"""
Filter non-equidistant signals (spectra, timeseries...).

Currently implemented:
    - Gaussian
    - Sinc
    - Box
    - Iterative Nonlinear filter

Example usage:

Generate some data:

>>> x = np.linspace(0,150,10000)
>>> x_= np.linspace(0,150,100)
>>> y = np.sin(2*pi/20.*x)+np.random.normal(size=len(x))

Apply some filter:

>>> x1,y1,pnts = filter_signal(x,y,"gauss",sigma=1)
>>> x2,y2,pnts = filter_signal(x,y,"pijpers",delta=1)
>>> x3,y3,pnts = filter_signal(x,y,"box",window_width=10)
>>> x3_,y3_,pnts = filter_signal(x,y,"box",window_width=10,x_template=x_,threads=2)

>>> import pylab as pl
>>> p = pl.plot(x,y,'ko')
>>> p = pl.plot(x1,y1,'ro',mec='r',label='Gauss')
>>> p = pl.plot(x2,y2,'bo',mec='b',label='Pijpers')
>>> p = pl.plot(x3,y3,'go',mec='g',label='Box')
>>> p = pl.plot(x3_,y3_,'gs',label='Box with template')
>>> p = pl.legend()

"""
import logging
import numpy as np
from numpy import sqrt,exp,pi,cos,sinc,trapz,average

#from scipy.integrate import trapz

from ivs.aux.decorators import make_parallel
from ivs.timeseries.decorators import parallel_pergram,defaults_filtering

logger = logging.getLogger("TS.FILTERING")

#{ Main filter program for convolution-based filters

@defaults_filtering
@parallel_pergram
@make_parallel
def filter_signal(x,y,ftype,f0=None,fn=None,step=1,x_template=None,**kwargs):
    """
    Filter a signal.

    Handles equidistant and non-equidistant data. C{x} coordinate array
    must be monotonically increasing, but does not need to be strict monotonically
    increasing (e.g. their can be duplicate C{x} coordinates).

    It is possible to define a new template C{x} coordinate array on which to
    filter to signal C{y}.

    For some filters, it is possible to set an adjustable window: that is,
    you can give an array to the C{window} parameter, but it needs to be the
    same length as C{x_template}.

    Example usage:

    Generate some data:

    >>> import time
    >>> x = np.linspace(0,150,10000)
    >>> y = np.sin(2*np.pi/20.*x)+np.random.normal(size=len(x))

    Apply some filter:

    >>> c0 = time.time()
    >>> x1,y1,pnts = filter_signal(x,y,"gauss",sigma=1)
    >>> print time.time()-c0
    >>> c0 = time.time()
    >>> x1,y1,pnts = filter_signal(x,y,"gauss",sigma=1,threads=2)
    >>> print time.time()-c0

    Output parameter C{pnts} shows you how many points of the original signal
    were used to compute the given point. E.g. for a box filter, it will give
    the number of points over which was averaged.

    @param ftype: one of 'gauss','pijpers','box','inl'
    @type ftype: string
    @rtype: tuple
    @return: output from the used filter: typically (x, y, pnts)
    """
    if x_template is None:
        x_template = x + 0.
    if f0 is None: f0 = 0
    if fn is None: fn = len(x_template)
    #-- set window and kernel function
    ftype = ftype.lower()
    window = globals()[ftype+'_window']
    kernel = globals()[ftype+'_kernel']
    logger.info("Applying filter: %s"%(ftype))

    #-- set window width
    lower_window,higher_window = window(**kwargs)

    #-- perhaps the window is a number, perhaps an array. Make sure it is an
    #   array
    if not isinstance(lower_window,np.ndarray):
        lower_window = lower_window*np.ones(len(x_template))[f0:fn:step]
    if not isinstance(higher_window,np.ndarray):
        higher_window = higher_window*np.ones(len(x_template))[f0:fn:step]

