/usr/lib/python2.7/dist-packages/pyFAI/geometryRefinement.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/kif/pyFAI
#
# 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__ = "Jerome Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "29/09/2014"
__status__ = "development"
import os
import tempfile
import subprocess
import logging
import numpy
import types
from math import pi
from . import azimuthalIntegrator
from .calibrant import Calibrant, ALL_CALIBRANTS
AzimuthalIntegrator = azimuthalIntegrator.AzimuthalIntegrator
from scipy.optimize import fmin, leastsq, fmin_slsqp, anneal
if os.name != "nt":
WindowsError = RuntimeError
logger = logging.getLogger("pyFAI.geometryRefinement")
# logger.setLevel(logging.DEBUG)
ROCA = "/opt/saxs/roca"
####################
# GeometryRefinement
####################
class GeometryRefinement(AzimuthalIntegrator):
def __init__(self, data, dist=1, poni1=None, poni2=None,
rot1=0, rot2=0, rot3=0,
pixel1=None, pixel2=None, splineFile=None, detector=None,
wavelength=None, calibrant=None):
"""
@param data: ndarray float64 shape = n, 3
col0: pos in dim0 (in pixels)
col1: pos in dim1 (in pixels)
col2: ring index in calibrant object
@param dist: guessed sample-detector distance (optional, in m)
@param poni1: guessed PONI coordinate along the Y axis (optional, in m)
@param poni2: guessed PONI coordinate along the X axis (optional, in m)
@param rot1: guessed tilt of the detector around the Y axis (optional, in rad)
@param rot2: guessed tilt of the detector around the X axis (optional, in rad)
@param rot3: guessed tilt of the detector around the incoming beam axis (optional, in rad)
@param pixel1: Pixel size along the vertical direction of the detector (in m), almost mandatory
@param pixel2: Pixel size along the horizontal direction of the detector (in m), almost mandatory
@param splineFile: file describing the detector as 2 cubic splines. Replaces pixel1 & pixel2
@param detector: name of the detector or Detector instance. Replaces splineFile, pixel1 & pixel2
@param wavelength: wavelength in m (1.54e-10)
@param calibrant: instance of pyFAI.calibrant.Calibrant containing the d-Spacing
"""
self.data = numpy.array(data, dtype=numpy.float64)
assert self.data.ndim == 2
assert self.data.shape[1] in [ 3, 4] #3 for non weighted, 4 for weighted refinement
assert self.data.shape[0]>0
if (pixel1 is None) and (pixel2 is None) and (splineFile is None) and (detector is None):
raise RuntimeError("Setting up the geometry refinement without knowing the detector makes little sense")
AzimuthalIntegrator.__init__(self, dist, 0, 0,
rot1, rot2, rot3,
pixel1, pixel2, splineFile, detector, wavelength=wavelength)
if calibrant is None:
self.calibrant = Calibrant()
else:
if isinstance(calibrant, Calibrant):
self.calibrant = calibrant
elif type(calibrant) in types.StringTypes:
if calibrant in ALL_CALIBRANTS:
self.calibrant = ALL_CALIBRANTS[calibrant]
else:
self.calibrant = Calibrant(filename=calibrant)
else:
self.calibrant = Calibrant(calibrant)
self.calibrant.wavelength = self.wavelength
if (poni1 is None) or (poni2 is None):
self.guess_poni()
else:
self.poni1 = float(poni1)
self.poni2 = float(poni2)
self._dist_min = 0
self._dist_max = 10
self._poni1_min = -10000 * self.pixel1
self._poni1_max = 15000 * self.pixel1
self._poni2_min = -10000 * self.pixel2
self._poni2_max = 15000 * self.pixel2
self._rot1_min = -pi
self._rot1_max = pi
self._rot2_min = -pi
self._rot2_max = pi
self._rot3_min = -pi
self._rot3_max = pi
self._wavelength_min = 1e-15
self._wavelength_max = 100.e-10
def guess_poni(self):
"""
Poni can be guessed by the centroid of the ring with lowest 2Theta
"""
if len(self.calibrant.dSpacing):
# logger.warning(self.calibrant.__repr__())s
tth = self.calc_2th(self.data[:, 2])
else: # assume rings are in decreasing dSpacing in the file
tth = self.data[:, 2]
asrt = tth.argsort()
tth = tth[asrt]
srtdata = self.data[asrt]
smallRing = srtdata[tth < (tth.min() + 1e-6)]
smallRing1 = smallRing[:, 0]
smallRing2 = smallRing[:, 1]
smallRing_in_m = self.detector.calc_cartesian_positions(smallRing1,
smallRing2)
l = len(smallRing)
self.poni1 = smallRing_in_m[0].sum() / l
self.poni2 = smallRing_in_m[1].sum() / l
def set_tolerance(self, value=10):
"""
Set the tolerance for a refinement of the geometry; in percent of the original value
@param value: Tolerance as a percentage
"""
low = 1.0 - value / 100.
