Source code for sas.sascalc.pr.invertor

# pylint: disable=invalid-name
"""
Module to perform P(r) inversion.
The module contains the Invertor class.

FIXME: The way the Invertor interacts with its C component should be cleaned up
"""
from __future__ import division

import numpy as np
import sys
import math
import time
import copy
import os
import re
import logging
from numpy.linalg import lstsq
from scipy import optimize


import os
import os.path
import unittest
import math
import numpy


from .p_invertor import Pinvertor
logger = logging.getLogger(__name__)

[docs]def help(): """ Provide general online help text Future work: extend this function to allow topic selection """ info_txt = "The inversion approach is based on Moore, J. Appl. Cryst. " info_txt += "(1980) 13, 168-175.\n\n" info_txt += "P(r) is set to be equal to an expansion of base functions " info_txt += "of the type " info_txt += "phi_n(r) = 2*r*sin(pi*n*r/D_max). The coefficient of each " info_txt += "base functions " info_txt += "in the expansion is found by performing a least square fit " info_txt += "with the " info_txt += "following fit function:\n\n" info_txt += "chi**2 = sum_i[ I_meas(q_i) - I_th(q_i) ]**2/error**2 +" info_txt += "Reg_term\n\n" info_txt += "where I_meas(q) is the measured scattering intensity and " info_txt += "I_th(q) is " info_txt += "the prediction from the Fourier transform of the P(r) " info_txt += "expansion. " info_txt += "The Reg_term term is a regularization term set to the second" info_txt += " derivative " info_txt += "d**2P(r)/dr**2 integrated over r. It is used to produce " info_txt += "a smooth P(r) output.\n\n" info_txt += "The following are user inputs:\n\n" info_txt += " - Number of terms: the number of base functions in the P(r)" info_txt += " expansion.\n\n" info_txt += " - Regularization constant: a multiplicative constant " info_txt += "to set the size of " info_txt += "the regularization term.\n\n" info_txt += " - Maximum distance: the maximum distance between any " info_txt += "two points in the system.\n" return info_txt
[docs]class Invertor(Pinvertor): """ Invertor class to perform P(r) inversion The problem is solved by posing the problem as Ax = b, where x is the set of coefficients we are looking for. Npts is the number of points. In the following i refers to the ith base function coefficient. The matrix has its entries j in its first Npts rows set to :: A[j][i] = (Fourier transformed base function for point j) We then choose a number of r-points, n_r, to evaluate the second derivative of P(r) at. This is used as our regularization term. For a vector r of length n_r, the following n_r rows are set to :: A[j+Npts][i] = (2nd derivative of P(r), d**2(P(r))/d(r)**2, evaluated at r[j]) The vector b has its first Npts entries set to :: b[j] = (I(q) observed for point j) The following n_r entries are set to zero. The result is found by using scipy.linalg.basic.lstsq to invert the matrix and find the coefficients x. Methods inherited from Cinvertor: * ``get_peaks(pars)``: returns the number of P(r) peaks * ``oscillations(pars)``: returns the oscillation parameters for the output P(r) * ``get_positive(pars)``: returns the fraction of P(r) that is above zero * ``get_pos_err(pars)``: returns the fraction of P(r) that is 1-sigma above zero """ ## Chisqr of the last computation chi2 = 0 ## Time elapsed for last computation elapsed = 0 ## Alpha to get the reg term the same size as the signal suggested_alpha = 0 ## Last number of base functions used nfunc = 10 ## Last output values out = None ## Last errors on output values cov = None ## Background value background = 0 ## Information dictionary for application use info = {} def __init__(self): Pinvertor.__init__(self) def __setstate__(self, state): """ restore the state of invertor for pickle """ (self.