pyqtgraph/flowchart/library/functions.py

import scipy
import numpy as np
from pyqtgraph.metaarray import MetaArray

def downsample(data, n, axis=0, xvals='subsample'):
    """Downsample by averaging points together across axis.
    If multiple axes are specified, runs once per axis.
    If a metaArray is given, then the axis values can be either subsampled
    or downsampled to match.
    """
    ma = None
    if (hasattr(data, 'implements') and data.implements('MetaArray')):
        ma = data
        data = data.view(np.ndarray)
        
    
    if hasattr(axis, '__len__'):
        if not hasattr(n, '__len__'):
            n = [n]*len(axis)
        for i in range(len(axis)):
            data = downsample(data, n[i], axis[i])
        return data
    
    nPts = int(data.shape[axis] / n)
    s = list(data.shape)
    s[axis] = nPts
    s.insert(axis+1, n)
    sl = [slice(None)] * data.ndim
    sl[axis] = slice(0, nPts*n)
    d1 = data[tuple(sl)]
    #print d1.shape, s
    d1.shape = tuple(s)
    d2 = d1.mean(axis+1)
    
    if ma is None:
        return d2
    else:
        info = ma.infoCopy()
        if 'values' in info[axis]:
            if xvals == 'subsample':
                info[axis]['values'] = info[axis]['values'][::n][:nPts]
            elif xvals == 'downsample':
                info[axis]['values'] = downsample(info[axis]['values'], n)
        return MetaArray(d2, info=info)


def applyFilter(data, b, a, padding=100, bidir=True):
    """Apply a linear filter with coefficients a, b. Optionally pad the data before filtering
    and/or run the filter in both directions."""
    d1 = data.view(np.ndarray)
    
    if padding > 0:
        d1 = np.hstack([d1[:padding], d1, d1[-padding:]])
    
    if bidir:
        d1 = scipy.signal.lfilter(b, a, scipy.signal.lfilter(b, a, d1)[::-1])[::-1]
    else:
        d1 = scipy.signal.lfilter(b, a, d1)
    
    if padding > 0:
        d1 = d1[padding:-padding]
        
    if (hasattr(data, 'implements') and data.implements('MetaArray')):
        return MetaArray(d1, info=data.infoCopy())
    else:
        return d1
    
def besselFilter(data, cutoff, order=1, dt=None, btype='low', bidir=True):
    """return data passed through bessel filter"""
    if dt is None:
        try:
            tvals = data.xvals('Time')
            dt = (tvals[-1]-tvals[0]) / (len(tvals)-1)
        except:
            dt = 1.0
    
    b,a = scipy.signal.bessel(order, cutoff * dt, btype=btype) 
    
    return applyFilter(data, b, a, bidir=bidir)
    #base = data.mean()
    #d1 = scipy.signal.lfilter(b, a, data.view(ndarray)-base) + base
    #if (hasattr(data, 'implements') and data.implements('MetaArray')):
        #return MetaArray(d1, info=data.infoCopy())
    #return d1

def butterworthFilter(data, wPass, wStop=None, gPass=2.0, gStop=20.0, order=1, dt=None, btype='low', bidir=True):
    """return data passed through bessel filter"""
    if dt is None:
        try:
            tvals = data.xvals('Time')
            dt = (tvals[-1]-tvals[0]) / (len(tvals)-1)
        except:
            dt = 1.0
    
    if wStop is None:
        wStop = wPass * 2.0
    ord, Wn = scipy.signal.buttord(wPass*dt*2., wStop*dt*2., gPass, gStop)
    #print "butterworth ord %f   Wn %f   c %f   sc %f" % (ord, Wn, cutoff, stopCutoff)
    b,a = scipy.signal.butter(ord, Wn, btype=btype) 
    
    return applyFilter(data, b, a, bidir=bidir)


def rollingSum(data, n):
    d1 = data.copy()
    d1[1:] += d1[:-1]  # integrate
    d2 = np.empty(len(d1) - n + 1, dtype=data.dtype)
    d2[0] = d1[n-1]  # copy first point
    d2[1:] = d1[n:] - d1[:-n]  # subtract
    return d2


def mode(data, bins=None):
    """Returns location max value from histogram."""
    if bins is None:
        bins = int(len(data)/10.)
        if bins < 2:
            bins = 2
    y, x = np.histogram(data, bins=bins)
    ind = np.argmax(y)
    mode = 0.5 * (x[ind] + x[ind+1])
    return mode
    
def modeFilter(data, window=500, step=None, bins=None):
    """Filter based on histogram-based mode function"""
    d1 = data.view(np.ndarray)
    vals = []
    l2 = int(window/2.)
    if step is None:
        step = l2
    i = 0
    while True:
        if i > len(data)-step:
            break
        vals.append(mode(d1[i:i+window], bins))
        i += step
            
    chunks = [np.linspace(vals[0], vals[0], l2)]
    for i in range(len(vals)-1):
        chunks.append(np.linspace(vals[i], vals[i+1], step))
    remain = len(data) - step*(len(vals)-1) - l2
    chunks.append(np.linspace(vals[-1], vals[-1], remain))
    d2 = np.hstack(chunks)
    
    if (hasattr(data, 'implements') and data.implements('MetaArray')):
        return MetaArray(d2, info=data.infoCopy())
    return d2

def denoise(data, radius=2, threshold=4):
    """Very simple noise removal function. Compares a point to surrounding points,
    replaces with nearby values if the difference is too large."""
    
