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H2_II.py
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#calibrate the delay drift for different measurement, cut the data if necessray
#do FFT and show FFT and phase
#Main function if self.show_FFT()
#smooth function doesn't influence the phase, checked
from fileinput import filename
from weakref import ref
import matplotlib as mpl
from matplotlib import pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from yaml import load
mpl.style.use('seaborn-poster')
from matplotlib.colors import Normalize
from matplotlib import cm
from matplotlib import gridspec
import numpy as np
import scipy as sp
import scipy.signal as sps
import scipy.fft as sft
import scipy.interpolate as spi
import pywt
import pycwt
import matplotlib as mpl
from obspy.signal.detrend import polynomial
import h5py
import pathlib as pl
import os
import pickle
from decimal import Decimal
from cal_intensity import cal_intensity
from calculate_k_b import Calibration_mass
from BaselineRemoval import BaselineRemoval
from lmfit import minimize, Parameters, Parameter, report_fit
import originpro as op
from skimage.restoration import denoise_wavelet
import math
my_path = os.path.abspath(__file__)
mpl.rcParams['lines.linewidth'] = 1
plt.rcParams["font.family"] = "arial"
mpl.rcParams['mathtext.fontset'] = 'custom'
mpl.rcParams['mathtext.it'] = 'Arial:italic'
mpl.rcParams['mathtext.rm'] = 'Arial'
SMALL_SIZE = 16
MEDIUM_SIZE = 22
BIGGER_SIZE = 26
plt.rc('font', size=SMALL_SIZE) # controls default text sizes
plt.rc('axes', titlesize=SMALL_SIZE) # fontsize of the axes title
plt.rc('axes', labelsize=SMALL_SIZE) # fontsize of the x and y labels
plt.rc('xtick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('ytick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('legend', fontsize=SMALL_SIZE) # legend fontsize
plt.rc('figure', titlesize=BIGGER_SIZE) # fontsize of the figure title
def save_obj(obj, filename):
with open(filename, 'wb+') as f:
pickle.dump(obj, f, pickle.HIGHEST_PROTOCOL)
def load_obj(filename):
with open(filename, 'rb') as f:
return pickle.load(f)
class FFT_ionS():
def __init__(self,folder,caliFolder=''):
'''
'''
self.folder = folder
self.caliFolder = caliFolder
self.filename = filename
self.saveRef = str(filename)
self.filepath = []
self.delayB,self.stepSize = np.linspace(start=0,stop=1300, num=13000,endpoint=False,retstep=True)
self.delayB = self.delayB*10**-15
self.stepSize = self.stepSize*10**-15
self.delayB_noPad = np.linspace(start=0,stop=1299.9, num=13000)*10**-15
self.rebin_delay = None
self.ifrebin = False
self.longstage = True
self.data = 0
self.specBigBottleB = {}
self.specBigBottleB_noPad = {}
self.interSpectraBottleB = {}
self.phaseSpecBottleB = {}
self.phaseBottleB = {}
self.filterPhase = {}
self.filterSpec = {}
self.fftSB = {}
self.fftSB_H2 = {}
self.stftSB = {}
self.specBigBottleB = {}
self.waveletsCoe = {}
self.zeroIndex = {}
self.zeroIndexMin = 10000000000000000000000000
self.zeroIndexMax = 0
self.retrivedPhase = {}
self.spec = None
self.scanNo = None
self.stage = 'piezo'
self.intensity = 8.9E14
self.molecule = str('H2')
#setting for data from digitizer
#self.channelSize = 12032#24000#1536
#self.scanLengthD = 3320#1200
#self.peakRange = [-100, 100] # range of the peak
#self.delayD = np.arange(self.scanLengthD)/self.scanLengthD*100*2*2*3.33564*10**-15#*3602/3647
#self.spectraBottleD = {}
#self.fftSD = {}
#self.stftSD = {}
#self.dataD = 0
self.rootPath= pl.PureWindowsPath(r'D:\SF_FFT')
self.savePath= pl.PureWindowsPath(os.path.join(r'D:\SF_FFT\processedData\inter',self.molecule,folder))
def read(self):
totalCounter = {}
#for gas in ['Ch0','Ch2','Ch4','Ch6','Ch8','Ch10']:
# self.fftSB[gas] = 0
for gas in ['Ch0','Ch2','Ch4','Ch6','Ch8','Ch10']:
self.specBigBottleB[gas] = np.zeros((1000,13000))
totalCounter[gas] = 0
#if not os.path.exists(os.path.join(self.savePath,r'plotData')):
# os.mkdir(os.path.join(self.savePath,r'plotData'))
for file in os.listdir(self.savePath):
filename = os.fsdecode(file)
print(filename)
if filename.endswith(".pkl"):
self.interSpectraBottleB = load_obj(os.path.abspath(os.path.join(self.savePath, filename)))
for gas in ['Ch0','Ch2','Ch4','Ch6','Ch8','Ch10']:
print(self.interSpectraBottleB[gas].shape)
for i in range(self.interSpectraBottleB[gas].shape[0]):
self.specBigBottleB[gas][totalCounter[gas]] = self.interSpectraBottleB[gas][i]
totalCounter[gas] = totalCounter[gas]+1
print(totalCounter)
for gas in ['Ch0','Ch2','Ch4','Ch6','Ch8','Ch10']:
self.specBigBottleB[gas] = self.specBigBottleB[gas][:totalCounter[gas]]
zeroIndex2 = self.findZeroDelay2()
zeroIndex2Min = np.amin(zeroIndex2)
#zeroIndex2Max = np.amax(zeroIndex2)
for gas in ['Ch0','Ch2','Ch4','Ch6','Ch8','Ch10']:
for i in range(self.specBigBottleB[gas].shape[0]):
self.specBigBottleB[gas][i] = np.concatenate((self.specBigBottleB[gas][i][(zeroIndex2[i]-zeroIndex2Min):], np.full(zeroIndex2[i]-zeroIndex2Min,self.specBigBottleB[gas][i][-1])))
print(self.specBigBottleB['Ch0'].shape)
def interFFT(self, y):
n = len(y)
delta = self.stepSize#/(self.interNum+1)
self.dw = 1/((n)*self.stepSize)/1E12*33.35641
#print('self.dw is '+str(self.dw))
f = np.fft.rfftfreq(n, delta)/1E12*33.35641 # frequency unit cm-1
f = f[f>0]
#y=np.fft.fftshift(y)
fft_y = np.fft.rfft(y)
fft_y=fft_y[:np.size(f)]
#plt.plot(f,np.abs(fft_y))
#plt.show()
return f, fft_y
def FFT3(self, windowSize = 100, delayRange=False, rebinF=1, paddingF=0, useWindow = False, zeroDirection = 'left', phaseCompensate = True, smooth=True, test=False):
'''
windowSize in fs, rebinF = inputShape/outputShape, padddingF means the length of the padding divided by length of the data.