__dict__, self.alpha, self.d_max, self.q_min, self.q_max, self.x, self.y, self.err, self.est_bck, self.slit_height, self.slit_width) = state def __reduce_ex__(self, proto): """ Overwrite the __reduce_ex__ """ state = (self.__dict__, self.alpha, self.d_max, self.q_min, self.q_max, self.x, self.y, self.err, self.est_bck, self.slit_height, self.slit_width, ) return (Invertor, tuple(), state, None, None) def __setattr__(self, name, value): """ Set the value of an attribute. Access the parent class methods for x, y, err, d_max, q_min, q_max and alpha """ if name == 'x': if 0.0 in value: msg = "Invertor: one of your q-values is zero. " msg += "Delete that entry before proceeding" raise ValueError(msg) return self.set_x(value) elif name == 'y': return self.set_y(value) elif name == 'err': value2 = abs(value) return self.set_err(value2) elif name == 'd_max': if value <= 0.0: msg = "Invertor: d_max must be greater than zero." msg += "Correct that entry before proceeding" raise ValueError(msg) return self.set_dmax(value) elif name == 'q_min': if value is None: return self.set_qmin(-1.0) return self.set_qmin(value) elif name == 'q_max': if value is None: return self.set_qmax(-1.0) return self.set_qmax(value) elif name == 'alpha': return self.set_alpha(value) elif name == 'slit_height': return self.set_slit_height(value) elif name == 'slit_width': return self.set_slit_width(value) elif name == 'est_bck': if value == True: return self.set_est_bck(1) elif value == False: return self.set_est_bck(0) else: raise ValueError("Invertor: est_bck can only be True or False") return Pinvertor.__setattr__(self, name, value) def __getattr__(self, name): """ Return the value of an attribute """ #import numpy if name == 'x': out = np.ones(self.get_nx()) self.get_x(out) return out elif name == 'y': out = np.ones(self.get_ny()) self.get_y(out) return out elif name == 'err': out = np.ones(self.get_nerr()) self.get_err(out) return out elif name == 'd_max': return self.get_dmax() elif name == 'q_min': qmin = self.get_qmin() if qmin < 0: return None return qmin elif name == 'q_max': qmax = self.get_qmax() if qmax < 0: return None return qmax elif name == 'alpha': return self.get_alpha() elif name == 'slit_height': return self.get_slit_height() elif name == 'slit_width': return self.get_slit_width() elif name == 'est_bck': value = self.get_est_bck() return value == 1 elif name in self.__dict__: return self.__dict__[name] return None
[docs] def clone(self): """ Return a clone of this instance """ #import copy invertor = Invertor() invertor.chi2 = self.chi2 invertor.elapsed = self.elapsed invertor.nfunc = self.nfunc invertor.alpha = self.alpha invertor.d_max = self.d_max invertor.q_min = self.q_min invertor.q_max = self.q_max invertor.x = self.x invertor.y = self.y invertor.err = self.err invertor.est_bck = self.est_bck invertor.background = self.background invertor.slit_height = self.slit_height invertor.slit_width = self.slit_width invertor.info = copy.deepcopy(self.info) return invertor
[docs] def invert(self, nfunc=10, nr=20): """ Perform inversion to P(r) The problem is solved by posing the problem as Ax = b, where x is the set of coefficients we are looking for. Npts is the number of points. In the following i refers to the ith base function coefficient. The matrix has its entries j in its first Npts rows set to :: A[i][j] = (Fourier transformed base function for point j) We then choose a number of r-points, n_r, to evaluate the second derivative of P(r) at. This is used as our regularization term. For a vector r of length n_r, the following n_r rows are set to :: A[i+Npts][j] = (2nd derivative of P(r), d**2(P(r))/d(r)**2, evaluated at r[j]) The vector b has its first Npts entries set to :: b[j] = (I(q) observed for point j) The following n_r entries are set to zero. The result is found by using scipy.linalg.basic.lstsq to invert the matrix and find the coefficients x. :param nfunc: number of base functions to use. :param nr: number of r points to evaluate the 2nd derivative at for the reg. term. :return: c_out, c_cov - the coefficients with covariance matrix """ # Reset the background value before proceeding # self.background = 0.0 if not self.est_bck: self.y -= self.background out, cov = self.lstsq(nfunc, nr=nr) if not self.est_bck: self.y += self.background return out, cov
