def __init__(self, sf, npts, nbins=18, pha_f=[2, 4], pha_meth='hilbert',
pha_cycle=3, amp_f=[60, 200], amp_meth='hilbert', amp_cycle=6,
window=None, width=None, step=None, time=None,
**kwargs):
# Check pha and amp methods:
_checkref('pha_meth', pha_meth, ['hilbert', 'hilbert1', 'hilbert2'])
_checkref('amp_meth', amp_meth, ['hilbert', 'hilbert1', 'hilbert2'])
# Check the type of f:
if (len(pha_f) == 4) and isinstance(pha_f[0], (int, float)):
pha_f = binarize(
pha_f[0], pha_f[1], pha_f[2], pha_f[3], kind='list')
if (len(amp_f) == 4) and isinstance(amp_f[0], (int, float)):
amp_f = binarize(
amp_f[0], amp_f[1], amp_f[2], amp_f[3], kind='list')
self.xvec = []
# Binarize phase vector :
self._binsize = 360 / nbins
self._phabin = np.arange(0, 360, self._binsize)
self.phabin = np.concatenate((self._phabin[:, np.newaxis],
self._phabin[:, np.newaxis]+self._binsize), axis=1)
# Initialize coupling:
_coupling.__init__(self, pha_f, 'phase', pha_meth, pha_cycle,
amp_f, 'amplitude', amp_meth, amp_cycle,
sf, npts, window, width, step, time, **kwargs)
self._nbins = nbins
def __init__(self,
sf,
npts,
Id='113',
pha_f=[2, 4],
pha_meth='hilbert',
pha_cycle=3,
amp_f=[60, 200],
amp_meth='hilbert',
amp_cycle=6,
nbins=18,
window=None,
width=None,
step=None,
time=None,
**kwargs):
# Check pha and amp methods:
_checkref('pha_meth', pha_meth, ['hilbert', 'hilbert1', 'hilbert2'])
_checkref('amp_meth', amp_meth, ['hilbert', 'hilbert1', 'hilbert2'])
# Check the type of f:
if (len(pha_f) == 4) and isinstance(pha_f[0], (int, float)):
pha_f = binarize(pha_f[0],
pha_f[1],
pha_f[2],
pha_f[3],
kind='list')
if (len(amp_f) == 4) and isinstance(amp_f[0], (int, float)):
amp_f = binarize(amp_f[0],
amp_f[1],
amp_f[2],
amp_f[3],
kind='list')
self.xvec = []
# Initalize pac object :
self.Id = Id
me = Id[0]
# Manage settings :
# 1 - Choose if we extract phase or amplitude :
# - Methods using phase // amplitude :
if me in ['1', '2', '3', '5', '6']:
pha_kind, amp_kind = 'phase', 'amplitude'
# - Methods using phase // phase :
elif me in ['4']:
pha_kind, amp_kind = 'phase', 'amplitude'
# 2 - Specific case of Ozkurt :
if me == '5':
Id = '500'
# Initialize cfc :
_coupling.__init__(self, pha_f, pha_kind, pha_meth, pha_cycle, amp_f,
amp_kind, amp_meth, amp_cycle, sf, npts, window,
width, step, time, **kwargs)
# Get pac model :
_, _, _, ModelStr, SurStr, NormStr = CfcSettings(Id, nbins)
self.model = [
'Method : ' + ModelStr, 'Surrogates : ' + SurStr,
'Normalization : ' + NormStr
]
self._nbins = nbins
def __init__(self, sf, npts, kind, f, baseline, norm, method, window,
width, step, split, time, meanT, **kwargs):
# Check the type of f:
if (len(f) == 4) and isinstance(f[0], (int, float)):
f = binarize(f[0], f[1], f[2], f[3], kind='list')
# Manage time and frequencies:
self._window, self.xvec = _manageWindow(npts,
window=window,
width=width,
step=step,
time=time)
self.f, self._fSplit, self._fSplitIndex = _manageFrequencies(
f, split=split)
# Get variables :
self._baseline = baseline
self._norm = norm
self._width = width
self._step = step
self._split = split
self._nf = len(self.f)
self._sf = sf
self._npts = npts
self.yvec = [round((k[0] + k[1]) / 2) for k in self.f]
self._kind = kind
self._fobj = fextract(method, kind, **kwargs)
self._meanT = meanT
def __init__(self,
sf,
npts,
f=[2, 4],
method='hilbert',
cycle=3,
sample=None,
time=None,
