def testWebsiteExample(self):
"""
Test from value given in the Egerton (2011) book website.
"""
# Drude(ep,ew,eb,epc,e0,beta,nn,tnm)
energies_eV, eps1, eps2, im_eps, im4_eps, re_eps, probabilities_total, probabilities_volume, probabilities_surface, ps, pv, mfp_volume_nm, mfp_free_nm = drude(15, 3, 0, 0.1, 200, 5, 500, 50)
self.assertEqual(500, len(eps1))
self.assertEqual(500, len(eps2))
self.assertEqual(500, len(im_eps))
self.assertEqual(500, len(im4_eps))
self.assertEqual(500, len(re_eps))
self.assertEqual(500, len(probabilities_total))
self.assertEqual(500, len(probabilities_volume))
self.assertEqual(500, len(probabilities_surface))
self.assertAlmostEqual(0.0163826, ps, 7)
# self.assertAlmostEqual(0.254905, pv, 6)
self.assertAlmostEqual(0.25491101951346251, pv, 6)
# self.assertAlmostEqual(196.151, mfp_volume_nm, 3)
self.assertAlmostEqual(196.14687546828225, mfp_volume_nm, 3)
self.assertAlmostEqual(183.836505, mfp_free_nm, 6)
test_data_file_path = get_current_module_path(__file__, "../../test_data/egerton2011/Drude.ssd")
if is_bad_file(test_data_file_path):
pytest.skip("File not found: {}".format(test_data_file_path))
with open(test_data_file_path, 'r') as ref_file:
lines = ref_file.readlines()
for channel_id, line in enumerate(lines):
items = line.split()
xx = float(items[0])
yy = float(items[1])
self.assertAlmostEqual(xx, energies_eV[channel_id], 7)
self.assertAlmostEqual(yy, probabilities_total[channel_id], 7, channel_id)
test_data_file_path = get_current_module_path(__file__, "../../test_data/egerton2011/Drude.eps")
if is_bad_file(test_data_file_path):
pytest.skip("File not found: {}".format(test_data_file_path))
with open(test_data_file_path, 'r') as ref_file:
lines = ref_file.readlines()
for channel_id, line in enumerate(lines):
items = line.split()
xx = float(items[0])
yy = float(items[1])
yy2 = float(items[2])
self.assertAlmostEqual(xx, energies_eV[channel_id], 7)
self.assertAlmostEqual(yy, eps1[channel_id], 7, channel_id)
self.assertAlmostEqual(yy2, eps2[channel_id], 7, channel_id)
def test_read_file_linescan(self):
"""
First test to check if the testcase is working with the testing framework.
"""
ana_file_path = get_current_module_path(
__file__,
"../../../../test_data/hitachi/eels_su/vacuum_linescan_07eV_i50_52pts/spectra_3.ana"
)
if is_bad_file(ana_file_path):
pytest.skip("File not found: {}".format(ana_file_path))
with open(ana_file_path, 'r') as ana_text_file:
ana_file = AnaFile()
ana_file.read(ana_text_file)
self.assertEqual("03/Mar/2017", ana_file.date)
self.assertEqual("15:32", ana_file.time)
self.assertEqual("", ana_file.comment)
self.assertEqual("0.5ms", ana_file.dose)
self.assertEqual("0.0eV", ana_file.le)
self.assertEqual(75.2, ana_file.raw)
self.assertEqual("7.0eV", ana_file.energy_width)
self.assertEqual("586ch", ana_file.dual_det_position)
self.assertEqual("133ch", ana_file.dual_det_post)
self.assertEqual("608ch", ana_file.dual_det_center)
self.assertEqual(13560, ana_file.q1)
self.assertEqual(4150, ana_file.q1s)
self.assertEqual(0, ana_file.q2)
self.assertEqual(0, ana_file.q2s)
self.assertEqual(2700, ana_file.q3)
self.assertEqual(0, ana_file.q3s)
self.assertEqual(3050, ana_file.h1)
self.assertEqual(5850, ana_file.h1s)
self.assertEqual(-650, ana_file.h2)
self.assertEqual(1250, ana_file.h2s)
self.assertEqual(0, ana_file.h3)
self.assertEqual(0, ana_file.h3s)
self.assertEqual(0, ana_file.elv_x)
self.assertEqual(0, ana_file.elv_y)
self.assertEqual(196, ana_file.spectrum_alignment_x)