[docs] def iq(self, out, q): """ Function to call to evaluate the scattering intensity :param args: c-parameters, and q :return: I(q) """ return Pinvertor.iq(self, out, q) + self.background
[docs] def invert_optimize(self, nfunc=10, nr=20): """ Slower version of the P(r) inversion that uses scipy.optimize.leastsq. This probably produce more reliable results, but is much slower. The minimization function is set to sum_i[ (I_obs(q_i) - I_theo(q_i))/err**2 ] + alpha * reg_term, where the reg_term is given by Svergun: it is the integral of the square of the first derivative of P(r), d(P(r))/dr, integrated over the full range of r. :param nfunc: number of base functions to use. :param nr: number of r points to evaluate the 2nd derivative at for the reg. term. :return: c_out, c_cov - the coefficients with covariance matrix """ self.nfunc = nfunc # First, check that the current data is valid if self.is_valid() <= 0: msg = "Invertor.invert: Data array are of different length" raise RuntimeError(msg) p = np.ones(nfunc) t_0 = time.time() out, cov_x, _, _, _ = optimize.leastsq(self.residuals, p, full_output=1) # Compute chi^2 res = self.residuals(out) chisqr = 0 for i in range(len(res)): chisqr += res[i] self.chi2 = chisqr # Store computation time self.elapsed = time.time() - t_0 if cov_x is None: cov_x = np.ones([nfunc, nfunc]) cov_x *= math.fabs(chisqr) return out, cov_x
[docs] def pr_fit(self, nfunc=5): """ This is a direct fit to a given P(r). It assumes that the y data is set to some P(r) distribution that we are trying to reproduce with a set of base functions. This method is provided as a test. """ # First, check that the current data is valid if self.is_valid() <= 0: msg = "Invertor.invert: Data arrays are of different length" raise RuntimeError(msg) p = np.ones(nfunc) t_0 = time.time() out, cov_x, _, _, _ = optimize.leastsq(self.pr_residuals, p, full_output=1) # Compute chi^2 res = self.pr_residuals(out) chisqr = 0 chisq = np.sum(res) self.chisqr = chisqr # Store computation time self.elapsed = time.time() - t_0 return out, cov_x
[docs] def pr_err(self, c, c_cov, r): """ Returns the value of P(r) for a given r, and base function coefficients, with error. :param c: base function coefficients :param c_cov: covariance matrice of the base function coefficients :param r: r-value to evaluate P(r) at :return: P(r) """ c_cov = np.ascontiguousarray(c_cov) return self.get_pr_err(c, c_cov, r)
def _accept_q(self, q): """ Check q-value against user-defined range """ if self.q_min is not None and q < self.q_min: return False if self.q_max is not None and q > self.q_max: return False return True
[docs] def lstsq(self, nfunc=5, nr=20): """ The problem is solved by posing the problem as Ax = b, where x is the set of coefficients we are looking for. Npts is the number of points. In the following i refers to the ith base function coefficient. The matrix has its entries j in its first Npts rows set to :: A[i][j] = (Fourier transformed base function for point j) We then choose a number of r-points, n_r, to evaluate the second derivative of P(r) at. This is used as our regularization term. For a vector r of length n_r, the following n_r rows are set to :: A[i+Npts][j] = (2nd derivative of P(r), d**2(P(r))/d(r)**2, evaluated at r[j]) The vector b has its first Npts entries set to :: b[j] = (I(q) observed for point j) The following n_r entries are set to zero. The result is found by using scipy.linalg.basic.lstsq to invert the matrix and find the coefficients x. :param nfunc: number of base functions to use. :param nr: number of r points to evaluate the 2nd derivative at for the reg. term. If the result