'''
self.smoothedT={}
self.smooth = smooth
self.stepSize = self.stepSize*rebinF
_size = self.specBigBottleB['Ch0'].size
paddingSize = int(_size*paddingF)
self.paddingSize = paddingSize
self.ifDelayRange = delayRange
self.delayRange4FFT = delayRange
for gas in self.phaseSpecBottleB.keys():
self.smoothedT[gas]=0
for i in range(self.phaseSpecBottleB[gas].shape[0]):
#becareful, here the sign of the amplitude is changed
interSpec = -self.phaseSpecBottleB[gas][i][-self.specBigBottleB[gas].size:]
#becareful, here the sign of the amplitude is changed
_,interSmoothedT,self.smoothedT['T'] = self.inter_window(interSpec,self.delayB,windowSize=0,direction=zeroDirection, useWindow=False, phaseCompensate=False,smooth = False)
self.smoothedT[gas]= self.smoothedT[gas] + interSmoothedT
if delayRange:
y=interSpec[np.where(np.logical_and(delayRange[0]<self.delayB,self.delayB<delayRange[1]))]
t=self.delayB[np.where(np.logical_and(delayRange[0]<self.delayB,self.delayB<delayRange[1]))]
_,y,t = self.inter_window(y,t,windowSize=0,direction=zeroDirection, useWindow=useWindow, phaseCompensate=phaseCompensate,smooth = smooth)
else:
_,y,t = self.inter_window(interSpec,self.delayB,windowSize=windowSize,direction=zeroDirection, useWindow=useWindow, phaseCompensate=phaseCompensate,smooth = smooth)
#_,y,t = self.inter_window(self.phaseSpecBottleB[gas][i],self.delayB,windowSize=windowSize,direction=zeroDirection, useWindow=useWindow, phaseCompensate=phaseCompensate,smooth = smooth)
#plt.plot(t,y)
#plt.plot(self.delayB,self.specBigBottleB['Ch8']-np.mean(self.specBigBottleB['Ch8']))
#plt.show()
y,t = self.inter_padding(y,t,paddingSize=paddingSize)
if test:
y=np.sin(2*np.pi/300*np.arange(np.size(t)))+np.sin(2*np.pi/100*np.arange(np.size(t))+np.pi)+np.sin(2*np.pi/200*np.arange(np.size(t)))
y,t = self.inter_padding(y,t,paddingSize=paddingSize)
#plt.plot(self.refSpectra4AbsPhase)
#plt.plot(y)
#plt.show()
if rebinF < 1.5:
pass
else:
y = self.rebin_factor(y,rebinF)
t = self.rebin_factor(t,rebinF)
#self.interNum = 100
#y = self.interInterp(t,y,self.interNum)
self.inputLength = np.size(y)
#print('Input length is '+str(self.inputLength)+' !')
f, Y = self.interFFT(y)
self.L=np.size(f)
if i == 0:
_interY = np.zeros((self.phaseSpecBottleB[gas].shape[0],Y.size),dtype=np.complex64)
_interY[i] = Y
self.fftSB['window_'+gas+'_fft'] = _interY
self.fftSB[gas] = 0
__, self.fftSB['ref4Phase'] = self.interFFT(self.refSpectra4AbsPhase)
self.fftSB['window_'+'fre'] = f
#print(self.folder)
self.smooth = smooth
save_obj(self.fftSB,os.path.join(self.savePath,str(smooth)+str(self.folder)+r'_fftSB.pkl'))
def transition(self):
self.specBigBottleB_noPad=self.specBigBottleB.copy()
#self.specBigBottleB_noPad['Ch2'] = self.specBigBottleB_noPad['Ch2']-self.specBigBottleB_noPad['Ch10']
self.delayB_noPad = self.delayB.copy()
if not os.path.exists(os.path.join(self.savePath,r'totalSpec.pkl')):
save_obj(self.specBigBottleB,os.path.join(self.savePath,r'totalSpec.pkl'))
save_obj(self.delayB_noPad,os.path.join(self.savePath,r'delay.pkl'))
else:
print('Total spectra Saved!\n')
for gas in self.specBigBottleB.keys():
n=5
print(self.specBigBottleB[gas].shape[0],n)
self.phaseSpecBottleB[gas] = self.specBigBottleB[gas][-int(self.specBigBottleB[gas].shape[0]/n)*n:].reshape(int(self.specBigBottleB[gas].shape[0]/n), n, self.specBigBottleB[gas].shape[1]).sum(axis=1)
self.specBigBottleB[gas] = self.specBigBottleB[gas].sum(axis = 0)#np.take(self.specBigBottleB[gas],[i for i in range(self.specBigBottleB[gas].shape[0]) if i not in self.goodSpecIndex],axis=0).sum(axis = 0)
self.specBigBottleB['Ch2'] = self.specBigBottleB['Ch2']-self.specBigBottleB['Ch10']
self.label = {}
self.label['Ch0'] = 'Mass1'
self.label['Ch2'] = 'Mass2'
self.label['Ch4'] = 'Mass16'
self.label['Ch6'] = 'Mass17'
self.label['Ch8'] = 'Mass18'
def checkSavedData(self):
if os.path.exists(os.path.join(self.savePath,r'totalSpec.pkl')):
self.specBigBottleB = load_obj(os.path.join(self.savePath,r'totalSpec.pkl'))
self.delayB = load_obj(os.path.join(self.savePath,r'delay.pkl'))
print('Saved total spectra detected!\n')
try:
self.phaseBottle = load_obj(os.path.join(self.savePath, r'phaseBottle.pkl'))
print('Saved phase detected!\n')
except:
print('No saved phase detected!\n')
return 0
else:
return 1
def _flip(self):
for gas in list(self.specBigBottleB):
self.specBigBottleB[gas] = np.flip(self.specBigBottleB[gas],axis=0)
def window(self, windowSize=0, direction='left', useWindow = True):
'''
windowSize is in fs.
'''
#windowSize = windowSize+np.abs(self.delayB[0])*1e15 #????????????????????????
for gas in list(self.specBigBottleB):
if 'rebin' not in gas:
self.specBigBottleB[gas], self.specBigBottleB['window_'+gas], self.delayB = self.inter_window(self.specBigBottleB[gas], self.delayB, windowSize=windowSize, direction=direction, useWindow=useWindow)
else:
self.specBigBottleB[gas], self.specBigBottleB['window_'+gas], self.rebin_delay = self.inter_window(self.specBigBottleB[gas], self.rebin_delay, windowSize=windowSize, direction=direction, useWindow=useWindow)
for gas in list(self.spectraBottleD):
if 'rebin' not in gas:
self.spectraBottleD[gas], self.spectraBottleD['window_'+gas], self.delayD = self.inter_window(self.spectraBottleD[gas], self.delayD, windowSize=windowSize, direction=direction, useWindow=useWindow)
else:
self.spectraBottleD[gas], self.spectraBottleD['window_rebin_'+gas], self.rebin_delay = self.inter_window(self.spectraBottleD[gas], self.rebin_delay, windowSize=windowSize, direction=direction, useWindow=useWindow)
self.windowSize = windowSize
def window2(self, windowSize=0, direction='left'):
'''
windowSize is in fs.