hi = 1.0 + value / 100.
self.dist_min = low * self.dist
self.dist_max = hi * self.dist
if abs(self.poni1) > (value / 100.) ** 2:
self.poni1_min = min(low * self.poni1, hi * self.poni1)
self.poni1_max = max(low * self.poni1, hi * self.poni1)
else:
self.poni1_min = -(value / 100.) ** 2
self.poni1_max = (value / 100.) ** 2
if abs(self.poni2) > (value / 100.) ** 2:
self.poni2_min = min(low * self.poni2, hi * self.poni2)
self.poni2_max = max(low * self.poni2, hi * self.poni2)
else:
self.poni2_min = -(value / 100.) ** 2
self.poni2_max = (value / 100.) ** 2
if abs(self.rot1) > (value / 100.) ** 2:
self.rot1_min = min(low * self.rot1, hi * self.rot1)
self.rot1_max = max(low * self.rot1, hi * self.rot1)
else:
self.rot1_min = -(value / 100.) ** 2
self.rot1_max = (value / 100.) ** 2
if abs(self.rot2) > (value / 100.) ** 2:
self.rot2_min = min(low * self.rot2, hi * self.rot2)
self.rot2_max = max(low * self.rot2, hi * self.rot2)
else:
self.rot2_min = -(value / 100.) ** 2
self.rot2_max = (value / 100.) ** 2
if abs(self.rot3) > (value / 100.) ** 2:
self.rot3_min = min(low * self.rot3, hi * self.rot3)
self.rot3_max = max(low * self.rot3, hi * self.rot3)
else:
self.rot3_min = -(value / 100.) ** 2
self.rot3_max = (value / 100.) ** 2
self.wavelength_min = low * self.wavelength
self.wavelength_max = hi * self.wavelength
def calc_2th(self, rings, wavelength=None):
"""
@param rings: indices of the rings. starts at 0 and self.dSpacing should be long enough !!!
@param wavelength: wavelength in meter
"""
if wavelength is None:
wavelength = self.wavelength
rings = numpy.ascontiguousarray(rings, dtype=numpy.int32)
if wavelength != self.calibrant.wavelength:
self.calibrant.setWavelength_change2th(wavelength)
return numpy.array(self.calibrant.get_2th(), dtype=numpy.float64)[rings]
def residu1(self, param, d1, d2, rings):
return self.tth(d1, d2, param) - self.calc_2th(rings, self.wavelength)
def residu1_wavelength(self, param, d1, d2, rings):
return self.tth(d1, d2, param) - self.calc_2th(rings, param[6] * 1e-10)
def residu2(self, param, d1, d2, rings):
return (self.residu1(param, d1, d2, rings) ** 2).sum()
def residu2_weighted(self, param, d1, d2, rings, weight):
return (weight * self.residu1(param, d1, d2, rings) ** 2).sum()
def residu2_wavelength(self, param, d1, d2, rings):
return (self.residu1_wavelength(param, d1, d2, rings) ** 2).sum()
def residu2_wavelength_weighted(self, param, d1, d2, rings, weight):
return (weight * self.residu1_wavelength(param, d1, d2, rings) ** 2).sum()
def refine1(self):
self.param = numpy.array([self._dist, self._poni1, self._poni2,
self._rot1, self._rot2, self._rot3],
dtype="float64")
newParam, rc = leastsq(self.residu1, self.param,
args=(self.data[:, 0],
self.data[:, 1],
self.data[:, 2]))
oldDeltaSq = self.chi2(tuple(self.param))
newDeltaSq = self.chi2(tuple(newParam))
logger.info("Least square retcode=%s %s --> %s",
rc, oldDeltaSq, newDeltaSq)
if newDeltaSq < oldDeltaSq:
i = abs(self.param - newParam).argmax()
d = ["dist", "poni1", "poni2", "rot1", "rot2", "rot3"]
logger.info("maxdelta on %s: %s --> %s ",
d[i], self.param[i], newParam[i])
self.param = newParam
self.dist, self.poni1, self.poni2, \
self.rot1, self.rot2, self.rot3 = tuple(newParam)
return newDeltaSq
else:
return oldDeltaSq