self.assertEqual(0, ana_file.spectrum_alignment_y)
self.assertEqual(-1280, ana_file.det_map_alignment_x)
self.assertEqual(1500, ana_file.det_map_alignment_y)
self.assertEqual(37443, ana_file.mag)
self.assertEqual(1024, len(ana_file.energies_eV))
self.assertEqual(52, len(ana_file.total_spectra))
self.assertEqual(1024, len(ana_file.total_spectra[0]))
self.assertEqual(1024, len(ana_file.total_spectra[51]))
self.assertEqual(-32.00, ana_file.energies_eV[0])
self.assertEqual(1.0, ana_file.total_spectra[0][0])
self.assertEqual(21.842, ana_file.energies_eV[-1])
self.assertEqual(0, ana_file.total_spectra[0][-1])
self.assertEqual(52, len(ana_file.spectra))
self.assertEqual(50, len(ana_file.spectra[0]))
self.assertEqual(49, ana_file.spectrum_id)
def test_read_oos_file(self):
"""
Test the method to read the oos file.
"""
file_path = get_current_module_path(__file__,
"../../test_data/mc/li_hcp.oos")
if is_bad_file(file_path):
pytest.skip("File not found: {}".format(file_path))
oos_file = OosFile()
oos_file.read_file(file_path)
self.assertEqual("OOS of li", oos_file.title)
self.assertEqual(20, oos_file.number_electrons)
self.assertAlmostEqual(6.941, oos_file.molecular_weight)
self.assertAlmostEqual(0.5, oos_file.density_g_cm3)
self.assertAlmostEqual(55.0, oos_file.switch_energy_eV)
self.assertEqual(346, len(oos_file.energies_eV))
self.assertEqual(346, len(oos_file.oos))
self.assertAlmostEqual(0.01361, oos_file.energies_eV[0])
self.assertAlmostEqual(4.2988e-09, oos_file.oos[0])
self.assertAlmostEqual(4.3295e+05, oos_file.energies_eV[-1])
self.assertAlmostEqual(4.6583e-13, oos_file.oos[-1])
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
if sys.platform != "win32":
pytest.skip("only run on windows")
self.name_ref = "TestRawSpectrum"
self.spectrum = RawSpectrum(self.name_ref)
self.test_data_path = get_current_module_path(__file__, '../test_data')
self.name_import_ref = "30kV_7eV"
self.import_sem_parameters = {
HDF5_ATTRIBUTE_ACCELERATING_VOLTAGE_V: 30.0e3
}
self.elv_file_path = os.path.join(self.test_data_path,
"hitachi/eels_su/30kV_7eV.elv")
if is_bad_file(self.elv_file_path):
pytest.skip("File not found: {}".format(self.elv_file_path))
filepath = self.elv_file_path
name = os.path.splitext(os.path.basename(filepath))[0]
self.spectrum_import = RawSpectrum(name)
self.spectrum_import.import_data(filepath, self.import_sem_parameters)
def test_import_data(self):
"""
Test import_data method.
"""
self.elv_file_path = os.path.join(self.test_data_path,
"hitachi/eels_su/30kV_7eV.elv")
if is_bad_file(self.elv_file_path):
pytest.skip("File not found: {}".format(self.elv_file_path))
filepath = self.elv_file_path
name = os.path.splitext(os.path.basename(filepath))[0]
spectrum = RawSpectrum(name)
spectrum.import_data(filepath)
self.assertEqual(-32.00, spectrum.energies_eV[0])
self.assertEqual(2282, spectrum.raw_counts[0])
self.assertEqual(21.84, spectrum.energies_eV[-1])
self.assertEqual(0, spectrum.raw_counts[-1])
self.assertEqual(1024, len(spectrum.energies_eV))
self.assertEqual(1024, len(spectrum.raw_counts))
self.assertEqual(0.918375, spectrum.gain_corrections[0])
self.assertEqual(0.000000, spectrum.gain_corrections[-1])
self.assertEqual(1024, len(spectrum.gain_corrections))
self.assertEqual(2313, spectrum.dark_currents[0])
self.assertEqual(0, spectrum.dark_currents[-1])
self.assertEqual(1024, len(spectrum.dark_currents))
def testWebsiteExample(self):
"""
Test from value given in the Egerton (2011) book website.
