def computeTimeFreq(self):
""" Compute the scalogram and returns a :class:`TimeFreq` object as
self.timeFreq. """
self.timeFreq = TimeFreq(
self.anaSig,
method=self.scalogram_method,
f_start=self.f_start,
f_stop=self.f_stop,
deltafreq=self.deltafreq,
sampling_rate=self.sampling_rate,
t_start=self.t_start,
t_stop=self.t_stop,
f0=self.f0,
normalisation=self.normalisation,
)
def computeTimeFreq(self):
""" Compute the scalogram and returns a :class:`TimeFreq` object as
self.timeFreq. """
self.timeFreq = TimeFreq( self.anaSig,
method = self.scalogram_method,
f_start=self.f_start,
f_stop=self.f_stop,
deltafreq = self.deltafreq,
sampling_rate = self.sampling_rate,
t_start = self.t_start,
t_stop = self.t_stop,
f0=self.f0,
normalisation = self.normalisation,
)
class LineDetector():
"""
LineDetector(anaSig,
scalogram_method = 'convolution_freq',
f_start=5.,
f_stop=100.,
deltafreq = 1.,
sampling_rate = 200.,
t_start = -inf,
t_stop = inf,
f0=2.5,
normalisation = 0.,
linedetection_method = 'detect_line_from_max',
detection_zone = [ 0, inf, 5, 100.],
manual_threshold = False,
abs_threshold = nan,
std_relative_threshold = 6.,
reference_zone = [ -inf, 0,5., 100.],
minimum_cycle_number= 0.,
eliminate_simultaneous = True,
regroup_full_overlap = True ,
eliminate_partial_overlap = True)
Class for line detection in the scalogram.
"""
def __init__(self,
anaSig,
scalogram_method = 'convolution_freq',
#scalogram
f_start=5.,
f_stop=100.,
deltafreq = 1.,
sampling_rate = 200.,
t_start = -inf,
t_stop = inf,
f0=2.5,
normalisation = 0.,
#~ linedetection_method = 'detect_all_lines',
linedetection_method = 'detect_line_from_max',
# detection_zone
detection_zone = [ 0, inf, 5, 100.],
# threshold
manual_threshold = False,
abs_threshold = nan,
std_relative_threshold = 6.,
reference_zone = [ -inf, 0,5., 100.],
# clean
minimum_cycle_number= 0.,
eliminate_simultaneous = True,
regroup_full_overlap = True ,
eliminate_partial_overlap = True,
):
"""
Construct a :class:`.LineDetector` object.
Parameters
----------
anaSig : AnalogSignal
The AnalogSignal in which oscillations will be detected.
Scalogram parameters:
f_start : float, optional
Lower frequency bound (Hz) of scalogram
f_stop : float, optional
Upper frequency bound (Hz) of scalogram
deltafreq : float, optional
Frequency resolution of scalogram
sampling_rate : float, optional
Sampling rate of scalogram (Hz)
t_start : float, optional
Starting point of scalogram (s)
t_stop : float, optional
End point of scalogram (s)
f0 : float, optional
Number of cycles within one standard deviation of the Morlet wavelet.
normalisation : float, optional
Normalisation exponent along the frequency dimension. Negative
(positive) values stress lower (higher) frequencies.
Detection parameters
detection_zone : array-like
Time-frequency zone for oscillations detection of shape
[t_start, t_stop, f_start, f_stop]
manual_threshold : bool, optional
Boolean switch for manual thresholding
abs_threshold : float, optional
Absolute power threshold for maxima detection
std_relative_threshold : float, optional
Threshold in units of of standard deviations from mean value in
reference_zone
reference_zone : array-like, optional
Time-frequency reference zone for relative thresholding of shape
[t_start, t_stop, f_start, f_stop]
Cleaning parameters
minimum_cycle_number : float, optional
Minimum number of cycles for cleaning of spurious oscillations
eliminate_simultaneous : bool, optional
Eliminate the less powerful oscillation of two oscillations overlapping
in time but not in frequency, e.g. for the elimination of harmonics
regroup_full_overlap : bool, optional
Merge oscillations completely overlapping in time and frequency, e.g.
