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 setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.elv_file_path = get_current_module_path(__file__, "../../test_data/hitachi/eels_su/30kV_7eV.elv")
self.hdf5_file_path = get_current_module_path(__file__, "../../test_data/hitachi/eels_su/30kV_7eV.hdf5")
if not os.path.isfile(self.elv_file_path): # pragma: no cover
pytest.skip("File not found: {}".format(self.elv_file_path))
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.path = get_current_module_path(__file__, r"../../test_data")
self.figures_file_path = get_current_module_path(__file__, r"../../test_data\hitachi\eels_su\SCNA9_EFSTEM_C_04\windows.png")
if not os.path.isdir(self.path): # pragma: no cover
pytest.skip("File not found: {}".format(self.path))
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 setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.name_ref = "TestProject"
self.project = Project(self.name_ref)
self.project.spectra.append(RawSpectrum("RawSpectrum_1"))
self.project.spectra.append(RawSpectrum("RawSpectrum_2"))
self.project.spectra.append(RawSpectrum("RawSpectrum_3"))
self.project.si_points.append(Point("Point_1"))
self.project.si_points.append(Point("Point_2"))
self.project.si_points.append(Point("Point_3"))
self.project.si_line_scans.append(Linescan("Linescan_1"))
self.project.si_line_scans.append(Linescan("Linescan_2"))
self.project.si_maps.append(Map("Map_3"))
self.project.energy_filtered_micrographs.append(Eftem("Eftem_1"))
self.test_data_path = get_current_module_path(__file__, '../test_data')
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 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 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 setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.path = get_current_module_path(
__file__,
r"../../test_data/hitachi/eels_su/vacuum_linescan_07eV_i50_52pts")
self.figures_file_path = get_current_module_path(
__file__,
r"../../test_data/hitachi/eels_su/vacuum_linescan_07eV_i50_52pts/vacuum_linescan_07eV_i50_52pts-all_spectra_3.pdf"
)
if not os.path.isdir(self.path): # pragma: no cover
pytest.skip("File not found: {}".format(self.path))
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 export_msa():
from pysemeels import get_current_module_path
elv_file_path = get_current_module_path(
__file__,
r"D:\Dropbox\hdemers\professional\results\experiments\2017\su9000\eels\2017\System_baseline_march2017/30kV_7eV.elv"
)
with open(elv_file_path, 'r') as elv_text_file:
elv_file = ElvFile()
elv_file.read(elv_text_file)
msa_file_path = get_current_module_path(
__file__,
r"D:\Dropbox\hdemers\professional\results\experiments\2017\su9000\eels\2017\System_baseline_march2017/30kV_7eV.msa"
)
elv_file.export_msa(msa_file_path)
for channel_id in range(len(elv_file.energies_eV) - 1):
print(elv_file.energies_eV[channel_id + 1] -
elv_file.energies_eV[channel_id])
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.name_ref = "TestEftem"
self.eftem = Eftem(self.name_ref)
self.test_data_path = get_current_module_path(__file__, '../test_data')
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.name_ref = "TestPoint"
self.point = Point(self.name_ref)
self.test_data_path = get_current_module_path(__file__, '../../test_data')
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.name_ref = "TestLinescan"
self.linescan = Linescan(self.name_ref)
self.test_data_path = get_current_module_path(__file__,
'../../test_data')
def test_is_git_lfs_file_good(self):
self.assertEqual(True, is_git_lfs_file(self.git_lfs_file))
self.assertEqual(True, is_git_lfs_file(self.git_lfs_file2))
file_path = get_current_module_path(__file__, "../test_data/30kV_7eV.elv.lfs")
self.assertEqual(True, os.path.isfile(file_path))
if not os.path.isfile(file_path):
pytest.skip("File not found: {}".format(file_path))
self.assertEqual(True, is_git_lfs_file(file_path))
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_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.")
self.fit_results_position_eV = values['center']
self.fit_results_fwhm_eV = values['fwhm']
self.fit_results_sigma_eV = values['sigma']
self.fit_results_gamma_eV = values['gamma']
self.fit_results_area = values['amplitude']
self.fit_results_height = values['height']
if __name__ == '__main__':
import matplotlib.pyplot as plt
from pysemeels import get_current_module_path
from pysemeels.hitachi.eels_su.elv_file import ElvFile
import numpy as np
elv_file_path = get_current_module_path(
__file__, "../../test_data/hitachi/eels_su/30kV_7eV.elv")
with open(elv_file_path, 'r') as elv_text_file:
elv_file = ElvFile()
elv_file.read(elv_text_file)
plt.figure()
plt.plot(
elv_file.energies_eV,
np.array(elv_file.raw_counts) - np.array(elv_file.dark_currents),
'.')
