def test_alphas(self, sample):
"""Test calculation with several model isotherms."""
sample = DATA[sample]
# exclude datasets where it is not applicable
if sample.get('as_area', None):
filepath = DATA_N77_PATH / sample['file']
isotherm = pygaps.isotherm_from_json(filepath)
ref_filepath = DATA_N77_PATH / DATA[sample['as_ref']]['file']
ref_isotherm = pygaps.isotherm_from_json(ref_filepath)
mref_isotherm = pygaps.ModelIsotherm.from_pointisotherm(
ref_isotherm, model='BET')
res = pygaps.alpha_s(isotherm, mref_isotherm)
results = res.get('results')
err_relative = 0.1 # 10 percent
err_absolute_area = 0.1 # units
err_absolute_volume = 0.01 # units
assert isclose(results[-1].get('adsorbed_volume'),
sample['as_volume'], err_relative,
err_absolute_area)
assert isclose(results[0].get('area'), sample['as_area'],
err_relative, err_absolute_volume)
def load_iast():
"""A fixture which loads files from the disk."""
filepath = DATA_IAST_PATH / DATA_IAST['CH4']['file']
ch4 = pygaps.isotherm_from_json(filepath)
filepath = DATA_IAST_PATH / DATA_IAST['C2H6']['file']
c2h6 = pygaps.isotherm_from_json(filepath)
return ch4, c2h6
def test_isotherm_from_json_nist(self):
"""Test the parsing of an isotherm from json."""
JSON_PATH_NIST = Path(
__file__
).parent.parent.parent / 'docs' / 'examples' / 'data' / 'parsing' / 'nist' / 'nist_iso.json'
with open(JSON_PATH_NIST) as file:
pygaps.isotherm_from_json(file.read(), fmt='NIST')
def test_isotherm_from_json_nist(self):
"""Test the parsing of an isotherm from json."""
JSON_PATH_NIST = os.path.join(
os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
'docs', 'examples', 'data', 'parsing', 'nist', 'nist_iso.json')
with open(JSON_PATH_NIST) as file:
pygaps.isotherm_from_json(file.read(), fmt='NIST')
def load_iast():
"""Load the files from disk."""
filepath = os.path.join(DATA_IAST_PATH, DATA_IAST['CH4'].get('file'))
with open(filepath, 'r') as text_file:
ch4 = pygaps.isotherm_from_json(text_file.read())
filepath = os.path.join(DATA_IAST_PATH, DATA_IAST['C2H6'].get('file'))
with open(filepath, 'r') as text_file:
c2h6 = pygaps.isotherm_from_json(text_file.read())
return ch4, c2h6
def test_iso_enthalpy_checks(self, use_material):
"""Test initial checks."""
isotherms = []
# load test data
for temp in DATA_ISOSTERIC:
filepath = os.path.join(DATA_ISOSTERIC_PATH,
DATA_ISOSTERIC.get(temp)['file'])
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
isotherms.append(isotherm)
# Check multiple isotherms
with pytest.raises(pygaps.ParameterError):
pygaps.isosteric_enthalpy([isotherms[0]])
# Check same sample
isotherms[0].material_name = 'Test'
with pytest.raises(pygaps.ParameterError):
pygaps.isosteric_enthalpy(isotherms)
isotherms[0].material_name = isotherms[1].material_name
# Check same basis
isotherms[0].convert_adsorbent(basis_to='volume', unit_to='cm3')
with pytest.raises(pygaps.ParameterError):
pygaps.isosteric_enthalpy(isotherms)
return
def test_read_excel(self, tmpdir_factory):
"""Test read excel files file."""
for index, path in enumerate(DATA_EXCEL_STD):
isotherm = pygaps.isotherm_from_xl(path=path)
with open(DATA_JSON_STD[index], 'r') as file:
isotherm2 = pygaps.isotherm_from_json(file.read())
assert isotherm.to_dict() == isotherm2.to_dict()
def test_read_excel_mic(self):
"""Test reading of micromeritics report files."""
for path in DATA_EXCEL_MIC:
isotherm = pygaps.isotherm_from_xl(path=path, fmt='mic')
json_path = path.replace('.xls', '.json')
with open(json_path, 'r') as file:
assert isotherm == pygaps.isotherm_from_json(file.read())
def test_pointisotherm_to_json(self, basic_pointisotherm):
"""Test the parsing of a PointIsotherm to json."""