'''
for gas in list(self.specBigBottleB):
if 'rebin' not in gas:
self.specBigBottleB[gas], self.specBigBottleB['window_'+gas], self.delayB = self.inter_window2(self.specBigBottleB[gas], self.delayB, windowSize=windowSize, direction=direction)
else:
self.specBigBottleB[gas], self.specBigBottleB['window_rebin_'+gas], self.rebin_delay = self.inter_window2(self.specBigBottleB[gas], self.rebin_delay, windowSize=windowSize, direction=direction)
for gas in list(self.spectraBottleD):
if 'rebin' not in gas:
self.spectraBottleD[gas], self.spectraBottleD['window_'+gas], self.delayD = self.inter_window2(self.spectraBottleD[gas], self.delayD, windowSize=windowSize, direction=direction)
else:
self.spectraBottleD[gas], self.spectraBottleD['window_rebin_'+gas], self.rebin_delay = self.inter_window2(self.spectraBottleD[gas], self.rebin_delay, windowSize=windowSize, direction=direction)
def inter_window(self, data, delay, windowSize=0, direction='left', useWindow = True, phaseCompensate = True, smooth = True):
'''
windowSize is in fs.
'''
if self.ifDelayRange:#
print('Using delay range!')
data = data[:int(np.size(data)/2)*2]
__len = np.size(data)
delay = delay[:__len]
windowSize = int(self.delayRange4FFT[0]/self.stepSize)
#print('window size is '+ str(windowSize)+str(' !'))
self.windowSize = windowSize
if smooth:
data=denoise_wavelet(data, sigma=5, wavelet='sym5', wavelet_levels=None)
#data=sps.savgol_filter(data, window_length=10, polyorder=1,deriv=1,delta=10, mode='nearest')
window=polynomial(data, order=1, plot=False)
refDelay = np.arange(np.size(window))*self.stepSize*1e15
omega=[588.26682,1346.61947,1479.61893,1588.32041,1704.69493,1821.06945,1945.11702,2053.8185,2189.37563,3294.29418,3530.87974,3771.30183,4161.34831,357.69977,815.04447,4518.73414,4718.93935,4911.44435,5110.36619,5463.29203,3081.36344]
oscA=np.sum(np.array([np.sin(2*np.pi*refDelay/33356.40952*f) for f in omega]),0)
self.refSpectra4AbsPhase = np.hanning(np.size(window))*oscA[-(__len-windowSize):]
if useWindow:
#window2=self.apply_triwindow(window)
window2=self.apply_hannwindow(window)
#window2=self.apply_hammwindow(window)
#plt.plot(self.refSpectra4AbsPhase)
#plt.show()
else:
window2=window
if phaseCompensate:
window2 = np.append(np.zeros(windowSize),window2,axis=0)
window = np.append(np.zeros(windowSize),window,axis=0)
self.refSpectra4AbsPhase = np.append(np.zeros(windowSize),self.refSpectra4AbsPhase,axis=0)
else:
data = data[:int(np.size(data)/2)*2]
__len = np.size(data)
delay = delay[:__len]
windowSize = int(windowSize*1e-15/self.stepSize)
#print('window size is '+ str(windowSize)+str(' !'))
self.windowSize = windowSize
refDelay = delay*1e15#np.arange(np.size(window))*self.stepSize*1e15
omega=[588.26682,1346.61947,1479.61893,1588.32041,1704.69493,1821.06945,1945.11702,2053.8185,2189.37563,3294.29418,3530.87974,3771.30183,4161.34831,357.69977,815.04447,4518.73414,4718.93935,4911.44435,5110.36619,5463.29203,3081.36344]
oscA=np.sum(np.array([np.sin(2*np.pi*refDelay/33356.40952*f) for f in omega]),0)
#data=self.butter_bandpass_filter(data, 300/33.35641*1e12, 18000/33.35641*1e12, 1/self.stepSize)
self.refSpectra4AbsPhase =oscA#self.butter_bandpass_filter(oscA, 300/33.35641*1e12, 18000/33.35641*1e12, 1/self.stepSize)
if smooth:
#pass
#data=denoise_wavelet(data, sigma=25, wavelet='sym5', wavelet_levels=None)
a,b,c,d = [20,1,1,3]
data=sps.savgol_filter(data, window_length=a, polyorder=b,deriv=c,delta=d, mode='nearest')
self.refSpectra4AbsPhase=sps.savgol_filter(self.refSpectra4AbsPhase, window_length=a, polyorder=b,deriv=c,delta=d, mode='nearest')
if direction == 'left':
window = data[-(__len-windowSize):]
self.refSpectra4AbsPhase = self.refSpectra4AbsPhase[-(__len-windowSize):]
if phaseCompensate:
pass
else:
delay = delay[-(__len-windowSize):]
elif direction == 'right':
window = data[:__len-windowSize]
delay = delay[:__len-windowSize]
elif direction == 'middle':
window = np.concatenate((
data[:round((__len-windowSize)/2)], # need to check again
(data[round((__len-windowSize)/2)] + \
data[round((__len+windowSize)/2)])/2*(np.zeros(windowSize)+1),
data[-(__len-round((__len+windowSize)/2)+1):]
))
window = polynomial(window, order=15, plot=False)
#window =self.baseLineRemove(window)#shift the base line to zero
#if not math.log2(np.size(window)).is_integer():
