargs['badval']
            except KeyError:
                badval = np.nan
                y_sea_m = ma.masked_where(np.isnan(y_sea), y_sea)
            else:
                y_sea_m = ma.masked_values(y_sea, badval)
            self.semean = [np.mean(y_sea_m[:,i].compressed()) for i in range(m)]
            self.semedian = [np.median(y_sea_m[:,i].compressed()) for i in range(m)]
            self.semean, self.semedian = np.array(self.semean), np.array(self.semedian)
            self.bound_low = np.zeros((m,1))
            self.bound_high = np.zeros((m,1))

            if kwargs['quartiles']:
                from matplotlib.mlab import prctile
                for i in range(m):
                    dum = np.sort(y_sea_m[:,i].compressed())
                    qul = prctile(dum,p=(25,75))
                    self.bound_low[i], self.bound_high[i] = qul[0], qul[1]
            elif kwargs['ci']: #bootstrapped confidence intervals (95%)
                from spacepy.poppy import boots_ci
                if kwargs['ci_quan'] == 'mean':
                    ci_func = lambda x: np.mean(x)
                else:
                    ci_func = lambda x: np.median(x)
                for i in range(m):
                    dum = np.sort(y_sea_m[:,i].compressed())
                    self.bound_low[i], self.bound_high[i] = \
                         boots_ci(dum, 800, 95, ci_func)
            elif kwargs['mad']: #median absolute deviation
                for i in range(m):
                    dum = np.sort(y_sea_m[:,i].compressed())
                    spread_mad = tb.medAbsDev(dum)
                    self.bound_low[i] = self.semedian[i]-spread_mad
                    self.bound_high[i] = self.semedian[i]+spread_mad

            self.x = np.linspace(-1.*self.window*self.delta, self.window*self.delta, \
             len(self.semedian))
            if kwargs['storedata']:
                self.datacube = y_sea_m
                if self.verbose:
                    print('sea(): datacube added as new attribute')

            if self.verbose:
                print('Superposed epoch analysis complete')

        #def sea_norm(self, epoch2, nbins=100, storedata=False, quartiles=True, ci=False, mad=False,
        #ci_quan='median'):
            #"""Method for normalized superposed epoch analysis (creates new object)

            #Examples
            #Assuming an already instantiated Sea object, xampl

            #>>> xampl_norm = xampl.sea_norm(epoch2)

            #Note that epoch2 must be a paired set with xampl.epochs

            #Inputs:
            #Uses object attributes obj.data, obj.times, obj.epochs, obj.delta.
            #all of which must be available on instantiation.
            #Also requires second set of epochs.

            #Other Parameters
            #nbins (default = 100) - number of bins for normalized SEA
            #storedata (default = False) - saves matrix of epoch windows as obj.datacube
            #quartiles calculates the quartiles as the upper and lower bounds (and is default);
            #ci will find the bootstrapped confidence intervals (and requires ci_quan to be set);
            #mad will use +/- the median absolute deviation for the bounds;
            #ci_quan can be set to 'median' or 'mean'

            #Output is a new SeaPy object with all Sea methods.
            #"""
            #import numpy as np
            #import numpy.ma as ma

            ##ensure all input is np array
            #delt = float(self.delta)
            #y = np.array(self.data, dtype=float)

            #if ci:
                #quartiles, mad = False, False
            #if mad:
                #quartiles, ci = False, False

            #time,t_epoch = self._timeepoch(delt)

            ##build SEA matrix and perform analysis
            #wind = self.window
            #m = int(2*wind + 1)
            #n = len(t_epoch)
            #y_sea = np.zeros((n,m), dtype=float)

            #for i in range(n):
                #t_a, t_b = abs(time-t_epoch1[i]), abs(time-t_epoch2[i])
                #j = np.where(t_a == np.min(t_a))
                #k = np.where(t_b == np.min(t_b))
                #norm_ax = np.linspace(t_epoch1[i], t_epoch2[i], nbins+1)
                #norm_event = np.interp(norm_ax, time[j[1]:k[1]], y[j[1]:k[1]]) #piecewise linear
                #norm_event[0], norm_event[-1] = y[j[0]], y[k[0]] #Fix endpoints
                #y_sea[i,0:] = norm_event