def refine2(self, maxiter=1000000, fix=["wavelength"]):
d = ["dist", "poni1", "poni2", "rot1", "rot2", "rot3"]
param = []
bounds = []
for i in d:
param.append(getattr(self, i))
if i in fix:
val = getattr(self, i)
bounds.append((val, val))
else:
bounds.append((getattr(self, "_%s_min" % i), getattr(self, "_%s_max" % i)))
self.param = numpy.array(param)
if self.data.shape[-1] == 3:
pos0 = self.data[:, 0]
pos1 = self.data[:, 1]
ring = self.data[:, 2].astype(numpy.int32)
weight = None
newParam = fmin_slsqp(self.residu2, self.param, iter=maxiter,
args=(pos0, pos1, ring),
bounds=bounds,
acc=1.0e-12,
iprint=(logger.getEffectiveLevel() <= logging.INFO))
elif self.data.shape[-1] == 4:
pos0 = self.data[:, 0]
pos1 = self.data[:, 1]
ring = self.data[:, 2].astype(numpy.int32)
weight = self.data[:, 3]
newParam = fmin_slsqp(self.residu2_weighted, self.param, iter=maxiter,
args=(pos0, pos1, ring, weight),
bounds=bounds,
acc=1.0e-12,
iprint=(logger.getEffectiveLevel() <= logging.INFO))
oldDeltaSq = self.chi2() / self.data.shape[0]
newDeltaSq = self.chi2(newParam) / self.data.shape[0]
logger.info("Constrained Least square %s --> %s",
oldDeltaSq, newDeltaSq)
if newDeltaSq < oldDeltaSq:
i = abs(self.param - newParam).argmax()
logger.info("maxdelta on %s: %s --> %s ",
d[i], self.param[i], newParam[i])
self.param = newParam
self.dist, self.poni1, self.poni2, \
self.rot1, self.rot2, self.rot3 = tuple(newParam)
return newDeltaSq
else:
return oldDeltaSq
def refine2_wavelength(self, maxiter=1000000, fix=["wavelength"]):
d = ["dist", "poni1", "poni2", "rot1", "rot2", "rot3", "wavelength"]
self.param = numpy.array([self.dist, self.poni1, self.poni2,
self.rot1, self.rot2, self.rot3, self.wavelength],
dtype="float64")
param = []
bounds = []
for i in d:
param.append(getattr(self, i))
if i in fix:
val = getattr(self, i)
bounds.append((val, val))
else:
bounds.append((getattr(self, "_%s_min" % i), getattr(self, "_%s_max" % i)))
# wavelength is multiplied to 10^10 to have values in the range 0.1-10: better numerical differentiation
bounds[-1] = (bounds[-1][0] * 1e10, bounds[-1][1] * 1e10)
param[-1] = 1e10 * param[-1]
self.param = numpy.array(param)
if self.data.shape[-1] == 3:
pos0 = self.data[:, 0]
pos1 = self.data[:, 1]
ring = self.data[:, 2].astype(numpy.int32)
weight = None
newParam = fmin_slsqp(self.residu2_wavelength,
self.param, iter=maxiter,
args=(pos0, pos1, ring),
bounds=bounds,
acc=1.0e-12,
iprint=(logger.getEffectiveLevel() <= logging.INFO))
elif self.data.shape[-1] == 4:
pos0 = self.data[:, 0]
pos1 = self.data[:, 1]
ring = self.data[:, 2].astype(numpy.int32)
weight = self.data[:, 3]
newParam = fmin_slsqp(self.residu2_wavelength_weighted,
self.param, iter=maxiter,
args=(pos0, pos1, ring, weight),
bounds=bounds,
acc=1.0e-12,
iprint=(logger.getEffectiveLevel() <= logging.INFO))
oldDeltaSq = self.chi2_wavelength() / self.data.shape[0]
newDeltaSq = self.chi2_wavelength(newParam) / self.data.shape[0]
logger.info("Constrained Least square %s --> %s",
oldDeltaSq, newDeltaSq)
if newDeltaSq < oldDeltaSq:
i = abs(self.param - newParam).argmax()
logger.info("maxdelta on %s: %s --> %s ",
d[i], self.param[i], newParam[i])
self.param = newParam
self.dist, self.poni1, self.poni2, self.rot1, self.rot2, self.rot3 = tuple(newParam[:-1])
self.wavelength = 1e-10 * newParam[-1]