# #print('Fill the data to length if power of 2!')
# window = np.append(window,np.zeros(2**(math.ceil(math.log2(np.size(window))))-np.size(window)),axis=0)
if useWindow:
#window2=self.apply_triwindow(window)
window2=self.apply_hannwindow(window)
self.refSpectra4AbsPhase = self.apply_hannwindow(self.refSpectra4AbsPhase)
#window2=self.apply_hammwindow(window)
#plt.plot(self.refSpectra4AbsPhase)
#plt.show()
else:
window2=window
if phaseCompensate:
window2 = np.append(np.zeros(windowSize),window2,axis=0)
window = np.append(np.zeros(windowSize),window,axis=0)
self.refSpectra4AbsPhase = np.append(np.zeros(windowSize),self.refSpectra4AbsPhase,axis=0)
return window, window2, delay
def apply_hannwindow(self,y):
hwindow = np.hanning(len(y))
return y*hwindow
def apply_hammwindow(self,y):
hwindow = np.hamming(len(y))
return y*hwindow
def apply_triwindow(self,y):
twindow = np.bartlett(len(y))
return y*twindow
def padding(self, paddingSize=0):
for gas in list(self.specBigBottleB):
if "rebin" not in gas:
self.specBigBottleB[gas], self.delayB = self.inter_padding(self.specBigBottleB[gas], self.delayB, paddingSize = paddingSize)
else:
self.specBigBottleB[gas], self.rebin_delay = self.inter_padding(self.specBigBottleB[gas], self.rebin_delay, paddingSize = paddingSize)
for gas in list(self.spectraBottleD):
if "rebin" not in gas:
self.spectraBottleD[gas], self.delayD = self.inter_padding(self.spectraBottleD[gas], self.delayD, paddingSize = paddingSize)
else:
self.spectraBottleD[gas], self.rebin_delay = self.inter_padding(self.specBigBottleB[gas], self.rebin_delay, paddingSize = paddingSize)
def inter_padding(self, inter_data, delay, paddingSize=0):
data = None
delayStep = self.stepSize
delay = np.concatenate((
#np.arange(delay[0]-(paddingSize+1) *
# delayStep, delay[0], delayStep),
delay,
np.arange(paddingSize)*delayStep+delay[-1]
))
data = np.concatenate(
#(np.zeros(paddingSize),inter_data, np.zeros(paddingSize)), axis=0)
(inter_data, np.zeros(paddingSize)), axis=0)
self.refSpectra4AbsPhase = np.concatenate(
#(np.zeros(paddingSize),inter_data, np.zeros(paddingSize)), axis=0)
(self.refSpectra4AbsPhase, np.zeros(paddingSize)), axis=0)
data = data[:int(np.size(data)/2)*2]
delay = delay[:len(data)]
return data, delay
def interpS(self, interNum=1):
interpDelay = np.arange(
self.delayB[0], self.delayB[-1], (self.delayB[1]-self.delayB[0])/(interNum+1))
for gas in self.specBigBottleB.keys():
iS = np.interp(interpDelay, self.delayB, self.specBigBottleB[gas])
self.specBigBottleB[gas] = iS
# #print(np.shape(iS))
self.delayB = interpDelay
def interInterp(self, t, S, interNum=1):
interpDelay = np.arange(
t[0], t[-1], self.stepSize/(interNum+1))
return np.interp(interpDelay, self.delayB, S)
def baseLineRemove(self,y):
baseObj=BaselineRemoval(y)
return baseObj.ZhangFit(lambda_=50, repitition=50)
def rmvExp(self):
for gas in self.specBigBottleB.keys():
self.specBigBottleB[gas] = self.interRmvLinear(self.specBigBottleB[gas])
def interRmvLinear(self,y):
a = np.array([[0, 1], [np.size(y), 1]])
b = np.array([y[0],y[-1]])
[k, b] = np.linalg.solve(a, b)
return y-(k*np.arange(np.size(y))+b)
#def runingAverage(self, n=5):
# def runAve(x, N): return np.convolve(x, np.ones(N)/N, mode='valid')
# for gas in self.specBigBottleB.keys():
# self.specBigBottleB[gas] = runAve(self.specBigBottleB[gas], n)
# new_size = len(self.specBigBottleB[gas])
# self.delayB = self.delayB[:new_size]
#
#def smooth(self, windowSize=100, order=3):
# for gas in self.specBigBottleB.keys():
# self.specBigBottleB[gas]=sps.savgol_filter(self.specBigBottleB[gas], windowSize, order) # window size 51, polynomial order 3
#
#def smooth2(self,data,windowSize=100,order=3):
# return sps.savgol_filter(data, windowSize, order)
def rebin_factor(self, a, factor):
'''Rebin an array to a new shape.^^
newshape must be a factor of a.shape.
'''
newshape = tuple(int(i/factor) for i in a.shape)
i1 = tuple(int(i*factor) for i in newshape)
a = a[:i1[0]]
return a.reshape(newshape+(-1,)).mean(axis=-1)
def rebinS(self, factor=10):
self.ifrebin = True
for gas in list(self.specBigBottleB.keys()):
self.specBigBottleB['rebin_'+gas] = self.rebin_factor(self.specBigBottleB[gas], factor)
self.rebin_delay = self.rebin_factor(self.delayB, factor)
self.stepSize = self.stepSize*factor
def dataProcess(self):
#self.mass_spectra()
self.fftSB()
def useFilter(self, lowcut, highcut):
for gas in list(self.specBigBottleB.keys()):
# if 'rebin' not in gas:
fs = 1/(self.delayB[1]-self.delayB[0])
# else:
# fs = 1/(self.rebin_delay[90]-self.rebin_delay[89])
self.specBigBottleB['filter_'+gas] = self.butter_bandpass_filter(self.specBigBottleB[gas], lowcut, highcut, fs)
def useFilter2(self, data, lowcut, highcut):
# if 'rebin' not in gas:
fs = 1/(self.delayB[1]-self.delayB[0])
# else:
# fs = 1/(self.rebin_delay[90]-self.rebin_delay[89])
return self.butter_bandpass_filter(data, lowcut, highcut, fs)