            ##for i in range(n):
                ##dif = np.abs(time-t_epoch[i])
                ##j = np.where(dif == np.min(dif))
                ##sea_slice = y[j[0][0]-wind:j[0][0]+wind+1]
                ##y_sea[i,0:] = sea_slice

            ##Instantiate new SeaPy object
            #outobj = Sea(self.data, self.times, self.epochs, self.window, self.delta)
            #print 'New Sea object created'

            ##find SEA mean, median and percentiles - exclude NaNs
            #y_sea_m = ma.masked_where(np.isnan(y_sea), y_sea)
            #outobj.semean = [np.mean(dum.compressed()) for dum in y_sea_m]
            #outobj.semedian = [np.median(dum.compressed()) for dum in y_sea_m]
            #outobj.bound_low = np.zeros((m,1))
            #outobj.bound_high = np.zeros((m,1))

            #if quartiles:
                #from matplotlib.mlab import prctile
                #for i in range(m):
                    #dum = np.sort(y_sea_m[:,i].compressed())
                    #qul = prctile(dum,p=(25,75))
                    #outobj.bound_low[i], outobj.bound_high[i] = qul[0], qul[1]
            #elif ci: #bootstrapped confidence intervals (95%)
                #from spacepy.poppy import boots_ci
                #if ci_quan == 'mean':
                    #ci_func = lambda x: np.mean(x)
                #else:
                    #ci_func = lambda x: np.median(x)
                #for i in range(m):
                    #dum = np.sort(y_sea_m[:,i].compressed())
                    #outobj.bound_low[i], outobj.bound_high[i] = \
                        #boots_ci(dum, 800, 95, ci_func)
            #elif mad: #median absolute deviation
                #from spacepy.toolbox import medabsdev
                #for i in range(m):
                    #dum = np.sort(y_sea_m[:,i].compressed())
                    #spread_mad = medabsdev(data)
                    #outobj.bound_low[i] = outobj.semedian[i]-spread_mad
                    #outobj.bound_high[i] = outobj.semedian[i]+spread_mad

            #outobj.x = np.linspace(0, nbins, len(outobj.semedian))
            #if storedata:
                #outobj.datacube = y_sea_m
                #print 'sea_norm(): datacube added to new object as attribute'

            #return 'Superposed epoch analysis complete'

        def plot(self, xquan = 'Time Since Epoch', yquan='', xunits='',
                    yunits='', epochline=False, usrlimy=[], show=True,
                    figsize=None, dpi=None, transparent=True, color='#7F7FFF'):
            """Method called to create basic plot of superposed epoch analysis.

            Parameters
    	==========
            Uses object attributes created by the obj.sea() method.

            Other Parameters
            ================
            xquan : str
    	    (default = 'Time since epoch' ) - x-axis label.
    	yquan : str
    	    default None - yaxus label
    	xunits : str
    	    (default = None) - x-axis units.
            yunits : str
    	    (default = None) - y-axis units.
            epochline : boolean
    	    (default = False) - put vertical line at zero epoch.
            usrlimy : list
    	    (default = []) - override automatic y-limits on plot.
            transparent : boolean
    	    (default True): make patch for low/high bounds transparent
            color : str
                Color to use for the patch if not transparent.
                (default #7F7FFF, a medium blue)

            Notes
            =====
            If both quan and units are supplied, axis label will read
            'Quantity Entered By User [Units]'
            """
            try:
                assert hasattr(self, 'semedian') or hasattr(self, 'semean')
            except AssertionError:
                raise ValueError('No superposed epoch results to plot')

            if len(xunits)<1:
                xlstr = '%s' % xquan
            else:
                xlstr = '%s [%s]' % (xquan, xunits)
            if len(yquan)>=1 and len(yunits)>=1:
                ylstr = '%s [%s]' % (yquan, yunits)
            elif len(yquan)>=1 and len(yunits)<1:
                ylstr = '%s' % yquan
            else:
                ylstr = ''

            if show==True and dpi==None:
                dpi=80
            elif show==False and dpi==None:
                dpi=300

            fig = plt.figure(figsize=figsize, dpi=dpi)
            ax0 = fig.add_subplot(111)