zlp = ZeroLossPeak(
elv_file.energies_eV,
np.array(elv_file.raw_counts) - np.array(elv_file.dark_currents))
zlp.compute_statistics()
def plot_spectrum():
import matplotlib.pyplot as plt
from pysemeels import get_current_module_path
from pysemeels.hitachi.eels_su.ana_file import AnaFile
import numpy as np
ana_file = AnaFile()
ana_file_path = get_current_module_path(
__file__,
r"D:\Dropbox\hdemers\professional\results\experiments\2017\su9000\eels\2017\System_baseline_march2017/30kV_7eV.ana"
)
with open(ana_file_path, 'r') as elv_text_file:
ana_file.read(elv_text_file)
elv_file_path = get_current_module_path(
__file__,
r"D:\Dropbox\hdemers\professional\results\experiments\2017\su9000\eels\2017\System_baseline_march2017/30kV_7eV.elv"
)
with open(elv_file_path, 'r') as elv_text_file:
elv_file = ElvFile()
elv_file.read(elv_text_file)
plt.figure()
plt.plot(elv_file.energies_eV, elv_file.raw_counts, '.')
plt.plot(ana_file.energies_eV, ana_file.counts, '-')
corrected_counts = (np.array(elv_file.raw_counts) - np.array(
elv_file.dark_currents)) / np.array(elv_file.gain_corrections)
#plt.plot(ana_file.energies_eV, corrected_counts, '.')
plt.plot(ana_file.energies_eV, elv_file.counts, '.')
#plt.close()
print(elv_file.raw_counts[0])
print(elv_file.gain_corrections[0])
print(elv_file.dark_currents[0])
print(ana_file.counts[0])
print(corrected_counts[0] - ana_file.counts[0])
print(
int(elv_file.raw_counts[0]) - int(elv_file.dark_currents[0]) -
int(ana_file.counts[0]))
print(elv_file.raw_counts[0] * elv_file.gain_corrections[0] -
elv_file.dark_currents[0])
print(elv_file.raw_counts[0] / elv_file.gain_corrections[0] -
elv_file.dark_currents[0])
print((elv_file.raw_counts[0] - elv_file.dark_currents[0]) *
elv_file.gain_corrections[0])
print((elv_file.raw_counts[0] - elv_file.dark_currents[0]) /
elv_file.gain_corrections[0])
print(elv_file.raw_counts[0] -
elv_file.dark_currents[0] * elv_file.gain_corrections[0])
print(ana_file.counts[0] -
(elv_file.raw_counts[0] - elv_file.dark_currents[0]) /
elv_file.gain_corrections[0])
plt.figure()
plt.plot(
ana_file.energies_eV,
np.array(ana_file.counts) -
(np.array(elv_file.raw_counts) - np.array(elv_file.dark_currents))
/ np.array(elv_file.gain_corrections))
plt.figure()
plt.plot(elv_file.energies_eV, elv_file.dark_currents, '-')
plt.figure()
plt.plot(elv_file.energies_eV, elv_file.gain_corrections, '-')
plt.close()
print(elv_file.energies_eV.index(0.0))
plt.figure()
plt.plot(elv_file.energies_eV, elv_file.raw_counts, '-')
for energy_eV in [-30.0, -20.0, -10.0, 0.0, 10, 20.0]:
plt.axvline(energy_eV, ls='--', color='b')
for min_index in [586, 443, 300]:
min_energy_eV = elv_file.energies_eV[min_index]
max_energy_eV = elv_file.energies_eV[min_index + 133]
plt.axvspan(min_energy_eV, max_energy_eV, color='r', alpha=0.5)
plt.xlim((elv_file.energies_eV[0], elv_file.energies_eV[-1]))
#plt.subplots_adjust(left=0.0, bottom=0.0, right=1.0, top=1.0)
plt.xlabel("Energy (eV)")
plt.show()
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_git_lfs_file_bad(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_git_lfs_file(file_path))
def read_hdf5(self, hdf5_file_path):
with h5py.File(hdf5_file_path, 'r') as hdf5_file:
self.energies_eV = hdf5_file["energy (eV)"][:]
self.total_spectra = hdf5_file["total spectra"][:]
if __name__ == '__main__':
import matplotlib.pyplot as plt
import numpy as np
from pysemeels import get_current_module_path
ana_file_path = get_current_module_path(
__file__,
"../../../../test_data/hitachi/eels_su/30kV_march2017_7eV/spectra_1.ana"
)
with open(ana_file_path, 'r') as ana_text_file:
ana_file = AnaFile()
ana_file.read(ana_text_file)
plt.figure()
plt.plot(ana_file.energies_eV, ana_file.total_spectra, '.')
energy_eV = ana_file.energies_eV[133]
plt.axvline(energy_eV)
energy_eV = ana_file.energies_eV[586]
plt.axvline(energy_eV)
energy_eV = ana_file.energies_eV[608]
plt.axvline(energy_eV)
plt.figure()
buffer = file.read(size)
if len(buffer) == 0:
break
counts = struct.unpack(format, buffer)
self.raw_spectra.append(counts)
self.raw_spectrum_id += 1
if __name__ == '__main__':
import matplotlib.pyplot as plt
import numpy as np
from pysemeels import get_current_module_path
file_path = get_current_module_path(
__file__,
"../../../../test_data/hitachi/eels_su/30kV_march2017_7eV/RawSpectra/rawspect-1.dat"
)
with open(file_path, 'rb') as raw_spectra_file:
raw_spectra = RawSpectra()
raw_spectra.read(raw_spectra_file)
xs = np.arange(1024)
plt.figure()
for spectrum in raw_spectra.raw_spectra:
plt.plot(xs, spectrum, '-')
plt.show()
