mirror of
https://github.com/fjosw/pyerrors.git
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1136 lines
47 KiB
Python
1136 lines
47 KiB
Python
import warnings
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from itertools import permutations
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import numpy as np
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import autograd.numpy as anp
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import matplotlib.pyplot as plt
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import scipy.linalg
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from .obs import Obs, reweight, correlate, CObs
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from .misc import dump_object, _assert_equal_properties
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from .fits import least_squares
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from .roots import find_root
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class Corr:
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"""The class for a correlator (time dependent sequence of pe.Obs).
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Everything, this class does, can be achieved using lists or arrays of Obs.
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But it is simply more convenient to have a dedicated object for correlators.
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One often wants to add or multiply correlators of the same length at every timeslice and it is inconvenient
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to iterate over all timeslices for every operation. This is especially true, when dealing with matrices.
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The correlator can have two types of content: An Obs at every timeslice OR a GEVP
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matrix at every timeslice. Other dependency (eg. spatial) are not supported.
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"""
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def __init__(self, data_input, padding=[0, 0], prange=None):
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""" Initialize a Corr object.
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Parameters
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----------
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data_input : list or array
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list of Obs or list of arrays of Obs or array of Corrs
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padding : list, optional
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List with two entries where the first labels the padding
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at the front of the correlator and the second the padding
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at the back.
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prange : list, optional
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List containing the first and last timeslice of the plateau
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region indentified for this correlator.
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"""
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if isinstance(data_input, np.ndarray):
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# This only works, if the array fulfills the conditions below
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if not len(data_input.shape) == 2 and data_input.shape[0] == data_input.shape[1]:
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raise Exception("Incompatible array shape")
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if not all([isinstance(item, Corr) for item in data_input.flatten()]):
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raise Exception("If the input is an array, its elements must be of type pe.Corr")
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if not all([item.N == 1 for item in data_input.flatten()]):
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raise Exception("Can only construct matrix correlator from single valued correlators")
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if not len(set([item.T for item in data_input.flatten()])) == 1:
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raise Exception("All input Correlators must be defined over the same timeslices.")
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T = data_input[0, 0].T
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N = data_input.shape[0]
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input_as_list = []
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for t in range(T):
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if any([(item.content[t] is None) for item in data_input.flatten()]):
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if not all([(item.content[t] is None) for item in data_input.flatten()]):
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warnings.warn("Input ill-defined at different timeslices. Conversion leads to data loss!", RuntimeWarning)
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input_as_list.append(None)
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else:
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array_at_timeslace = np.empty([N, N], dtype="object")
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for i in range(N):
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for j in range(N):
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array_at_timeslace[i, j] = data_input[i, j][t]
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input_as_list.append(array_at_timeslace)
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data_input = input_as_list
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if isinstance(data_input, list):
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if all([isinstance(item, (Obs, CObs)) for item in data_input]):
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_assert_equal_properties(data_input)
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self.content = [np.asarray([item]) for item in data_input]
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if all([isinstance(item, (Obs, CObs)) or item is None for item in data_input]):
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_assert_equal_properties([o for o in data_input if o is not None])
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self.content = [np.asarray([item]) if item is not None else None for item in data_input]
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self.N = 1
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elif all([isinstance(item, np.ndarray) or item is None for item in data_input]) and any([isinstance(item, np.ndarray) for item in data_input]):
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self.content = data_input
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noNull = [a for a in self.content if not (a is None)] # To check if the matrices are correct for all undefined elements
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self.N = noNull[0].shape[0]
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if self.N > 1 and noNull[0].shape[0] != noNull[0].shape[1]:
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raise Exception("Smearing matrices are not NxN")
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if (not all([item.shape == noNull[0].shape for item in noNull])):
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raise Exception("Items in data_input are not of identical shape." + str(noNull))
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else:
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raise Exception("data_input contains item of wrong type")
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else:
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raise Exception("Data input was not given as list or correct array")
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self.tag = None
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# An undefined timeslice is represented by the None object
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self.content = [None] * padding[0] + self.content + [None] * padding[1]
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self.T = len(self.content)
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self.prange = prange
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def __getitem__(self, idx):
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"""Return the content of timeslice idx"""
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if self.content[idx] is None:
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return None
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elif len(self.content[idx]) == 1:
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return self.content[idx][0]
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else:
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return self.content[idx]
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@property
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def reweighted(self):
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bool_array = np.array([list(map(lambda x: x.reweighted, o)) for o in [x for x in self.content if x is not None]])
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if np.all(bool_array == 1):
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return True
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elif np.all(bool_array == 0):
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return False
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else:
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raise Exception("Reweighting status of correlator corrupted.")
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def gamma_method(self, **kwargs):
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"""Apply the gamma method to the content of the Corr."""
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for item in self.content:
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if not(item is None):
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if self.N == 1:
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item[0].gamma_method(**kwargs)
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else:
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for i in range(self.N):
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for j in range(self.N):
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item[i, j].gamma_method(**kwargs)
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def projected(self, vector_l=None, vector_r=None, normalize=False):
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"""We need to project the Correlator with a Vector to get a single value at each timeslice.
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The method can use one or two vectors.
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If two are specified it returns v1@G@v2 (the order might be very important.)
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By default it will return the lowest source, which usually means unsmeared-unsmeared (0,0), but it does not have to
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"""
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if self.N == 1:
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raise Exception("Trying to project a Corr, that already has N=1.")
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if vector_l is None:
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vector_l, vector_r = np.asarray([1.] + (self.N - 1) * [0.]), np.asarray([1.] + (self.N - 1) * [0.])
