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#!/usr/bin/env python
# coding: utf-8
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2015-2018 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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.
"""Test suites for calibrants"""
__author__ = "Jérôme Kieffer"
__contact__ = "Jérôme.Kieffer@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "16/10/2020"
import unittest
import logging
import sys
import copy
import numpy
from .utilstest import UtilsTest
logger = logging.getLogger(__name__)
from ..calibrant import Calibrant, get_calibrant, Cell, CALIBRANT_FACTORY
from ..detectors import ALL_DETECTORS
from ..azimuthalIntegrator import AzimuthalIntegrator
class TestCalibrant(unittest.TestCase):
"""
Test calibrant installation and loading
"""
def test_factory(self):
# by default we provide 11 calibrants
count = len(CALIBRANT_FACTORY)
self.assertTrue(count > 10, "at least 11 calibrants are available, got %s" % count)
self.assertTrue("LaB6" in CALIBRANT_FACTORY, "LaB6 is a calibrant")
# ensure each calibrant instance is unique
cal1 = get_calibrant("LaB6")
cal1.wavelength = 1e-10
cal2 = get_calibrant("LaB6")
self.assertTrue(cal2.wavelength is None, "calibrant is delivered without wavelength")
# check that it is possible to instantiate all calibrant
for _k, v in CALIBRANT_FACTORY.items():
self.assertTrue(isinstance(v, Calibrant))
def test_2th(self):
lab6 = get_calibrant("LaB6")
lab6.wavelength = 1.54e-10
tth = lab6.get_2th()
self.assertEqual(len(tth), 25, "We expect 25 rings for LaB6")
lab6.setWavelength_change2th(1e-10)
tth = lab6.get_2th()
self.assertEqual(len(tth), 59, "We expect 59 rings for LaB6")
lab6.setWavelength_change2th(2e-10)
tth = lab6.get_2th()
self.assertEqual(len(tth), 15, "We expect 15 rings for LaB6")
self.assertEqual(lab6.get_2th_index(1.0, 0.04), 3, "right index picked")
def test_fake(self):
"""test for fake image generation"""
detectors = set(ALL_DETECTORS.values())
for _idx, detector in enumerate(detectors):
det = detector()
# Skip generic detectors
if "MAX_SHAPE" not in dir(det):
continue
# skip the big detectors for now
if max(det.MAX_SHAPE) > 2000:
continue
ai = AzimuthalIntegrator(dist=0.01, poni1=0, poni2=0, detector=det)
calibrant = get_calibrant("LaB6")
calibrant.set_wavelength(1e-10)
img = calibrant.fake_calibration_image(ai)
logger.info("%s min: %s max: %s ", det.name, img.min(), img.max())
self.assertTrue(img.shape == det.shape, "Image (%s) has the right size" % (det.name,))
self.assertTrue(img.sum() > 0, "Image (%s) contains some data" % (det.name,))
sys.stderr.write(".")