            #ax0.plot(self.x, self.semean, 'b-', lw=1.5)
            #plt.hold(True)
            #ax0.plot(self.x, self.semedian, 'k-', lw=2.5)
            #ax0.plot(self.x, self.bound_low, 'k-.', lw=2)
            #ax0.plot(self.x, self.bound_high, 'k-.', lw=2)

            if transparent:
                ax0.fill_between(self.x, self.bound_low.ravel(), self.bound_high.ravel(),
                                 edgecolor='none', facecolor=color, interpolate=True, alpha=0.25)
            else:
                ax0.fill_between(self.x, self.bound_low.ravel(), self.bound_high.ravel(),
                                 edgecolor='none', facecolor=color, interpolate=True)
            plt.hold(True)
            ax0.plot(self.x, self.semedian, 'k-', lw=2.0)
            ax0.plot(self.x, self.semean, 'r--', lw=1.25)

            plt.xlabel(xlstr)
            plt.ylabel(ylstr)

            if usrlimy:
                ax0.set_ylim(usrlimy)

            if epochline:
                yr = ax0.get_ylim()
                if yr[0] < 0:
                    yrlo = yr[0]+yr[0]
                else:
                    yrlo = yr[0]-yr[0]
                if yr[1] < 0:
                    yrhi = yr[1]-yr[1]
                else:
                    yrhi = yr[1]+yr[1]
                ax0.plot([0,0], [yrlo,yrhi], 'k:', lw=1)
                plt.ylim(yr)

            if show:
                plt.show()
                return None
            else:
                return fig

    class Sea2d(SeaBase):
        """SeaPy 2D Superposed epoch analysis object

        Initialize object with data (n element vector), times(y*n array),
        epochs, window (half-width), delta (optional), and
        y (two-element vector with max and min of y;optional)
        'times' and epochs should be in some useful format
        Includes method to perform superposed epoch analysis of input data series

        Parameters
        ==========
        data : array_like
            2-D array of data (0th dimension is quantity y, 1st dimension is time)
        times : array_like
            list of datetime objects (or list of serial times)
        epochs : array_like
            list of datetime objects (or serial times) for zero epochs in SEA
        window : datetime.timedelta
            size of the half-window for the SEA (can also be given as serial time)
        delta : datetime.timedelta
            resolution of the input data series, which must be uniform (can also be
            given as serial time)

        Notes
        =====
        Output can be nicely plotted with :meth:`plot`, or for multiple
        objects use the :func:`multisea` function

        .. currentmodule:: spacepy.seapy
        .. autosummary::
            ~Sea2d.sea
            ~Sea2d.plot
        .. automethod:: sea
        .. automethod:: plot
        """
        def __init__(self, data, times, epochs, window=3., delta=1., verbose=False, y=[]):
            super(Sea2d, self).__init__(data, times, epochs, window=window, \
                  delta=delta, verbose=False, y=[])

            if y:
                self.y = np.linspace(y[0], y[1], data.shape[0]+1)
            else:
                self.y = np.linspace(0, data.shape[0]-1, data.shape[0]+1)

        def sea(self, storedata=False, quartiles=True, ci=False, mad=False,
            ci_quan='median', nmask=1, **kwargs):
            """Perform 2D superposed epoch analysis on data in object

            Uses object attributes obj.data, obj.times, obj.epochs, obj.delta,
            obj.window, all of which must be available on instantiation.