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elif(vector_r is None):
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vector_r = vector_l
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if isinstance(vector_l, list) and not isinstance(vector_r, list):
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if len(vector_l) != self.T:
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raise Exception("Length of vector list must be equal to T")
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vector_r = [vector_r] * self.T
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if isinstance(vector_r, list) and not isinstance(vector_l, list):
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if len(vector_r) != self.T:
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raise Exception("Length of vector list must be equal to T")
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vector_l = [vector_l] * self.T
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if not isinstance(vector_l, list):
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if not vector_l.shape == vector_r.shape == (self.N,):
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raise Exception("Vectors are of wrong shape!")
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if normalize:
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vector_l, vector_r = vector_l / np.sqrt((vector_l @ vector_l)), vector_r / np.sqrt(vector_r @ vector_r)
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newcontent = [None if (item is None) else np.asarray([vector_l.T @ item @ vector_r]) for item in self.content]
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else:
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# There are no checks here yet. There are so many possible scenarios, where this can go wrong.
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if normalize:
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for t in range(self.T):
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vector_l[t], vector_r[t] = vector_l[t] / np.sqrt((vector_l[t] @ vector_l[t])), vector_r[t] / np.sqrt(vector_r[t] @ vector_r[t])
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newcontent = [None if (self.content[t] is None or vector_l[t] is None or vector_r[t] is None) else np.asarray([vector_l[t].T @ self.content[t] @ vector_r[t]]) for t in range(self.T)]
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return Corr(newcontent)
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def item(self, i, j):
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"""Picks the element [i,j] from every matrix and returns a correlator containing one Obs per timeslice.
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Parameters
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----------
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i : int
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First index to be picked.
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j : int
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Second index to be picked.
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"""
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if self.N == 1:
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raise Exception("Trying to pick item from projected Corr")
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newcontent = [None if(item is None) else item[i, j] for item in self.content]
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return Corr(newcontent)
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def plottable(self):
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"""Outputs the correlator in a plotable format.
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Outputs three lists containing the timeslice index, the value on each
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timeslice and the error on each timeslice.
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"""
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if self.N != 1:
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raise Exception("Can only make Corr[N=1] plottable")
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x_list = [x for x in range(self.T) if not self.content[x] is None]
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y_list = [y[0].value for y in self.content if y is not None]
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y_err_list = [y[0].dvalue for y in self.content if y is not None]
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return x_list, y_list, y_err_list
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def symmetric(self):
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""" Symmetrize the correlator around x0=0."""
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if self.T % 2 != 0:
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raise Exception("Can not symmetrize odd T")
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if np.argmax(np.abs(self.content)) != 0:
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warnings.warn("Correlator does not seem to be symmetric around x0=0.", RuntimeWarning)
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newcontent = [self.content[0]]
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for t in range(1, self.T):
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if (self.content[t] is None) or (self.content[self.T - t] is None):
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newcontent.append(None)
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else:
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newcontent.append(0.5 * (self.content[t] + self.content[self.T - t]))
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if(all([x is None for x in newcontent])):
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raise Exception("Corr could not be symmetrized: No redundant values")
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return Corr(newcontent, prange=self.prange)
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def anti_symmetric(self):
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"""Anti-symmetrize the correlator around x0=0."""
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if self.T % 2 != 0:
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raise Exception("Can not symmetrize odd T")
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test = 1 * self
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test.gamma_method()
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if not all([o.is_zero_within_error(3) for o in test.content[0]]):
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warnings.warn("Correlator does not seem to be anti-symmetric around x0=0.", RuntimeWarning)
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newcontent = [self.content[0]]
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for t in range(1, self.T):
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if (self.content[t] is None) or (self.content[self.T - t] is None):
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newcontent.append(None)
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else:
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newcontent.append(0.5 * (self.content[t] - self.content[self.T - t]))
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if(all([x is None for x in newcontent])):
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raise Exception("Corr could not be symmetrized: No redundant values")
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return Corr(newcontent, prange=self.prange)
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def matrix_symmetric(self):
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"""Symmetrizes the correlator matrices on every timeslice."""
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if self.N > 1:
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transposed = [None if (G is None) else G.T for G in self.content]
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return 0.5 * (Corr(transposed) + self)
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if self.N == 1:
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raise Exception("Trying to symmetrize a correlator matrix, that already has N=1.")
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def GEVP(self, t0, ts=None, state=0, sorted_list=None):
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"""Solve the general eigenvalue problem on the current correlator
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Parameters
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----------
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t0 : int
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The time t0 for G(t)v= lambda G(t_0)v
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ts : int
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fixed time G(t_s)v= lambda G(t_0)v if return_list=False
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If return_list=True and sorting=Eigenvector it gives a reference point for the sorting method.
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state : int
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The state one is interested in ordered by energy. The lowest state is zero.
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sorted_list : string
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if this argument is set, a list of vectors (len=self.T) is returned. If it is left as None, only one vector is returned.
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"Eigenvalue" - The eigenvector is chosen according to which eigenvalue it belongs individually on every timeslice.
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"Eigenvector" - Use the method described in arXiv:2004.10472 [hep-lat] to find the set of v(t) belonging to the state.
