def test_run_comparison_function():
a = parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_a.txt'),
skiprows=1)
b = parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_b.txt'),
skiprows=1)
compare_spectrum(a, b, method='pearson')
def test_spectrum_comparison_basic():
"""
Compares a spectrum to itself to verify the similarity measures
are running
:return:
"""
specA = parse_spectrum(os.path.join(TEST_FILE_DIR,
'sample_spectrum_a.txt'),
skiprows=1)
specB = parse_spectrum(os.path.join(TEST_FILE_DIR,
'sample_spectrum_b.txt'),
skiprows=1)
pers_aa = compare_spectrum(specA, specA, 'pearson')
eucl_aa = compare_spectrum(specA, specA, 'euclidean')
cos_aa = compare_spectrum(specA, specA, 'cosine')
ruz_aa = compare_spectrum(specA, specA, 'ruzicka')
pers_bb = compare_spectrum(specB, specB, 'pearson')
eucl_bb = compare_spectrum(specB, specB, 'euclidean')
cos_bb = compare_spectrum(specB, specB, 'cosine')
ruz_bb = compare_spectrum(specB, specB, 'ruzicka')
assert (pers_aa == 1.0)
assert (eucl_aa == 0.0)
assert (ruz_aa == 1.0)
assert isclose(cos_aa, 1.0)
assert (pers_bb == 1.0)
assert (eucl_bb == 0.0)
assert (ruz_bb == 1.0)
assert isclose(cos_bb, 1.0)
def test_all_comparisons():
a = parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_a.txt'),
skiprows=1)
b = parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_b.txt'),
skiprows=1)
all_comparisons = get_all_comparisons()
for key in all_comparisons.keys():
_ = compare_spectrum(a, b, method=key)
def test_run_comparison_function_alt_x():
c = parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_c.txt'),
kind='json')
d = parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_d.txt'),
kind='json')
compare_spectrum(c, c, method='pearson', alt_x='Enorm')
assert compare_spectrum(c, c, method='pearson', alt_x='Enorm') == 1
assert 0 < compare_spectrum(c, d, method='pearson', alt_x='Enorm') < 1
assert compare_spectrum(d, c, method='pearson', alt_x='Enorm') == \
compare_spectrum(d, c, method='pearson', alt_x='Enorm')
def test_XAS_shift():
spec1 = parse_spectrum(os.path.join(TEST_FILE_DIR,
'sample_spectrum_c.txt'),
kind='json')
spec2 = deepcopy(spec1)
spec1.x = np.subtract(spec1.x, 5.0)
assert (abs(5.0 +
spec1.get_shift_alignment(spec2, fidelity=20, iterations=3)[0])
< .1)
def test_parse_spectrum():
"""
Tests that the parse spectrum function can import a simple
2D CSV file
:return:
"""
speca = parse_spectrum(os.path.join(TEST_FILE_DIR,
'sample_spectrum_a.txt'),
skiprows=1)
assert isinstance(speca, Spectrum)
assert len(speca) == 417
assert speca.x[0] == 7570
assert speca.x[-1] == 8277.18
assert speca.y[0] == 0.00267023
assert speca.y[-1] == 0.9949
specb = parse_spectrum(os.path.join(TEST_FILE_DIR,
'sample_spectrum_b.txt'),
skiprows=1)
assert isinstance(specb, Spectrum)
assert len(specb) == 417
def test_parse_spectrum_json():
"""
Tests that the parse spectrum function can import a simple
2D CSV file
:return:
"""
specc = parse_spectrum(os.path.join(TEST_FILE_DIR,
'sample_spectrum_c.txt'),
kind='json')
# print(specc.full_spectrum)
# TODO FINISH THIS
assert isinstance(specc, XAS_Spectrum)
def sample_spectrum():
yield parse_spectrum(os.path.join(TEST_FILE_DIR, 'sample_spectrum_a.txt'),
skiprows=1)