            Other Parameters
            ================
            storedata : boolean
                saves matrix of epoch windows as obj.datacube (default = False)
            quartiles : list
                calculates the inter-quartile range to show the spread
                (and is default);
            ci : float
                will find the bootstrapped confidence interval
                (and requires ci_quan to be set)
            mad : float
                will use the median absolute deviation for the spread;
            ci_quan : string
                can be set to 'median' or 'mean'

            Notes
            =====
            A basic plot can be raised with :meth:`plot`
            """
            #ensure all input is np array or correct form
            delt = float(self.delta)
            y = np.asarray(self.data, dtype=float)
            time,t_epoch = self._timeepoch(delt)
            if not nmask:
                nmask = 0 #set mask to exclude none

            #build SEA matrix and perform analysis
            wind = self.window
            l = y.shape[0]
            m = 2*int(wind) + 1
            n = len(t_epoch)
            y_sea = np.zeros((l,m,n), dtype=float)
            for i in range(n):
                dif = np.abs(time-t_epoch[i])
                j = np.where(dif == np.min(dif))
                sea_slice = y[:,j[0][0]-wind:j[0][0]+wind+1]
                y_sea[:,:,i] = sea_slice

            #find SEA mean, median and percentiles - exclude NaNs
            #y_sea_m = ma.masked_where(y_sea < 0., y_sea)
            try:
                badval = kwargs['badval']
            except KeyError:
                badval = np.nan
                y_sea_m = ma.masked_where(np.isnan(y_sea), y_sea)
            else:
                y_sea_m = ma.masked_values(y_sea, badval)
            #now get SEA quantities
            self.semean, self.semedian, self.countmask = np.empty((l,m)), np.empty((l,m)), np.empty((l,m))
            yj=0
            for ti in range(int(m)):
                for yj in range(l):
                    self.semean[yj,ti] = np.mean(y_sea_m[yj,ti,:].compressed()) #np.mean(y_sea_m, axis=2)
                    self.semedian[yj,ti] = np.median(y_sea_m[yj,ti,:].compressed())
                    self.countmask[yj,ti] = len(y_sea_m[yj,ti,:].compressed())
            self.semean = ma.masked_where(self.countmask<nmask, self.semean)#(np.isnan(self.semean), self.semean)
            self.semedian = ma.masked_where(self.countmask<nmask, self.semedian)#(np.isnan(self.semedian), self.semedian)
            self.perc25 = np.zeros((l,m))
            self.perc50 = np.zeros((l,m))
            self.perc75 = np.zeros((l,m))

            #maybe use median absolute deviation?
            #p75 = np.around(75*n/100)
            #p25 = np.around(25*n/100)
            #sea_sort = y_sea_m.copy()
            #sea_sort.sort(axis=0)
            ##self.perc25 = sea_sort[p25,0:]
            ##self.perc75 = sea_sort[p75,0:]

            self.x = np.linspace(-1.*self.window*delt,self.window*delt, \
            self.semedian.shape[1]+1)

            if storedata:
                self.datacube = y_sea_m
                print('sea(): datacube added as new attribute')

            if self.verbose:
                print('Superposed epoch analysis complete')

        def plot(self, xquan = 'Time Since Epoch', yquan='', xunits='',
                    yunits='', zunits='', epochline=False, usrlimy=[],
                    show=True, zlog=True, figsize=None, dpi=300):
            """Method called to create basic plot of 2D superposed epoch analysis.

            Uses object attributes created by :meth:`sea`.

            Other Parameters
            ================
            x(y)quan : str
                x(y)-axis label.  (default = 'Time since epoch' (None))
            x(y/z)units : str
                x(y/z)-axis units. (default = None (None))
            epochline : boolean
                put vertical line at zero epoch. (default = False)
            usrlimy : list
                override automatic y-limits on plot. (default = [])
            show : boolean
                shows plot; set to false to output plot object to variable
                (default = True)
            figsize : tuple
                (width, height) in inches
            dpi : int
                figure resolution in dots per inch (default=300)

            Notes
            =====
            If both quan and units are supplied, axis label will read
            'Quantity Entered By User [Units]'
            """
            try:
                dum = self.semedian
            except AttributeError:
                return 'Error: No superposed epoch results to plot'

            from matplotlib.colors import LogNorm

            if len(xunits)<1:
                xlstr = '%s' % xquan
            else:
                xlstr = '%s [%s]' % (xquan, xunits)
            if len(yquan)>=1 and len(yunits)>=1:
                ylstr = '%s [%s]' % (yquan, yunits)
            elif len(yquan)>=1 and len(yunits)<1:
                ylstr = '%s' % yquan
            else:
                ylstr = ''

