def __init__(self, center, lower=None, upper=None, depth=0.0, volume=0.0):
self.center = center
self.lower = lower if lower is not None else center
self.upper = upper if upper is not None else center
self.depth = depth
self.volume = volume
self.sign = int_sign(self.depth)
def __init__(self, center, lower=None, upper=None, depth=0.0, volume=0.0):
self.center = center
self.lower = lower if lower is not None else center
self.upper = upper if upper is not None else center
self.depth = depth
self.volume = volume
self.sign = int_sign(self.depth)
def locate_peak(sig):
"""
Return
------
an array with the same shape as sig, where 0: not peak or valley; 1/-1: peak/valley; 2/-2: pos valley/neg peak.
"""
sig = np.array(sig)
cr1 = np.zeros_like(sig, dtype='i')
cr2 = np.zeros_like(sig, dtype='i')
cr1[1:] = int_sign(sig[1:] - sig[:-1])
cr2[:-1] = int_sign(sig[:-1] - sig[1:])
sigsign = int_sign(sig)
cr = cr1 * cr2
cr[cr <= 0] = 0
cr[np.where((cr == 1) & (cr1 * sigsign == -1))] = 2
cr[np.where((cr == 1) & (cr2 * sigsign == -1))] = 2
# cr[cr==1] = 2
# print cr
# print sigsign
cr *= sigsign
return cr
def locate_peak(sig):
"""
Return
------
an array with the same shape as sig, where 0: not peak or valley; 1/-1: peak/valley; 2/-2: pos valley/neg peak.
"""
sig = np.array(sig)
cr1 = np.zeros_like(sig, dtype='i')
cr2 = np.zeros_like(sig, dtype='i')
cr1[1:] = int_sign(sig[1:] - sig[:-1])
cr2[:-1] = int_sign(sig[:-1] - sig[1:])
sigsign = int_sign(sig)
cr = cr1 * cr2
cr[cr <= 0] = 0
cr[np.where((cr==1) & (cr1 * sigsign == -1))] = 2
cr[np.where((cr==1) & (cr2 * sigsign == -1))] = 2
# cr[cr==1] = 2
# print cr
# print sigsign
cr *= sigsign
return cr
def measure_peak(sig, use_inflection=True, return_allinfo=False):
"""measure_peak measures peaks from 1D/2D signal (2D signal are regarded as columns of individual signal lines), with all the information for the Peak class, e.g., peak center position (indices), peak size (lower/upper position), peak depth and peak volume.
Parameters
----------
sig:
use_inflection: whether to use inflection points to split peaks.
return_allinfo: whether to return raw peak array, crossing zero point array and inflection point array.
Return
------
list/lists of Peak. And if return_allinfo is True, also returns 3 more arrays: raw peaks, crossing zero points and inflection points.
For all the arrays:
0: not anything.
For raw peak array:
1/-1: peak/valley; 2/-2: pos valley/neg peak;
For crossing zero array and inflection point array:
4/-4: pos/neg crossing zero; 8/-8: pos/neg inflection point.
"""
sig = np.array(sig)
cr = locate_peak(sig)
cr_crosszero = np.zeros_like(cr)
cr_inflection = np.zeros_like(cr)
# cross zero points
cr_cr1 = -int_sign(sig[1:] * sig[:-1])
cr_cr2 = -int_sign(sig[:-1] * sig[1:])
cr_cr1[cr_cr1 < 0] = 0
cr_cr2[cr_cr2 < 0] = 0
cr_crosszero[1:] = cr_cr1
cr_crosszero[:-1] += cr_cr2
cr_crosszero = int_sign(cr_crosszero * sig) * 4
# inflection points
d2 = second_derivate(sig)
d2p = locate_peak(d2)
d2p[np.where(np.abs(d2p) != 1)] = 0
d2p[np.where(((d2p == 1) & (sig < 0)) | ((d2p == -1) & (sig > 0)))] = 0
cr_inflection[np.where(d2p == -1)] = 8
cr_inflection[np.where(d2p == 1)] = -8
if use_inflection:
cr_combine = cr + cr_inflection + cr_crosszero
else:
cr_combine = cr + cr_crosszero
oned = False
if len(np.shape(sig)) == 1:
oned = True
sig = sig[:, np.newaxis]
peaks_list = []
for i in range(np.shape(sig)[1]):
pvs = np.where(np.abs(cr[:, i]) == 1)[0]
lims = np.where(np.abs(cr_combine[:, i]) >= 2)[0]
if len(pvs) == 0:
peaks_list.append([])
continue
if np.shape(lims)[0] == 0:
lower_pos = pvs
upper_pos = pvs
else:
lower_arr = (pvs > lims[:, np.newaxis])
upper_arr = (pvs < lims[:, np.newaxis])
lower_arr_r = np.flipud(lower_arr)
upper_pos_i = np.argmax(upper_arr, axis=0)
upper_pos = lims[(upper_pos_i, )]
w_upper_none = np.where(upper_arr[-1, :] == False)
upper_pos[w_upper_none] = pvs[w_upper_none]
lower_pos_r_i = np.argmax(lower_arr_r, axis=0)
lower_pos_i = len(lims) - 1 - lower_pos_r_i
lower_pos = lims[(lower_pos_i, )]
w_lower_none = np.where(lower_arr[0, :] == False)
lower_pos[w_lower_none] = 0
peaks = []
for center, lower, upper in zip(pvs, lower_pos, upper_pos):
depth = sig[center, i]
sig_range = sig[lower:upper + 1, i]
sig_range[np.where(int_sign(sig_range) != int_sign(depth))] = 0.0
volume = np.sum(sig_range)
peaks.append(
Peak(center=center,
lower=lower,
upper=upper,
depth=depth,
volume=volume))
peaks_list.append(peaks)
if oned:
peaks_list = peaks_list[0]
if return_allinfo:
return peaks_list, cr, cr_crosszero, cr_inflection
else:
return peaks_list
def measure_peak(sig, use_inflection=True, return_allinfo=False):
"""measure_peak measures peaks from 1D/2D signal (2D signal are regarded as columns of individual signal lines), with all the information for the Peak class, e.g., peak center position (indices), peak size (lower/upper position), peak depth and peak volume.