**kwargs):
# Check pha and amp methods:
_checkref('pha_meth', method, ['hilbert', 'hilbert1', 'hilbert2'])
# Check the type of f:
if (len(f) == 4) and isinstance(f[0], (int, float)):
f = binarize(f[0], f[1], f[2], f[3], kind='list')
# Initialize PLV :
_coupling.__init__(self, f, 'phase', method, cycle, f, 'phase', method,
cycle, sf, npts, None, None, None, time, **kwargs)
if time is None:
time = np.arange(npts)
else:
time = time
if sample is None:
sample = slice(npts)
self._sample = sample
self.time = time[sample]
del self.amp
def __init__(self, sf, npts, kind, f, baseline, norm, method, window,
width, step, split, time, meanT, **kwargs):
# Check the type of f:
if (len(f) == 4) and isinstance(f[0], (int, float)):
f = binarize(f[0], f[1], f[2], f[3], kind='list')
# Manage time and frequencies:
self._window, self.xvec = _manageWindow(
npts, window=window, width=width, step=step, time=time)
self.f, self._fSplit, self._fSplitIndex = _manageFrequencies(
f, split=split)
# Get variables :
self._baseline = baseline
self._norm = norm
self._width = width
self._step = step
self._split = split
self._nf = len(self.f)
self._sf = sf
self._npts = npts
self.yvec = [round((k[0]+k[1])/2) for k in self.f]
self._kind = kind
self._fobj = fextract(method, kind, **kwargs)
self._meanT = meanT
if (self._window is not None) and (time is not None):
self.xvec = binArray(time, self._window)[0]
self.xvec = list(self.xvec)
def __init__(self, sf, npts, f=[60, 200], step=None, width=None,
time=None):
# Check the type of f:
if (len(f) == 4) and isinstance(f[0], (int, float)):
self.yvec = binarize(f[0], f[1], f[2], f[3], kind='list')
else:
self.yvec = f
if not isinstance(f[0], list):
self.yvec = [f]
self._psd = PSD(sf, npts, step=step, width=width, time=time)
def __init__(self, sf, npts, pha_f=[2, 4], pha_meth='hilbert',
pha_cycle=3, amp_f=[60, 200], amp_meth='hilbert', amp_cycle=6,
window=None, step=None, width=None, time=None, **kwargs):
# Check pha and amp methods:
_checkref('pha_meth', pha_meth, ['hilbert', 'hilbert1', 'hilbert2'])
_checkref('amp_meth', amp_meth, ['hilbert', 'hilbert1', 'hilbert2'])
# Check the type of f:
if (len(pha_f) == 4) and isinstance(pha_f[0], (int, float)):
pha_f = binarize(
pha_f[0], pha_f[1], pha_f[2], pha_f[3], kind='list')
if (len(amp_f) == 4) and isinstance(amp_f[0], (int, float)):
amp_f = binarize(
amp_f[0], amp_f[1], amp_f[2], amp_f[3], kind='list')
# Initialize cfc :
_coupling.__init__(self, pha_f, 'phase', pha_meth, pha_cycle,
amp_f, 'amplitude', amp_meth, amp_cycle,
sf, npts, window, width, step, time, **kwargs)
def __init__(self, sf, npts, Id='113', pha_f=[2, 4], pha_meth='hilbert',
pha_cycle=3, amp_f=[60, 200], amp_meth='hilbert', amp_cycle=6,
nbins=18, window=None, width=None, step=None, time=None,
**kwargs):
# Check pha and amp methods:
_checkref('pha_meth', pha_meth, ['hilbert', 'hilbert1', 'hilbert2'])
_checkref('amp_meth', amp_meth, ['hilbert', 'hilbert1', 'hilbert2'])
# Check the type of f:
if (len(pha_f) == 4) and isinstance(pha_f[0], (int, float)):
pha_f = binarize(
pha_f[0], pha_f[1], pha_f[2], pha_f[3], kind='list')
if (len(amp_f) == 4) and isinstance(amp_f[0], (int, float)):
amp_f = binarize(
amp_f[0], amp_f[1], amp_f[2], amp_f[3], kind='list')
self.xvec = []
# Initalize pac object :
self.Id = Id
me = Id[0]
# Manage settings :
# 1 - Choose if we extract phase or amplitude :
# - Methods using phase // amplitude :
if me in ['1', '2', '3', '5', '6']:
pha_kind, amp_kind = 'phase', 'amplitude'
# - Methods using phase // phase :
elif me in ['4']:
pha_kind, amp_kind = 'phase', 'amplitude'
# 2 - Specific case of Ozkurt :
if me == '5':
Id = '500'
# Initialize cfc :
_coupling.__init__(self, pha_f, pha_kind, pha_meth, pha_cycle,
amp_f, amp_kind, amp_meth, amp_cycle,
sf, npts, window, width, step, time, **kwargs)
# Get pac model :
_, _, _, ModelStr, SurStr, NormStr = CfcSettings(Id, nbins)
self.model = ['Method : '+ModelStr, 'Surrogates : '+SurStr,
'Normalization : '+NormStr]
self._nbins = nbins
def _manageWindow(npts, window=None, width=None, step=None, kind='tuple',
time=None):
"""Manage window definition
Parameters
----------
npts : int
Number of points in the time signal
window : tuple, list, None, optional [def: None]
List/tuple: [100,1500]
List of list/tuple: [(100,500),(200,4000)]
None and the width and step paameters will be considered
width : int, optional [def : None]
width of a single window
step : int, optional [def : None]
Each window will be spaced by the "step" value
kind : string, optional, [def: 'list']
Return either a list or a tuple
"""
if window and (len(window) == 2) and (type(window[0]) == int):
window = [window]
else:
if width is not None:
if step is None:
step = round(width/2)
window = binarize(0, npts, width, step, kind=kind)
if window:
xvec = [round((k[0]+k[1])/2) for k in window]
else:
xvec = list(n.arange(0, npts))
if (time is not None) and not isinstance(time, list):
tme = list(time)
if (time is not None) and (len(time) == npts):
xvec = time
elif time and (len(time) != npts):
warnings.warn("The length of 'time' ["+str(len(time))+"] must be equal"
"to the length of the defined window ["+str(len(xvec)) +
". A default vector is going to used.")
return window, xvec
def _manageWindow(npts, window=None, width=None, step=None, kind="tuple", time=None):
"""Manage window definition
Parameters
----------
npts : int
Number of points in the time signal
window : tuple, list, None, optional [def: None]
List/tuple: [100,1500]
List of list/tuple: [(100,500),(200,4000)]
None and the width and step paameters will be considered
width : int, optional [def : None]
width of a single window
step : int, optional [def : None]
Each window will be spaced by the "step" value
kind : string, optional, [def: 'list']
Return either a list or a tuple
"""
if window and (len(window) == 2) and (type(window[0]) == int):
window = [window]
else:
if width is not None:
if step is None:
step = round(width / 2)
window = binarize(0, npts, width, step, kind=kind)
if window:
xvec = [round((k[0] + k[1]) / 2) for k in window]
else:
xvec = list(n.arange(0, npts))
if (time is not None) and not isinstance(time, list):
tme = list(time)
if (time is not None) and (len(time) == npts):
xvec = time
elif time and (len(time) != npts):
warnings.warn(
"The length of 'time' [" + str(len(time)) + "] must be equal"
"to the length of the defined window [" + str(len(xvec)) + ". A default vector is going to used."
)
return window, xvec
def _manageFrequencies(f, split=None):
"""Manage frequency bands definition
Parameters
----------
f : list
List containing the couple of frequency bands.
Each couple can be either a list or a tuple.
Ex: f = [(2,4),(5,7)]
split : int or list of int, optional [def: None]
Split the frequency band f in "split" band width.
If f is a list which contain couple of frequencies,
split is a list too.