when one oscillations has several maximas in its envelope
eliminate_partial_overlap : bool, optional
Keep the more powerful oscillation of two partially overlapping
oscillations, e.g. for the case of two forking ones
Examples
--------
>>> ana = AnalogSignal.load(id)
>>> lid = LineDetector(ana)
>>> lid.computeAllStep()
"""
self.anaSig = anaSig
self.scalogram_method = scalogram_method
#scalogram
self.f_start=f_start
self.f_stop=f_stop
self.deltafreq = deltafreq
self.sampling_rate = sampling_rate
self.t_start = t_start
self.t_stop = t_stop
self.f0= f0
self.normalisation = normalisation
#~ self.t_start = max(self.t_start , self.anaSig.t_start)
#~ self.t_stop = min(self.t_stop , self.anaSig.t()[-1] )
self.linedetection_method = linedetection_method
# detection_zone
self.detection_zone = detection_zone
#~ self.detection_zone[1] = min(self.detection_zone[1], self.anaSig.t()[-1] )
# threshold
self.manual_threshold = manual_threshold
self.abs_threshold = abs_threshold
self.std_relative_threshold = std_relative_threshold
self.reference_zone = reference_zone
#~ self.reference_zone[0] = max(self.reference_zone[0], self.anaSig.t()[0] )
# clean
self.minimum_cycle_number= minimum_cycle_number
self.eliminate_simultaneous =eliminate_simultaneous
self.regroup_full_overlap = regroup_full_overlap
self.eliminate_partial_overlap = eliminate_partial_overlap
self.checkParam()
self.timeFreq = None
self.threshold = inf
self.list_max = None
def update(self, **params):
self.__dict__.update(params)
def checkParam(self):
""" Perform checks and corrections to parameters t_start, t_stop,
sampling_rate, detection_zone[0] and detection_zone[1]. """
self.t_start = max(self.t_start , self.anaSig.t_start)
self.t_stop = min(self.t_stop , self.anaSig.t()[-1]+1./self.anaSig.sampling_rate )
self.sampling_rate = max(self.f_stop*2, self.sampling_rate)
self.detection_zone[1] = min(self.detection_zone[1], self.anaSig.t()[-1]+1./self.anaSig.sampling_rate )
self.reference_zone[0] = max(self.reference_zone[0], self.anaSig.t()[0] )
def computeAllStep(self):
""" Compute the scalogram (:func:`computeTimeFreq`), detects maxima
(:func:`detectMax`) and lines (:func:`detectLine`), and cleans the
detected oscillations (:func:`cleanLine`. """
#~ self.checkParam()
self.computeTimeFreq()
self.detectMax()
self.detectLine()
self.cleanLine()
def computeTimeFreq(self):
""" Compute the scalogram and returns a :class:`TimeFreq` object as
self.timeFreq. """
self.timeFreq = TimeFreq( self.anaSig,
method = self.scalogram_method,
f_start=self.f_start,
f_stop=self.f_stop,
deltafreq = self.deltafreq,
sampling_rate = self.sampling_rate,
t_start = self.t_start,
t_stop = self.t_stop,
f0=self.f0,
normalisation = self.normalisation,
)
def computeThreshold(self):
""" Either set self.threshold to the specified self.abs_threshold or
(re)compute the relative threshold and sets it. In both cases the
the threshold is returned. """
if self.manual_threshold:
self.threshold = self.abs_threshold
else:
map = self.timeFreq.map
t = self.timeFreq.t()
f = self.timeFreq.f()
t1,t2,f1,f2 = self.reference_zone
subMap = map[ (t>=t1) & (t<t2), :][: , (f>=f1) & (f<f2)]
subMap = abs(subMap)
self.threshold = numpy.mean(subMap) + self.std_relative_threshold*numpy.std(subMap)
return self.threshold
def detectMax(self):
""" Detect the maxima in the scalogram using :func:`max_detection`."""