return newDeltaSq
else:
return oldDeltaSq
def simplex(self, maxiter=1000000):
self.param = numpy.array([self.dist, self.poni1, self.poni2,
self.rot1, self.rot2, self.rot3],
dtype="float64")
newParam = fmin(self.residu2, self.param,
args=(self.data[:, 0],
self.data[:, 1],
self.data[:, 2]),
maxiter=maxiter,
xtol=1.0e-12)
oldDeltaSq = self.chi2(tuple(self.param)) / self.data.shape[0]
newDeltaSq = self.chi2(tuple(newParam)) / self.data.shape[0]
logger.info("Simplex %s --> %s", oldDeltaSq, newDeltaSq)
if newDeltaSq < oldDeltaSq:
i = abs(self.param - newParam).argmax()
d = ["dist", "poni1", "poni2", "rot1", "rot2", "rot3"]
logger.info("maxdelta on %s : %s --> %s ",
d[i], self.param[i], newParam[i])
self.param = newParam
self.dist, self.poni1, self.poni2, \
self.rot1, self.rot2, self.rot3 = tuple(newParam)
return newDeltaSq
else:
return oldDeltaSq
def anneal(self, maxiter=1000000):
self.param = [self.dist, self.poni1, self.poni2,
self.rot1, self.rot2, self.rot3]
result = anneal(self.residu2, self.param,
args=(self.data[:, 0],
self.data[:, 1],
self.data[:, 2]),
lower=[self._dist_min,
self._poni1_min,
self._poni2_min,
self._rot1_min,
self._rot2_min,
self._rot3_min],
upper=[self._dist_max,
self._poni1_max,
self._poni2_max,
self._rot1_max,
self._rot2_max,
self._rot3_max],
maxiter=maxiter)
newParam = result[0]
oldDeltaSq = self.chi2() / self.data.shape[0]
newDeltaSq = self.chi2(newParam) / self.data.shape[0]
logger.info("Anneal %s --> %s", oldDeltaSq, newDeltaSq)
if newDeltaSq < oldDeltaSq:
i = abs(self.param - newParam).argmax()
d = ["dist", "poni1", "poni2", "rot1", "rot2", "rot3"]
logger.info("maxdelta on %s : %s --> %s ",
d[i], self.param[i], newParam[i])
self.param = newParam
self.dist, self.poni1, self.poni2, \
self.rot1, self.rot2, self.rot3 = tuple(newParam)
return newDeltaSq
else:
return oldDeltaSq
def chi2(self, param=None):
if param is None:
param = self.param[:]
return self.residu2(param,
self.data[:, 0], self.data[:, 1], self.data[:, 2])
def chi2_wavelength(self, param=None):
if param is None:
param = self.param
if len(param) == 6:
param.append(1e10 * self.wavelength)
return self.residu2_wavelength(param,
self.data[:, 0], self.data[:, 1], self.data[:, 2].astype(numpy.int32))
def roca(self):
"""
run roca to optimise the parameter set
"""
tmpf = tempfile.NamedTemporaryFile()
for line in self.data:
tmpf.write("%s %s %s %s" % (line[2], line[0], line[1], os.linesep))
tmpf.flush()
roca = subprocess.Popen(
[ROCA, "debug=8", "maxdev=1", "input=" + tmpf.name,
str(self.pixel1), str(self.pixel2),
str(self.poni1 / self.pixel1), str(self.poni2 / self.pixel2),
str(self.dist), str(self.rot1), str(self.rot2), str(self.rot3)],
stdout=subprocess.PIPE)
newParam = [self.dist, self.poni1, self.poni2,
self.rot1, self.rot2, self.rot3]
for line in roca.stdout:
word = line.split()
if len(word) == 3:
if word[0] == "cen1":
newParam[1] = float(word[1]) * self.pixel1
if word[0] == "cen2":
newParam[2] = float(word[1]) * self.pixel2
if word[0] == "dis":
newParam[0] = float(word[1])
if word[0] == "rot1":
newParam[3] = float(word[1])
if word[0] == "rot2":
newParam[4] = float(word[1])
if word[0] == "rot3":
newParam[5] = float(word[1])
print("Roca %s --> %s" % (self.chi2() / self.data.shape[0], self.chi2(newParam) / self.data.shape[0]))
