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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 suite for non regression on some bugs.
Please refer to their respective bug number
https://github.com/silx-kit/pyFAI/issues
"""
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@esrf.fr"
__license__ = "MIT"
__copyright__ = "2015-2018 European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "01/02/2021"
import sys
import os
import unittest
import numpy
import subprocess
import logging
from .utilstest import UtilsTest
logger = logging.getLogger(__name__)
import fabio
from .. import load
from ..azimuthalIntegrator import AzimuthalIntegrator
from .. import detectors
from .. import units
from math import pi
try:
import importlib.util
if "module_from_spec" not in dir(importlib.util):
raise ImportError
except ImportError:
import importlib
def load_source(module_name, file_path):
"""Plugin loader which does not pollute sys.module,
Not as powerful as the v3.5+
"""
return importlib.import_module(module_name, module_name.split(".")[0])
else:
def load_source(module_name, file_path):
"""Plugin loader which does not pollute sys.module,
Python Version >=3.5"""
spec = importlib.util.spec_from_file_location(module_name, file_path)
module = importlib.util.module_from_spec(spec)
spec.loader.exec_module(module)
return module
class TestBug170(unittest.TestCase):
"""
Test a mar345 image with 2300 pixels size
"""
def setUp(self):
ponitxt = """
Detector: Mar345
PixelSize1: 0.00015
PixelSize2: 0.00015
Distance: 0.446642915189
Poni1: 0.228413453499
Poni2: 0.272291324302
Rot1: 0.0233130647508
Rot2: 0.0011735285628
Rot3: -7.22446379865e-08
SplineFile: None
Wavelength: 7e-11
"""
self.ponifile = os.path.join(UtilsTest.tempdir, "bug170.poni")
with open(self.ponifile, "w") as poni:
poni.write(ponitxt)
self.data = numpy.random.random((2300, 2300))
def tearDown(self):
if os.path.exists(self.ponifile):
os.unlink(self.ponifile)
self.data = None
@unittest.skipIf(UtilsTest.low_mem, "test using >100Mb")
def test_bug170(self):
ai = load(self.ponifile)
logger.debug(ai.mask.shape)
logger.debug(ai.detector.pixel1)
logger.debug(ai.detector.pixel2)
ai.integrate1d_ng(self.data, 2000)
class TestBug211(unittest.TestCase):
"""
Check the quantile filter in pyFAI-average
"""
def setUp(self):
shape = (100, 100)
dtype = numpy.float32
self.image_files = []
self.outfile = os.path.join(UtilsTest.tempdir, "out.edf")
res = numpy.zeros(shape, dtype=dtype)
for i in range(5):
fn = os.path.join(UtilsTest.tempdir, "img_%i.edf" % i)
if i == 3:
data = numpy.zeros(shape, dtype=dtype)
elif i == 4:
data = numpy.ones(shape, dtype=dtype)
else:
data = numpy.random.random(shape).astype(dtype)
res += data
e = fabio.edfimage.edfimage(data=data)
e.write(fn)
self.image_files.append(fn)
self.res = res / 3.0
# It is not anymore a script, but a module
import pyFAI.app.average
self.exe = pyFAI.app.average.__file__
self.env = UtilsTest.get_test_env()
def tearDown(self):
for fn in self.image_files:
os.unlink(fn)
if os.path.exists(self.outfile):
os.unlink(self.outfile)
self.image_files = None
self.res = None
self.exe = self.env = None
def test_quantile(self):
command_line = [sys.executable, self.exe, "--quiet", "-q", "0.2-0.8", "-o", self.outfile] + self.image_files
p = subprocess.Popen(command_line,
shell=False, env=self.env,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
rc = p.wait()
if rc:
logger.info(p.stdout.read())
logger.error(p.stderr.read())
logger.error(os.linesep + (" ".join(command_line)))
env = "Environment:"
for k, v in self.env.items():
env += "%s %s: %s" % (os.linesep, k, v)
logger.error(env)
self.fail()
if fabio.hexversion < 262147:
logger.error("Error: the version of the FabIO library is too old: %s, please upgrade to 0.4+. Skipping test for now", fabio.version)
return
self.assertEqual(rc, 0, msg="pyFAI-average return code %i != 0" % rc)
self.assertTrue(numpy.allclose(fabio.open(self.outfile).data, self.res),
"pyFAI-average with quantiles gives good results")
class TestBugRegression(unittest.TestCase):
"just a bunch of simple tests"
def test_bug_232(self):
"""
Check the copy and deepcopy methods of Azimuthal integrator
"""
det = detectors.ImXPadS10()
ai = AzimuthalIntegrator(dist=1, detector=det)
data = numpy.random.random(det.shape)