    #-- start running through timeseries (make searchsorted local for speedup)
    logger.debug("FILTER between index %d-%d with step %d"%(f0,fn,step))
    x_template = x_template[f0:fn:step]
    searchsorted = x.searchsorted
    out = [kernel(x,y,t,index=searchsorted([t-1e-30-lower_window[i],t+1e-30+higher_window[i]]),
                        **kwargs) for i,t in enumerate(x_template)]
    #-- that's it!
    return tuple([x_template] + list(np.array(out).T))

#}

#{ Basic functions for convolution-based filters

def _fixed_window(window_width=0):
    """
    Define general window
    @rtype: (float,float)
    @return: window limits
    """
    lower_window = window_width/2.
    higher_window = window_width/2.
    #logger.debug("Window: width=%f"%(window_width))
    return lower_window,higher_window
#}
#{ Convolution-based filter kernels and Windows

def gauss_window(sigma=1.,limit=4.):
    """
    Define Gaussian_window
    @rtype: (float,float)
    @return: window limits
    """
    if isinstance(sigma,np.ndarray):
        sigma = sigma.max()
    return _fixed_window(window_width=2*sigma*limit)


def gauss_kernel(times, signal, t,sigma=1.,index=(0,-1),norm_weights=True):
    """
    Define Gaussian kernel.

    #Import necessary modules:
        #>>> from pylab import plot,figure,title,subplot
        #>>> from sigproc.timeseries import tfreq

    #Generate some data:
        #>>> x = linspace(0,150,10000)
        #>>> y = random.normal(size=len(x))

    #Apply Gaussian filter twice, subtract and calculate periodogram:
        #>>> y1,pnts = filter_signal(x,y,"gauss",sigma=1)
        #>>> y2,pnts = filter_signal(x,y,"gauss",sigma=3)

    #Plot the results:
        #>>> p=figure(figsize=(8,18))
        #>>> p=subplot(311);p=title("GAUSSIAN FILTER")
        #>>> p=plot(x,y,'ko')
        #>>> p=plot(x,y1,'r-',linewidth=2)
        #>>> p=plot(x,y2,'b-',linewidth=2)
        #>>> p=subplot(312)
        #>>> p=plot(x,y1-y2,'ko')
        #>>> p=subplot(313)
        #>>> p=plot(per1[0],per1[1],'k-')
        #>>> p=plot(per2[0],per2[1],'r-')

    @rtype: (ndarray,)
    """
    index0,indexn = index
    #-- maybe sigma is changing
    if isinstance(sigma,np.ndarray):
        sigma = sigma[(indexn+index0)/2]
    #-- compute convolution kernel -- should we normalize? so that sum(weights)=1
    times_ = times[index0:indexn]
    signal_ = signal[index0:indexn]
    weights = 1./(sqrt(2.*pi)*sigma) * exp( -(times_-t)**2./(2.*sigma**2.))
    if norm_weights and len(times)>1:
        convolved = trapz(weights*signal_,x=times_-t)
        norm_fact = trapz(weights,x=times_-t)
    else:
        convolved = average(signal_,weights=weights)
        norm_fact = 1
    convolved_signal = convolved/norm_fact
    return convolved_signal,len(times_)

def mad(a, c=0.6745):
    """
    Median Absolute Deviation of a 1D array:

    median(abs(a - median(a))) / c

    @rtype: float
    """
    return np.median(np.abs(a-np.median(a)))/c

def inl_window(**kwargs):
    """
    Defines the INL window

    @rtype: (float,float)
    @return: window limits
    """
    return _fixed_window(**kwargs)

def inl_kernel(times_in,signal_in,t,c=0.6745,sig_level=3.,tolerance=0.01,index=(0,-1),window_width=None):
    """
    Iterative Nonlinear Filter (Aigrain).