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The reference state is identified by its eigenvalue at t=ts
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"""
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if sorted_list is None:
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if (ts is None):
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raise Exception("ts is required if sorted_list=None")
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if (self.content[t0] is None) or (self.content[ts] is None):
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raise Exception("Corr not defined at t0/ts")
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G0, Gt = np.empty([self.N, self.N], dtype="double"), np.empty([self.N, self.N], dtype="double")
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symmetric_corr = self.matrix_symmetric()
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for i in range(self.N):
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for j in range(self.N):
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G0[i, j] = symmetric_corr.content[t0][i, j].value
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Gt[i, j] = symmetric_corr[ts][i, j].value
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sp_vecs = _GEVP_solver(Gt, G0)
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sp_vec = sp_vecs[state]
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return sp_vec
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else:
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all_vecs = []
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for t in range(self.T):
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try:
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G0, Gt = np.empty([self.N, self.N], dtype="double"), np.empty([self.N, self.N], dtype="double")
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for i in range(self.N):
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for j in range(self.N):
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G0[i, j] = self.content[t0][i, j].value
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Gt[i, j] = self.content[t][i, j].value
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sp_vecs = _GEVP_solver(Gt, G0)
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if sorted_list == "Eigenvalue":
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sp_vec = sp_vecs[state]
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all_vecs.append(sp_vec)
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else:
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all_vecs.append(sp_vecs)
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except Exception:
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all_vecs.append(None)
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if sorted_list == "Eigenvector":
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if (ts is None):
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raise Exception("ts is required for the Eigenvector sorting method.")
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all_vecs = _sort_vectors(all_vecs, ts)
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all_vecs = [a[state] for a in all_vecs]
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return all_vecs
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def Eigenvalue(self, t0, ts=None, state=0, sorted_list=None):
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"""Determines the eigenvalue of the GEVP by solving and projecting the correlator
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Parameters
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----------
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t0 : int
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The time t0 for G(t)v= lambda G(t_0)v
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ts : int
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fixed time G(t_s)v= lambda G(t_0)v if return_list=False
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If return_list=True and sorting=Eigenvector it gives a reference point for the sorting method.
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state : int
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The state one is interested in ordered by energy. The lowest state is zero.
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sorted_list : string
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if this argument is set, a list of vectors (len=self.T) is returned. If it is left as None, only one vector is returned.
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"Eigenvalue" - The eigenvector is chosen according to which eigenvalue it belongs individually on every timeslice.
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"Eigenvector" - Use the method described in arXiv:2004.10472 [hep-lat] to find the set of v(t) belonging to the state.
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The reference state is identified by its eigenvalue at t=ts
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"""
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vec = self.GEVP(t0, ts=ts, state=state, sorted_list=sorted_list)
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return self.projected(vec)
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def Hankel(self, N, periodic=False):
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"""Constructs an NxN Hankel matrix
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C(t) c(t+1) ... c(t+n-1)
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C(t+1) c(t+2) ... c(t+n)
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.................
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C(t+(n-1)) c(t+n) ... c(t+2(n-1))
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Parameters
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----------
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N : int
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Dimension of the Hankel matrix
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periodic : bool, optional
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determines whether the matrix is extended periodically
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"""
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if self.N != 1:
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raise Exception("Multi-operator Prony not implemented!")
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array = np.empty([N, N], dtype="object")
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new_content = []
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for t in range(self.T):
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new_content.append(array.copy())
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def wrap(i):
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while i >= self.T:
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i -= self.T
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return i
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for t in range(self.T):
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for i in range(N):
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for j in range(N):
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if periodic:
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new_content[t][i, j] = self.content[wrap(t + i + j)][0]
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elif (t + i + j) >= self.T:
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new_content[t] = None
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else:
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new_content[t][i, j] = self.content[t + i + j][0]
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return Corr(new_content)
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def roll(self, dt):
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"""Periodically shift the correlator by dt timeslices
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Parameters
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----------
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dt : int
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number of timeslices
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"""
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return Corr(list(np.roll(np.array(self.content, dtype=object), dt)))
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def reverse(self):
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"""Reverse the time ordering of the Corr"""
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return Corr(self.content[:: -1])
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def thin(self, spacing=2, offset=0):
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"""Thin out a correlator to suppress correlations
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Parameters
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----------
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spacing : int
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Keep only every 'spacing'th entry of the correlator
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offset : int
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Offset the equal spacing
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"""
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new_content = []
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for t in range(self.T):
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if (offset + t) % spacing != 0:
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new_content.append(None)
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else:
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new_content.append(self.content[t])
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return Corr(new_content)
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def correlate(self, partner):
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"""Correlate the correlator with another correlator or Obs
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Parameters
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----------
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partner : Obs or Corr
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partner to correlate the correlator with.
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Can either be an Obs which is correlated with all entries of the
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correlator or a Corr of same length.
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"""
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new_content = []
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for x0, t_slice in enumerate(self.content):
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if t_slice is None:
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new_content.append(None)
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else:
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if isinstance(partner, Corr):
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if partner.content[x0] is None:
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new_content.append(None)
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else:
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new_content.append(np.array([correlate(o, partner.content[x0][0]) for o in t_slice]))
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elif isinstance(partner, Obs): # Should this include CObs?
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new_content.append(np.array([correlate(o, partner) for o in t_slice]))
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else:
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raise Exception("Can only correlate with an Obs or a Corr.")
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return Corr(new_content)
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def reweight(self, weight, **kwargs):
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"""Reweight the correlator.
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Parameters
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----------
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weight : Obs
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Reweighting factor. An Observable that has to be defined on a superset of the
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configurations in obs[i].idl for all i.
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all_configs : bool
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if True, the reweighted observables are normalized by the average of
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the reweighting factor on all configurations in weight.idl and not
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on the configurations in obs[i].idl.
