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I changed the name from range to prange (hope i did not miss something)

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There is now an Eigenvalue method using the cholesky method you put in the example. I do not really use that, but it seems like a logical inclusion.
I gave the standard fit an option to seht the number of fit parameters by hand, because it does not work automatically
 if the function is not consistent between calls.
This commit is contained in:
JanNeuendorf 2021-10-06 13:16:04 +02:00
parent 014c0d12ce
commit 7c03cff42f
2 changed files with 80 additions and 38 deletions
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96
pyerrors/correlators.py
View file

@ -3,6 +3,7 @@ import autograd.numpy as anp
#from scipy.special.orthogonal import _IntegerType #from scipy.special.orthogonal import _IntegerType
from .pyerrors import * from .pyerrors import *
from .fits import standard_fit from .fits import standard_fit
from .linalg import *
from .roots import find_root from .roots import find_root
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
from matplotlib.ticker import NullFormatter # useful for `logit` scale from matplotlib.ticker import NullFormatter # useful for `logit` scale
@ -23,7 +24,7 @@ class Corr:
""" """
def __init__(self, data_input, padding_front=0, padding_back=0,range=None): def __init__(self, data_input, padding_front=0, padding_back=0,prange=None):
#All data_input should be a list of things at different timeslices. This needs to be verified #All data_input should be a list of things at different timeslices. This needs to be verified
if not (isinstance(data_input, list)): if not (isinstance(data_input, list)):
@ -61,7 +62,7 @@ class Corr:
#This is useful for keeping track of plateaus and fitranges. #This is useful for keeping track of plateaus and fitranges.
#The range can be inherited from other Corrs, if the operation should not alter a chosen range eg. multiplication with a constant. #The range can be inherited from other Corrs, if the operation should not alter a chosen range eg. multiplication with a constant.
if not range is None: if not range is None:
self.range=range self.prange=prange
self.gamma_method() self.gamma_method()
@ -143,7 +144,7 @@ class Corr:
if(all([x is None for x in newcontent])): if(all([x is None for x in newcontent])):
raise Exception("Corr could not be symmetrized: No redundant values") raise Exception("Corr could not be symmetrized: No redundant values")
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
def anti_symmetric(self): def anti_symmetric(self):
@ -158,7 +159,7 @@ class Corr:
newcontent.append(0.5 * (self.content[t] - self.content[self.T - t])) newcontent.append(0.5 * (self.content[t] - self.content[self.T - t]))
if(all([x is None for x in newcontent])): if(all([x is None for x in newcontent])):
raise Exception("Corr could not be symmetrized: No redundant values") raise Exception("Corr could not be symmetrized: No redundant values")
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
#This method will symmetrice the matrices and therefore make them positive definit. #This method will symmetrice the matrices and therefore make them positive definit.
@ -186,6 +187,32 @@ class Corr:
return sp_vec return sp_vec
def Eigenvalue(self,t0,state=1):
G=self.smearing_symmetric()
G0=G.content[t0]
L = mat_mat_op(anp.linalg.cholesky, G0)
Li = mat_mat_op(anp.linalg.inv, L)
LT=L.T
LTi=mat_mat_op(anp.linalg.inv, LT)
newcontent=[]
for t in range(self.T):
Gt=G.content[t]
M=Li@Gt@LTi
eigenvalues = eigh(M)[0]
#print(eigenvalues)
eigenvalue=eigenvalues[-state]
newcontent.append(eigenvalue)
return Corr(newcontent)
def roll(self, dt): def roll(self, dt):
return Corr(list(np.roll(np.array(self.content, dtype=object), dt))) return Corr(list(np.roll(np.array(self.content, dtype=object), dt)))
@ -260,6 +287,17 @@ class Corr:
raise Exception('m_eff is undefined at all timeslices') raise Exception('m_eff is undefined at all timeslices')
return Corr(newcontent, padding_back=1) return Corr(newcontent, padding_back=1)
elif variant is 'arccosh':
newcontent=[]
for t in range(1,self.T-1):
if (self.content[t] is None) or (self.content[t+1] is None)or (self.content[t-1] is None):
newcontent.append(None)
else:
newcontent.append((self.content[t+1]+self.content[t-1])/(2*self.content[t]))
if(all([x is None for x in newcontent])):
raise Exception("m_eff is undefined at all timeslices")
return np.arccosh(Corr(newcontent,padding_back=1,padding_front=1))
else: else:
raise Exception('Unkown variant.') raise Exception('Unkown variant.')
