import os
import numpy as np
import numpy.testing
import pytest
import lazy5
from crikit.io.hdf5 import hdf_import_data
from crikit.data.spectrum import Spectrum
from crikit.data.spectra import Spectra
from crikit.data.hsi import Hsi
[docs]@pytest.fixture(scope="function")
def make_datasets():
""" Setups and tears down a series of datasets """
data_m, data_n, data_p = [20, 22, 24]
spectrum = np.random.randn(data_p)**2 + 1
spectra = np.random.randn(data_n, data_p)**2 + 1
hsi = np.random.randn(data_m, data_n, data_p)**2 + 1
return spectrum, spectra, hsi, np.array([data_m, data_n, data_p])
[docs]def test_mean_axes_static():
""" Ensure mean_axes_static raises an error"""
with pytest.raises(NotImplementedError):
Hsi._mean_axes()
[docs]def test_reshape_axes_static(make_datasets):
""" Test reshape axes static method """
spectrum, spectra, hsi, make_dataset_shape = make_datasets
Hsi._reshape_axes(shape=hsi.shape, spectral_axis=-1) == (-1, hsi.shape[-1])
Hsi._reshape_axes(shape=spectra.shape, spectral_axis=-1) == (-1, spectra.shape[-1])
Hsi._reshape_axes(shape=spectrum.shape, spectral_axis=-1) == (-1, spectrum.shape[-1])
[docs]def test_hsi_to_hsi(make_datasets):
""" Import an hsi into an hsi """
spectrum, spectra, hsi, make_dataset_shape = make_datasets
new_dataset = Hsi()
new_dataset.data = hsi
assert new_dataset.size == hsi.size
np.testing.assert_array_equal(new_dataset.data, hsi)
[docs]def test_hsi_to_hsi_rng(make_datasets):
""" Import an hsi into an hsi -- defined range"""
spectrum, spectra, hsi, make_dataset_shape = make_datasets
rng = [10,11]
new_dataset = Hsi()
new_dataset.freq.data = np.arange(hsi.shape[-1])
new_dataset.data = hsi
new_dataset.freq.op_list_pix = rng
new_dataset.data = hsi
assert new_dataset.size == hsi.size
assert (new_dataset.data != 0).sum() == len(rng)*np.prod(hsi.shape[:-1])
np.testing.assert_almost_equal(new_dataset.data[..., rng], hsi[..., rng])
[docs]def test_spectrum_to_hsi(make_datasets):
""" Import a spectrum into an hsi """
spectrum, spectra, hsi, make_dataset_shape = make_datasets
new_dataset = Hsi()
new_dataset.data = spectrum
assert new_dataset.size == spectrum.size
np.testing.assert_array_equal(np.squeeze(new_dataset.data), spectrum)
[docs]def test_spectrum_to_hsi_rng(make_datasets):
""" Import a spectrum into an hsi -- defined range"""
spectrum, spectra, hsi, make_dataset_shape = make_datasets
rng = [10,11]
new_dataset = Hsi()
new_dataset.freq.data = np.arange(hsi.shape[-1])
new_dataset.data = spectrum
new_dataset.freq.op_list_pix = rng
new_dataset.data = spectrum
assert new_dataset.size == spectrum.size
assert (new_dataset.data != 0).sum() == len(rng)
np.testing.assert_almost_equal(np.squeeze(new_dataset.data[..., rng]), spectrum[rng])
[docs]def test_spectra_to_hsi(make_datasets):
""" Import spectra into an hsi """
spectrum, spectra, hsi, make_dataset_shape = make_datasets
new_dataset = Hsi()
new_dataset.data = spectra
assert new_dataset.size == spectra.size
np.testing.assert_array_equal(np.squeeze(new_dataset.data), spectra)
[docs]def test_spectra_to_hsi_rng(make_datasets):
""" Import spectra into an hsi -- defined range"""
spectrum, spectra, hsi, make_dataset_shape = make_datasets
rng = [10,11]
new_dataset = Hsi()
new_dataset.freq.data = np.arange(hsi.shape[-1])
new_dataset.data = spectra
new_dataset.freq.op_list_pix = rng
new_dataset.data = spectra
assert new_dataset.size == spectra.size
assert (new_dataset.data != 0).sum() == len(rng)*spectra.shape[0]
np.testing.assert_almost_equal(np.squeeze(new_dataset.data[..., rng]), spectra[..., rng])