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"""
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new_content = []
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for t_slice in self.content:
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if t_slice is None:
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new_content.append(None)
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else:
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new_content.append(np.array(reweight(weight, t_slice, **kwargs)))
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return Corr(new_content)
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def T_symmetry(self, partner, parity=+1):
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"""Return the time symmetry average of the correlator and its partner
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Parameters
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----------
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partner : Corr
|
|
Time symmetry partner of the Corr
|
|
partity : int
|
|
Parity quantum number of the correlator, can be +1 or -1
|
|
"""
|
|
if not isinstance(partner, Corr):
|
|
raise Exception("T partner has to be a Corr object.")
|
|
if parity not in [+1, -1]:
|
|
raise Exception("Parity has to be +1 or -1.")
|
|
T_partner = parity * partner.reverse()
|
|
|
|
t_slices = []
|
|
test = (self - T_partner)
|
|
test.gamma_method()
|
|
for x0, t_slice in enumerate(test.content):
|
|
if t_slice is not None:
|
|
if not t_slice[0].is_zero_within_error(5):
|
|
t_slices.append(x0)
|
|
if t_slices:
|
|
warnings.warn("T symmetry partners do not agree within 5 sigma on time slices " + str(t_slices) + ".", RuntimeWarning)
|
|
|
|
return (self + T_partner) / 2
|
|
|
|
def deriv(self, variant="symmetric"):
|
|
"""Return the first derivative of the correlator with respect to x0.
|
|
|
|
Parameters
|
|
----------
|
|
variant : str
|
|
decides which definition of the finite differences derivative is used.
|
|
Available choice: symmetric, forward, backward, improved, default: symmetric
|
|
"""
|
|
if variant == "symmetric":
|
|
newcontent = []
|
|
for t in range(1, self.T - 1):
|
|
if (self.content[t - 1] is None) or (self.content[t + 1] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(0.5 * (self.content[t + 1] - self.content[t - 1]))
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception('Derivative is undefined at all timeslices')
|
|
return Corr(newcontent, padding=[1, 1])
|
|
elif variant == "forward":
|
|
newcontent = []
|
|
for t in range(self.T - 1):
|
|
if (self.content[t] is None) or (self.content[t + 1] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t + 1] - self.content[t])
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception("Derivative is undefined at all timeslices")
|
|
return Corr(newcontent, padding=[0, 1])
|
|
elif variant == "backward":
|
|
newcontent = []
|
|
for t in range(1, self.T):
|
|
if (self.content[t - 1] is None) or (self.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] - self.content[t - 1])
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception("Derivative is undefined at all timeslices")
|
|
return Corr(newcontent, padding=[1, 0])
|
|
elif variant == "improved":
|
|
newcontent = []
|
|
for t in range(2, self.T - 2):
|
|
if (self.content[t - 2] is None) or (self.content[t - 1] is None) or (self.content[t + 1] is None) or (self.content[t + 2] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append((1 / 12) * (self.content[t - 2] - 8 * self.content[t - 1] + 8 * self.content[t + 1] - self.content[t + 2]))
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception('Derivative is undefined at all timeslices')
|
|
return Corr(newcontent, padding=[2, 2])
|
|
else:
|
|
raise Exception("Unknown variant.")
|
|
|
|
def second_deriv(self, variant="symmetric"):
|
|
"""Return the second derivative of the correlator with respect to x0.
|
|
|
|
Parameters
|
|
----------
|
|
variant : str
|
|
decides which definition of the finite differences derivative is used.
|
|
Available choice: symmetric, improved, default: symmetric
|
|
"""
|
|
if variant == "symmetric":
|
|
newcontent = []
|
|
for t in range(1, self.T - 1):
|
|
if (self.content[t - 1] is None) or (self.content[t + 1] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append((self.content[t + 1] - 2 * self.content[t] + self.content[t - 1]))
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception("Derivative is undefined at all timeslices")
|
|
return Corr(newcontent, padding=[1, 1])
|
|
elif variant == "improved":
|
|
newcontent = []
|
|
for t in range(2, self.T - 2):
|
|
if (self.content[t - 2] is None) or (self.content[t - 1] is None) or (self.content[t] is None) or (self.content[t + 1] is None) or (self.content[t + 2] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append((1 / 12) * (-self.content[t + 2] + 16 * self.content[t + 1] - 30 * self.content[t] + 16 * self.content[t - 1] - self.content[t - 2]))
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception("Derivative is undefined at all timeslices")
|
|
return Corr(newcontent, padding=[2, 2])
|
|
else:
|
|
raise Exception("Unknown variant.")
|
|
|
|
def m_eff(self, variant='log', guess=1.0):
|
|
"""Returns the effective mass of the correlator as correlator object
|
|
|
|
Parameters
|
|
----------
|
|
variant : str
|
|
log : uses the standard effective mass log(C(t) / C(t+1))
|
|
cosh, periodic : Use periodicitiy of the correlator by solving C(t) / C(t+1) = cosh(m * (t - T/2)) / cosh(m * (t + 1 - T/2)) for m.
|
|
sinh : Use anti-periodicitiy of the correlator by solving C(t) / C(t+1) = sinh(m * (t - T/2)) / sinh(m * (t + 1 - T/2)) for m.
