"""
Tests for reading spectra with different dimensions organisation
(X, Y, Channels), (Channels, Y, X), (Y, Channels, X)
"""
import warnings
import h5py
import numpy
import pytest
from silx.io.url import DataUrl
from ..core.io.read_xas import read_from_url
from ..core.types.xasobject import XASObject
from ..core.units import ur
[docs]
@pytest.fixture()
def testDimensionsXYEnergy(tmpdir):
"""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 = saveSpectra(tmpdir, spectra)
channel_url = saveChannel(tmpdir, channel=channel)
# if dims are incoherent with energy, should raise an error
dims = (2, 1, 0)
with pytest.raises(ValueError):
read_from_url(spectra_url=spectra_url, channel_url=channel_url, dimensions=dims)
dims = (0, 1, 2)
xas_obj = read_from_url(
spectra_url=spectra_url, channel_url=channel_url, dimensions=dims
)
assert isinstance(xas_obj, XASObject)
assert xas_obj.n_spectrum == x_dim * y_dim
numpy.testing.assert_array_equal(xas_obj.spectra.data.flat[1].mu, spectra[1, 0, :])
numpy.testing.assert_array_equal(xas_obj.spectra.data.flat[2].energy, channel)
[docs]
@pytest.fixture()
def testDimensionsChannelYX(tmpdir):
"""Test that spectra stored as Energy, 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 = saveSpectra(tmpdir, spectra)
channel_url = saveChannel(tmpdir, channel=channel)
# if dims are incoherent with energy, should raise an error
dims = (0, 1, 2)
with warnings.catch_warnings(record=True):
read_from_url(spectra_url=spectra_url, channel_url=channel_url, dimensions=dims)
dims = (2, 1, 0)
xas_obj = read_from_url(
spectra_url=spectra_url, channel_url=channel_url, dimensions=dims
)
assert isinstance(xas_obj, XASObject)
assert xas_obj.n_spectrum == x_dim * y_dim
numpy.testing.assert_array_equal(xas_obj.spectra.data.flat[1].mu, spectra[:, 0, 1])
numpy.testing.assert_array_equal(
xas_obj.spectra.data.flat[2].energy, (channel * ur.eV).m
)
[docs]
def saveSpectra(tmpdir, spectra):
"""Save the spectra to the spectra file defined in setup and return the
associated silx url"""
filename = str(tmpdir / "myfile.h5")
data_path = "/data/NXdata/data"
with h5py.File(filename, "a") as f:
f[data_path] = spectra
return DataUrl(file_path=filename, data_path=data_path, scheme="silx")
[docs]
def saveChannel(tmpdir, channel):
"""Save the energy to the spectra file defined in setup and return the
associated silx url"""
filename = str(tmpdir / "myfile.h5")
data_path = "/data/NXdata/channel"
with h5py.File(filename, "a") as f:
f[data_path] = channel
return DataUrl(file_path=filename, data_path=data_path, scheme="silx")