    
    r2 = radius * 2
    d1 = data.view(np.ndarray)
    d2 = data[radius:] - data[:-radius] #a derivative
    #d3 = data[r2:] - data[:-r2]
    #d4 = d2 - d3
    stdev = d2.std()
    #print "denoise: stdev of derivative:", stdev
    mask1 = d2 > stdev*threshold #where derivative is large and positive
    mask2 = d2 < -stdev*threshold #where derivative is large and negative
    maskpos = mask1[:-radius] * mask2[radius:] #both need to be true
    maskneg = mask1[radius:] * mask2[:-radius]
    mask = maskpos + maskneg
    d5 = np.where(mask, d1[:-r2], d1[radius:-radius]) #where both are true replace the value with the value from 2 points before
    d6 = np.empty(d1.shape, dtype=d1.dtype) #add points back to the ends
    d6[radius:-radius] = d5
    d6[:radius] = d1[:radius]
    d6[-radius:] = d1[-radius:]
    
    if (hasattr(data, 'implements') and data.implements('MetaArray')):
        return MetaArray(d6, info=data.infoCopy())
    return d6

def adaptiveDetrend(data, x=None, threshold=3.0):
    """Return the signal with baseline removed. Discards outliers from baseline measurement."""
    if x is None:
        x = data.xvals(0)
    
    d = data.view(np.ndarray)
    
    d2 = scipy.signal.detrend(d)
    
    stdev = d2.std()
    mask = abs(d2) < stdev*threshold
    #d3 = where(mask, 0, d2)
    #d4 = d2 - lowPass(d3, cutoffs[1], dt=dt)
    
    lr = stats.linregress(x[mask], d[mask])
    base = lr[1] + lr[0]*x
    d4 = d - base
    
    if (hasattr(data, 'implements') and data.implements('MetaArray')):
        return MetaArray(d4, info=data.infoCopy())
    return d4
    

def histogramDetrend(data, window=500, bins=50, threshold=3.0):
    """Linear detrend. Works by finding the most common value at the beginning and end of a trace, excluding outliers."""
    
    d1 = data.view(np.ndarray)
    d2 = [d1[:window], d1[-window:]]
    v = [0, 0]
    for i in [0, 1]:
        d3 = d2[i]
        stdev = d3.std()
        mask = abs(d3-np.median(d3)) < stdev*threshold
        d4 = d3[mask]
        y, x = np.histogram(d4, bins=bins)
        ind = np.argmax(y)
        v[i] = 0.5 * (x[ind] + x[ind+1])
        
    base = np.linspace(v[0], v[1], len(data))
    d3 = data.view(np.ndarray) - base
    
    if (hasattr(data, 'implements') and data.implements('MetaArray')):
        return MetaArray(d3, info=data.infoCopy())
    return d3
    
def concatenateColumns(data):
    """Returns a single record array with columns taken from the elements in data. 
    data should be a list of elements, which can be either record arrays or tuples (name, type, data)
    """
    
    ## first determine dtype
    dtype = []
    names = set()
    maxLen = 0
    for element in data:
        if isinstance(element, np.ndarray):
            ## use existing columns
            for i in range(len(element.dtype)):
                name = element.dtype.names[i]
                dtype.append((name, element.dtype[i]))
            maxLen = max(maxLen, len(element))
        else:
            name, type, d = element
            if type is None:
                type = suggestDType(d)
            dtype.append((name, type))
            if isinstance(d, list) or isinstance(d, np.ndarray):
                maxLen = max(maxLen, len(d))
        if name in names:
            raise Exception('Name "%s" repeated' % name)
        names.add(name)
            
            
    
    ## create empty array
    out = np.empty(maxLen, dtype)
    
    ## fill columns
    for element in data:
        if isinstance(element, np.ndarray):
            for i in range(len(element.dtype)):
                name = element.dtype.names[i]
                try:
                    out[name] = element[name]
                except:
                    print("Column:", name)
                    print("Input shape:", element.shape, element.dtype)
                    print("Output shape:", out.shape, out.dtype)
                    raise
        else:
            name, type, d = element
            out[name] = d
            
    return out
    
def suggestDType(x):
    """Return a suitable dtype for x"""
    if isinstance(x, list) or isinstance(x, tuple):
        if len(x) == 0:
            raise Exception('can not determine dtype for empty list')
        x = x[0]
        
    if hasattr(x, 'dtype'):
        return x.dtype
    elif isinstance(x, float):
        return float
    elif isinstance(x, int):
        return int
    #elif isinstance(x, basestring):  ## don't try to guess correct string length; use object instead.
        #return '<U%d' % len(x)
    else:
        return object