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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 masked arrays"""
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "15/01/2021"
import unittest
import numpy
import logging
import fabio
from .utilstest import UtilsTest
logger = logging.getLogger(__name__)
if logger.getEffectiveLevel() <= logging.INFO:
import pylab
from .. import load, detectors
from ..azimuthalIntegrator import AzimuthalIntegrator
class TestMask(unittest.TestCase):
dataFile = "testMask.edf"
poniFile = "Pilatus1M.poni"
def setUp(self):
"""Download files"""
self.dataFile = UtilsTest.getimage(self.__class__.dataFile)
self.poniFile = UtilsTest.getimage(self.__class__.poniFile)
self.ai = load(self.poniFile)
self.data = fabio.open(self.dataFile).data
self.mask = self.data < 0
def tearDown(self):
unittest.TestCase.tearDown(self)
self.dataFile = self.data = self.ai = self.mask = self.poniFile = None
def test_mask_hist(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = ("no", "histogram", "cython")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="no mask")
pylab.plot(*x2, label="with mask")
pylab.plot(*x3, label="with dummy")
pylab.title("test_mask_splitBBox")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually Nan (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
def test_mask_splitBBox(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = ("bbox", "histogram", "cython")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="no mask")
pylab.plot(*x2, label="with mask")
pylab.plot(*x3, label="with dummy")
pylab.title("test_mask_splitBBox")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually Nan (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
def test_mask_splitfull(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = ("full", "histogram", "cython")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="no mask")
pylab.plot(*x2, label="with mask")
pylab.plot(*x3, label="with dummy")
pylab.title("test_mask_splitBBox")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually Nan (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
def test_mask_LUT(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = ("bbox", "lut", "cython")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, mask=numpy.zeros(shape=self.mask.shape, dtype="uint8"), dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="nomask")
pylab.plot(*x2, label="mask")
pylab.plot(*x3, label="dummy")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually Nan (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
def test_mask_CSR(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = meth = ("bbox", "csr", "cython")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, mask=numpy.zeros(shape=self.mask.shape, dtype="uint8"), dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="nomask")
pylab.plot(*x2, label="mask")
pylab.plot(*x3, label="dummy")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually Nan (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
@unittest.skipIf(UtilsTest.opencl is False, "User request to skip OpenCL tests")
def test_mask_LUT_OCL(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = ("bbox", "lut", "opencl")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="nomask")
pylab.plot(*x2, label="mask")
pylab.plot(*x3, label="dummy")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually around 0 (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
@unittest.skipIf(UtilsTest.opencl is False, "User request to skip OpenCL tests")
def test_mask_CSR_OCL(self):
"""
The masked image has a masked ring around 1.5deg with value -10
without mask the pixels should be at -10 ; with mask they are at 0
"""
meth = ("bbox", "csr", "opencl")
x1 = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method=meth)
x2 = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method=meth)
x3 = self.ai.integrate1d_ng(self.data, 1000, dummy=-20.0, delta_dummy=19.5, unit="2th_deg", method=meth)
res1 = numpy.interp(1.5, *x1)
res2 = numpy.interp(1.5, *x2)
res3 = numpy.interp(1.5, *x3)
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(*x1, label="nomask")
pylab.plot(*x2, label="mask")
pylab.plot(*x3, label="dummy")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(res1, -10., 1, msg="Without mask the bad pixels are around -10 (got %.4f)" % res1)
self.assertAlmostEqual(res2, 0, 1, msg="With mask the bad pixels are actually around 0 (got %.4f)" % res2)
self.assertAlmostEqual(res3, -20., 4, msg="Without mask but dummy=-20 the dummy pixels are actually at -20 (got % .4f)" % res3)
class TestMaskBeamstop(unittest.TestCase):
"""
Test for https://github.com/silx-kit/pyFAI/issues/76
"""
dataFile = "mock.tif"
def setUp(self):
"""
Download files
Create a mask for tth<3.7 deg
"""
self.dataFile = UtilsTest.getimage(self.__class__.dataFile)
detector = detectors.Detector(pixel1=0.0001, pixel2=0.0001)
self.ai = AzimuthalIntegrator(dist=0.1, poni1=0.03, poni2=0.03, detector=detector)
self.data = fabio.open(self.dataFile).data
self.tth, self.I = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg")
self.mask = self.ai.ttha < numpy.deg2rad(3.7)
def test_nomask(self):
"""
without mask, tth value should start at 0
"""
if logger.getEffectiveLevel() == logging.DEBUG:
pylab.plot(self.tth, self.I, label="nomask")
pylab.legend()
pylab.show()
input()
self.assertAlmostEqual(self.tth[0], 0.0, 1, "tth without mask starts at 0")
def test_mask_splitBBox(self):
"""
With a mask with and without limits
"""
tth, _ = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method="splitBBox")
self.assertAlmostEqual(tth[0], 3.7, 1, msg="tth range starts at 3.7 (got %.4f)" % tth[0])
tth, _ = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method="splitBBox", radial_range=[1, 10])
self.assertAlmostEqual(tth[0], 1.0, 1, msg="tth range should start at 1.0 (got %.4f)" % tth[0])
def test_mask_LUT(self):
"""
With a mask with and without limits
"""
tth, _ = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method="LUT")
self.assertAlmostEqual(tth[0], 3.7, 1, msg="tth range starts at 3.7 (got %.4f)" % tth[0])
tth, _ = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method="LUT", radial_range=[1, 10])
self.assertAlmostEqual(tth[0], 1.0, 1, msg="tth range should start at 1.0 (got %.4f)" % tth[0])
@unittest.skipIf(UtilsTest.opencl is False, "User request to skip OpenCL tests")
def test_mask_LUT_OCL(self):
"""
With a mask with and without limits
"""
tth, _ = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method="lut_ocl")
self.assertTrue(tth[0] > 3.5, msg="tth range starts at 3.7 (got %.4f)" % tth[0])
tth, _ = self.ai.integrate1d_ng(self.data, 1000, mask=self.mask, unit="2th_deg", method="lut_ocl", radial_range=[1, 10])
self.assertAlmostEqual(tth[0], 1.0, 1, msg="tth range should start at 1.0 (got %.4f)" % tth[0])
def test_nomask_LUT(self):
"""
without mask, tth value should start at 0
"""
tth, _ = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method="lut")
self.assertAlmostEqual(tth[0], 0.0, 1, msg="tth range starts at 3.7 (got %.4f)" % tth[0])
tth, _ = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method="lut", radial_range=[1, 10])
self.assertAlmostEqual(tth[0], 1.0, 1, msg="tth range should start at 1.0 (got %.4f)" % tth[0])
@unittest.skipIf(UtilsTest.opencl is False, "User request to skip OpenCL tests")
def test_nomask_LUT_OCL(self):
"""
without mask, tth value should start at 0
"""
tth, _ = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method="lut_ocl")
self.assertAlmostEqual(tth[0], 0.0, 1, msg="tth range starts at 3.7 (got %.4f)" % tth[0])
tth, _ = self.ai.integrate1d_ng(self.data, 1000, unit="2th_deg", method="lut_ocl", radial_range=[1, 10])
self.assertAlmostEqual(tth[0], 1.0, 1, msg="tth range should start at 1.0 (got %.4f)" % tth[0])
def suite():
testsuite = unittest.TestSuite()
loader = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite.addTest(loader(TestMask))
testsuite.addTest(loader(TestMaskBeamstop))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
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