map = self.timeFreq.map
t = self.timeFreq.t()
f = self.timeFreq.f()
t1,t2,f1,f2 = self.detection_zone
subMap = map[ (t>=t1) & (t<t2), :][: , (f>=f1) & (f<f2)]
new_t = t[ (t>=t1) & (t<t2) ]
new_f = f[ (f>=f1) & (f<f2)]
self.computeThreshold()
ind_t,ind_f = numpy.array(max_detection(abs(subMap),threshold= self.threshold))
self.list_max = numpy.recarray(ind_t.size , formats = ['f8', 'f8'], names=['time', 'freq'] , )
self.list_max.time = new_t[ind_t]
self.list_max.freq = new_f[ind_f]
def detectLine(self):
""" Detect lines in the scalogram using self.linedetection_method. """
map = self.timeFreq.map
t = self.timeFreq.t()
f = self.timeFreq.f()
t1,t2,f1,f2 = self.detection_zone
subMap = map[ (t>=t1) & (t<t2), :][: , (f>=f1) & (f<f2)]
new_t = t[ (t>=t1) & (t<t2) ]
new_f = f[ (f>=f1) & (f<f2)]
self.computeThreshold()
if self.linedetection_method == 'detect_all_lines':
self.list_oscillation = detectalllines.detect_oscillations(subMap,
new_t[0], #self.detection_zone[0],
self.sampling_rate,
new_f[0], #self.detection_zone[3],
self.deltafreq,
self.threshold,
list_max = self.list_max,
)
elif self.linedetection_method == 'detect_line_from_max':
self.list_oscillation = detectlinefrommax.detect_oscillations(subMap,
new_t[0], #self.detection_zone[0],
self.sampling_rate,
new_f[0], #self.detection_zone[3],
self.deltafreq,
self.threshold,
list_max =self.list_max,
)
def recomputeSelection(self , ind):
pass
def cleanLine(self):
""" Clean all oscillations with selected parameters and sort them in time. """
self.list_oscillation = clean_oscillations_list(self.list_oscillation,
minimum_cycle_number=self.minimum_cycle_number,
eliminate_simultaneous = self.eliminate_simultaneous,
regroup_full_overlap = self.regroup_full_overlap,
eliminate_partial_overlap = self.eliminate_partial_overlap,
)
self.sortOscillations()
def cleanSelection(self, ind):
""" Clean only selected oscillations and sort them in time. """
not_selected = [ ]
selected = []
for i in range(len(self.list_oscillation)):
if i in ind:
selected.append( self.list_oscillation[i] )
else:
not_selected.append( self.list_oscillation[i] )
list_cleaned = clean_oscillations_list(selected,
minimum_cycle_number=self.minimum_cycle_number,
eliminate_simultaneous = self.eliminate_simultaneous,
regroup_full_overlap = self.regroup_full_overlap,
eliminate_partial_overlap = self.eliminate_partial_overlap,
)
self.list_oscillation = list_cleaned + not_selected
self.sortOscillations()
def sortOscillations(self):
""" Sort the detected oscillations by time. """
t = [ ]
for osci in self.list_oscillation:
t.append( osci.time_max )
ind = numpy.argsort(t)
sorted = [ self.list_oscillation[i] for i in ind ]
self.list_oscillation = sorted
class LineDetector():
"""
LineDetector(anaSig,
scalogram_method = 'convolution_freq',
f_start=5.,
f_stop=100.,
deltafreq = 1.,
sampling_rate = 200.,
t_start = -inf,
t_stop = inf,
f0=2.5,
normalisation = 0.,
linedetection_method = 'detect_line_from_max',
detection_zone = [ 0, inf, 5, 100.],
manual_threshold = False,
abs_threshold = nan,
std_relative_threshold = 6.,
reference_zone = [ -inf, 0,5., 100.],
minimum_cycle_number= 0.,
eliminate_simultaneous = True,
regroup_full_overlap = True ,
eliminate_partial_overlap = True)
Class for line detection in the scalogram.
"""
def __init__(
self,
anaSig,
scalogram_method='convolution_freq',
#scalogram
f_start=5.,
f_stop=100.,
deltafreq=1.,
sampling_rate=200.,
t_start=-inf,
t_stop=inf,
f0=2.5,
normalisation=0.,
#~ linedetection_method = 'detect_all_lines',
linedetection_method='detect_line_from_max',
# detection_zone
detection_zone=[0, inf, 5, 100.],
# threshold
manual_threshold=False,
abs_threshold=nan,
std_relative_threshold=6.,
reference_zone=[-inf, 0, 5., 100.],
# clean
minimum_cycle_number=0.,
eliminate_simultaneous=True,
regroup_full_overlap=True,
eliminate_partial_overlap=True,
):
"""
Construct a :class:`.LineDetector` object.
Parameters
----------
anaSig : AnalogSignal
The AnalogSignal in which oscillations will be detected.