Parameters
----------
sig:
use_inflection: whether to use inflection points to split peaks.
return_allinfo: whether to return raw peak array, crossing zero point array and inflection point array.
Return
------
list/lists of Peak. And if return_allinfo is True, also returns 3 more arrays: raw peaks, crossing zero points and inflection points.
For all the arrays:
0: not anything.
For raw peak array:
1/-1: peak/valley; 2/-2: pos valley/neg peak;
For crossing zero array and inflection point array:
4/-4: pos/neg crossing zero; 8/-8: pos/neg inflection point.
"""
sig = np.array(sig)
cr = locate_peak(sig)
cr_crosszero = np.zeros_like(cr)
cr_inflection = np.zeros_like(cr)
# cross zero points
cr_cr1 = -int_sign(sig[1:] * sig[:-1])
cr_cr2 = -int_sign(sig[:-1] * sig[1:])
cr_cr1[cr_cr1<0] = 0
cr_cr2[cr_cr2<0] = 0
cr_crosszero[1:] = cr_cr1
cr_crosszero[:-1] += cr_cr2
cr_crosszero = int_sign(cr_crosszero * sig) * 4
# inflection points
d2 = second_derivate(sig)
d2p = locate_peak(d2)
d2p[np.where( np.abs(d2p) != 1 )] = 0
d2p[np.where( ((d2p==1) & (sig<0)) | ((d2p==-1) & (sig>0)) )] = 0
cr_inflection[np.where(d2p==-1)] = 8
cr_inflection[np.where(d2p==1)] = -8
if use_inflection:
cr_combine = cr + cr_inflection + cr_crosszero
else:
cr_combine = cr + cr_crosszero
oned = False
if len(np.shape(sig)) == 1:
oned = True
sig = sig[:, np.newaxis]
peaks_list = []
for i in range(np.shape(sig)[1]):
pvs = np.where(np.abs(cr[:,i]) == 1)[0]
lims = np.where(np.abs(cr_combine[:,i]) >= 2)[0]
if len(pvs) == 0 :
peaks_list.append([])
continue
if np.shape(lims)[0] == 0:
lower_pos = pvs
upper_pos = pvs
else:
lower_arr = (pvs > lims[:, np.newaxis])
upper_arr = (pvs < lims[:, np.newaxis])
lower_arr_r = np.flipud(lower_arr)
upper_pos_i = np.argmax(upper_arr, axis=0)
upper_pos = lims[(upper_pos_i, )]
w_upper_none = np.where(upper_arr[-1,:] == False)
upper_pos[w_upper_none] = pvs[w_upper_none]
lower_pos_r_i = np.argmax(lower_arr_r, axis=0)
lower_pos_i = len(lims) - 1 - lower_pos_r_i
lower_pos = lims[(lower_pos_i, )]
w_lower_none = np.where(lower_arr[0, :] == False)
lower_pos[w_lower_none] = 0
peaks = []
for center, lower, upper in zip(pvs, lower_pos, upper_pos):
depth = sig[center, i]
sig_range = sig[lower:upper+1, i]
sig_range[np.where(int_sign(sig_range) != int_sign(depth))] = 0.0
volume = np.sum(sig_range)
peaks.append(Peak(center=center, lower=lower, upper=upper, depth=depth, volume=volume))
peaks_list.append(peaks)
if oned:
peaks_list = peaks_list[0]
if return_allinfo:
return peaks_list, cr, cr_crosszero, cr_inflection
else:
return peaks_list