    Example usage:

    #Import necessary modules:
        #>>> from pylab import plot,figure,title,subplot
        #>>> from sigproc.timeseries import tfreq

    #Generate some data:
        #>>> x = linspace(0,150,10000)
        #>>> y = sin(2*pi*x/20.*x)+random.normal(size=len(x))

    #Apply INL filter twice, subtract and calculate periodogram:
        #>>> y1,pnts1,mads = filter_signal(x,y,"inl",window_width=1)
        #>>> y2,pnts2,mads = filter_signal(x,y,"inl",window_width=10)
        #>>> freq1,per1,stat1 = tfreq.scargle(x,y,norm='amplitude',fn=4)
        #>>> freq2,per2,stat2 = tfreq.scargle(x,y1-y2,norm='amplitude',fn=4)

    #Plot the results:
        #>>> p=figure(figsize=(8,18))
        #>>> p=subplot(311);p=title("INL FILTER")
        #>>> p=plot(x,y,'ko')
        #>>> p=plot(x,y1,'r-',linewidth=2)
        #>>> p=plot(x,y2,'b-',linewidth=2)
        #>>> p=subplot(312)
        #>>> p=plot(x,y1-y2,'ko')
        #>>> p=subplot(313)
        #>>> p=plot(per1[0],per1[1],'k-')
        #>>> p=plot(per2[0],per2[1],'r-')

    @rtype: (ndarray,ndarray)
    @return: continuum,sigma
    """
    index0,indexn = index
    times = times_in[index0:indexn]
    signal = signal_in[index0:indexn]
    sigma = mad(signal,c=c)
    continuum = np.median(signal)
    outliers = (np.abs(continuum-signal)>sig_level*sigma)
    max_iter = 3
    for iteration in range(max_iter):
        signal_ = signal[outliers==0]
        sigma = mad(signal_,c=c)
        continuum_ = np.median(signal_)
        if abs((continuum_-continuum)/continuum_)<tolerance:
            break
        else:
            continuum = continuum_
            outliers = (np.abs(continuum - signal_)>sig_level*sigma)

    return continuum_, sigma,len(times)

def pijpers_window(delta=1.):
    """
    Defines the window for the Pijpers filter.

    @rtype: (float,float)
    @return: window limits
    """
    return _fixed_window(window_width=100*delta)
    return _fixed_window(**kwargs)


def pijpers_kernel(times_in, signal_in,t,limit=0.000001,delta=1.,sigma=1.,gamma=0,
                         r=0.0001,index0=0,indexn=-1,index=(0,-1),norm_weights=True):
    """
    Defines the Pijpers (2006) filter kernel.

    Equals box-multiplying in the frequency domain.

    Example usage:

    #Import necessary modules:
        #>>> from pylab import plot,figure,title,subplot
        #>>> from sigproc.timeseries import tfreq

    #Generate some data:
        #>>> x = linspace(0,150,10000)
        #>>> y = random.normal(size=len(x))

    #Apply Gaussian filter twice, subtract and calculate periodogram:
        #>>> y1,pnts1 = filter_signal(x,y,"pijpers",delta=1)
        #>>> y2,pnts2 = filter_signal(x,y,"pijpers",delta=3)
        #>>> freq1,per1,stat1 = tfreq.scargle(x,y,norm='amplitude',fn=4)
        #>>> freq2,per2,stat2 = tfreq.scargle(x,y1-y2,norm='amplitude',fn=4)

    #Plot the results:
        #>>> p=figure(figsize=(8,18))
        #>>> p=subplot(311);p=title("PIJPERS FILTER")
        #>>> p=plot(x,y,'ko')
        #>>> p=plot(x,y1,'r-',linewidth=2)
        #>>> p=plot(x,y2,'b-',linewidth=2)
        #>>> p=subplot(312)
        #>>> p=plot(x,y1-y2,'ko')
        #>>> p=subplot(313)
        #>>> p=plot(per1[0],per1[1],'k-')
        #>>> p=plot(per2[0],per2[1],'r-')

    @rtype: (ndarray,)
    @return: convolved signal
    """
    index0,indexn = index
    times = times_in[index0:indexn]
    signal = signal_in[index0:indexn]

    delta = delta*2*pi

    x = delta * (times-t)
    #-- compute convolution kernel -- should we normalize? so that sum(weights)=1
    weights = delta/pi * sinc(x/pi) * exp(-1/4. * r**2 * x**2) * cos(gamma*x)
    #-- compensate for severe unequidistant sampling
    convolved = np.trapz(weights*signal,x=times-t)
    norm_fact = np.trapz(weights,x=times-t)
    convolved_signal = convolved/norm_fact
    return convolved_signal,len(times)

def box_window(**kwargs):
    """
    Defines the window for the box-filter.