"""
eout, outssd, outpsd = spec_gen(16.7, 3.2, 1, 5, 0.1, 10000, 1.5, 1000,
2, 0.5, 10)
self.assertEqual(1000, len(eout))
self.assertEqual(1000, len(outssd))
self.assertEqual(1000, len(outpsd))
test_data_file_path = get_current_module_path(
__file__, "../../test_data/egerton2011/SpecGen.ssd")
if is_bad_file(test_data_file_path):
pytest.skip("File not found: {}".format(test_data_file_path))
with open(test_data_file_path, 'r') as ref_file:
lines = ref_file.readlines()
for channel_id, line in enumerate(lines):
items = line.split()
xx = float(items[0])
yy = float(items[1])
self.assertAlmostEqual(xx, eout[channel_id], 7)
self.assertAlmostEqual(yy, outssd[channel_id], 7, channel_id)
test_data_file_path = get_current_module_path(
__file__, "../../test_data/egerton2011/SpecGen.psd")
if is_bad_file(test_data_file_path):
pytest.skip("File not found: {}".format(test_data_file_path))
with open(test_data_file_path, 'r') as ref_file:
lines = ref_file.readlines()
for channel_id, line in enumerate(lines):
items = line.split()
xx = float(items[0])
yy = float(items[1])
self.assertAlmostEqual(xx, eout[channel_id], 7)
self.assertAlmostEqual(yy, outpsd[channel_id], 7, channel_id)
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.elv_text_file_path = get_current_module_path(__file__, "../../../test_data/hitachi/eels_su/30kV_7eV.txt")
if is_bad_file(self.elv_text_file_path):
pytest.skip("File not found: {}".format(self.elv_text_file_path))
def test_read_hdf5(self):
"""
Test read_hdf5 method.
"""
filepath = os.path.join(self.test_data_path, "test_map_read_hdf5.hdf5")
if is_bad_file(filepath):
pytest.skip("File not found: {}".format(filepath))
with h5py.File(filepath, "r") as hdf5_file:
self.map.read_hdf5(hdf5_file)
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.ana_file_path = get_current_module_path(
__file__,
"../../../../test_data/hitachi/eels_su/30kV_march2017_7eV/spectra_1.ana"
)
if is_bad_file(self.ana_file_path):
pytest.skip("File not found: {}".format(self.ana_file_path))
def test_read_hdf5_bad_project(self):
"""
Test read_hdf5 method with a different project name.
"""
name_ref = "TestMap_init"
map = Map(name_ref)
filepath = os.path.join(self.test_data_path, "test_map_read_hdf5.hdf5")
if is_bad_file(filepath):
pytest.skip("File not found: {}".format(filepath))
with h5py.File(filepath, "r") as hdf5_file:
self.assertRaises(ValueError, map.read_hdf5, hdf5_file)
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.elv_file_path = get_current_module_path(
__file__,
r"../../test_data\hitachi\eels_su\SCNA9_EFSTEM_C_04\windows.elv")
self.figures_file_path = get_current_module_path(
__file__,
r"../../test_data\hitachi\eels_su\SCNA9_EFSTEM_C_04\windows.png")
if is_bad_file(self.elv_file_path):
pytest.skip("File not found: {}".format(self.elv_file_path))
def test_read_hdf5(self):
"""
Test read_hdf5 method.