Scalogram parameters:
f_start : float, optional
Lower frequency bound (Hz) of scalogram
f_stop : float, optional
Upper frequency bound (Hz) of scalogram
deltafreq : float, optional
Frequency resolution of scalogram
sampling_rate : float, optional
Sampling rate of scalogram (Hz)
t_start : float, optional
Starting point of scalogram (s)
t_stop : float, optional
End point of scalogram (s)
f0 : float, optional
Number of cycles within one standard deviation of the Morlet wavelet.
normalisation : float, optional
Normalisation exponent along the frequency dimension. Negative
(positive) values stress lower (higher) frequencies.
Detection parameters
detection_zone : array-like
Time-frequency zone for oscillations detection of shape
[t_start, t_stop, f_start, f_stop]
manual_threshold : bool, optional
Boolean switch for manual thresholding
abs_threshold : float, optional
Absolute power threshold for maxima detection
std_relative_threshold : float, optional
Threshold in units of of standard deviations from mean value in
reference_zone
reference_zone : array-like, optional
Time-frequency reference zone for relative thresholding of shape
[t_start, t_stop, f_start, f_stop]
Cleaning parameters
minimum_cycle_number : float, optional
Minimum number of cycles for cleaning of spurious oscillations
eliminate_simultaneous : bool, optional
Eliminate the less powerful oscillation of two oscillations overlapping
in time but not in frequency, e.g. for the elimination of harmonics
regroup_full_overlap : bool, optional
Merge oscillations completely overlapping in time and frequency, e.g.
when one oscillations has several maximas in its envelope
eliminate_partial_overlap : bool, optional
Keep the more powerful oscillation of two partially overlapping
oscillations, e.g. for the case of two forking ones
Examples
--------
>>> ana = AnalogSignal.load(id)
>>> lid = LineDetector(ana)
>>> lid.computeAllStep()
"""
self.anaSig = anaSig
self.scalogram_method = scalogram_method
#scalogram
self.f_start = f_start
self.f_stop = f_stop
self.deltafreq = deltafreq
self.sampling_rate = sampling_rate
self.t_start = t_start
self.t_stop = t_stop
self.f0 = f0
self.normalisation = normalisation
#~ self.t_start = max(self.t_start , self.anaSig.t_start)
#~ self.t_stop = min(self.t_stop , self.anaSig.t()[-1] )
self.linedetection_method = linedetection_method
# detection_zone
self.detection_zone = detection_zone
#~ self.detection_zone[1] = min(self.detection_zone[1], self.anaSig.t()[-1] )
# threshold
self.manual_threshold = manual_threshold
self.abs_threshold = abs_threshold
self.std_relative_threshold = std_relative_threshold
self.reference_zone = reference_zone
#~ self.reference_zone[0] = max(self.reference_zone[0], self.anaSig.t()[0] )
# clean
self.minimum_cycle_number = minimum_cycle_number
self.eliminate_simultaneous = eliminate_simultaneous
self.regroup_full_overlap = regroup_full_overlap
self.eliminate_partial_overlap = eliminate_partial_overlap
self.checkParam()
self.timeFreq = None
self.threshold = inf
self.list_max = None
def update(self, **params):
self.__dict__.update(params)
def checkParam(self):
""" Perform checks and corrections to parameters t_start, t_stop,
sampling_rate, detection_zone[0] and detection_zone[1]. """
self.t_start = max(self.t_start, self.anaSig.t_start)
self.t_stop = min(self.t_stop,
self.anaSig.t()[-1] + 1. / self.anaSig.sampling_rate)
self.sampling_rate = max(self.f_stop * 2, self.sampling_rate)
self.detection_zone[1] = min(
self.detection_zone[1],
self.anaSig.t()[-1] + 1. / self.anaSig.sampling_rate)
self.reference_zone[0] = max(self.reference_zone[0],
self.anaSig.t()[0])
def computeAllStep(self):
""" Compute the scalogram (:func:`computeTimeFreq`), detects maxima
(:func:`detectMax`) and lines (:func:`detectLine`), and cleans the
detected oscillations (:func:`cleanLine`. """
#~ self.checkParam()
self.computeTimeFreq()
self.detectMax()
self.detectLine()
self.cleanLine()
def computeTimeFreq(self):
""" Compute the scalogram and returns a :class:`TimeFreq` object as
self.timeFreq. """
self.timeFreq = TimeFreq(
self.anaSig,
method=self.scalogram_method,
f_start=self.f_start,
f_stop=self.f_stop,
deltafreq=self.deltafreq,
sampling_rate=self.sampling_rate,
t_start=self.t_start,
t_stop=self.t_stop,
f0=self.f0,
normalisation=self.normalisation,
)
def computeThreshold(self):
""" Either set self.threshold to the specified self.abs_threshold or
(re)compute the relative threshold and sets it. In both cases the
the threshold is returned. """
if self.manual_threshold:
self.threshold = self.abs_threshold
else:
map = self.timeFreq.map
t = self.timeFreq.t()
f = self.timeFreq.f()
t1, t2, f1, f2 = self.reference_zone
subMap = map[(t >= t1) & (t < t2), :][:, (f >= f1) & (f < f2)]
subMap = abs(subMap)
self.threshold = numpy.mean(
subMap) + self.std_relative_threshold * numpy.std(subMap)
return self.threshold
def detectMax(self):
""" Detect the maxima in the scalogram using :func:`max_detection`."""