Returns
----------
f : the modified list
fSplit : the splitted f
fSplitIndex : index of the splitted bands
"""
if (len(f) == 2) and (type(f[0]) in [int, float]):
f = [f]
nf = len(f)
if (split is None) or (type(split) == int):
split = [split]
if len(split) != nf:
split = split*nf
fSplit, fSplitIndex, lenOld = [], [], 0
for k, i in enumerate(f):
if split[k] is None:
fSplit.append(f[k])
elif type(split[k]) == int:
fSplit.extend(binarize(i[0], i[1], split[k], split[k],
kind='tuple'))
fSplitIndex.append([lenOld, len(fSplit)])
lenOld = len(fSplit)
return f, fSplit, fSplitIndex
def _kl_hr(pha, amp, nbins):
nPha, npts, nAmp = *pha.shape, amp.shape[0]
step = 2 * np.pi / nbins
vecbin = binarize(-np.pi, np.pi + step, step, step)
if len(vecbin) > nbins:
vecbin = vecbin[0:-1]
abin = np.zeros((nAmp, nPha, nbins))
for k, i in enumerate(vecbin):
# Find where phase take vecbin values :
pL, pC = np.where((pha >= i[0]) & (pha < i[1]))
# Matrix to do amp x binMat :
binMat = np.zeros((npts, nPha))
binMat[pC, pL] = 1
meanMat = np.matlib.repmat(binMat.sum(axis=0), nAmp, 1)
meanMat[meanMat == 0] = 1
# Multiply matrix :
abin[:, :, k] = np.divide(np.dot(amp, binMat), meanMat)
abinsum = np.array([abin.sum(axis=2) for k in range(nbins)])
return abin, abinsum
def _kl_hr(pha, amp, nbins):
nPha, npts, nAmp = *pha.shape, amp.shape[0]
step = 2 * np.pi / nbins
vecbin = binarize(-np.pi, np.pi + step, step, step)
if len(vecbin) > nbins:
vecbin = vecbin[0:-1]
abin = np.zeros((nAmp, nPha, nbins))
for k, i in enumerate(vecbin):
# Find where phase take vecbin values :
pL, pC = np.where((pha >= i[0]) & (pha < i[1]))
# Matrix to do amp x binMat :
binMat = np.zeros((npts, nPha))
binMat[pC, pL] = 1
meanMat = np.matlib.repmat(binMat.sum(axis=0), nAmp, 1)
meanMat[meanMat == 0] = 1
# Multiply matrix :
abin[:, :, k] = np.divide(np.dot(amp, binMat), meanMat)
abinsum = np.array([abin.sum(axis=2) for k in range(nbins)])
return abin, abinsum
def __init__(self, sf, npts, f=[2, 4], method='hilbert', cycle=3,
sample=None, time=None, **kwargs):
# Check pha and amp methods:
_checkref('pha_meth', method, ['hilbert', 'hilbert1', 'hilbert2'])
# Check the type of f:
if (len(f) == 4) and isinstance(f[0], (int, float)):
f = binarize(f[0], f[1], f[2], f[3], kind='list')
# Initialize PLV :
_coupling.__init__(self, f, 'phase', method, cycle,
f, 'phase', method, cycle,
sf, npts, None, None, None, time, **kwargs)
if time is None:
time = np.arange(npts)
else:
time = time
if sample is None:
sample = slice(npts)
self._sample = sample
self.time = time[sample]
del self.amp
def _manageFrequencies(f, split=None):
"""Manage frequency bands definition
Parameters
----------
f : list
List containing the couple of frequency bands.
Each couple can be either a list or a tuple.
Ex: f = [(2,4),(5,7)]
split : int or list of int, optional [def: None]
Split the frequency band f in "split" band width.
If f is a list which contain couple of frequencies,
split is a list too.
Returns
----------
f : the modified list
fSplit : the splitted f
fSplitIndex : index of the splitted bands
"""
if (len(f) == 2) and (type(f[0]) in [int, float]):
f = [f]
nf = len(f)
if (split is None) or (type(split) == int):
split = [split]
if len(split) != nf:
split = split * nf
fSplit, fSplitIndex, lenOld = [], [], 0
for k, i in enumerate(f):
if split[k] is None:
fSplit.append(f[k])
elif type(split[k]) == int:
fSplit.extend(binarize(i[0], i[1], split[k], split[k], kind="tuple"))
fSplitIndex.append([lenOld, len(fSplit)])
lenOld = len(fSplit)
return f, fSplit, fSplitIndex