def butter_bandpass_filter(self, data, lowcut, highcut, fs, order=2):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
sos = sps.butter(order, [low, high], analog=False, btype='band', output='sos')
y = sps.sosfiltfilt(sos, data)
#w, h = sps.sosfreqz(sos, worN=2000)
#plt.plot(w, h)
#plt.show()
return y
def findZeroDelay(self):
zeroIndex = []
for i in range(self.interSpectraBottleB['Ch0'].shape[0]):
_Spec = self.interSpectraBottleB['Ch0'][i]
_Spec = self.butter_bandpass_filter(_Spec, 100/33.35641*1e12, 1000/33.35641*1e12, 1/(self.delayB[1]-self.delayB[0]))
#plt.plot(_Spec)
zeroIndex =zeroIndex + [(_Spec[:2000]).argmax()]
#plt.show()
return zeroIndex
def findZeroDelay2(self):
zeroIndex = []
for i in range(self.specBigBottleB['Ch2'].shape[0]):
_Spec = np.abs(self.specBigBottleB['Ch2'][i])+np.abs(self.specBigBottleB['Ch0'][i])
_Spec = self.butter_bandpass_filter(_Spec, 100/33.35641*1e12, 1000/33.35641*1e12, 1/(self.delayB[1]-self.delayB[0]))
plt.plot(_Spec)
zeroIndex =zeroIndex + [np.abs((_Spec[:2000])).argmax()]
plt.show()
return zeroIndex
def findZeroDelay3(self):
zeroIndex = []
_Spec = np.abs(self.specBigBottleB['Ch0'])/np.max(np.abs(self.specBigBottleB['Ch0']))#+np.abs(self.specBigBottleB['Ch8'])/np.max(np.abs(self.specBigBottleB['Ch8']))
_Spec = self.butter_bandpass_filter(_Spec, 300/33.35641*1e12, 4500/33.35641*1e12, 1/(self.delayB[1]-self.delayB[0]))
zeroIndex =np.abs((_Spec[:2000])).argmax()
self.zeroIndex = zeroIndex # this number will be used for phase correction
__inter = self.specBigBottleB_noPad.copy()
self.specBigBottleB_noPad = {}
for gas in self.specBigBottleB.keys():
self.specBigBottleB[gas] = self.specBigBottleB[gas][zeroIndex:]
self.specBigBottleB_noPad[gas]={}
for j in range(__inter[gas].shape[0]):
self.specBigBottleB_noPad[gas][j]=-1*__inter[gas][j][zeroIndex:] #change the sign of the amplitude
#self.specBigBottleB[gas] = self.specBigBottleB[gas][:zeroIndex]
self.delayB = np.arange(self.specBigBottleB['Ch8'].size)*self.stepSize
return zeroIndex
def phaseCorrection(self,spectra):
spectra = self.interRmvLinear(spectra)
interSpectra =spectra[:(self.zeroIndex*2)]
L=np.size(spectra)-(self.zeroIndex*2)
padded=np.concatenate((interSpectra[self.zeroIndex:self.zeroIndex*2],np.zeros(L),interSpectra[:self.zeroIndex]))
Y=sp.fft.fft(padded)
#plt.plot(np.unwrap(np.arctan(np.imag(Y)/np.real(Y))))
#plt.show()
F = sp.fft.idct(np.cos(np.unwrap(np.arctan(np.imag(Y)/np.real(Y)))),type=2,norm=None)+sp.fft.idst(np.sin(np.unwrap(np.arctan(np.imag(Y)/np.real(Y)))),type=2,norm=None)
b=np.convolve(F,spectra)
plt.plot(b)
plt.show()
#P_inter = np.unwrap(np.where(P_inter<0,P_inter+np.pi,P_inter))
return b
def show_FFT(self, ifsaveFFT=False, ifsaveT=False):
self.interfftSB = load_obj(os.path.abspath(os.path.join(d.savePath, str(self.smooth)+str(self.folder)+r'_fftSB.pkl')))
self.dcRange=0
fig, ax = plt.subplots(nrows=2, ncols=1, sharex=True, sharey=True,figsize=(10,10))
fig.add_subplot(111, frameon=False)
plt.tick_params(labelcolor='none', which='both', top=False, bottom=False, left=False, right=False)
plt.xlabel("Frequency ($\mathrm{cm^{-1}}$)")
plt.ylabel("Amplitude (a.u.)", labelpad=25)
plt.text(1.18,0.35,'Relative Phase v.s. Mass 2 ($\pi$)', rotation = 270)
axPP = []
for axx in ax.flatten():
axPP = axPP + [axx.twinx()]
axPP[0].get_shared_y_axes().join(axPP[0], axPP[1])
lab=['Mass 2','Mass 1']
i=0
if ifsaveFFT:
op.set_show(show=True)
self.wksFFT = op.new_sheet('w',lname=str('FFT')+str('_')+self.folder)
if ifsaveT:
op.set_show(show=True)
self.wksT = op.new_sheet('w',lname=str('Time')+str('_')+self.folder)
_preP = 'window'+'_'
self.result = {}
self.result['phase'] = {}
self.result['amplitude'] = {}
boxcarA={}
boxcarA['Ch0'],boxcarA['Ch2'] = [1,0.01]
for gas in ['Ch2','Ch0']:
if 'filter' in gas or 'window' in gas or 'rebin' in gas or 'com' in gas:
continue
elif gas not in ['Ch2','Ch0']:
continue
axF=ax[i]
axP = axPP[i]
#axP.set_ylim([-np.pi,np.pi])
label=lab[i]
f_window = self.fftSB[_preP+'fre']
Y = np.array([np.mean(self.fftSB[_preP+gas+'_fft'],axis=0), np.std(self.fftSB[_preP+gas+'_fft'],axis=0)])
Y_window = np.array([np.mean(np.abs(self.fftSB[_preP+gas+'_fft']),axis=0), np.std(np.abs(self.fftSB[_preP+gas+'_fft']),axis=0)])
Y_window=np.where(f_window>=100,Y_window,0)/np.amax(Y_window)
Y_window_im = np.array([np.mean(np.imag(self.fftSB[_preP+gas+'_fft']),axis=0), np.std(np.imag(self.fftSB[_preP+gas+'_fft']),axis=0)])
Y_window_re = np.array([np.mean(np.real(self.fftSB[_preP+gas+'_fft']),axis=0), np.std(np.real(self.fftSB[_preP+gas+'_fft']),axis=0)])
#if self.smooth and self.folder==r'7.2E+14_H2O':
# P_inter = np.angle(self.interfftSB[_preP+gas+'_fft'])
#else:
P_inter = np.angle(self.fftSB[_preP+gas+'_fft'])
if gas == 'Ch2':
P_ref = P_inter
P_window = np.array([np.mean(P_inter,axis=0)-np.angle(self.fftSB['ref4Phase']), np.std(P_inter,axis=0)])#np.mean(P_inter,axis=0)-np.angle(self.fftSB['ref4Phase'])
