/usr/lib/python2.7/dist-packages/pyFAI/calibrant.py is in pyfai 0.10.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/kif
#
# 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/>.
#
"""
Calibrant
A module containing classical calibrant and also tools to generate d-spacing.
"""
__author__ = "Jerome Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "06/10/2014"
__status__ = "production"
import os
import logging
import numpy
from math import sin, asin
import threading
logger = logging.getLogger("pyFAI.calibrant")
epsilon = 1.0e-6 # for floating point comparison
class Calibrant(object):
"""
A calibrant is a reference compound where the d-spacing (interplanar distances)
are known. They are expressed in Angstrom (in the file)
"""
def __init__(self, filename=None, dSpacing=None, wavelength=None):
object.__init__(self)
self._filename = filename
self._wavelength = wavelength
self._sem = threading.Semaphore()
self._2th = []
if dSpacing is None:
self._dSpacing = []
else:
self._dSpacing = list(dSpacing)
if self._dSpacing and self._wavelength:
self._calc_2th()
def __repr__(self):
name = "undefined"
if self._filename:
name = os.path.splitext(os.path.basename(self._filename))[0]
name += " Calibrant "
if len(self._dSpacing):
name += "with %i reflections " % len(self._dSpacing)
if self._wavelength:
name += "at wavelength %s" % self._wavelength
return name
def load_file(self, filename=None):
with self._sem:
if filename:
self._filename = filename
if not os.path.isfile(self._filename):
logger.error("No such calibrant file: %s" % self._filename)
return
self._filename = os.path.abspath(self._filename)
self._dSpacing = numpy.unique(numpy.loadtxt(self._filename))
self._dSpacing = list(self._dSpacing[-1::-1]) #reverse order
# self._dSpacing.sort(reverse=True)
if self._wavelength:
self._calc_2th()
def save_dSpacing(self, filename=None):
"""
save the d-spacing to a file
"""
if filename == None and self._filename is not None:
filename = self._filename
else:
return
with open(filename) as f:
f.write("# %s Calibrant" % filename)
for i in self.dSpacing:
f.write("%s\n" % i)
def get_dSpacing(self):
if not self._dSpacing and self._filename:
self.load_file()
return self._dSpacing
def set_dSpacing(self, lst):
self._dSpacing = list(lst)
self._filename = "Modified"
if self._wavelength:
self._calc_2th()
dSpacing = property(get_dSpacing, set_dSpacing)
def append_dSpacing(self, value):
with self._sem:
delta = [abs(value - v) / v for v in self._dSpacing if v is not None]
if not delta or min(delta) > epsilon:
self._dSpacing.append(value)
self._dSpacing.sort(reverse=True)
self._calc_2th()
def append_2th(self, value):
with self._sem:
if value not in self._2th:
self._2th.append(value)
self._2th.sort()
self._calc_dSpacing()
def setWavelength_change2th(self, value=None):
with self._sem:
if value:
self._wavelength = float(value)
if self._wavelength < 1e-15 or self._wavelength > 1e-6:
logger.warning("This is an unlikely wavelength (in meter): %s" % self._wavelength)
self._calc_2th()
def setWavelength_changeDs(self, value=None):
"""
This is probably not a good idea, but who knows !
"""
with self._sem:
if value:
self._wavelength = float(value)
if self._wavelength < 1e-15 or self._wavelength > 1e-6:
logger.warning("This is an unlikely wavelength (in meter): %s" % self._wavelength)
self._calc_dSpacing()
def set_wavelength(self, value=None):
updated = False
with self._sem:
if self._wavelength is None:
if value:
self._wavelength = float(value)
if (self._wavelength < 1e-15) or (self._wavelength > 1e-6):
logger.warning("This is an unlikely wavelength (in meter): %s" % self._wavelength)
updated = True
elif abs(self._wavelength - value) / self._wavelength > epsilon:
logger.warning("Forbidden to change the wavelength once it is fixed !!!!")
