test_io.py

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


import unittest
from est.core.types import Dim
from est.core.io import XASReader
from silx.io.url import DataUrl
from est.core.types import XASObject
from est.units import ur
import numpy
import os
import tempfile
import h5py
import shutil


class TestSpectraDimensions(unittest.TestCase):
    """
    Test reading spectra with different dimensions organisation
    (X, Y, Channels), (Channels, Y, X), (Y, Channels, X)
    """

    def setUp(self) -> None:
        self.spectra_path = "/data/NXdata/data"
        self.channel_path = "/data/NXdata/Channel"
        self.output_dir = tempfile.mkdtemp()
        self.filename = os.path.join(self.output_dir, "myfile.h5")

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

    def saveSpectra(self, spectra):
        """Save the spectra to the spectra file defined in setup and return the
        associated silx url"""
        with h5py.File(self.filename, "a") as f:
            f[self.spectra_path] = spectra

        return DataUrl(
            file_path=self.filename, data_path=self.spectra_path, scheme="silx"
        )

    def saveChannel(self, channel):
        """Save the energy to the spectra file defined in setup and return the
        associated silx url"""
        with h5py.File(self.filename, "a") as f:
            f[self.channel_path] = channel

        return DataUrl(
            file_path=self.filename, data_path=self.channel_path, scheme="silx"
        )

    def testDimensionsXYEnergy(self):
        """Test that spectra stored as X, Y Energy can be read"""
        x_dim = 4
        y_dim = 2
        energy_dim = 3
        shape = (x_dim, y_dim, energy_dim)
        spectra = numpy.arange(x_dim * y_dim * energy_dim).reshape(shape)
        channel = numpy.linspace(0, 1, energy_dim)
        spectra_url = self.saveSpectra(spectra)
        channel_url = self.saveChannel(channel=channel)

        # if dims are incoherent with energy, should raise an error
        dims = (Dim.CHANNEL_ENERGY_DIM, Dim.Y_DIM, Dim.X_DIM)
        with self.assertRaises(ValueError):
            XASReader().read_frm_url(
                spectra_url=spectra_url, channel_url=channel_url, dimensions=dims
            )

        dims = (Dim.X_DIM, Dim.Y_DIM, Dim.CHANNEL_ENERGY_DIM)
        xas_obj = XASReader().read_frm_url(
            spectra_url=spectra_url, channel_url=channel_url, dimensions=dims
        )
        self.assertTrue(isinstance(xas_obj, XASObject))
        self.assertTrue(xas_obj.n_spectrum == x_dim * y_dim)
        numpy.testing.assert_array_equal(xas_obj.spectra[1].mu, spectra[1, 0, :])
        numpy.testing.assert_array_equal(xas_obj.spectra[2].energy, channel)

    def testDimensionsChannelYX(self):
        """Test that spectra stored as Channel, Y, X can be read"""
        x_dim = 10
        y_dim = 5
        energy_dim = 30
        shape = (energy_dim, y_dim, x_dim)
        spectra = numpy.arange(x_dim * y_dim * energy_dim).reshape(shape)
        channel = numpy.linspace(0, 100, energy_dim)
        spectra_url = self.saveSpectra(spectra)
        channel_url = self.saveChannel(channel=channel)

        # if dims are incoherent with energy, should raise an error
        dims = (Dim.X_DIM, Dim.Y_DIM, Dim.CHANNEL_ENERGY_DIM)
        with self.assertRaises(ValueError):
            XASReader().read_frm_url(
                spectra_url=spectra_url, channel_url=channel_url, dimensions=dims
            )

        dims = (Dim.CHANNEL_ENERGY_DIM, Dim.Y_DIM, Dim.X_DIM)
        xas_obj = XASReader().read_frm_url(
            spectra_url=spectra_url, channel_url=channel_url, dimensions=dims
        )
        self.assertTrue(isinstance(xas_obj, XASObject))
        self.assertTrue(xas_obj.n_spectrum == x_dim * y_dim)
        numpy.testing.assert_array_equal(xas_obj.spectra[1].mu, spectra[:, 0, 1])
        numpy.testing.assert_array_equal(xas_obj.spectra[2].energy.m,
                                         (channel * ur.eV).m)


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


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