test_isotherm_json = pygaps.isotherm_to_json(basic_pointisotherm)
new_isotherm = pygaps.isotherm_from_json(test_isotherm_json)
assert basic_pointisotherm == new_isotherm
def test_psd_micro(self, sample):
"""Test psd calculation with several model isotherms"""
sample = DATA[sample]
# exclude datasets where it is not applicable
if sample.get('psd_micro_pore_size', None):
filepath = DATA_N77_PATH / sample['file']
isotherm = pygaps.isotherm_from_json(filepath)
result_dict = pmic.psd_microporous(
isotherm, psd_model='HK', pore_geometry='slit'
)
loc = np.where(
result_dict['pore_distribution'] ==
max(result_dict['pore_distribution'])
)
principal_peak = result_dict['pore_widths'][loc]
err_relative = 0.05 # 5 percent
err_absolute = 0.01 # 0.01
assert np.isclose(
principal_peak, sample['psd_micro_pore_size'], err_relative,
err_absolute
)
def test_modelisotherm_to_json(self, basic_modelisotherm):
"""Test the parsing of an ModelIsotherm to json."""
test_isotherm_json = pygaps.isotherm_to_json(basic_modelisotherm)
new_isotherm = pygaps.isotherm_from_json(test_isotherm_json)
assert basic_modelisotherm.to_dict() == new_isotherm.to_dict()
def test_read_bel(self):
"""Tests reading of a bel data file"""
for path in DATA_BEL:
isotherm = pygaps.isotherm_from_bel(path=path)
json_path = str(path).replace('.DAT', '.json')
assert isotherm == pygaps.isotherm_from_json(json_path)
def test_read_excel_bel(self):
"""Test reading of bel report files."""
for path in DATA_EXCEL_BEL:
isotherm = pygaps.isotherm_from_xl(path=path, fmt='bel')
json_path = path.replace('.xls', '.json')
with open(json_path, 'r') as file:
new_iso = pygaps.isotherm_from_json(file.read())
assert isotherm == new_iso
def test_isotherm_from_json_file(self, basic_pointisotherm,
tmpdir_factory):
"""Test the parsing of an isotherm to a json file."""
path = tmpdir_factory.mktemp('json').join('isotherm.json').strpath
pygaps.isotherm_to_json(basic_pointisotherm, path)
isotherm = pygaps.isotherm_from_json(path)
assert isotherm == basic_pointisotherm
def test_iso_enthalpy_output(self):
"""Test verbosity."""
isotherms = []
for sample in DATA_ISOSTERIC:
filepath = DATA_ISOSTERIC_PATH / DATA_ISOSTERIC[sample]['file']
isotherm = pygaps.isotherm_from_json(filepath)
isotherms.append(isotherm)
ie.isosteric_enthalpy(isotherms, verbose=True)
def test_da_display(self, file, exp_vol, exp_pot):
"""Test isotherm display."""
if exp_vol is None:
return
filepath = os.path.join(DATA_N77_PATH, file)
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
pygaps.da_plot(isotherm, verbose=True)
def test_read_bel(self):
"""Tests reading of a bel data file"""
for path in DATA_BEL:
isotherm = pygaps.isotherm_from_bel(path=path)
json_path = path.replace('.DAT', '.json')
with open(json_path, 'r') as file:
assert isotherm == pygaps.isotherm_from_json(file.read())
def test_area_BET_output(self, noplot):
"""Test verbosity"""
data = DATA['MCM-41']
filepath = os.path.join(DATA_N77_PATH, data['file'])
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
pygaps.area_BET(isotherm, verbose=True)
def test_iso_enthalpy(self):
"""Test calculation with several model isotherms."""
isotherms = []
for sample in DATA_ISOSTERIC:
filepath = DATA_ISOSTERIC_PATH / DATA_ISOSTERIC[sample]['file']
isotherm = pygaps.isotherm_from_json(filepath)
isotherms.append(isotherm)
result_dict = ie.isosteric_enthalpy(isotherms)
assert isclose(average(result_dict['isosteric_enthalpy']), 29, 0.5)
def test_ienthalpy_comb(self, sample):
"""The combined polynomial method"""
sample = DATA_CALO[sample]
filepath = DATA_CALO_PATH / sample['file']
isotherm = pygaps.isotherm_from_json(filepath)
ienth_poly = pygaps.initial_enthalpy_comp(isotherm, 'enthalpy'
).get('initial_enthalpy')
err_relative = 0.1 # 10 percent
err_absolute = 1 #
assert isclose(ienth_poly, sample['ienth'], err_relative, err_absolute)
def test_area_BET_choice(self):
"""Test choice of points."""