            usry = self.y
            if usrlimy:
                st = (self.y>=usrlimy[0]).nonzero()
                st = st[0][0]
                en = (self.y<=usrlimy[1]).nonzero()
                en = en[0][-1]
                pld = self.semedian[st:en+1,:]
                usry = self.y[st:en+1]
                #ax0.set_ylim(usrlimy)

            if show==True and dpi==None:
                dpi=80
            elif show==False and dpi==None:
                dpi=300

            fig = plt.figure(figsize=figsize, dpi=dpi)
            ax0 = fig.add_subplot(111)
            if zlog:
                cax = ax0.pcolor(self.x, usry, pld, norm=LogNorm(vmin=np.nanmin(pld), vmax=np.nanmax(pld)))
            else:
                cax = ax0.pcolor(self.x, usry, pld)

            plt.xlabel(xlstr)
            plt.ylabel(ylstr)

            if usrlimy:
                ax0.set_ylim(usrlimy)

            if epochline:
                yr = ax0.get_ylim()
                if yr[0] < 0:
                    yrlo = yr[0]+yr[0]
                else:
                    yrlo = yr[0]-yr[0]
                if yr[1] < 0:
                    yrhi = yr[1]-yr[1]
                else:
                    yrhi = yr[1]+yr[1]
                ax0.plot([0,0], [yrlo,yrhi], 'k:', lw=2)
                plt.ylim(yr)

            ax0.set_xlim([self.x[0],self.x[-1]])
            hc1 = plt.colorbar(cax)
            if len(zunits)>=1:
                hc1.set_label(zunits)

            if show:
                plt.show()
                return None
            else:
                return fig

    def seadict(objlist, namelist):
        """Function to create dictionary of SeaPy.Sea objects.

        Parameters
        ==========
            - objlist: List of Sea objects.
            - namelist: List of variable labels for input objects.

        Other Parameters
        ================
        namelist = List containing names for y-axes.

        """
        try:
            assert type(objlist) == \
            list, 'seadict(): Inputs must be in lists'
        except AssertionError as args:
            raise ValueError('%s -- %s' % (args.__class__.__name__, args))

        nobj, nname = len(objlist), len(namelist)
        if nobj!=nname:
            raise ValueError('seadict(): Lengths of object list and names list must be equal')
        else:
            pass

        outdict = {}
        for i  in range(nobj):
            outdict[namelist[i]] = objlist[i]

        return outdict

    def multisea(dictobj, n_cols=1, epochline=False, usrlimx=[], usrlimy=[],
        xunits='', show=True, zunits='', zlog=True, figsize=None, dpi=300):
        """Function to create multipanel plot of superposed epoch analyses.

        Parameters
        ==========
        Dictionary of Sea objects (from superposedepoch.seadict()).

        Other Parameters
        ================
            - epochline (default = False) - put vertical line at zero epoch.
            - usrlimy (default = []) - override automatic y-limits on plot (same for all plots).
            - show (default = True) - shows plot; set to false to output plot object to variable
            - x/zunits - Units for labeling x and z axes, if required
            - figsize - tuple of (width, height) in inches
            - dpi (default=300) - figure resolution in dots per inch
            - n_cols - Number of columns: not yet implemented.

        Returns
        =======
        Plot of input object median and bounds (ci, mad, quartiles - see sea()).
        If keyword 'show' is False, output is a plot object.

        """
        import matplotlib.ticker as tik

        keys = list(dictobj.keys())
        pld, ply, plx, ylab = [], [], [], []
        qup, qlo = [], []
        keylist = sorted(keys)
        for key in keylist:
            tmp = dictobj[key].semedian
            pld.append(tmp) #pld (PLot Data)
            plx.append(dictobj[key].x) #plx (PLot X)
            qup.append(dictobj[key].bound_high)
            qlo.append(dictobj[key].bound_low)
            ylab.append(key) #ylab (Y-axis LABel)
            if tmp.ndim==2:
                ply.append(dictobj[key].y) #ply (Plot Y)

        if show==True and dpi==None:
            dpi=80
        elif show==False and dpi==None:
            dpi=300