map = self.timeFreq.map
t = self.timeFreq.t()
f = self.timeFreq.f()
t1, t2, f1, f2 = self.detection_zone
subMap = map[(t >= t1) & (t < t2), :][:, (f >= f1) & (f < f2)]
new_t = t[(t >= t1) & (t < t2)]
new_f = f[(f >= f1) & (f < f2)]
self.computeThreshold()
ind_t, ind_f = numpy.array(
max_detection(abs(subMap), threshold=self.threshold))
self.list_max = numpy.recarray(
ind_t.size,
formats=['f8', 'f8'],
names=['time', 'freq'],
)
self.list_max.time = new_t[ind_t]
self.list_max.freq = new_f[ind_f]
def detectLine(self):
""" Detect lines in the scalogram using self.linedetection_method. """
map = self.timeFreq.map
t = self.timeFreq.t()
f = self.timeFreq.f()
t1, t2, f1, f2 = self.detection_zone
subMap = map[(t >= t1) & (t < t2), :][:, (f >= f1) & (f < f2)]
new_t = t[(t >= t1) & (t < t2)]
new_f = f[(f >= f1) & (f < f2)]
self.computeThreshold()
if self.linedetection_method == 'detect_all_lines':
self.list_oscillation = detectalllines.detect_oscillations(
subMap,
new_t[0], #self.detection_zone[0],
self.sampling_rate,
new_f[0], #self.detection_zone[3],
self.deltafreq,
self.threshold,
list_max=self.list_max,
)
elif self.linedetection_method == 'detect_line_from_max':
self.list_oscillation = detectlinefrommax.detect_oscillations(
subMap,
new_t[0], #self.detection_zone[0],
self.sampling_rate,
new_f[0], #self.detection_zone[3],
self.deltafreq,
self.threshold,
list_max=self.list_max,
)
def recomputeSelection(self, ind):
pass
def cleanLine(self):
""" Clean all oscillations with selected parameters and sort them in time. """
self.list_oscillation = clean_oscillations_list(
self.list_oscillation,
minimum_cycle_number=self.minimum_cycle_number,
eliminate_simultaneous=self.eliminate_simultaneous,
regroup_full_overlap=self.regroup_full_overlap,
eliminate_partial_overlap=self.eliminate_partial_overlap,
)
self.sortOscillations()
def cleanSelection(self, ind):
""" Clean only selected oscillations and sort them in time. """
not_selected = []
selected = []
for i in range(len(self.list_oscillation)):
if i in ind:
selected.append(self.list_oscillation[i])
else:
not_selected.append(self.list_oscillation[i])
list_cleaned = clean_oscillations_list(
selected,
minimum_cycle_number=self.minimum_cycle_number,
eliminate_simultaneous=self.eliminate_simultaneous,
regroup_full_overlap=self.regroup_full_overlap,
eliminate_partial_overlap=self.eliminate_partial_overlap,
)
self.list_oscillation = list_cleaned + not_selected
self.sortOscillations()
def sortOscillations(self):
""" Sort the detected oscillations by time. """
t = []
for osci in self.list_oscillation:
t.append(osci.time_max)
ind = numpy.argsort(t)
sorted = [self.list_oscillation[i] for i in ind]
self.list_oscillation = sorted