"""
filepath = os.path.join(self.test_data_path,
"test_project_read_hdf5.hdf5")
if is_bad_file(filepath):
pytest.skip("File not found: {}".format(filepath))
with h5py.File(filepath, "r") as hdf5_file:
self.project.read_hdf5(hdf5_file)
author_ref = "Hendrix Demers"
self.assertEqual(author_ref, self.project.author)
self.assertEqual(3, len(self.project.spectra))
self.assertEqual(3, len(self.project.si_points))
self.assertEqual(2, len(self.project.si_line_scans))
self.assertEqual(1, len(self.project.si_maps))
self.assertEqual(1, len(self.project.energy_filtered_micrographs))
def test_make_oos(self):
"""
Test the method to make the oos data.
"""
oos_maker = OosMaker()
oos_maker.title = "OOS of li"
oos_maker.number_electrons = 20
oos_maker.molecular_weight = 6.941
oos_maker.density_g_cm3 = 0.5
oos_maker.switch_energy_eV = 55.0
oos_maker.transition_energy_eV = 55.0
oos_file = oos_maker.get_oos_file()
file_path = get_current_module_path(__file__, "../../test_data/mc/li_hcp.oos")
if is_bad_file(file_path):
pytest.skip("File not found: {}".format(file_path))
oos_file_ref = OosFile()
oos_file_ref.read_file(file_path)
self.assertEqual(oos_file_ref.title, oos_file.title)
self.assertEqual(oos_file_ref.number_electrons, oos_file.number_electrons)
self.assertEqual(oos_file_ref.molecular_weight, oos_file.molecular_weight)
self.assertEqual(oos_file_ref.density_g_cm3, oos_file.density_g_cm3)
self.assertEqual(oos_file_ref.switch_energy_eV, oos_file.switch_energy_eV)
self.assertAlmostEqual(0.01361, oos_file.energies_eV[0])
self.assertAlmostEqual(4.2988e-09, oos_file.oos[0])
self.assertAlmostEqual(4.3295e+05, oos_file.energies_eV[-1])
self.assertAlmostEqual(4.6583e-13, oos_file.oos[-1])
for energy_ref_eV, df_dw_ref, energy_eV, df_dw in zip(oos_file_ref.energies_eV, oos_file_ref.oos,
oos_file.energies_eV, oos_file.oos):
self.assertAlmostEqual(energy_ref_eV, energy_eV)
self.assertAlmostEqual(df_dw_ref, df_dw)
self.fail("Test if the testcase is working.")
def test_is_bad_file_no_file(self):
file_path = get_current_module_path(__file__, "../../test_data/this_file_does_not_exist.txt")
self.assertEqual(True, is_bad_file(file_path))
def test_is_bad_file_git_lfs(self):
self.assertEqual(True, is_bad_file(self.git_lfs_file))
def test_is_bad_file(self):
file_path = get_current_module_path(__file__, "test_pysemeels.py")
if not os.path.isfile(file_path):
pytest.skip("File not found: {}".format(file_path))
self.assertEqual(False, is_bad_file(file_path))
def test_import_data_read_hdf5(self):
"""
Test read_hdf5 method.
"""
filepath = self.elv_file_path
name = os.path.splitext(os.path.basename(filepath))[0]
spectrum_read = RawSpectrum(name)
filepath = os.path.join(
self.test_data_path,
"test_raw_spectrum_import_data_read_hdf5.hdf5")
if is_bad_file(filepath):
pytest.skip("File not found: {}".format(filepath))
with h5py.File(filepath, "r") as hdf5_file:
spectrum_read.read_hdf5(hdf5_file)
self.assertEqual(self.name_import_ref, spectrum_read.name)
self.assertTrue(HDF5_ATTRIBUTE_ACCELERATING_VOLTAGE_V in
spectrum_read.extra_parameters)
self.assertAlmostEqual(
self.
import_sem_parameters[HDF5_ATTRIBUTE_ACCELERATING_VOLTAGE_V],
spectrum_read.