does not allow us to compute the covariance matrix, a matrix filled with zeros will be returned. """ # Note: To make sure an array is contiguous: # blah = np.ascontiguousarray(blah_original) # ... before passing it to C if self.is_valid() < 0: msg = "Invertor: invalid data; incompatible data lengths." raise RuntimeError(msg) self.nfunc = nfunc # a -- An M x N matrix. # b -- An M x nrhs matrix or M vector. npts = len(self.x) nq = nr sqrt_alpha = math.sqrt(math.fabs(self.alpha)) if sqrt_alpha < 0.0: nq = 0 # If we need to fit the background, add a term if self.est_bck: nfunc_0 = nfunc nfunc += 1 a = np.zeros([npts + nq, nfunc]) b = np.zeros(npts + nq) err = np.zeros([nfunc, nfunc]) # Construct the a matrix and b vector that represent the problem t_0 = time.time() try: a, b = self._get_matrix(nfunc, nq) except Exception as exc: raise RuntimeError("Invertor: could not invert I(Q)\n %s" % str(exc)) # Perform the inversion (least square fit) # CRUFT: numpy>=1.14.0 allows rcond=None for the following default rcond = np.finfo(float).eps * max(a.shape) c, chi2, _, _ = lstsq(a, b, rcond=rcond) # Sanity check try: float(chi2) except: chi2 = -1.0 self.chi2 = chi2 inv_cov = np.zeros([nfunc, nfunc]) # Get the covariance matrix, defined as inv_cov = a_transposed * a inv_cov = self._get_invcov_matrix(nfunc, nr, a) # Compute the reg term size for the output sum_sig, sum_reg = self._get_reg_size(nfunc, nr, a) if math.fabs(self.alpha) > 0: new_alpha = sum_sig / (sum_reg / self.alpha) else: new_alpha = 0.0 self.suggested_alpha = new_alpha try: cov = np.linalg.pinv(inv_cov) err = math.fabs(chi2 / (npts - nfunc)) * cov except Exception as exc: # We were not able to estimate the errors # Return an empty error matrix logger.error(exc) # Keep a copy of the last output if not self.est_bck: self.out = c self.cov = err else: self.background = c[0] err_0 = np.zeros([nfunc, nfunc]) c_0 = np.zeros(nfunc) c_0[:-1] = c[1:] err_0[:-1, :-1] = err[1:, 1:] self.out = c_0 self.cov = err_0 # Store computation time self.elapsed = time.time() - t_0 return self.out, self.cov
[docs] def estimate_numterms(self, isquit_func=None): """ Returns a reasonable guess for the number of terms :param isquit_func: reference to thread function to call to check whether the computation needs to be stopped. :return: number of terms, alpha, message """ from .num_term import NTermEstimator estimator = NTermEstimator(self.clone()) try: return estimator.num_terms(isquit_func) except Exception as exc: # If we fail, estimate alpha and return the default # number of terms best_alpha, _, _ = self.estimate_alpha(self.nfunc) logger.warning("Invertor.estimate_numterms: %s" % exc) return self.nfunc, best_alpha, "Could not estimate number of terms"
[docs] def estimate_alpha(self, nfunc): """ Returns a reasonable guess for the regularization constant alpha :param nfunc: number of terms to use in the expansion. :return: alpha, message, elapsed where alpha is the estimate for alpha, message is a message for the user, elapsed is the computation time """ #import time try: pr = self.clone() # T_0 for computation time starttime = time.time() elapsed = 0 # If the current alpha is zero, try # another value if pr.alpha <= 0: pr.alpha = 0.0001 # Perform inversion to find the largest alpha out, _ = pr.invert(nfunc) elapsed = time.time() - starttime initial_alpha = pr.alpha initial_peaks = pr.get_peaks(out) # Try the inversion with the estimated alpha pr.alpha = pr.suggested_alpha out, _ = pr.invert(nfunc) npeaks = pr.get_peaks(out) # if more than one peak to start with # just return the estimate if npeaks > 1: #message = "Your P(r) is not smooth, #please check your inversion parameters" message = None return pr.suggested_alpha, message, elapsed else: # Look at smaller values # We assume that for the suggested alpha, we have 1 peak # if not, send a message to change parameters alpha = pr.suggested_alpha best_alpha = pr.suggested_alpha found = False