    @rtype: (float,float)
    @return: window limits
    """
    return _fixed_window(**kwargs)

def box_kernel(times_in,signal_in,t,window_width=None,index=(0,-1),norm_weights=True):
    """
    Defines the Box filter kernel (moving average).

    Equals sinc-multiplication of frequency domain.

    Example usage:

    #Import necessary modules:
        #>>> from pylab import plot,figure,title,subplot
        #>>> from sigproc.timeseries import tfreq

    #Generate some data:
        #>>> x = linspace(0,150,10000)
        #>>> y = random.normal(size=len(x))

    #Apply Gaussian filter twice, subtract and calculate periodogram:
        #>>> y1,pnts = filter_signal(x,y,"box",window_width=1)
        #>>> y2,pnts = filter_signal(x,y,"box",window_width=3)

    @rtype: (ndarray,)
    @return: convolved signal
    """
    index0,indexn = index
    times = times_in[index0:indexn]
    signal = signal_in[index0:indexn]
    weights = np.ones(len(times))
    if norm_weights:
        weights /= np.sum(weights)

    convolved_signal = np.sum(weights*signal)
    return convolved_signal,len(times)




#def box_kernel(times_in,signal_in,t,window_width=None,index=(0,-1),
         #norm_weights=True,is_error_array=False):
    #"""
    #Defines the Box filter kernel (moving average).

    #Equals sinc-multiplication in frequency domain.

    #When C{is_error_array} is C{True}, the integration will be done differently.
    #Instead of the usual

    #F_j = sum_i (F_i dx_{i,j}) / sum_i (dx_{i,j})

    #it will be

    #s_j = sqrt(sum_i (s_i dx_{i,j})**2) / sum_i (dx_{i,j})

    #You can only set C{is_error_array} to C{True} when C{norm_weights=True}.

    #Example usage:

    ##Import necessary modules:
        ##>>> from pylab import plot,figure,title,subplot
        ##>>> from sigproc.timeseries import tfreq

    ##Generate some data:
        ##>>> x = linspace(0,150,10000)
        ##>>> y = random.normal(size=len(x))

    ##Apply Gaussian filter twice, subtract and calculate periodogram:
        ##>>> y1,pnts = filter_signal(x,y,"box",window_width=1)
        ##>>> y2,pnts = filter_signal(x,y,"box",window_width=3)

    #@rtype: (ndarray,)
    #@return: convolved signal
    #"""
    #index0,indexn = index
    #times = times_in[index0:indexn]
    #signal = signal_in[index0:indexn]
    #weights = np.ones(len(times))
    #if norm_weights:
        #if is_error_array:
            #convolved = sqrt(trapz((weights*signal)**2,x=times-t))/np.trapz(weights,x=times-t)
        #else:
            #convolved =      trapz( weights*signal,    x=times-t) /np.trapz(weights,x=times-t)
        #norm_fact = 1
            ##trapz(weights*signal,x=times-t)
            ##norm_fact = trapz(weights,x=times-t)
    #else:
        #assert(is_error_array==False)
        #convolved = average(signal,weights=weights)
        #norm_fact = 1

    #convolved_signal = convolved/norm_fact
    ##weights /= np.sum(weights)
    ##convolved_signal = np.sum(weights*signal)
    #return convolved_signal,len(times)









#}

def test():
    """

    >>> from pylab import show
    >>> p=show()

    """
    import doctest
    doctest.testmod()


if __name__ == "__main__":
    test()