|
|
See, e.g., arXiv:1205.5380
|
|
arccosh : Uses the explicit form of the symmetrized correlator (not recommended)
|
|
guess : float
|
|
guess for the root finder, only relevant for the root variant
|
|
"""
|
|
if self.N != 1:
|
|
raise Exception('Correlator must be projected before getting m_eff')
|
|
if variant == 'log':
|
|
newcontent = []
|
|
for t in range(self.T - 1):
|
|
if (self.content[t] is None) or (self.content[t + 1] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] / self.content[t + 1])
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception('m_eff is undefined at all timeslices')
|
|
|
|
return np.log(Corr(newcontent, padding=[0, 1]))
|
|
|
|
elif variant in ['periodic', 'cosh', 'sinh']:
|
|
if variant in ['periodic', 'cosh']:
|
|
func = anp.cosh
|
|
else:
|
|
func = anp.sinh
|
|
|
|
def root_function(x, d):
|
|
return func(x * (t - self.T / 2)) / func(x * (t + 1 - self.T / 2)) - d
|
|
|
|
newcontent = []
|
|
for t in range(self.T - 1):
|
|
if (self.content[t] is None) or (self.content[t + 1] is None):
|
|
newcontent.append(None)
|
|
# Fill the two timeslices in the middle of the lattice with their predecessors
|
|
elif variant == 'sinh' and t in [self.T / 2, self.T / 2 - 1]:
|
|
newcontent.append(newcontent[-1])
|
|
else:
|
|
newcontent.append(np.abs(find_root(self.content[t][0] / self.content[t + 1][0], root_function, guess=guess)))
|
|
if(all([x is None for x in newcontent])):
|
|
raise Exception('m_eff is undefined at all timeslices')
|
|
|
|
return Corr(newcontent, padding=[0, 1])
|
|
|
|
elif variant == '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=[1, 1]))
|
|
|
|
else:
|
|
raise Exception('Unknown variant.')
|
|
|
|
def fit(self, function, fitrange=None, silent=False, **kwargs):
|
|
"""Fits function to the data
|
|
|
|
Parameters
|
|
----------
|
|
function : obj
|
|
function to fit to the data. See fits.least_squares for details.
|
|
fitrange : list
|
|
Two element list containing the timeslices on which the fit is supposed to start and stop.
|
|
If not specified, self.prange or all timeslices are used.
|
|
silent : bool
|
|
Decides whether output is printed to the standard output.
|
|
"""
|
|
if self.N != 1:
|
|
raise Exception("Correlator must be projected before fitting")
|
|
|
|
if fitrange is None:
|
|
if self.prange:
|
|
fitrange = self.prange
|
|
else:
|
|
fitrange = [0, self.T - 1]
|
|
else:
|
|
if not isinstance(fitrange, list):
|
|
raise Exception("fitrange has to be a list with two elements")
|
|
if len(fitrange) != 2:
|
|
raise Exception("fitrange has to have exactly two elements [fit_start, fit_stop]")
|
|
|
|
xs = [x for x in range(fitrange[0], fitrange[1] + 1) if not self.content[x] is None]
|
|
ys = [self.content[x][0] for x in range(fitrange[0], fitrange[1] + 1) if not self.content[x] is None]
|
|
result = least_squares(xs, ys, function, silent=silent, **kwargs)
|
|
return result
|
|
|
|
def plateau(self, plateau_range=None, method="fit", auto_gamma=False):
|
|
""" Extract a plateau value from a Corr object
|
|
|
|
Parameters
|
|
----------
|
|
plateau_range : list
|
|
list with two entries, indicating the first and the last timeslice
|
|
of the plateau region.
|
|
method : str
|
|
method to extract the plateau.
|
|
'fit' fits a constant to the plateau region
|
|
'avg', 'average' or 'mean' just average over the given timeslices.
|
|
auto_gamma : bool
|
|
apply gamma_method with default parameters to the Corr. Defaults to None
|
|
"""
|
|
if not plateau_range:
|
|
if self.prange:
|
|
plateau_range = self.prange
|
|
else:
|
|
raise Exception("no plateau range provided")
|
|
if self.N != 1:
|
|
raise Exception("Correlator must be projected before getting a plateau.")
|
|
if(all([self.content[t] is None for t in range(plateau_range[0], plateau_range[1] + 1)])):
|
|
raise Exception("plateau is undefined at all timeslices in plateaurange.")
|
|
if auto_gamma:
|
|
self.gamma_method()
|
|
if method == "fit":
|
|
def const_func(a, t):
|
|
return a[0]
|
|
return self.fit(const_func, plateau_range)[0]
|
|
elif method in ["avg", "average", "mean"]:
|
|
returnvalue = np.mean([item[0] for item in self.content[plateau_range[0]:plateau_range[1] + 1] if item is not None])
|
|
return returnvalue
|
|
|
|
else:
|
|
raise Exception("Unsupported plateau method: " + method)
|
|
|
|
def set_prange(self, prange):
|
|
"""Sets the attribute prange of the Corr object."""
|
|
if not len(prange) == 2:
|
|
raise Exception("prange must be a list or array with two values")
|
|
if not ((isinstance(prange[0], int)) and (isinstance(prange[1], int))):
|
|
raise Exception("Start and end point must be integers")
|
|
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")
|
|
|
|
self.prange = prange
|
|
return
|
|
|
|
def show(self, x_range=None, comp=None, y_range=None, logscale=False, plateau=None, fit_res=None, ylabel=None, save=None, auto_gamma=False):
|
|
"""Plots the correlator using the tag of the correlator as label if available.
|
|
|
|
Parameters
|
|
----------
|
|
x_range : list
|
|
list of two values, determining the range of the x-axis e.g. [4, 8]
|
|
comp : Corr or list of Corr
|
|
Correlator or list of correlators which are plotted for comparison.
|
|
The tags of these correlators are used as labels if available.