_result = ai.integrate1d_ng(data, 100, unit="r_mm")
import copy
ai2 = copy.copy(ai)
self.assertNotEqual(id(ai), id(ai2), "copy instances are different")
self.assertEqual(id(ai.ra), id(ai2.ra), "copy arrays are the same after copy")
self.assertEqual(id(ai.detector), id(ai2.detector), "copy detector are the same after copy")
ai3 = copy.deepcopy(ai)
self.assertNotEqual(id(ai), id(ai3), "deepcopy instances are different")
self.assertNotEqual(id(ai.ra), id(ai3.ra), "deepcopy arrays are different after copy")
self.assertNotEqual(id(ai.detector), id(ai3.detector), "deepcopy arrays are different after copy")
def test_bug_174(self):
"""
wavelength change not taken into account (memoization error)
"""
ai = load(UtilsTest.getimage("Pilatus1M.poni"))
data = fabio.open(UtilsTest.getimage("Pilatus1M.edf")).data
wl1 = 1e-10
wl2 = 2e-10
ai.wavelength = wl1
q1, i1 = ai.integrate1d_ng(data, 1000)
# ai.reset()
ai.wavelength = wl2
q2, i2 = ai.integrate1d_ng(data, 1000)
dq = (abs(q1 - q2).max())
_di = (abs(i1 - i2).max())
# print(dq)
self.assertAlmostEqual(dq, 3.79, 2, "Q-scale difference should be around 3.8, got %s" % dq)
def test_bug_758(self):
"""check the stored "h*c" constant is almost 12.4"""
hc = 12.398419292004204 # Old reference value from pyFAI
hc = 12.398419739640717 # calculated from scipy 1.3
self.assertAlmostEqual(hc, units.hc, 6, "hc is correct, got %s" % units.hc)
def test_import_all_modules(self):
"""Try to import every single module in the package
"""
import pyFAI
pyFAI_root = os.path.split(pyFAI.__file__)[0]
def must_be_skipped(path):
path = os.path.relpath(path, pyFAI_root)
path = path.replace("\\", "/")
elements = path.split("/")
if "test" in elements:
# Always skip test modules
logger.warning("Skip test module %s", path)
return True
if not UtilsTest.WITH_OPENCL_TEST:
if "opencl" in elements:
logger.warning("Skip %s. OpenCL tests disabled", path)
return True
if not UtilsTest.WITH_QT_TEST:
if "gui" in elements:
logger.warning("Skip %s. Qt tests disabled", path)
return True
return False
for root, dirs, files in os.walk(pyFAI_root, topdown=True):
for adir in dirs:
subpackage_path = os.path.join(root, adir, "__init__.py")
if must_be_skipped(subpackage_path):
continue
subpackage = "pyFAI" + subpackage_path[len(pyFAI_root):-12].replace(os.sep, ".")
if os.path.isdir(subpackage_path):
logger.info("Loading subpackage: %s from %s", subpackage, subpackage_path)
sys.modules[subpackage] = load_source(subpackage, subpackage_path)
for name in files:
if not name.endswith(".py"):
continue
path = os.path.join(root, name)
if must_be_skipped(path):
continue
fqn = "pyFAI" + path[len(pyFAI_root):-3].replace(os.sep, ".")
logger.info("Importing %s from %s", fqn, path)
try:
load_source(fqn, path)
except Exception as err:
if ((isinstance(err, ImportError) and
"No Qt wrapper found" in err.__str__() or
"pyopencl is not installed" in err.__str__() or
"PySide" in err.__str__()) or
(isinstance(err, SystemError) and
"Parent module" in err.__str__())):
logger.info("Expected failure importing %s from %s with error: %s",
fqn, path, err)
else:
logger.error("Failed importing %s from %s with error: %s%s: %s",
fqn, path, os.linesep,
err.__class__.__name__, err)
raise err
def test_bug_816(self):
"Ensure the chi-disontinuity is properly set"
detector = detectors.detector_factory("Pilatus 300k")
positions = detector.get_pixel_corners()
# y_min = positions[..., 1].min()
y_max = positions[..., 1].max()
# x_min = positions[..., 0].min()
x_max = positions[..., 2].max()
expected = { # poni -> azimuthal range in both convention
(0, 0): [(0, pi / 2), (0, pi / 2)],
(y_max / 2, x_max / 2): [(-pi, pi), (0, 2 * pi)],
(y_max, 0): [(-pi / 2, 0), (3 * pi / 2, 2 * pi)],
(0, x_max): [(pi / 2, pi), (pi / 2, pi)],
(y_max, x_max): [(-pi, -pi / 2), (pi, 3 * pi / 2)],
}
for poni, chi_range in expected.items():
logger.debug("%s, %s", poni, chi_range)
ai = AzimuthalIntegrator(0.1, *poni, detector=detector)
chi_pi_center = ai.chiArray()
logger.debug("disc @pi center: poni: %s; expected: %s; got: %.2f, %.2f", poni, chi_range, chi_pi_center.min(), chi_pi_center.max())
chi_pi_corner = ai.array_from_unit(typ="corner", unit="r_m", scale=False)[1:-1, 1:-1,:, 1]
logger.debug("disc @pi corner: poni: %s; expected: %s; got: %.2f, %.2f", poni, chi_range, chi_pi_corner.min(), chi_pi_corner.max())