#plt.plot(f_window,np.angle(self.fftSB['ref4Phase']))
#plt.plot(f_window,np.unwrap(np.mean(P_inter,axis=0)))
#plt.plot(np.arctan2(Y_window_im[0],Y_window_re[0]))
#plt.xlim([3500,3600])
#plt.show()
else:
P_inter = P_inter-P_ref
for iii in range(10):
P_inter.sort(axis=0)
P_inter2=P_inter.copy()
P_inter3=P_inter.copy()
P_inter2[-1]=P_inter2[-1]-2*np.pi
P_inter3[0]=P_inter3[0]+2*np.pi
P_inter[-1]=np.where(np.std(P_inter,axis=0)<np.std(P_inter2,axis=0),P_inter[-1],P_inter2[-1])
P_inter[0]=np.where(np.std(P_inter,axis=0)<np.std(P_inter3,axis=0),P_inter[0],P_inter3[0])
#P_window = np.array([np.mean(P_inter,axis=0), np.sqrt(np.std(P_inter,axis=0)**2+np.std(P_ref,axis=0)**2)])
P_window = np.array([np.mean(P_inter,axis=0), np.sqrt(np.std(P_inter,axis=0)**2+0)])
aa = len(f_window[(f_window<100)])
bb=len(f_window[(f_window<20000)])
#aa = len(f_window[(f_window<100)])
#bb=len(f_window[(f_window<50000)])
f_window = f_window[aa:bb]
#print('The step of frequency is '+str(np.mean(f_window[1:10]-f_window[0:9])))
Y = Y[:,aa:bb]
Y_window = Y_window[:,aa:bb]
Y_window_im = Y_window_im[:,aa:bb]
Y_window_re = Y_window_re[:,aa:bb]
P_window = P_window[:,aa:bb]
P_window[0]=np.where(P_window[0]<-np.pi+1,P_window[0]+2*np.pi,P_window[0])
P_window[0]=np.where(P_window[0]>np.pi-1,P_window[0]-2*np.pi,P_window[0])
P_window = P_window/np.pi
self.result['frequency'] = f_window
self.result['phase'][gas] = P_window
omega=[588.26682,1346.61947,1479.61893,1588.32041,1704.69493,1821.06945,1945.11702,2053.8185,2189.37563,3294.29418,3530.87974,3771.30183,4161.34831,357.69977,815.04447,4518.73414,4718.93935,4911.44435,5110.36619,5463.29203,3081.36344,5684]
for om in omega:
if i>0:
axF.axvline(x=om,ymin=0,ymax=1.3,clip_on=False,c='k',linestyle='--',alpha=0.3)
else:
axF.axvline(x=om,clip_on=False,c='k',linestyle='--',alpha=0.3)
axF.text(x=om-70, y=1.1, s=str(int(om)),fontsize='8')
if om==1594.43209:
axF.text(x=om-70, y=1.8, s='H2O+ Bend',fontsize='8')
if om==3655.52723:
axF.text(x=om-70, y=1.8, s='H2O a1 Sym',fontsize='8')
inter = 0
for w in omega:
inter = inter + np.where(np.abs(f_window-w)<20,P_window,0)
inter = np.where(inter==0,np.inf,inter)
P_window = inter
_interF = self.baseLineRemove(sps.savgol_filter(Y_window[0], window_length=20, polyorder=0,deriv=0,delta=2, mode='nearest'))
axF.plot(f_window, _interF/np.max(_interF), 'k', clip_on=True, label=label)
#self.result['amplitude'][gas] = self.baseLineRemove(Y_window[0]/np.amax(Y_window[0]))
#axF.plot(f_window, Y_window_re[0]/(np.amax(Y_window_re[0])-np.amin(Y_window_re[0])), label=label+'_re')
#axF.plot(f_window, Y_window_im[0]/(np.amax(Y_window_im[0])-np.amin(Y_window_im[0])), label=label+'_im')
#axF.plot(f_window, self.baseLineRemove(Y_window_re[0]/np.amax(Y_window[0])))#, label=label+'_re')
#axF.plot(f_window, self.baseLineRemove(Y_window_im[0]/np.amax(Y_window[0])))#, label=label+'_im')
axP.errorbar(f_window,P_window[0],yerr=P_window[1], color='r', ecolor='r',linewidth=2,label='Phase')
#plot(f_window,P_window,'r')
#axF.set_ylim([0,0.2])
#axF.set_xlim([200,4500])
axP.set_yticks([-1,-0.5,0,0.5,1])
axP.grid(visible=True,linestyle='--',linewidth='0.3',c='b')
axP.set_ylim([-1.3,1.3])
axP.legend(loc=(0.02,0.6),ncol=2,fontsize=10)
#axF.set_yscale('log')
#axF.set_ylim([10**-2.5,10**0])
axF.legend(loc=(0.02,0.8),ncol=2,fontsize=10)
i=i+1
if ifsaveFFT:
self.wksFFT.from_list(0, f_window, lname="Frequency", axis='X')
self.wksFFT.from_list(i*3-2, _interF/np.max(_interF), lname=label, axis='Y')
self.wksFFT.from_list(i*3-1, P_window[0], lname=label, axis='Y')
self.wksFFT.from_list(i*3, P_window[1], lname=label, axis='E')
#self.wksFFT.from_list(i*3-3, f_window, lname="Frequency", axis='X', units = 'wavenumber')
#self.wksFFT.from_list(i*3-2, self.baseLineRemove(Y_window[0]/np.amax(Y_window[0])), lname=label, axis='Y')
#self.wksFFT.from_list(i*3-2, Y_window_re[0], lname=label, axis='Y', comments = 're')
#self.wksFFT.from_list(i*3-1, Y_window_im[0], lname=label, axis='Y', comments = 'im')
if ifsaveT:
#self.wks.from_list(0, self.rebin_factor(self.delayB,10), 'X')
#self.wks.from_list(i, self.rebin_factor((self.specBigBottleB[gas]-np.mean(self.specBigBottleB[gas])),10), lname=gas, axis='Y')
self.wksT.from_list(0, self.smoothedT['T']*1e15, 'X')
self.wksT.from_list(i, self.smoothedT[gas], lname=gas, axis='Y')
fig.tight_layout()
save_obj(self.result, pl.PureWindowsPath(self.savePath, self.folder+'_result'+r'.pkl'))
save_obj(self.fftSB, pl.PureWindowsPath(self.savePath, self.folder+'_fftSB'+r'.pkl'))
#plt.savefig(os.path.join(os.path.join(self.savePath,r'fft_logy.png')),dpi=720,bbox_inches='tight',pad_inches=0,transparent=True)
#plt.savefig(os.path.join(os.path.join(self.savePath,r'fft.png')),dpi=720,bbox_inches='tight',pad_inches=0,transparent=True)
plt.show()
#def show_FFTD(self):