|
|
logscale : bool
|
|
Sets y-axis to logscale
|
|
plateau : Obs
|
|
Plateau value to be visualized in the figure
|
|
fit_res : Fit_result
|
|
Fit_result object to be visualized
|
|
ylabel : str
|
|
Label for the y-axis
|
|
save : str
|
|
path to file in which the figure should be saved
|
|
auto_gamma : bool
|
|
Apply the gamma method with standard parameters to all correlators and plateau values before plotting.
|
|
"""
|
|
if self.N != 1:
|
|
raise Exception("Correlator must be projected before plotting")
|
|
|
|
if auto_gamma:
|
|
self.gamma_method()
|
|
|
|
if x_range is None:
|
|
x_range = [0, self.T - 1]
|
|
|
|
fig = plt.figure()
|
|
ax1 = fig.add_subplot(111)
|
|
|
|
x, y, y_err = self.plottable()
|
|
ax1.errorbar(x, y, y_err, label=self.tag)
|
|
if logscale:
|
|
ax1.set_yscale('log')
|
|
else:
|
|
if y_range is None:
|
|
try:
|
|
y_min = min([(x[0].value - x[0].dvalue) for x in self.content[x_range[0]: x_range[1] + 1] if (x is not None) and x[0].dvalue < 2 * np.abs(x[0].value)])
|
|
y_max = max([(x[0].value + x[0].dvalue) for x in self.content[x_range[0]: x_range[1] + 1] if (x is not None) and x[0].dvalue < 2 * np.abs(x[0].value)])
|
|
ax1.set_ylim([y_min - 0.1 * (y_max - y_min), y_max + 0.1 * (y_max - y_min)])
|
|
except Exception:
|
|
pass
|
|
else:
|
|
ax1.set_ylim(y_range)
|
|
if comp:
|
|
if isinstance(comp, (Corr, list)):
|
|
for corr in comp if isinstance(comp, list) else [comp]:
|
|
if auto_gamma:
|
|
corr.gamma_method()
|
|
x, y, y_err = corr.plottable()
|
|
plt.errorbar(x, y, y_err, label=corr.tag, mfc=plt.rcParams['axes.facecolor'])
|
|
else:
|
|
raise Exception("'comp' must be a correlator or a list of correlators.")
|
|
|
|
if plateau:
|
|
if isinstance(plateau, Obs):
|
|
if auto_gamma:
|
|
plateau.gamma_method()
|
|
ax1.axhline(y=plateau.value, linewidth=2, color=plt.rcParams['text.color'], alpha=0.6, marker=',', ls='--', label=str(plateau))
|
|
ax1.axhspan(plateau.value - plateau.dvalue, plateau.value + plateau.dvalue, alpha=0.25, color=plt.rcParams['text.color'], ls='-')
|
|
else:
|
|
raise Exception("'plateau' must be an Obs")
|
|
if self.prange:
|
|
ax1.axvline(self.prange[0], 0, 1, ls='-', marker=',')
|
|
ax1.axvline(self.prange[1], 0, 1, ls='-', marker=',')
|
|
|
|
if fit_res:
|
|
x_samples = np.arange(x_range[0], x_range[1] + 1, 0.05)
|
|
ax1.plot(x_samples,
|
|
fit_res.fit_function([o.value for o in fit_res.fit_parameters], x_samples),
|
|
ls='-', marker=',', lw=2)
|
|
|
|
ax1.set_xlabel(r'$x_0 / a$')
|
|
if ylabel:
|
|
ax1.set_ylabel(ylabel)
|
|
ax1.set_xlim([x_range[0] - 0.5, x_range[1] + 0.5])
|
|
|
|
handles, labels = ax1.get_legend_handles_labels()
|
|
if labels:
|
|
ax1.legend()
|
|
plt.draw()
|
|
|
|
if save:
|
|
if isinstance(save, str):
|
|
fig.savefig(save)
|
|
else:
|
|
raise Exception("'save' has to be a string.")
|
|
|
|
def spaghetti_plot(self, logscale=True):
|
|
"""Produces a spaghetti plot of the correlator suited to monitor exceptional configurations.
|
|
|
|
Parameters
|
|
----------
|
|
logscale : bool
|
|
Determines whether the scale of the y-axis is logarithmic or standard.
|
|
"""
|
|
if self.N != 1:
|
|
raise Exception("Correlator needs to be projected first.")
|
|
|
|
mc_names = list(set([item for sublist in [o[0].mc_names for o in self.content if o is not None] for item in sublist]))
|
|
x0_vals = [n for (n, o) in zip(np.arange(self.T), self.content) if o is not None]
|
|
|
|
for name in mc_names:
|
|
data = np.array([o[0].deltas[name] + o[0].r_values[name] for o in self.content if o is not None]).T
|
|
|
|
fig = plt.figure()
|
|
ax = fig.add_subplot(111)
|
|
for dat in data:
|
|
ax.plot(x0_vals, dat, ls='-', marker='')
|
|
|
|
if logscale is True:
|
|
ax.set_yscale('log')
|
|
|
|
ax.set_xlabel(r'$x_0 / a$')
|
|
plt.title(name)
|
|
plt.draw()
|
|
|
|
def dump(self, filename, datatype="json.gz", **kwargs):
|
|
"""Dumps the Corr into a file of chosen type
|
|
Parameters
|
|
----------
|
|
filename : str
|
|
Name of the file to be saved.
|
|
datatype : str
|
|
Format of the exported file. Supported formats include
|
|
"json.gz" and "pickle"
|
|
path : str
|
|
specifies a custom path for the file (default '.')