self.assertAlmostEquals(chi_pi_center.min(), chi_range[0][0], msg="chi_pi_center.min", delta=0.1)
self.assertAlmostEquals(chi_pi_corner.min(), chi_range[0][0], msg="chi_pi_corner.min", delta=0.1)
self.assertAlmostEquals(chi_pi_center.max(), chi_range[0][1], msg="chi_pi_center.max", delta=0.1)
self.assertAlmostEquals(chi_pi_corner.max(), chi_range[0][1], msg="chi_pi_corner.max", delta=0.1)
ai.reset()
ai.setChiDiscAtZero()
logger.debug("Updated range %s %s %s %s", chi_range[0], chi_range[1], ai.chiDiscAtPi, list(ai._cached_array.keys()))
chi_0_center = ai.chiArray()
logger.debug("disc @0 center: poni: %s; expected: %s; got: %.2f, %.2f", poni, chi_range[1], chi_0_center.min(), chi_0_center.max())
chi_0_corner = ai.array_from_unit(typ="corner", unit="r_m", scale=False)[1:-1, 1:-1,:, 1] # Discard pixel from border...
logger.debug("disc @0 corner: poni: %s; expected: %s; got: %.2f, %.2f", poni, chi_range[1], chi_0_corner.min(), chi_0_corner.max())
dmin = lambda v: v - chi_range[1][0]
dmax = lambda v: v - chi_range[1][1]
self.assertAlmostEquals(dmin(chi_0_center.min()), 0, msg="chi_0_center.min", delta=0.1)
self.assertAlmostEquals(dmin(chi_0_corner.min()), 0, msg="chi_0_corner.min", delta=0.1)
self.assertAlmostEquals(dmax(chi_0_center.max()), 0, msg="chi_0_center.max", delta=0.1)
self.assertAlmostEquals(dmax(chi_0_corner.max()), 0, msg="chi_0_corner.max", delta=0.1)
def test_bug_924(self):
"Regression on spline calculation for single pixel coordinate"
dp = detectors.detector_factory("Pilatus100k")
aip = AzimuthalIntegrator(detector=dp)
aip.chi(numpy.array([1, 2]), numpy.array([3, 4]))
aip.chi(numpy.array([1]), numpy.array([3]))
# so far, so good
df = detectors.detector_factory("Frelon",
{"splineFile": UtilsTest.getimage("frelon.spline")})
print(df.spline.splineFuncX(numpy.array([1, 2]), numpy.array([3, 4]), True))
aif = AzimuthalIntegrator(detector=df)
aif.chi(numpy.array([1, 2]), numpy.array([3, 4]))
aif.chi(numpy.array([1]), numpy.array([3]))
def test_bug_1275(self):
"This bug about major sectors not taken into account when performing intgrate1d on small azimuthal sectors"
shape = (128, 128)
detector = detectors.Detector(100e-4, 100e-4, max_shape=shape)
ai = AzimuthalIntegrator(detector=detector, wavelength=1e-10)
ai.setFit2D(1000, shape[1] / 2, shape[0] / 2)
data = numpy.ones(shape)
nb_pix = ai.integrate1d_ng(data, 100).count.sum()
self.assertAlmostEqual(nb_pix, numpy.prod(shape), msg="All pixels are counted", delta=0.01)
delta = 45
target = numpy.prod(shape) / 360 * 2 * delta
ai.setChiDiscAtPi()
angles = numpy.arange(-180, 400, 90)
for method in [("no", "histogram", "python"),
("no", "histogram", "cython"),
("no", "csr", "cython"),
("no", "lut", "cython")]:
# print(method)
for angle in angles:
res = ai.integrate1d_ng(data, 100, azimuth_range=(angle - delta, angle + delta), method=method)
# print(res.compute_engine, res.count)
res = res.count.sum()
if angle in (-180, 180):
# We expect only half of the pixel
self.assertLess(abs(res / target - 0.5), 0.1, "ChiDiscAtPi we expect half the pixels to be missing %s %s %s=%s/2" % (method, angle, res, target))
else:
self.assertLess(abs(res / target - 1), 0.1, "ChiDiscAtPi we expect the pixel to be present %s %s %s=%s" % (method, angle, res, target))
# Now with the azimuthal integrator set with the chi discontinuity at 0
ai.setChiDiscAtZero()
for method in [("no", "histogram", "python"),
("no", "histogram", "cython"),
("no", "csr", "cython"),
("no", "lut", "cython")]:
# print(method)
for angle in angles:
res = ai.integrate1d_ng(data, 100, azimuth_range=(angle - delta, angle + delta), method=method).count.sum()
if angle in (0, 360):
# We expect only half of the pixel
self.assertLess(abs(res / target - 0.5), 0.1, "ChiDiscAtZero we expect half the pixels to be missing %s %s %s=%s/2" % (method, angle, res, target))
else:
self.assertLess(abs(res / target - 1), 0.1, "ChiDiscAtZero we expect the pixel to be present method:%s angle:%s expected:%s=%s" % (method, angle, target, res))
def test_bug_1421(self):
"""This bug is about geometry refinement not working with SAXS-constrains in certain conditions
Inspired by the Recalib tutorial
"""
from .. import geometry
from ..calibrant import CALIBRANT_FACTORY
from ..goniometer import SingleGeometry
filename = UtilsTest.getimage("Pilatus1M.edf")