@ -275,8 +313,8 @@ class Corr:
if fitrange is None: if fitrange is None:
if hasattr(self,"range"): if hasattr(self,"prange"):
fitrange=self.range fitrange=self.prange
else: else:
fitrange=[0, self.T] fitrange=[0, self.T]
@ -294,8 +332,8 @@ class Corr:
#we want to quickly get a plateau #we want to quickly get a plateau
def plateau(self, plateau_range=None, method="fit"): def plateau(self, plateau_range=None, method="fit"):
if not plateau_range: if not plateau_range:
if hasattr(self,"range"): if hasattr(self,"prange"):
plateau_range=self.range plateau_range=self.prange
else: else:
raise Exception("no plateau range provided") raise Exception("no plateau range provided")
if self.N != 1: if self.N != 1:
@ -316,15 +354,15 @@ class Corr:
def set_range(self,range): def set_prange(self,prange):
if not len(range)==2: if not len(prange)==2:
raise Exception("range must be a list or array with two values") raise Exception("range must be a list or array with two values")
if not ((isinstance(range[0],int)) and (isinstance(range[1],int))): if not ((isinstance(prange[0],int)) and (isinstance(prange[1],int))):
raise Exception("start and end point must be integers") raise Exception("start and end point must be integers")
if not (0<=range[0]<=self.T and 0<=range[1]<=self.T and range[0]<range[1] ): if not (0<=prange[0]<=self.T and 0<=prange[1]<=self.T and prange[0]<prange[1] ):
raise Exception("start and end point must define a range in the interval 0,T") raise Exception("start and end point must define a range in the interval 0,T")
self.range=range self.prange=prange
return return
@ -380,9 +418,9 @@ class Corr:
ax1.axhspan(plateau.value - plateau.dvalue, plateau.value + plateau.dvalue, alpha=0.25, color=plt.rcParams['text.color'], ls='-') ax1.axhspan(plateau.value - plateau.dvalue, plateau.value + plateau.dvalue, alpha=0.25, color=plt.rcParams['text.color'], ls='-')
else: else:
raise Exception('plateau must be an Obs') raise Exception('plateau must be an Obs')
if hasattr(self,"range"): if hasattr(self,"prange"):
ax1.axvline(self.range[0],0,1) ax1.axvline(self.prange[0],0,1)
ax1.axvline(self.range[1],0,1) ax1.axvline(self.prange[1],0,1)
if fit_res: if fit_res:
x_samples = np.arange(x_range[0], x_range[1] + 1, 0.05) x_samples = np.arange(x_range[0], x_range[1] + 1, 0.05)
@ -458,7 +496,7 @@ class Corr:
newcontent.append(None) newcontent.append(None)
else: else:
newcontent.append(self.content[t]+y) newcontent.append(self.content[t]+y)
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
else: else:
raise TypeError("Corr + wrong type") raise TypeError("Corr + wrong type")
@ -481,7 +519,7 @@ class Corr:
newcontent.append(None) newcontent.append(None)
else: else:
newcontent.append(self.content[t]*y) newcontent.append(self.content[t]*y)
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
else: else:
raise TypeError("Corr * wrong type") raise TypeError("Corr * wrong type")
@ -519,11 +557,11 @@ class Corr:
newcontent.append(None) newcontent.append(None)
else: else:
newcontent.append(self.content[t]/y) newcontent.append(self.content[t]/y)
if hasattr(self,"range"): if hasattr(self,"prange"):
newrange=self.range newrange=self.prange
else: else:
newrange=None newrange=None
return Corr(newcontent,range=newrange) return Corr(newcontent,prange=newrange)
elif isinstance(y, int) or isinstance(y,float): elif isinstance(y, int) or isinstance(y,float):
if y==0: if y==0:
@ -534,17 +572,17 @@ class Corr:
newcontent.append(None) newcontent.append(None)
else: else:
newcontent.append(self.content[t]/y) newcontent.append(self.content[t]/y)
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
else: else:
raise TypeError("Corr / wrong type") raise TypeError("Corr / wrong type")
def __neg__(self): def __neg__(self):
newcontent=[None if (item is None) else -1.*item for item in self.content] newcontent=[None if (item is None) else -1.*item for item in self.content]
if hasattr(self,"range"): if hasattr(self,"prange"):
newrange=self.range newrange=self.prange
else: else:
newrange=None newrange=None
return Corr(newcontent,range=newrange) return Corr(newcontent,prange=newrange)
def __sub__(self,y): def __sub__(self,y):
return self +(-y) return self +(-y)
@ -552,13 +590,13 @@ class Corr:
def __pow__(self, y): def __pow__(self, y):
if isinstance(y, Obs) or isinstance(y,int) or isinstance(y,float): if isinstance(y, Obs) or isinstance(y,int) or isinstance(y,float):
newcontent=[None if (item is None) else item**y for item in self.content] newcontent=[None if (item is None) else item**y for item in self.content]
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
else: else:
raise TypeError("type of exponent not supported") raise TypeError("type of exponent not supported")
def __abs__(self): def __abs__(self):
newcontent=[None if (item is None) else np.abs(item) for item in self.content] newcontent=[None if (item is None) else np.abs(item) for item in self.content]
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
#The numpy functions: #The numpy functions:
def sqrt(self): def sqrt(self):
@ -566,11 +604,11 @@ class Corr:
def log(self): def log(self):
newcontent=[None if (item is None) else np.log(item) for item in self.content] newcontent=[None if (item is None) else np.log(item) for item in self.content]
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
def exp(self): def exp(self):
newcontent=[None if (item is None) else np.exp(item) for item in self.content] newcontent=[None if (item is None) else np.exp(item) for item in self.content]
return Corr(newcontent,range= self.range if hasattr(self,"range") else None) return Corr(newcontent,prange= self.prange if hasattr(self,"prange") else None)
def sin(self): def sin(self):
newcontent=[None if (item is None) else np.sin(item) for item in self.content] newcontent=[None if (item is None) else np.sin(item) for item in self.content]

22
pyerrors/fits.py
View file

@ -14,7 +14,7 @@ from autograd import elementwise_grad as egrad
from .pyerrors import Obs, derived_observable, covariance, pseudo_Obs from .pyerrors import Obs, derived_observable, covariance, pseudo_Obs
def standard_fit(x, y, func, silent=False, **kwargs): def standard_fit(x, y, func,n_parms="auto", silent=False, **kwargs):
"""Performs a non-linear fit to y = func(x) and returns a list of Obs corresponding to the fit parameters. """Performs a non-linear fit to y = func(x) and returns a list of Obs corresponding to the fit parameters.
x has to be a list of floats. x has to be a list of floats.
@ -68,15 +68,19 @@ def standard_fit(x, y, func, silent=False, **kwargs):
if not callable(func): if not callable(func):
raise TypeError('func has to be a function.') raise TypeError('func has to be a function.')
for i in range(25): if n_parms=="auto":
try: for i in range(25):
func(np.arange(i), x.T[0]) try:
except: func(np.arange(i), x.T[0])
pass except:
else: pass
break else:
break
n_parms = i
n_parms = i
if not silent: if not silent:
print('Fit with', n_parms, 'parameters') print('Fit with', n_parms, 'parameters')