/usr/bin/refine_wavelength is in pyfai 0.10.2-1.
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# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/kif/pyFAI
#
# File: "$Id$"
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "12/07/2011"
__doc__ = """
Refine the wavelength from a set of images taken with various geometries.
For numerical efficiency, the wavelength has to be in ANGSTROM
Usage:
$ refine_wavelength -w=1.54 poni1 poni2 poni3 poni4
"""
import sys, os, logging
import numpy
from numpy import sin, arcsin
from scipy.optimize import fmin_slsqp
from pyFAI.geometryRefinement import GeometryRefinement
class RefineWavelength(object):
def __init__(self, wavelength, listFiles=None):
self.wavelength_init = wavelength
self.wavelength = wavelength
self.listFiles = []
self.listPoni = []
self.listPoints = []
self.listRefiner = []
self.bounds = []
self.param = []
if listFiles:
for oneFile in listFiles:
self.addFile(oneFile)
self.param.append(wavelength)
self.bounds.append((0.9 * wavelength, 1.1 * wavelength))
self.nbImg = len(self.listPoni)
def __repr__(self):
lstTxt = [ "%s\t%6.3f\t%6.3f\t%6.3f\t%6.3f\t%6.3f\t%6.3f" % (j, i.dist, i.poni1, i.poni2, i.rot1, i.rot2, i.rot3) for i, j in zip(self.listRefiner, self.listFiles)]
lstTxt.append("Wavelength: %s" % self.wavelength)
return os.linesep.join(lstTxt)
def addFile(self, filename):
if filename in self.listFiles:
return
basename = os.path.splitext(filename)[0]
if filename.endswith(".poni") and os.path.isfile(basename + ".py"):
poni = filename
pointFile = basename + ".py"
elif filename.endswith(".py") and os.path.isfile(basename + ".poni"):
poni = filename
pointFile = basename + ".py"
try:
points = eval(open(pointFile).read().replace("data=", ""))
except:
logging.error("error in reading %s" % pointFile)
return
refinement = GeometryRefinement(points)
refinement.load(poni)
# print refinement
self.listPoints.append(numpy.array(points).astype("float64"))
self.listPoni.append(refinement.param)
refinement.dist_min = 0.5 * refinement.dist
refinement.dist_max = 2 * refinement.dist
refinement.poni1_min = min(0.9 * refinement.poni1, 1.1 * refinement.poni1)
refinement.poni1_max = max(0.9 * refinement.poni1, 1.1 * refinement.poni1)
refinement.poni2_min = min(0.9 * refinement.poni2, 1.1 * refinement.poni2)
refinement.poni2_max = max(0.9 * refinement.poni2, 1.1 * refinement.poni2)
refinement.rot1_min = min(0.9 * refinement.rot1, 1.1 * refinement.rot1)
refinement.rot1_max = max(0.9 * refinement.rot1, 1.1 * refinement.rot1)
refinement.rot2_min = min(0.9 * refinement.rot2, 1.1 * refinement.rot2)
refinement.rot2_max = max(0.9 * refinement.rot2, 1.1 * refinement.rot2)
refinement.rot3_min = min(0.9 * refinement.rot3, 1.1 * refinement.rot3)
refinement.rot3_max = max(0.9 * refinement.rot3, 1.1 * refinement.rot3)
self.listRefiner.append(refinement)
self.listFiles.append(poni)
# self.listFiles.append(pointFile)
self.param += refinement.param
self.bounds += [(refinement.dist_min, refinement.dist_max),
(refinement.poni1_min, refinement.poni1_max),
(refinement.poni2_min, refinement.poni2_max),
(refinement.rot1_min, refinement.rot1_max),
(refinement.rot2_min, refinement.rot2_max),
(refinement.rot3_min, refinement.rot3_max)]
def residu1(self, param):
res = []
for i, ref in enumerate(self.listRefiner):
points = self.listPoints[i]
d1 = points[:, 0]
d2 = points[:, 1]
tth = 2 * arcsin(param[-1] * sin(points[:, 2] / 2.0) / self.wavelength_init)
res.append(ref.tth(d1, d2, param[i * 6: (i + 1) * 6]) - tth)
return numpy.concatenate(tuple(res))
def residu2(self, param):
return (self.residu1(param) ** 2).sum()
def chi2(self, param=None):
if param is not None:
return self.residu2(param)
else:
return self.residu2(self.param)
# sum = 0.0
# for oneRef in self.listRefiner:
# sum += oneRef.chi2()
# return sum
def refine2(self, maxiter=1000):
param = []
for i in self.listRefiner:
param.append(i.param)
param.append([self.wavelength])
self.param = numpy.concatenate(tuple(param)).astype("float64")
newParam = fmin_slsqp(self.residu2, self.param, iter=maxiter,
bounds=self.bounds, iprint=2,
acc=1.0e-12)
print newParam
print "Constrained Least square", self.chi2(), "--> ", self.chi2(newParam)
if self.chi2(newParam) < self.chi2():
i = abs(self.param - newParam).argmax()
print "maxdelta on: ", i, self.param[i], "-->", newParam[i]
self.param = newParam
self.wavelength = newParam[-1]
for i, ref in enumerate(self.listRefiner):
ref.param = newParam[6 * i:6 * (i + 1) ]
ref.dist = newParam[6 * i]
ref.poni1 = newParam[6 * i + 1]
ref.poni2 = newParam[6 * i + 2]
ref.rot1 = newParam[6 * i + 3]
ref.rot2 = newParam[6 * i + 4]
ref.rot3 = newParam[6 * i + 5]
if __name__ == "__main__":
if len(sys.argv) == 1:
print __doc__
sys.exit(1)
wavelength = None
listFiles = []
for arg in sys.argv[1:]:
if arg.find("-h") in [0, 1]:
print(__doc__)
sys.exit(0)
elif arg.find("-w=") in [0, 1]:
wavelength = float(arg.split("=")[1])
elif os.path.isfile(arg):
listFiles.append(arg)
if wavelength is None:
wavelength = raw_input("WaveLength (A) ? ")
refinement = RefineWavelength(wavelength, listFiles)
print refinement
last = refinement.chi2() + 1
# print last - 1
while refinement.chi2() < last:
last = refinement.chi2()
refinement.refine2()
print refinement
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