frame = fabio.open(filename).data
# Approximatively the position of the beam center ...
x = 200 # x-coordinate of the beam-center in pixels
y = 300 # y-coordinate of the beam-center in pixels
d = 1600 # This is the distance in mm (unit used by Fit2d)
wl = 1e-10 # The wavelength is 1 Å
# Definition of the detector and of the calibrant:
pilatus = detectors.detector_factory("Pilatus1M")
behenate = CALIBRANT_FACTORY("AgBh")
behenate.wavelength = wl
# Set the guessed geometry
initial = geometry.Geometry(detector=pilatus, wavelength=wl)
initial.setFit2D(d, x, y)
# print(initial)
# The SingleGeometry object (from goniometer) allows to extract automatically ring and calibrate
sg = SingleGeometry("demo", frame, calibrant=behenate, detector=pilatus, geometry=initial)
sg.extract_cp(max_rings=5)
# Refine the geometry ... here in SAXS geometry, the rotation is fixed in orthogonal setup
sg.geometry_refinement.refine2(fix=["rot1", "rot2", "rot3", "wavelength"])
refined = sg.get_ai()
self.assertNotEqual(initial.dist, refined.dist, "Distance got refined")
self.assertNotEqual(initial.poni1, refined.poni1, "Poni1 got refined")
self.assertNotEqual(initial.poni2, refined.poni2, "Poni2 got refined")
self.assertEqual(initial.rot1, refined.rot1, "Rot1 is unchanged")
self.assertEqual(initial.rot2, refined.rot2, "Rot2 is unchanged")
self.assertEqual(initial.rot3, refined.rot3, "Rot3 is unchanged")
self.assertEqual(initial.wavelength, refined.wavelength, "Wavelength is unchanged")
sg.geometry_refinement.refine2(fix=[])
# print(refined)
refined2 = sg.get_ai()
self.assertNotEqual(refined2.dist, refined.dist, "Distance got refined")
self.assertNotEqual(refined2.poni1, refined.poni1, "Poni1 got refined")
self.assertNotEqual(refined2.poni2, refined.poni2, "Poni2 got refined")
self.assertNotEqual(refined2.rot1, refined.rot1, "Rot1 got refined")
self.assertNotEqual(refined2.rot2, refined.rot2, "Rot2 got refined")
# self.assertNotEqual(refined2.rot3, refined.rot3, "Rot3 got refined") #Rot can change or not ...
self.assertEqual(refined2.wavelength, refined.wavelength, "Wavelength is unchanged (refine2)")
# print(refined2)
# raise
sg.geometry_refinement.refine3(fix=[])
# print(refined)
refined2 = sg.get_ai()
self.assertNotEqual(refined2.dist, refined.dist, "Distance got refined")
self.assertNotEqual(refined2.poni1, refined.poni1, "Poni1 got refined")
self.assertNotEqual(refined2.poni2, refined.poni2, "Poni2 got refined")
self.assertNotEqual(refined2.rot1, refined.rot1, "Rot1 got refined")
self.assertNotEqual(refined2.rot2, refined.rot2, "Rot2 got refined")
# self.assertNotEqual(refined2.rot3, refined.rot3, "Rot3 got refined")
self.assertNotEqual(refined2.wavelength, refined.wavelength, "Wavelength got refined (refine3)")
def suite():
loader = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loader(TestBug170))
testsuite.addTest(loader(TestBug211))
testsuite.addTest(loader(TestBugRegression))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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