for i in range(10): pr.alpha = (0.33) ** (i + 1) * alpha out, _ = pr.invert(nfunc) peaks = pr.get_peaks(out) if peaks > 1: found = True break best_alpha = pr.alpha # If we didn't find a turning point for alpha and # the initial alpha already had only one peak, # just return that if not found and initial_peaks == 1 and \ initial_alpha < best_alpha: best_alpha = initial_alpha # Check whether the size makes sense message = '' if not found: message = None elif best_alpha >= 0.5 * pr.suggested_alpha: # best alpha is too big, return a # reasonable value message = "The estimated alpha for your system is too " message += "large. " message += "Try increasing your maximum distance." return best_alpha, message, elapsed except Exception as exc: message = "Invertor.estimate_alpha: %s" % exc return 0, message, elapsed
[docs] def to_file(self, path, npts=100): """ Save the state to a file that will be readable by SliceView. :param path: path of the file to write :param npts: number of P(r) points to be written """ file = open(path, 'w') file.write("#d_max=%g\n" % self.d_max) file.write("#nfunc=%g\n" % self.nfunc) file.write("#alpha=%g\n" % self.alpha) file.write("#chi2=%g\n" % self.chi2) file.write("#elapsed=%g\n" % self.elapsed) file.write("#qmin=%s\n" % str(self.q_min)) file.write("#qmax=%s\n" % str(self.q_max)) file.write("#slit_height=%g\n" % self.slit_height) file.write("#slit_width=%g\n" % self.slit_width) file.write("#background=%g\n" % self.background) if self.est_bck: file.write("#has_bck=1\n") else: file.write("#has_bck=0\n") file.write("#alpha_estimate=%g\n" % self.suggested_alpha) if self.out is not None: if len(self.out) == len(self.cov): for i in range(len(self.out)): file.write("#C_%i=%s+-%s\n" % (i, str(self.out[i]), str(self.cov[i][i]))) file.write("<r> <Pr> <dPr>\n") r = np.arange(0.0, self.d_max, self.d_max / npts) (value, err) = self.pr_err(self.out, self.cov, r) all_data = np.vstack([r, value, err]) np.savetxt(file, all_data.T) file.close()
[docs] def from_file(self, path): """ Load the state of the Invertor from a file, to be able to generate P(r) from a set of parameters. :param path: path of the file to load """ #import os #import re if os.path.isfile(path): try: fd = open(path, 'r') buff = fd.read() lines = buff.split('\n') for line in lines: if line.startswith('#d_max='): toks = line.split('=') self.d_max = float(toks[1]) elif line.startswith('#nfunc='): toks = line.split('=') self.nfunc = int(toks[1]) self.out = np.zeros(self.nfunc) self.cov = np.zeros([self.nfunc, self.nfunc]) elif line.startswith('#alpha='): toks = line.split('=') self.alpha = float(toks[1]) elif line.startswith('#chi2='): toks = line.split('=') self.chi2 = float(toks[1]) elif line.startswith('#elapsed='): toks = line.split('=') self.elapsed = float(toks[1]) elif line.startswith('#alpha_estimate='): toks = line.split('=') self.suggested_alpha = float(toks[1]) elif line.startswith('#qmin='): toks = line.split('=') try: self.q_min = float(toks[1]) except: self.q_min = None elif line.startswith('#qmax='): toks = line.split('=') try: self.q_max = float(toks[1]) except: self.q_max = None elif line.startswith('#slit_height='): toks = line.split('=') self.slit_height = float(toks[1]) elif line.startswith('#slit_width='): toks = line.split('=') self.slit_width = float(toks[1]) elif line.startswith('#background='): toks = line.split('=') self.background = float(toks[1]) elif line.startswith('#has_bck='): toks = line.split('=') self.est_bck = int(toks[1]) == 1 # Now read in the parameters elif line.startswith('#C_'): toks = line.split('=') p = re.compile('#C_([0-9]+)') m = p.search(toks[0]) toks2 = toks[1].split('+-') i = int(m.group(1)) self.out[i] = float(toks2[0]) self.cov[i][i] = float(toks2[1]) except Exception as exc: msg = "Invertor.from_file: corrupted file\n%s" % exc raise RuntimeError(msg) else: msg = "Invertor.from_file: '%s' is not a file" % str(path) raise RuntimeError(msg)