def test_get_peaks(self):
calibrant = get_calibrant("LaB6")
calibrant.wavelength = 1e-10
ref = calibrant.get_2th()
delta = abs(calibrant.get_peaks() - numpy.rad2deg(ref))
self.assertLess(delta.max(), 1e-10, "results are the same")
self.assertEqual(len(calibrant.get_peaks("q_A^-1")), len(ref), "length is OK")
def test_amount_of_calibrant(self):
c = get_calibrant("LaB6")
nb = c.count_registered_dSpacing()
c.setWavelength_change2th(0.00000000002)
c.setWavelength_change2th(0.0000000002)
c.setWavelength_change2th(0.00000000002)
c.setWavelength_change2th(0.0000000002)
self.assertEqual(c.count_registered_dSpacing(), nb)
def test_factory_create_calibrant(self):
c1 = get_calibrant("LaB6")
c2 = get_calibrant("LaB6")
self.assertIsNot(c1, c2)
self.assertEquals(c1, c2)
def test_same(self):
c1 = get_calibrant("LaB6")
c2 = get_calibrant("LaB6")
self.assertEquals(c1, c2)
def test_same2(self):
c1 = get_calibrant("LaB6")
c2 = get_calibrant("LaB6")
c1.set_wavelength(1e-10)
c2.set_wavelength(1e-10)
self.assertEquals(c1, c2)
def test_not_same_dspace(self):
# this 2 calibrant must only be used there to test the lazy-loading
c1 = get_calibrant("LaB6_SRM660a")
c2 = get_calibrant("LaB6_SRM660b")
self.assertNotEquals(c1, c2)
def test_not_same_wavelength(self):
c1 = get_calibrant("LaB6")
c1.set_wavelength(1e-10)
c2 = get_calibrant("LaB6")
self.assertNotEquals(c1, c2)
def test_copy(self):
c1 = get_calibrant("AgBh")
c2 = copy.copy(c1)
self.assertIsNot(c1, c2)
self.assertEquals(c1, c2)
c2.set_wavelength(1e-10)
self.assertNotEquals(c1, c2)
def test_hash(self):
c1 = get_calibrant("AgBh")
c2 = get_calibrant("AgBh")
c3 = get_calibrant("AgBh")
c3.set_wavelength(1e-10)
c4 = get_calibrant("LaB6")
store = {}
store[c1] = True
self.assertTrue(c1 in store)
self.assertTrue(c2 in store)
self.assertTrue(c3 not in store)
self.assertTrue(c4 not in store)
class TestCell(unittest.TestCase):
"""
Test generation of a calibrant from a cell
"""
def test_class(self):
c = Cell()
self.assertAlmostEqual(c.volume, 1.0, msg="Volume of triclinic 1,1,1,90,90,90 == 1.0, got %s" % c.volume)
c = Cell(1, 2, 3)
self.assertAlmostEqual(c.volume, 6.0, msg="Volume of triclinic 1,2,3,90,90,90 == 6.0, got %s" % c.volume)
c = Cell(1, 2, 3, 90, 30, 90)
self.assertAlmostEqual(c.volume, 3.0, msg="Volume of triclinic 1,2,3,90,30,90 == 3.0, got %s" % c.volume)
def test_classmethods(self):
c = Cell.cubic(1)
self.assertAlmostEqual(c.volume, 1.0, msg="Volume of cubic 1 == 1.0, got %s" % c.volume)
c = Cell.tetragonal(2, 3)
self.assertAlmostEqual(c.volume, 12.0, msg="Volume of tetragonal 2,3 == 12.0, got %s" % c.volume)
c = Cell.orthorhombic(1, 2, 3)
self.assertAlmostEqual(c.volume, 6.0, msg="Volume of orthorhombic 1,2,3 == 6.0, got %s" % c.volume)
def test_dspacing(self):
c = Cell.cubic(1)
cd = c.d_spacing(0.1)
cds = list(cd.keys())
cds.sort()
t = Cell()
td = t.d_spacing(0.1)
tds = list(td.keys())
tds.sort()
self.assertEquals(cds, tds, msg="d-spacings are the same")
for k in cds:
self.assertEquals(cd[k], td[k], msg="plans are the same for d=%s" % k)
def test_helium(self):
# self.skipTest("Not working")
a = 4.242
href = "A.F. Schuch and R.L. Mills, Phys. Rev. Lett., 1961, 6, 596."
he = Cell.cubic(a)
self.assertTrue(len(he.d_spacing(1)) == 15, msg="got 15 lines for He")
he.save("He", "Helium", href, 1.0, UtilsTest.tempdir)
def test_hydrogen(self):
# self.skipTest("Not working")
href = "DOI: 10.1126/science.239.4844.1131"
h = Cell.hexagonal(2.6590, 4.3340)
self.assertAlmostEqual(h.volume, 26.537, places=3, msg="Volume for H cell is correct")
self.assertTrue(len(h.d_spacing(1)) == 14, msg="got 14 lines for H")
h.save("H", "Hydrogen", href, 1.0, UtilsTest.tempdir)
def suite():
loader = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loader(TestCalibrant))
testsuite.addTest(loader(TestCell))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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