# #plt.figure()
# #unused_f, ref = self.fftS['CH3OH+']
# i=12
# for gas in self.fftSD.keys():
# #if 'filter' not in gas:
# # continue
# [f, Y, _] = self.fftSD[gas]
# #Y=np.where(np.logical_and(f>=10, f<=4500),Y,0)
# if gas == 'window_H2+':
# plt.plot(f[self.dcRange:], Y[self.dcRange:]/1000, label=r'$\mathrm{H_2^+}$')
# #if gas == 'H+':
# # plt.plot(f[self.dcRange:], Y[self.dcRange:]/1000, label=r'$\mathrm{H^+}$')
# if gas == 'window_O+':
# plt.plot(f[self.dcRange:], Y[self.dcRange:]/1000, label=r'$\mathrm{O^+}$')
# if gas == 'window_O+H2':
# plt.plot(f[self.dcRange:], Y[self.dcRange:]/1000, label=r'$\mathrm{H_2^++O^+}$')
# #print("The max of the FFT is ",np.amax( Y[self.dcRange:]/1000))
# if gas == 'window_O-H2':
# plt.plot(f[self.dcRange:], Y[self.dcRange:]/1000, label=r'$\mathrm{H_2^+-O^+}$')
# else:
# #plt.plot(f[self.dcRange:], Y[self.dcRange:]/1000, label=gas)
# pass
# plt.xlabel(r'$\mathrm{Frequency (cm^{-1})}$')
# plt.ylabel('a.u.')
# plt.legend(loc=2)
# #plt.xlabel('Frequency/cm-1')
# #plt.ylim([0,np.max(Y[self.dcRange:1000])*3/2])
# plt.xlim([0,4500])
# i=i+1
# if ifsave:
# self.wks.from_list(7, f[self.dcRange:], 'X')
# self.wks.from_list(i, np.abs(Y[self.dcRange:]), lname=gas, axis='Y')
# #plt.legend()
# plt.tight_layout()
# d='_100_120'
def show_Spectra(self, ifsaveT=False):
gs = gridspec.GridSpec(2, 3)
#gs = gridspec.GridSpec(1, 1)
fig = plt.figure(figsize=(20,8))
#ax = fig.add_subplot(111)
lab=['Mass1','Mass2','Mass16','Mass17','Mass18','Ch2+Ch4','Mass1+Mass16', 'Mass1+Mass17', 'Mass16+Mass17','Mass17+Mass18']
i=0
if ifsaveT:
op.set_show(show=True)
self.wks = op.new_sheet('w',lname=str('Time')+str('_')+self.molecule+str('_')+self.folder)
for gas in self.specBigBottleB.keys():
#print(gas)
if 'filter' in gas or 'window' in gas or 'rebin' in gas or 'com' in gas:
continue
if gas in ['Ch0','Ch2','Ch4','Ch6','Ch8','Ch10']:
pass
else:
#print('Skip!')
continue
label=lab[i]
ax = fig.add_subplot(gs[i])
i=i+1
delay = self.delayB
rebindelay = self.rebin_delay
#else:
# delay = self.rebin_delay
ax.plot(delay*10**15,
self.specBigBottleB[gas]/(np.amax(self.specBigBottleB[gas][5500:6000])-np.amin(self.specBigBottleB[gas][5500:6000])), label=gas)#/np.amax(self.specBigBottleB[gas])
#ax.plot(delay*10**15+shift,
# self.specBigBottleB['window_filter_'+gas], label=label)
#ax.plot(delay*10**15+shift,
# self.specBigBottleB['window_'+gas], label='window_'+gas)
#ax.plot(rebindelay*10**15+shift,
# self.specBigBottleB['rebin_window_'+gas], label='rebin_window_'+gas)
ax.set_xlabel("Delay/fs")
ax.set_ylabel('a.u.')
#plt.xlim([300,400])
ax.legend()
if ifsaveT:
self.wks.from_list(0, delay*10**15, 'X')
self.wks.from_list(i, self.specBigBottleB['filter_'+gas], lname=label, axis='Y')
#plt.legend()
fig.tight_layout()
plt.show()
def calDrift(self, _cRange, gas='Ch8'):
plt.clf()
_iS = np.array(np.zeros(self.specBigBottleB[gas].shape))
for i in range(self.specBigBottleB[gas].shape[0]):
#_iS[i]=self.butter_bandpass_filter(self.specBigBottleB[gas][i], (3643.52883-0.1)/33.35641*1e12, (3643.52883+0.1)/33.35641*1e12, 1/(self.delayB[1]-self.delayB[0]))
_iS[i]=self.butter_bandpass_filter(self.specBigBottleB[gas][i], 100/33.35641*1e12, 4000/33.35641*1e12, 1/(self.delayB[1]-self.delayB[0]))
iS = sp.interpolate.RectBivariateSpline(range(_iS.shape[0]), self.delayB*1e15, _iS)
_delayRange = np.linspace(start=_cRange[0],stop=_cRange[1], num=2000)
indexMax = []
for i in range(self.specBigBottleB[gas].shape[0]):
_inter=iS.ev(i,_delayRange)
plt.plot(_delayRange,_inter,label=str(i))
#indexMax = indexMax + [sps.argrelextrema(_inter, np.greater)[0][-1]]
indexMax = indexMax + [np.argmax(_inter)]
plt.xlabel('Delay (fs)')
plt.ylabel('a.u.')
plt.legend()
plt.show()
_ref = indexMax[int(self.specBigBottleB[gas].shape[0]/2)]
_shift = (np.array(indexMax)-_ref)*(_cRange[1]-_cRange[0])/2000
for i in range(self.specBigBottleB[gas].shape[0]):
_inter=iS.ev(i,_delayRange+_shift[i])
plt.plot(_delayRange,_inter, label=str(i))
plt.xlabel('Delay (fs)')
plt.ylabel('a.u.')
plt.legend()
plt.show()
return _shift
def calDrift2(self, _cRange, gas='Ch8'):
'''
calibrate by drift of the strech mode oscillation
'''
plt.clf()
standard = 0
standard = self.specBigBottleB['Ch8']-self.specBigBottleB['Ch0']#-self.specBigBottleB['Ch6']
_iS = np.array(np.zeros(self.specBigBottleB[gas].shape))
#_iS2 = np.array(np.zeros(self.specBigBottleB[gas].shape))
for i in range(self.specBigBottleB[gas].shape[0]):
#_iS[i]=self.butter_bandpass_filter(standard[i], (3655.52723-20)/33.35641*1e12, (3655.52723+20)/33.35641*1e12, 1/self.stepSize)
#_iS[i]=self.butter_bandpass_filter(self.specBigBottleB[gas][i], 500/33.35641*1e12, 3800/33.35641*1e12, 1/self.stepSize)
_iS[i]=self.butter_bandpass_filter(standard[i], 100/33.35641*1e12, 1500/33.35641*1e12, 1/self.stepSize)
#_iS2[i]=self.butter_bandpass_filter(self.specBigBottleB[gas][i], 100/33.35641*1e12, 4000/33.35641*1e12, 1/(self.delayB[1]-self.delayB[0]))
iS = sp.interpolate.RectBivariateSpline(range(_iS.shape[0]), self.delayB*1e15, _iS)
#iS2 = sp.interpolate.RectBivariateSpline(range(_iS2.shape[0]), self.delayB*1e15, _iS2)
_delayRange = np.linspace(start=_cRange[0],stop=_cRange[1], num=20000)
indexMax = []
for i in range(self.specBigBottleB[gas].shape[0]):
_inter=iS.ev(i,_delayRange)
plt.plot(_delayRange,_inter)
#indexMax = indexMax + [sps.argrelextrema(_inter, np.greater)[0][-1]]
indexMax = indexMax + [np.argmax(np.abs(_inter))]
#print(indexMax)
plt.xlabel('Delay (fs)')
plt.ylabel('a.u.')