        if n_cols > 1:
            print('multisea(): Multiple column output not yet implemented')
            n_fig = len(dictobj) #force single column output for now
            fignum = list(range(1,n_fig+1))
            fig = plt.figure()
        else:
            n_fig = len(dictobj)
            fignum = list(range(1,n_fig+1))
            fig = plt.figure(figsize=figsize, dpi=dpi)

        for i in range(n_fig):
            #loop over each subplot
            #create subplot panel number
            dum = str(n_fig)+'1'+str(fignum[i])
            ax = fig.add_subplot(dum)
            if pld[i].ndim==2: #if semean/median 2D, do colour-plot
                if zlog:
                    cax = ax0.pcolor(plx[i], ply[i], pld[i], norm=LogNorm(vmin=np.nanmin(pld), vmax=np.nanmax(pld)))
                else:
                    cax = ax.pcolor(plx[i],ply[i],pld[i])
                plt.ylabel(ylab[i])
                hc1 = plt.colorbar(cax)
                if len(zunits)>=1:
                    hc1.set_label(zunits)
            else: #else do line plot
                ax.plot(plx[i],pld[i], 'k-', lw=2)
                plt.hold(True)
                ax.plot(plx[i],qup[i], 'k-', lw=1.5)
                ax.plot(plx[i],qlo[i], 'k-', lw=1.5)
                plt.ylabel(ylab[i])

            if i==n_fig-1:
                #Add x-label to bottom panel
                if xunits:
                    xlab = 'Time since epoch [' + xunits + ']'
                else:
                    xlab = 'Time since epoch'
                plt.xlabel(xlab)

            if epochline:
                yr = plt.ylim()
                if yr[0] < 0:
                    yrlo = yr[0]+yr[0]
                else:
                    yrlo = yr[0]-yr[0]
                if yr[1] < 0:
                    yrhi = yr[1]-yr[1]
                else:
                    yrhi = yr[1]+yr[1]
                ax.plot([0,0], [yrlo,yrhi], 'k:', lw=1)
                plt.ylim(yr)

            if usrlimx:
                plt.xlim(usrlimx)

            if usrlimy:
                plt.ylim(usrlimy)

            majorticky=tik.MaxNLocator(7)
            ax.yaxis.set_major_locator(majorticky)

        if show:
            plt.show()
            return None
        else:
            return fig

    def readepochs(fname, iso=False, isofmt="%Y-%m-%dT%H:%M:%S"):
        """Read epochs from text file assuming YYYY MM DD hh mm ss format

        Parameters
        ==========
        Filename (include path)

        Other Parameters
        ================
        iso (default = False), read in ISO date format
        isofmt (default is YYYY-mm-ddTHH:MM:SS, code is %Y-%m-%dT%H:%M:%S)

        Returns
        =======
        epochs (type=list)

        """
        if iso==False:
            from numpy import loadtxt, zeros

            intime = loadtxt(fname)
            dum = zeros([intime.shape[0],6])
            for i in range(intime.shape[1]):
                dum[:,i] = intime[:,i]

            epochs=[]
            for i in range(dum.shape[0]):
                dtobj = dt.datetime(int(dum[i,0]), int(dum[i,1]), \
                int(dum[i,2]), int(dum[i,3]), int(dum[i,4]), int(dum[i,5]))
                epochs.append(dtobj)
        else:
            fh = open(fname,'r')
            intime = fh.readlines()
            epochs=[]
            for d in intime:
                d = d.strip()
                dtobj = dt.datetime.strptime(d, isofmt)
                epochs.append(dtobj)
        return epochs

    def sea_signif(obj1, obj2, test='KS', show=True, xquan = 'Time Since Epoch',
            yquan='', xunits='', yunits='', epochline=True, usrlimy=[]):
        """Test for similarity between distributions at each lag in two 1-D SEAs

        Parameters
        ==========
        Two seapy.Sea() instances for comparison

        Other Parameters
        ================
            - show (default = True)
            - x(y)quan (default = 'Time since epoch' (None)) - x(y)-axis label.
            - x(y)units (default = None (None)) - x(y)-axis units.
            - epochline (default = True) - put vertical line at zero epoch.
            - usrlimy (default = []) - override automatic y-limits on plot.