|
|
"""
|
|
if datatype == "json.gz":
|
|
from .input.json import dump_to_json
|
|
if 'path' in kwargs:
|
|
file_name = kwargs.get('path') + '/' + filename
|
|
else:
|
|
file_name = filename
|
|
dump_to_json(self, file_name)
|
|
elif datatype == "pickle":
|
|
dump_object(self, filename, **kwargs)
|
|
else:
|
|
raise Exception("Unknown datatype " + str(datatype))
|
|
|
|
def print(self, range=[0, None]):
|
|
print(self.__repr__(range))
|
|
|
|
def __repr__(self, range=[0, None]):
|
|
content_string = ""
|
|
|
|
content_string += "Corr T=" + str(self.T) + " N=" + str(self.N) + "\n" # +" filled with"+ str(type(self.content[0][0])) there should be a good solution here
|
|
|
|
if self.tag is not None:
|
|
content_string += "Description: " + self.tag + "\n"
|
|
if self.N != 1:
|
|
return content_string
|
|
|
|
if range[1]:
|
|
range[1] += 1
|
|
content_string += 'x0/a\tCorr(x0/a)\n------------------\n'
|
|
for i, sub_corr in enumerate(self.content[range[0]:range[1]]):
|
|
if sub_corr is None:
|
|
content_string += str(i + range[0]) + '\n'
|
|
else:
|
|
content_string += str(i + range[0])
|
|
for element in sub_corr:
|
|
content_string += '\t' + ' ' * int(element >= 0) + str(element)
|
|
content_string += '\n'
|
|
return content_string
|
|
|
|
def __str__(self):
|
|
return self.__repr__()
|
|
|
|
# We define the basic operations, that can be performed with correlators.
|
|
# While */+- get defined here, they only work for Corr*Obs and not Obs*Corr.
|
|
# This is because Obs*Corr checks Obs.__mul__ first and does not catch an exception.
|
|
# One could try and tell Obs to check if the y in __mul__ is a Corr and
|
|
|
|
def __add__(self, y):
|
|
if isinstance(y, Corr):
|
|
if ((self.N != y.N) or (self.T != y.T)):
|
|
raise Exception("Addition of Corrs with different shape")
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None) or (y.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] + y.content[t])
|
|
return Corr(newcontent)
|
|
|
|
elif isinstance(y, (Obs, int, float, CObs)):
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] + y)
|
|
return Corr(newcontent, prange=self.prange)
|
|
elif isinstance(y, np.ndarray):
|
|
if y.shape == (self.T,):
|
|
return Corr(list((np.array(self.content).T + y).T))
|
|
else:
|
|
raise ValueError("operands could not be broadcast together")
|
|
else:
|
|
raise TypeError("Corr + wrong type")
|
|
|
|
def __mul__(self, y):
|
|
if isinstance(y, Corr):
|
|
if not((self.N == 1 or y.N == 1 or self.N == y.N) and self.T == y.T):
|
|
raise Exception("Multiplication of Corr object requires N=N or N=1 and T=T")
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None) or (y.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] * y.content[t])
|
|
return Corr(newcontent)
|
|
|
|
elif isinstance(y, (Obs, int, float, CObs)):
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] * y)
|
|
return Corr(newcontent, prange=self.prange)
|
|
elif isinstance(y, np.ndarray):
|
|
if y.shape == (self.T,):
|
|
return Corr(list((np.array(self.content).T * y).T))
|
|
else:
|
|
raise ValueError("operands could not be broadcast together")
|
|
else:
|
|
raise TypeError("Corr * wrong type")
|
|
|
|
def __truediv__(self, y):
|
|
if isinstance(y, Corr):
|
|
if not((self.N == 1 or y.N == 1 or self.N == y.N) and self.T == y.T):
|
|
raise Exception("Multiplication of Corr object requires N=N or N=1 and T=T")
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None) or (y.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] / y.content[t])
|
|
for t in range(self.T):
|
|
if newcontent[t] is None:
|
|
continue
|
|
if np.isnan(np.sum(newcontent[t]).value):
|
|
newcontent[t] = None
|
|
|
|
if all([item is None for item in newcontent]):
|
|
raise Exception("Division returns completely undefined correlator")
|
|
return Corr(newcontent)
|
|
|
|
elif isinstance(y, (Obs, CObs)):
|
|
if isinstance(y, Obs):
|
|
if y.value == 0:
|
|
raise Exception('Division by zero will return undefined correlator')
|
|
if isinstance(y, CObs):
|
|
if y.is_zero():
|
|
raise Exception('Division by zero will return undefined correlator')
|
|
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] / y)
|
|
return Corr(newcontent, prange=self.prange)
|
|
|
|
elif isinstance(y, (int, float)):
|
|
if y == 0:
|
|
raise Exception('Division by zero will return undefined correlator')
|
|
newcontent = []
|
|
for t in range(self.T):
|
|
if (self.content[t] is None):
|
|
newcontent.append(None)
|
|
else:
|
|
newcontent.append(self.content[t] / y)
|
|
return Corr(newcontent, prange=self.prange)
|
|