logger.warning("%s != %s, delta= %s" % (self._wavelength, value, self._wavelength - value))
if updated:
self._calc_2th()
def get_wavelength(self):
return self._wavelength
wavelength = property(get_wavelength, set_wavelength)
def _calc_2th(self):
if self._wavelength is None:
logger.error("Cannot calculate 2theta angle without knowing wavelength")
return
self._2th = []
for ds in self._dSpacing:
try:
tth = 2.0 * asin(5.0e9 * self._wavelength / ds)
except ValueError:
tth = None
if self._2th:
self._dSpacing = self._dSpacing[:len(self._2th)]
#avoid turning around...
break
else:
self._2th.append(tth)
def _calc_dSpacing(self):
if self._wavelength is None:
logger.error("Cannot calculate 2theta angle without knowing wavelength")
return
self._dSpacing = [5.0e9 * self._wavelength / sin(tth / 2.0) for tth in self._2th]
def get_2th(self):
if not self._2th:
ds = self.dSpacing #forces the file reading if not done
with self._sem:
if not self._2th:
self._calc_2th()
return self._2th
def get_2th_index(self, angle):
"""
return the index in the 2theta angle index
"""
idx = None
if angle:
idx = self._2th.find(angle)
if idx == -1:
idx = None
return idx
def fake_calibration_image(self, ai, shape=None, Imax=1.0, U=0, V=0, W=0.0001):
"""
Generates a fake calibration image from an azimuthal integrator
@param ai: azimuthal integrator
@param Imax: maximum intensity of rings
@param U, V, W: width of the peak from Caglioti's law (FWHM^2 = Utan(th)^2 + Vtan(th) + W)
"""
if shape is None:
if ai.detector.shape:
shape = ai.detector.shape
elif ai.detector.max_shape:
shape = ai.detector.max_shape
if shape is None:
raise RuntimeError("No shape available")
tth = ai.twoThetaArray(shape)
tth_min = tth.min()
tth_max = tth.max()
dim = int(numpy.sqrt(shape[0] * shape[0] + shape[1] * shape[1]))
tth_1d = numpy.linspace(tth_min, tth_max, dim)
tanth = numpy.tan(tth_1d / 2.0)
fwhm2 = U * tanth ** 2 + V * tanth + W
sigma2 = 8.0 * numpy.log(2.0) * fwhm2
signal = numpy.zeros_like(sigma2)
for t in self.get_2th():
if t >= tth_max:
break
else:
signal += Imax * numpy.exp(-(tth_1d - t) ** 2 / (2 * sigma2))
res = ai.calcfrom1d(tth_1d, signal, shape=shape, mask=ai.mask,
dim1_unit='2th_rad', correctSolidAngle=True)
return res
class calibrant_factory(object):
"""
Behaves like a dict but is actually a factory:
Each time one retrieves an object it is a new geniune new calibrant (unmodified)
"""
def __init__(self, basedir=None):
"""
Constructor
@param basedir: directory name where to search for the calibrants
"""
if basedir is None:
basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "calibration")
self.directory = basedir
if not os.path.isdir(self.directory):
logger.warning("No calibrant directory: %s" % self.directory)
self.all = {}
else:
self.all = dict([(os.path.splitext(i)[0], os.path.join(self.directory, i))
for i in os.listdir(self.directory)
if i.endswith(".D")])
def __getitem__(self, what):
return Calibrant(self.all[what])
def get(self, what, notfound=None):
if what in self.all:
return Calibrant(self.all[what])
else:
return notfound
def __contains__(self, k):
return k in self.all
def __repr__(self):
return "Calibrants available: %s" % (", ".join(self.all.keys()))
def __len__(self):
return len(self.all)
def keys(self):
return self.all.keys()
def values(self):
return map(Calibrant, self.all.values())
def items(self):
return [(i, Calibrant(j)) for i, j in self.all.items()]
__call__ = __getitem__
has_key = __contains__
ALL_CALIBRANTS = calibrant_factory()
|