test_spectra.py 3.02 KB
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# coding: utf-8
# /*##########################################################################
#
# Copyright (c) 2017-2019 European Synchrotron Radiation Facility
#
# 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.
#
# ###########################################################################*/
__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "06/26/2019"


import tempfile
import os
import unittest
from est.core.types import Spectrum
from est.core.utils import spectra as spectra_utils
from est.core.types import XASObject
import shutil

try:
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PEP8    
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    import PyMca5  # noqa
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except ImportError:
    has_pymca = False
else:
    has_pymca = True
    from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR
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    from est.io.utils.spec import read_spectrum
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class TestSpectra(unittest.TestCase):
    """Test the spectrum class"""

    def setUp(self) -> None:
        self._tmp_dir = tempfile.mkdtemp()

    def tearDown(self) -> None:
        shutil.rmtree(self._tmp_dir)

    @unittest.skipIf(has_pymca is False, "PyMca5 is not installed")
    def test_from_dat(self):
        """check that we can create a Spectrum from a pymca .dat file"""
        data_file = os.path.join(PYMCA_DATA_DIR, "EXAFS_Cu.dat")
        energy, mu = read_spectrum(
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            data_file,
            energy_col_name="Column 1",
            absorption_col_name="Column 2",
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        )
        spectrum = Spectrum(energy=energy, mu=mu)

        self.assertTrue(spectrum.energy is not None)
        self.assertTrue(spectrum.mu is not None)

    def test_from_mock(self):
        """check that we can create a Spectrum from numpy arrays"""
        self.output_dir = tempfile.mkdtemp()
        energy, spectra = spectra_utils.create_dataset(shape=(256, 20, 10))
        self.xas_obj = XASObject(spectra=spectra, energy=energy, dim1=20, dim2=10)
        spectra = self.xas_obj.spectra
        self.assertEqual(self.xas_obj.n_spectrum, 20 * 10)
        self.assertEqual(self.xas_obj.n_spectrum, 20 * 10)
        spectra.keys()
        self.assertTrue(spectra.data.flat[0] == spectra[0, 0])
        spectra.map_to("mu")