elif isinstance(y, np.ndarray):
|
|
if y.shape == (self.T,):
|
|
return Corr(list((np.array(self.content).T / y).T))
|
|
else:
|
|
raise ValueError("operands could not be broadcast together")
|
|
else:
|
|
raise TypeError('Corr / wrong type')
|
|
|
|
def __neg__(self):
|
|
newcontent = [None if (item is None) else -1. * item for item in self.content]
|
|
return Corr(newcontent, prange=self.prange)
|
|
|
|
def __sub__(self, y):
|
|
return self + (-y)
|
|
|
|
def __pow__(self, y):
|
|
if isinstance(y, (Obs, int, float, CObs)):
|
|
newcontent = [None if (item is None) else item**y for item in self.content]
|
|
return Corr(newcontent, prange=self.prange)
|
|
else:
|
|
raise TypeError('Type of exponent not supported')
|
|
|
|
def __abs__(self):
|
|
newcontent = [None if (item is None) else np.abs(item) for item in self.content]
|
|
return Corr(newcontent, prange=self.prange)
|
|
|
|
# The numpy functions:
|
|
def sqrt(self):
|
|
return self**0.5
|
|
|
|
def log(self):
|
|
newcontent = [None if (item is None) else np.log(item) for item in self.content]
|
|
return Corr(newcontent, prange=self.prange)
|
|
|
|
def exp(self):
|
|
newcontent = [None if (item is None) else np.exp(item) for item in self.content]
|
|
return Corr(newcontent, prange=self.prange)
|
|
|
|
def _apply_func_to_corr(self, func):
|
|
newcontent = [None if (item is None) else func(item) for item in self.content]
|
|
for t in range(self.T):
|
|
if newcontent[t] is None:
|
|
continue
|
|
if np.isnan(np.sum(newcontent[t]).value):
|
|
newcontent[t] = None
|
|
if all([item is None for item in newcontent]):
|
|
raise Exception('Operation returns undefined correlator')
|
|
return Corr(newcontent)
|
|
|
|
def sin(self):
|
|
return self._apply_func_to_corr(np.sin)
|
|
|
|
def cos(self):
|
|
return self._apply_func_to_corr(np.cos)
|
|
|
|
def tan(self):
|
|
return self._apply_func_to_corr(np.tan)
|
|
|
|
def sinh(self):
|
|
return self._apply_func_to_corr(np.sinh)
|
|
|
|
def cosh(self):
|
|
return self._apply_func_to_corr(np.cosh)
|
|
|
|
def tanh(self):
|
|
return self._apply_func_to_corr(np.tanh)
|
|
|
|
def arcsin(self):
|
|
return self._apply_func_to_corr(np.arcsin)
|
|
|
|
def arccos(self):
|
|
return self._apply_func_to_corr(np.arccos)
|
|
|
|
def arctan(self):
|
|
return self._apply_func_to_corr(np.arctan)
|
|
|
|
def arcsinh(self):
|
|
return self._apply_func_to_corr(np.arcsinh)
|
|
|
|
def arccosh(self):
|
|
return self._apply_func_to_corr(np.arccosh)
|
|
|
|
def arctanh(self):
|
|
return self._apply_func_to_corr(np.arctanh)
|
|
|
|
# Right hand side operations (require tweak in main module to work)
|
|
def __radd__(self, y):
|
|
return self + y
|
|
|
|
def __rsub__(self, y):
|
|
return -self + y
|
|
|
|
def __rmul__(self, y):
|
|
return self * y
|
|
|
|
def __rtruediv__(self, y):
|
|
return (self / y) ** (-1)
|
|
|
|
@property
|
|
def real(self):
|
|
def return_real(obs_OR_cobs):
|
|
if isinstance(obs_OR_cobs, CObs):
|
|
return obs_OR_cobs.real
|
|
else:
|
|
return obs_OR_cobs
|
|
|
|
return self._apply_func_to_corr(return_real)
|
|
|
|
@property
|
|
def imag(self):
|
|
def return_imag(obs_OR_cobs):
|
|
if isinstance(obs_OR_cobs, CObs):
|
|
return obs_OR_cobs.imag
|
|
else:
|
|
return obs_OR_cobs * 0 # So it stays the right type
|
|
|
|
return self._apply_func_to_corr(return_imag)
|
|
|
|
|
|
def _sort_vectors(vec_set, ts):
|
|
"""Helper function used to find a set of Eigenvectors consistent over all timeslices"""
|
|
reference_sorting = np.array(vec_set[ts])
|
|
N = reference_sorting.shape[0]
|
|
sorted_vec_set = []
|
|
for t in range(len(vec_set)):
|
|
if vec_set[t] is None:
|
|
sorted_vec_set.append(None)
|
|
elif not t == ts:
|
|
perms = [list(o) for o in permutations([i for i in range(N)], N)]
|
|
best_score = 0
|
|
for perm in perms:
|
|
current_score = 1
|
|
for k in range(N):
|
|
new_sorting = reference_sorting.copy()
|
|
new_sorting[perm[k], :] = vec_set[t][k]
|
|
current_score *= abs(np.linalg.det(new_sorting))
|
|
if current_score > best_score:
|
|
best_score = current_score
|
|
best_perm = perm
|
|
sorted_vec_set.append([vec_set[t][k] for k in best_perm])
|
|
else:
|
|
sorted_vec_set.append(vec_set[t])
|
|
|
|
return sorted_vec_set
|
|
|
|
|
|
def _GEVP_solver(Gt, G0): # Just so normalization an sorting does not need to be repeated. Here we could later put in some checks
|
|
sp_val, sp_vecs = scipy.linalg.eigh(Gt, G0)
|
|
sp_vecs = [sp_vecs[:, np.argsort(sp_val)[-i]] for i in range(1, sp_vecs.shape[0] + 1)]
|
|
sp_vecs = [v / np.sqrt((v.T @ G0 @ v)) for v in sp_vecs]
|
|
return sp_vecs
|