plt.show()
#_ref = sum(indexMax[int(self.specBigBottleB[gas].shape[0]/2)-5:int(self.specBigBottleB[gas].shape[0]/2)+5])/10
_ref =indexMax[int(self.specBigBottleB[gas].shape[0]/2)]
_shift = (np.array(indexMax)-_ref)*(_cRange[1]-_cRange[0])/20000
for i in range(self.specBigBottleB[gas].shape[0]):
_inter=iS.ev(i,_delayRange+_shift[i])
#delayRangeA = np.linspace(start=50,stop=100, num=2000)#Used to compare the zreo delay when calibrating using stretch mode frequency to calibrate
#_inter2 = iS2.ev(i,delayRangeA+_shift[i])#
plt.plot(_delayRange,_inter)
#plt.plot(delayRangeA,_inter2)
#plt.xlabel('Delay (fs)')
#plt.ylabel('a.u.')
plt.show()
return _shift
#def delayCorrection(self, _cRange = [300,307]):
def delayCorrection(self, _cRange = [1,150]):
#def delayCorrection(self, _cRange = [900,1300]):
xxx = 0
while True:
try:
#_shift = self.calDrift(_cRange = _cRange)
_shift = self.calDrift2(_cRange = _cRange)
break
except IndexError:
#print('Wrong Region! Try again!')
if xxx>10:
_cRange = [np.array(_cRange)[0], np.array(_cRange)[1]+0.5]
_cRange = np.array(_cRange)+0.5
xxx = xxx+1
iinter = {}
for gas in self.specBigBottleB.keys():
iS = sp.interpolate.RectBivariateSpline(range(self.specBigBottleB[gas].shape[0]), self.delayB_noPad*1e15, self.specBigBottleB[gas])
inter = np.zeros(self.specBigBottleB[gas].shape)
for i in range(self.specBigBottleB[gas].shape[0]):
inter[i] = iS.ev(i, self.delayB_noPad*1e15+_shift[i])
iinter[gas] = inter
self.specBigBottleB = iinter
def removeHydrogenS(self):
savePathH2= pl.PureWindowsPath(os.path.join(r'C:\Users\user\Desktop\Data_newTOF\dataProcessing\H2',self.caliFolder))
if os.path.exists(os.path.join(savePathH2,r'totalSpec.pkl')):
self.specBigBottleB_H2 = load_obj(os.path.join(savePathH2,r'totalSpec.pkl'))
for gas in self.specBigBottleB_H2.keys():
self.specBigBottleB_H2[gas] = self.specBigBottleB_H2[gas].sum(axis = 0)
def phaseRetrive(self,omega=[3655.52723]):
#[526.49165,625.20883,699.99458,810.67748,882.47179,1145.71762,1343.15199,1594.43209,1696.1407,2153.82946,2324.34096,2677.32968,3212.79562,3655.52723]
self.interSpectraBottleB = {}
for gas in self.specBigBottleB_noPad.keys():
_shape = self.specBigBottleB_noPad[gas].shape[0]
_shape = _shape-_shape%6
self.interSpectraBottleB[gas] = self.specBigBottleB_noPad[gas][:_shape]
self.interSpectraBottleB[gas] = self.interSpectraBottleB[gas].reshape(int(_shape/6), 6, self.interSpectraBottleB[gas].shape[1]).sum(axis=1)
self.filterPhase[gas]={}
self.filterSpec[gas]={}
for i in range(self.interSpectraBottleB[gas].shape[0]):
self.filterPhase[gas][str(i)]={}
self.filterSpec[gas][str(i)]={}
for f in omega:
f0=(f-1)/33.35641*1e12
f1=(f+1)/33.35641*1e12
#dd,t=self.inter_padding(self.interSpectraBottleB[gas][i],self.delayB,paddingSize=10000000)
self.filterSpec[gas][str(i)][str(f)] = self.useFilter2(self.interSpectraBottleB[gas][i],f0,f1)
#if gas=='Ch6' and f==3643.52883:
# plt.plot(self.filterSpec[gas][str(i)][str(f)]*3000-382,label='noPad')
# dd,t=self.inter_padding(self.interSpectraBottleB[gas][i],self.delayB,paddingSize=10000000)
# plt.plot(self.useFilter2(dd,f0,f1)-382,label='Pad')
# plt.plot(self.interSpectraBottleB[gas][i])
# plt.legend()
# plt.show()
self.filterPhase[gas][str(i)][str(f)] = np.angle(sps.hilbert(self.filterSpec[gas][str(i)][str(f)]))
#zeroIndex = self.findZeroDelay()
#sampleIndex = np.zeros(self.delayB_noPad.size)+1
#sampleIndex = np.where(np.abs(self.filterPhase['Ch8'][str(i)][str(f)]-np.pi)<2*np.pi*2/9.15*(self.delayB[1]-self.delayB[0])*1e15,sampleIndex,0)
#sampleIndex = np.where(self.delayB_noPad*1e15<900, sampleIndex, 0)
#sampleIndex = np.where(self.delayB_noPad*1e15>200, sampleIndex, 0)
for gas in self.interSpectraBottleB.keys():
self.phaseBottleB[gas] = {}
for f in omega:
self.phaseBottleB[gas][str(f)] = {}
for i in range(self.interSpectraBottleB[gas].shape[0]):
zeroIndex = self.findZeroDelay3(i)
#print(zeroIndex)
#delay = (self.delayB_noPad-zeroIndex[i]*self.delayStep)*10**15
delay = (self.delayB_noPad-zeroIndex*self.delayStep)*10**15
delay = delay[(delay>200)]
phi = np.unwrap(self.filterPhase[gas][str(i)][str(f)])
phi = phi[-delay.size:]
delay = delay[(delay<200+9.15497*60)]
phi = phi[:delay.size]
#plt.plot(phi)
#plt.plot(delay/(33356.40952/f)*2*np.pi)
#plt.show()
phi = phi-delay/(33356.40952/f)*2*np.pi
#plt.plot(phi)
#plt.show()
phi = phi%(2*np.pi)
if i==0:
inter = np.zeros((self.interSpectraBottleB[gas].shape[0],phi.size))
inter[0] = phi
else:
inter[i] = phi
self.phaseBottleB[gas][str(f)]=inter
#if phi[]
for gas in self.phaseBottleB.keys():
if gas == 'Ch8':
continue
for f in omega:
plt.plot(np.mean(self.phaseBottleB[gas][str(f)],axis=1), label = str(f))
plt.legend()
plt.show()
#save_obj(self.)
def fit_sin(self, tt, yy, fre):
'''Fit sin to the input time sequence, and return fitting parameters "amp", "omega", "phase", "offset", "freq", "period" and "fitfunc"'''
tt = np.array(tt)
yy = np.array(yy)
ff = np.fft.fftfreq(len(tt), (tt[1]-tt[0])) # assume uniform spacing
Fyy = abs(np.fft.fft(yy))
guess_freq = abs(ff[np.argmax(Fyy[2:])+2]) # excluding the zero frequency "peak", which is related to offset
guess_amp = np.std(yy) * 2.**0.5