if self.chi2(tuple(newParam)) < self.chi2(tuple(self.param)):
self.param = newParam
self.dist, self.poni1, self.poni2, \
self.rot1, self.rot2, self.rot3 = tuple(newParam)
tmpf.close()
def set_dist_max(self, value):
if isinstance(value, float):
self._dist_max = value
else:
self._dist_max = float(value)
def get_dist_max(self):
return self._dist_max
dist_max = property(get_dist_max, set_dist_max)
def set_dist_min(self, value):
if isinstance(value, float):
self._dist_min = value
else:
self._dist_min = float(value)
def get_dist_min(self):
return self._dist_min
dist_min = property(get_dist_min, set_dist_min)
def set_poni1_min(self, value):
if isinstance(value, float):
self._poni1_min = value
else:
self._poni1_min = float(value)
def get_poni1_min(self):
return self._poni1_min
poni1_min = property(get_poni1_min, set_poni1_min)
def set_poni1_max(self, value):
if isinstance(value, float):
self._poni1_max = value
else:
self._poni1_max = float(value)
def get_poni1_max(self):
return self._poni1_max
poni1_max = property(get_poni1_max, set_poni1_max)
def set_poni2_min(self, value):
if isinstance(value, float):
self._poni2_min = value
else:
self._poni2_min = float(value)
def get_poni2_min(self):
return self._poni2_min
poni2_min = property(get_poni2_min, set_poni2_min)
def set_poni2_max(self, value):
if isinstance(value, float):
self._poni2_max = value
else:
self._poni2_max = float(value)
def get_poni2_max(self):
return self._poni2_max
poni2_max = property(get_poni2_max, set_poni2_max)
def set_rot1_min(self, value):
if isinstance(value, float):
self._rot1_min = value
else:
self._rot1_min = float(value)
def get_rot1_min(self):
return self._rot1_min
rot1_min = property(get_rot1_min, set_rot1_min)
def set_rot1_max(self, value):
if isinstance(value, float):
self._rot1_max = value
else:
self._rot1_max = float(value)
def get_rot1_max(self):
return self._rot1_max
rot1_max = property(get_rot1_max, set_rot1_max)
def set_rot2_min(self, value):
if isinstance(value, float):
self._rot2_min = value
else:
self._rot2_min = float(value)
def get_rot2_min(self):
return self._rot2_min
rot2_min = property(get_rot2_min, set_rot2_min)
def set_rot2_max(self, value):
if isinstance(value, float):
self._rot2_max = value
else:
self._rot2_max = float(value)
def get_rot2_max(self):
return self._rot2_max
rot2_max = property(get_rot2_max, set_rot2_max)
def set_rot3_min(self, value):
if isinstance(value, float):
self._rot3_min = value
else:
self._rot3_min = float(value)
def get_rot3_min(self):
return self._rot3_min
rot3_min = property(get_rot3_min, set_rot3_min)
def set_rot3_max(self, value):
if isinstance(value, float):
self._rot3_max = value
else:
self._rot3_max = float(value)
def get_rot3_max(self):
return self._rot3_max
rot3_max = property(get_rot3_max, set_rot3_max)
def set_wavelength_min(self, value):
if isinstance(value, float):
self._wavelength_min = value
else:
self._wavelength_min = float(value)
def get_wavelength_min(self):
return self._wavelength_min
wavelength_min = property(get_wavelength_min, set_wavelength_min)
def set_wavelength_max(self, value):
if isinstance(value, float):
self._wavelength_max = value
else:
self._wavelength_max = float(value)
def get_wavelength_max(self):
return self._wavelength_max
wavelength_max = property(get_wavelength_max, set_wavelength_max)
|