# -*- coding: utf-8 -*-
#
# Project: freesas
# https://github.com/kif/freesas
#
# Copyright (C) 2020 European Synchrotron Radiation Facility, Grenoble, France
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""
Set of namedtuples defined a bit everywhere
"""
__authors__ = ["Jérôme Kieffer"]
__license__ = "MIT"
__copyright__ = "2020 ESRF"
__date__ = "13/10/2020"
from collections import namedtuple
from os import linesep
import numpy
# Used in AutoRg
RG_RESULT = namedtuple(
"RG_RESULT",
"Rg sigma_Rg I0 sigma_I0 start_point end_point quality aggregated",
)
def _RG_RESULT_repr(self):
return f"Rg={self.Rg:6.4f}(±{self.sigma_Rg:6.4f}) I0={self.I0:6.4f}(±{self.sigma_I0:6.4f}) [{self.start_point}-{self.end_point}] {100.0*self.quality:5.2f}% {'aggregated' if self.aggregated>0.1 else ''}"
RG_RESULT.__repr__ = _RG_RESULT_repr
FIT_RESULT = namedtuple(
"FIT_RESULT",
"slope sigma_slope intercept sigma_intercept, R, R2, chi2, RMSD",
)
RT_RESULT = namedtuple("RT_RESULT", "Vc sigma_Vc Qr sigma_Qr mass sigma_mass")
def _RT_RESULT_repr(self):
return f"Vc={self.Vc:6.4f}(±{self.sigma_Vc:6.4f}) Qr={self.Qr:6.4f}(±{self.sigma_Qr:6.4f}) mass={self.mass:6.4f}(±{self.sigma_mass:6.4f})"
RT_RESULT.__repr__ = _RT_RESULT_repr
# Used in BIFT
RadiusKey = namedtuple("RadiusKey", "Dmax npt")
PriorKey = namedtuple("PriorKey", "type npt")
TransfoValue = namedtuple("TransfoValue", "transfo B sum_dia")
EvidenceKey = namedtuple("EvidenceKey", "Dmax alpha npt")
EvidenceResult = namedtuple(
"EvidenceResult", "evidence chi2r regularization radius density converged"
)
StatsResult = namedtuple(
"StatsResult",
"radius density_avg density_std evidence_avg evidence_std Dmax_avg Dmax_std alpha_avg, alpha_std chi2r_avg chi2r_std regularization_avg regularization_std Rg_avg Rg_std I0_avg I0_std",
)
[docs]def save_bift(stats, filename, source=None):
"Save the results of the fit to the file"
res = [
"Dmax= %.2f±%.2f" % (stats.Dmax_avg, stats.Dmax_std),
"𝛂= %.1f±%.1f" % (stats.alpha_avg, stats.alpha_std),
"S₀= %.4f±%.4f" % (stats.regularization_avg, stats.regularization_std),
"χ²= %.2f±%.2f" % (stats.chi2r_avg, stats.chi2r_std),
"logP= %.2f±%.2f" % (stats.evidence_avg, stats.evidence_std),
"Rg= %.2f±%.2f" % (stats.Rg_avg, stats.Rg_std),
"I₀= %.2f±%.2f" % (stats.I0_avg, stats.I0_std),
]
with open(filename, "wt", encoding="utf-8") as out:
out.write("# %s %s" % (source or filename, "\n"))
for txt in res:
out.write("# %s %s" % (txt, "\n"))
out.write("%s# r\tp(r)\tsigma_p(r)%s" % ("\n", "\n"))
for r, p, s in zip(
stats.radius.astype(numpy.float32),
stats.density_avg.astype(numpy.float32),
stats.density_std.astype(numpy.float32),
):
out.write("%s\t%s\t%s%s" % (r, p, s, "\n"))
return filename + ": " + "; ".join(res)
StatsResult.save = save_bift
# Used in Cormap
GOF = namedtuple("GOF", ["n", "c", "P"])