sample = DATA['MCM-41']
filepath = DATA_N77_PATH / sample['file']
isotherm = pygaps.isotherm_from_json(filepath)
bet_area = ab.area_BET(isotherm, limits=[0.05, 0.30]).get("area")
err_relative = 0.1 # 10 percent
err_absolute = 0.1 # 0.1 m2
assert isclose(bet_area, sample['s_bet_area'], err_relative,
err_absolute)
def test_area_BET(self, file, expected_bet):
"""Test calculation with several model isotherms"""
filepath = os.path.join(DATA_N77_PATH, file)
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
bet_area = pygaps.area_BET(isotherm).get("area")
err_relative = 0.1 # 10 percent
err_absolute = 0.1 # 0.1 m2
assert isclose(bet_area, expected_bet, err_relative, err_absolute)
def from_json(cls, json_string, **isotherm_parameters):
"""
Construct a PointIsotherm from a standard json-represented isotherm.
This function is just a wrapper around the more powerful .isotherm_from_json
function.
Parameters
----------
json_string : str
A json standard isotherm representation.
isotherm_parameters :
Any other options to be passed to the isotherm creation, like mode, basis or unit.
"""
return pygaps.isotherm_from_json(json_string, **isotherm_parameters)
def test_psd_dft(self, file):
"""Test psd calculation with several model isotherms."""
filepath = os.path.join(DATA_N77_PATH, file)
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
result_dict = pygaps.dft_size_distribution(isotherm,
'internal',
verbose=True)
# max_error = 0.1 # 10 percent
assert result_dict is not None
def test_ienthalpy_point(self, file, expected):
"""The point method."""
filepath = os.path.join(DATA_CALO_PATH, file)
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
ienth_poly = pygaps.initial_enthalpy_point(
isotherm, 'enthalpy', verbose=True).get('initial_enthalpy')
err_relative = 0.1 # 10 percent
err_absolute = 1 #
assert isclose(ienth_poly, expected, err_relative, err_absolute)
def test_ihenry_virial(self, sample):
"""Test virial method with several model isotherms."""
sample = DATA[sample]
# exclude datasets where it is not applicable
if sample.get('Khi_slope', None):
filepath = DATA_N77_PATH / sample['file']
isotherm = pygaps.isotherm_from_json(filepath)
ihenry_virial = pygaps.initial_henry_virial(isotherm)
err_relative = 0.1 # 10 percent
err_absolute = 10 #
assert isclose(ihenry_virial, sample['Khi_virial'], err_relative,
err_absolute)
def test_area_bet(self, sample):
"""Test calculation with several model isotherms."""
sample = DATA[sample]
# exclude datasets where it is not applicable
if sample.get('bet_area', None):
filepath = DATA_N77_PATH / sample['file']
isotherm = pygaps.isotherm_from_json(filepath)
bet_area = ab.area_BET(isotherm).get("area")
err_relative = 0.1 # 10 percent
err_absolute = 0.1 # 0.1 m2
assert isclose(bet_area, sample['bet_area'], err_relative,
err_absolute)
def test_convert(self, basic_pointisotherm, tmpdir_factory):
tempdir = tmpdir_factory.mktemp('cli')
path = tempdir.join('isotherm.json').strpath
outpath = tempdir.join('model.json').strpath
basic_pointisotherm.adsorbate = 'N2'
basic_pointisotherm.to_json(path)
command = [
"pygaps", "-cv", "pressure_mode=relative", "-o", outpath, path
]
out, err, exitcode = capture(command)
print(out, err)
assert exitcode == 0
assert pygaps.isotherm_from_json(outpath).pressure_mode == 'relative'
def test_psd_micro(self, file, method):
"""Test psd calculation with several model isotherms"""
filepath = os.path.join(DATA_N77_PATH, file)
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
result_dict = pygaps.micropore_size_distribution(isotherm,
psd_model=method,
pore_geometry='slit',
verbose=True)
# max_error = 0.1 # 10 percent
assert result_dict is not None
def test_iso_enthalpy_output(self):
"""Test verbosity."""
isotherms = []
# load test data
for temp in DATA_ISOSTERIC:
filepath = os.path.join(DATA_ISOSTERIC_PATH,
DATA_ISOSTERIC.get(temp)['file'])
with open(filepath, 'r') as text_file:
isotherm = pygaps.isotherm_from_json(text_file.read())
isotherms.append(isotherm)
pygaps.isosteric_enthalpy(isotherms, verbose=True)