test_normalization.py

# coding: utf-8
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__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "06/11/2019"


import unittest
from xas.core.process.normalization import pymca_normalization
from xas.core.types import Spectrum, XASObject
from xas.io.utils.pymca import read_spectrum
from xas.core.utils import spectra as spectra_utils
from xas.core.io import read as read_xas
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR
from silx.io.url import DataUrl
import os
import numpy
import tempfile
import shutil
import h5py


class TestNormalizationSingleSpectrum(unittest.TestCase):
    """Make sure the process have valid io"""
    def setUp(self):
        data_file = os.path.join(PYMCA_DATA_DIR, "EXAFS_Cu.dat")
        energy, mu = read_spectrum(data_file)
        self.spectrum = Spectrum(energy=energy, mu=mu)
        self.xas_obj = XASObject(spectra=(self.spectrum,), energy=energy,
                                 dim1=1, dim2=1)

    def testWithXASObjAsInput(self):
        res = pymca_normalization(xas_obj=self.xas_obj)
        self.assertTrue(isinstance(res, XASObject))
        self.assertTrue(isinstance(res.spectra, (tuple, list)))
        res_spectrum = res.spectra[0]
        self.assertTrue(isinstance(res_spectrum, Spectrum))
        self.assertTrue('NormalizedMu' in res_spectrum)
        self.assertTrue('NormalizedEnergy' in res_spectrum)
        self.assertTrue('NormalizedSignal' in res_spectrum)

    def testWithDictAsInput(self):
        res = pymca_normalization(xas_obj=self.xas_obj.to_dict())
        self.assertTrue(isinstance(res, XASObject))
        self.assertTrue('NormalizedMu' in res.spectra[0])
        self.assertTrue('NormalizedEnergy' in res.spectra[0])
        self.assertTrue('NormalizedSignal' in res.spectra[0])


class TestNormalizationMultipleSpectrum(unittest.TestCase):
    """"""
    def setUp(self):
        self.spectra = spectra_utils.create_dataset(shape=(256, 20, 10))
        self.energy = numpy.linspace(start=3.26, stop=3.96, num=256)
        self.output_dir = tempfile.mkdtemp()
        spectra_path = '/data/NXdata/data'
        channel_path = '/data/NXdata/Channel'
        filename = os.path.join(self.output_dir, 'myfile.h5')
        with h5py.File(filename) as f:
            f[spectra_path] = self.spectra
            f[channel_path] = self.energy

        self.xas_obj = read_xas(spectra_url=DataUrl(file_path=filename,
                                                    data_path=spectra_path,
                                                    scheme='silx'),
                                channel_url=DataUrl(file_path=filename,
                                                    data_path=channel_path,
                                                    scheme='silx'),
                                )

    def tearDown(self):
        shutil.rmtree(path=self.output_dir)

    def testWithXASObjAsInput(self):
        res = pymca_normalization(xas_obj=self.xas_obj)
        self.assertTrue(isinstance(res, XASObject))
        for spectrum in self.xas_obj.spectra:
            self.assertTrue('NormalizedMu' in spectrum)
            self.assertTrue('NormalizedEnergy' in spectrum)
            self.assertTrue('NormalizedSignal' in spectrum)

    def testWithDictAsInput(self):
        pass


def suite():
    test_suite = unittest.TestSuite()
    for ui in (TestNormalizationSingleSpectrum,
               TestNormalizationMultipleSpectrum):
        test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
    return test_suite


if __name__ == '__main__':
    unittest.main(defaultTest="suite")