        Examples
        ========
        >>> obj1 = seapy.Sea(data1, times1, epochs1)
        >>> obj2 = seapy.Sea(data2, times2, epochs2)
        >>> obj1.sea(storedata=True)
        >>> obj2.sea(storedata=True)
        >>> seapy.sea_signif(obj1, obj2)

        """
        try:
            assert isinstance(obj1, Sea)
            assert isinstance(obj2, Sea)
        except:
            raise TypeError("Inputs must both be seapy.Sea() instances of same length")

        keylist, S, prob = ['KS','U'], [], []
        try:
            assert test.upper() in keylist
        except:
            raise NotImplementedError("Test "+self.dtype+" not implemented, only "+str(keylist))

        from scipy.stats import ks_2samp, mannwhitneyu

        if test.upper() == 'KS':
            try:
                for x in range(obj1.datacube.shape[1]):
                    tD, tprobKS2 = ks_2samp(obj1.datacube[:,x].compressed(),
                        obj2.datacube[:,x].compressed())
                    S.append(tD)
                    prob.append(tprobKS2)
            except:
                raise AttributeError('''KS significance testing requires datacube attribute\n
                    Run sea() with kwarg storedata''')

        if test.upper() == 'U':
            for x,y in zip(obj1.datacube.transpose(), obj2.datacube.transpose()):
                tU, tprobU = mannwhitneyu(x, y)
                S.append(tU)
                prob.append(tprobU*2)

        def add_epochline(ax):
            yr = ax.get_ylim()
            if yr[0] < 0:
                yrlo = yr[0]+yr[0]
            else:
                yrlo = yr[0]-yr[0]
            if yr[1] < 0:
                yrhi = yr[1]-yr[1]
            else:
                yrhi = yr[1]+yr[1]

            return (yr, yrlo, yrhi)

        if len(xunits)<1:
            xlstr = '%s' % xquan
        else:
            xlstr = '%s [%s]' % (xquan, xunits)
        if len(yquan)>=1 and len(yunits)>=1:
            ylstr = '%s [%s]' % (yquan, yunits)
        elif len(yquan)>=1 and len(yunits)<1:
            ylstr = '%s' % yquan
        else:
            ylstr = ''

        #set up plot panels
        fig = plt.figure()
        ax0 = fig.add_subplot(211)
        pos = ax0.get_position()
        ax0.set_position([pos.bounds[0], 0.4, pos.bounds[2], 0.55])
        ax1 = fig.add_subplot(212, position=[pos.bounds[0], 0.1, pos.bounds[2], 0.25])
        #overlay superposed epochs
        ax0.plot(obj1.x, obj1.semedian, 'b-', lw=1.5)
        plt.hold(True)
        ax0.plot(obj1.x, obj1.bound_high, 'b--')
        ax0.plot(obj1.x, obj1.bound_low, 'b--')
        ax0.plot(obj2.x, obj2.semedian, 'r-', lw=1.5)
        ax0.plot(obj2.x, obj2.bound_high, 'r--')
        ax0.plot(obj2.x, obj2.bound_low, 'r--')
        if epochline:
            yr, yrlo, yrhi = add_epochline(ax0)
            ax0.plot([0,0], [yrlo,yrhi], 'k:', lw=1)
            ax0.set_ylim(yr)
        ax0.set_ylabel(ylstr)
        #plot prob in lower panel
        ax1.plot(obj1.x, prob, 'r-', lw=1.5, drawstyle='steps-mid')
        ax1.plot([obj1.x[0], obj1.x[-1]], [0.05, 0.05], 'b-')
        if epochline:
            yr, yrlo, yrhi = add_epochline(ax1)
            ax1.plot([0,0], [yrlo,yrhi], 'k:', lw=1)
            ax1.set_ylim(yr)
        ax1.set_xlabel(xlstr)
        ax1.set_ylabel('Prob. of H0')

        if show:
            plt.show()
            return None
        else:
            return fig

            #now make an output object to store the test stats and prob.
        #return None

### Navigation

- index
- modules |
- modules |
- homepage|
- search|
- documentation »
- Module code »