extra_parameters[HDF5_ATTRIBUTE_ACCELERATING_VOLTAGE_V])
self.assertEqual(-32.00, spectrum_read.energies_eV[0])
self.assertEqual(21.84, spectrum_read.energies_eV[-1])
self.assertEqual(1024, len(spectrum_read.energies_eV))
self.assertEqual(2282, spectrum_read.raw_counts[0])
self.assertEqual(0, spectrum_read.raw_counts[-1])
self.assertEqual(1024, len(spectrum_read.raw_counts))
self.assertEqual(0.918375, spectrum_read.gain_corrections[0])
self.assertEqual(0.000000, spectrum_read.gain_corrections[-1])
self.assertEqual(1024, len(spectrum_read.gain_corrections))
self.assertEqual(2313, spectrum_read.dark_currents[0])
self.assertEqual(0, spectrum_read.dark_currents[-1])
self.assertEqual(1024, len(spectrum_read.dark_currents))
self.assertEqual(-33.755274261603375, spectrum_read.counts[0])
self.assertTrue(np.isnan(spectrum_read.counts)[-1])
self.assertEqual(1024, len(spectrum_read.counts))
parameters = spectrum_read.eels_parameters
self.assertEqual("SU-EELS", parameters[HDF5_ATTRIBUTE_MODEL])
self.assertEqual(0.0, parameters[HDF5_ATTRIBUTE_SAMPLE_HEIGHT_mm])
self.assertEqual(r"D:\2017\System_baseline_march2017\30kV_7eV.elv",
parameters[HDF5_ATTRIBUTE_FILEPATH])
self.assertEqual("", parameters[HDF5_ATTRIBUTE_COMMENT])
self.assertEqual("01/Mar/2017", parameters[HDF5_ATTRIBUTE_DATE])
self.assertEqual("10:59", parameters[HDF5_ATTRIBUTE_TIME])
self.assertEqual(30000,
parameters[HDF5_ATTRIBUTE_ACCELERATING_VOLTAGE_V])
self.assertEqual(7.0, parameters[HDF5_ATTRIBUTE_ENERGY_WIDTH_eV])
self.assertEqual(0.0, parameters[HDF5_ATTRIBUTE_ENERGY_LOSS_eV])
self.assertEqual(500, parameters[HDF5_ATTRIBUTE_SPEED_us])
self.assertEqual("01/Mar/2017", parameters[HDF5_DATE])
self.assertEqual("10:59", parameters[HDF5_TIME])
self.assertEqual("", parameters[HDF5_COMMENT])
self.assertEqual(500.0, parameters[HDF5_ACQUISITION_SPEED])
self.assertEqual(0.0, parameters[HDF5_ENERGY_LOSS])
self.assertEqual(98.7, parameters[HDF5_RAW])
self.assertEqual(7.0, parameters[HDF5_ENERGY_WIDTH_eV])
self.assertEqual(586, parameters[HDF5_DUAL_DET_POSITION])
self.assertEqual(133, parameters[HDF5_DUAL_DET_POST])
self.assertEqual(608, parameters[HDF5_DUAL_DET_CENTER])
self.assertEqual(13575, parameters[HDF5_Q1])
self.assertEqual(3850, parameters[HDF5_Q1S])
self.assertEqual(0, parameters[HDF5_Q2])
self.assertEqual(0, parameters[HDF5_Q2S])
self.assertEqual(2700, parameters[HDF5_Q3])
self.assertEqual(2900, parameters[HDF5_H1])
self.assertEqual(6150, parameters[HDF5_H1S])
self.assertEqual(-600, parameters[HDF5_H2])
self.assertEqual(350, parameters[HDF5_H2S])
self.assertEqual(0, parameters[HDF5_H4])
self.assertEqual(0, parameters[HDF5_ELV_X])
self.assertEqual(0, parameters[HDF5_ELV_Y])
self.assertEqual(259, parameters[HDF5_SPECTRUM_ALIGNMENT_X])
self.assertEqual(0, parameters[HDF5_SPECTRUM_ALIGNMENT_Y])
self.assertEqual(-1500, parameters[HDF5_DET_SPEC_ALIGNMENT_X])
self.assertEqual(470, parameters[HDF5_DET_SPEC_ALIGNMENT_Y])
self.assertEqual(-1500, parameters[HDF5_DET_MAP_ALIGNMENT_X])
self.assertEqual(1500, parameters[HDF5_DET_MAP_ALIGNMENT_Y])
self.assertEqual(37443, parameters[HDF5_MAGNIFICATION])
