def test_isotopequantity_from_comparison(iq):
"""Test IsotopeQuantity.from_comparison calculation"""
counts1 = 1e3
start = iq.ref_date
stop = start + datetime.timedelta(seconds=3600)
interval1 = (start, stop)
iq2 = IsotopeQuantity.from_comparison(iq, counts1, interval1, counts1,
interval1)
assert iq2 == iq
f = 3.1
counts2 = counts1 * f
iq3 = IsotopeQuantity.from_comparison(iq, counts1, interval1, counts2,
interval1)
assert iq3 == iq * f
if iq.half_life < 1000 * 3.156e7:
dt = datetime.timedelta(seconds=iq.half_life)
interval2 = (start + dt, stop + dt)
iq4 = IsotopeQuantity.from_comparison(iq, counts1, interval1, counts1,
interval2)
assert iq4 == iq * 2
iq5 = IsotopeQuantity.from_comparison(iq, counts1, interval1, counts2,
interval2)
assert iq5 == iq * 2 * f
interval3 = (start - dt, stop - dt)
iq6 = IsotopeQuantity.from_comparison(iq, counts1, interval1, counts1,
interval3)
assert iq6 == iq / 2
def test_irradiation_activate_errors():
"""Test NeutronIrradiation.activate() bad args"""
iso0 = Isotope("Na-23")
iso1 = Isotope("Na-24")
iq0 = IsotopeQuantity(iso0, atoms=1e24)
iq1 = IsotopeQuantity(iso1, atoms=1e24)
start = datetime.datetime.now()
stop = start
n_cm2 = 1e15
ni = NeutronIrradiation(start, stop, n_cm2=n_cm2)
barns = 10
with pytest.raises(NeutronIrradiationError):
ni.activate(barns, initial=iq0, activated=iq1)
with pytest.raises(NeutronIrradiationError):
ni.activate(barns, initial=iso0, activated=iso1)
with pytest.raises(TypeError):
ni.activate(barns, initial=iq0, activated="asdf")
iso2 = Isotope("Na-25")
with pytest.raises(NotImplementedError):
ni.activate(barns, initial=iq1, activated=iso2)
def test_isotopequantity_ref_atoms_stable(stable_isotope):
"""Test IsotopeQuantity.ref_atoms for a stable isotope"""
atoms = 1e24
iq = IsotopeQuantity(stable_isotope, atoms=atoms)
assert iq.ref_atoms == atoms
g = 1e-5
iq = IsotopeQuantity(stable_isotope, g=g)
assert iq.ref_atoms == g / stable_isotope.A * N_AV
def test_isotopequantity_init_stable(stable_isotope, iq_date, iq_kwargs):
"""Test IsotopeQuantity.__init__() for radioactive isotopes"""
if "bq" in iq_kwargs or "uci" in iq_kwargs:
with pytest.raises(IsotopeQuantityError):
iq = IsotopeQuantity(stable_isotope, date=iq_date, **iq_kwargs)
return None
iq = IsotopeQuantity(stable_isotope, date=iq_date, **iq_kwargs)
assert iq.isotope is stable_isotope
assert iq.half_life == stable_isotope.half_life
assert iq.decay_const == stable_isotope.decay_const
def test_isotopequantity_init_rad(radioisotope, iq_date, iq_kwargs):
"""Test IsotopeQuantity.__init__() for radioactive isotopes"""
iq = IsotopeQuantity(radioisotope, date=iq_date, **iq_kwargs)
assert iq.isotope is radioisotope
assert iq.half_life == radioisotope.half_life
assert iq.decay_const == radioisotope.decay_const
# check string input
iq = IsotopeQuantity(str(radioisotope), date=iq_date, **iq_kwargs)
assert iq.isotope == radioisotope
assert iq.half_life == radioisotope.half_life
assert iq.decay_const == radioisotope.decay_const
def test_isotopequantity_from_decays(iq):
"""Test IsotopeQuantity.from_decays instantiation"""
start = iq.ref_date
stop = start + datetime.timedelta(seconds=3600)
# qualitative
IsotopeQuantity.from_decays(
iq.isotope, n_decays=1000, start_time=start, stop_time=stop)
# quantitative
if iq.half_life < 1000 * 3.156e7: # floating point precision #65
n = iq.decays_from(start, stop)
iq2 = IsotopeQuantity.from_decays(
iq.isotope, n_decays=n, start_time=start, stop_time=stop)
assert np.isclose(iq.atoms_at(start), iq2.atoms_at(start))
def test_irradiation_activate_extended(activation_pair):
"""Test NeutronIrradiation.activate() with decay"""
start = datetime.datetime.now()
t_irr = 3600 * 12
stop = start + datetime.timedelta(seconds=t_irr)
n_cm2_s = 1e11
iso0, iso1 = activation_pair
barns = 1
iq0 = IsotopeQuantity(iso0, date=start, atoms=1e24)
expected_atoms = (n_cm2_s * barns * 1e-24 * iq0.ref_atoms *
(1 - np.exp(-iso1.decay_const * t_irr)))
ni = NeutronIrradiation(start, stop, n_cm2_s=n_cm2_s)
# forward calculation
iq1 = ni.activate(barns, initial=iq0, activated=iso1)
assert iq1.ref_date == stop
assert np.isclose(iq1.bq_at(iq1.ref_date), expected_atoms)
# backward calculation
iq0a = ni.activate(barns, initial=iso0, activated=iq1)
assert iq0a.ref_date == start
assert np.isclose(iq0a.ref_atoms, iq0.ref_atoms)
def test_isotopequantity_init_stable(stable_isotope, iq_date, iq_kwargs):
"""Test IsotopeQuantity.__init__() for radioactive isotopes"""
if "bq" in iq_kwargs or "uci" in iq_kwargs:
with pytest.raises(IsotopeQuantityError):
iq = IsotopeQuantity(stable_isotope, date=iq_date, **iq_kwargs)
return None
iq = IsotopeQuantity(stable_isotope, date=iq_date, **iq_kwargs)
assert iq.isotope is stable_isotope
assert iq.half_life == stable_isotope.half_life
assert iq.decay_const == stable_isotope.decay_const
assert iq.bq_at() == iq.bq_at(iq.ref_date) == 0.0
assert iq.uci_at() == iq.uci_at(iq.ref_date) == 0.0
if "g" in iq_kwargs:
assert np.isclose(iq.g_at(), iq_kwargs["g"])
if "atoms" in iq_kwargs:
assert np.isclose(iq.atoms_at(), iq_kwargs["atoms"])
def test_isotopequantity_ref_date_rad(radioisotope, iq_date):
"""Test IsotopeQuantity.ref_date for a radioisotope"""
iq = IsotopeQuantity(radioisotope, date=iq_date, atoms=1e24)
if isinstance(iq_date, datetime.datetime):
assert iq.ref_date == iq_date
elif bq.core.utils.isstring(iq_date):
assert iq.ref_date == dateutil_parse(iq_date)
else:
assert (datetime.datetime.now() - iq.ref_date).total_seconds() < 5
def test_isotopequantity_eq(iq):
"""Test IsotopeQuantity equality magic method"""
iq2 = copy.deepcopy(iq)
assert iq == iq2
dt_s = min(iq.half_life, 10 * 86400)
date = iq.ref_date + datetime.timedelta(seconds=dt_s)
iq3 = IsotopeQuantity(iq.isotope, date=date, atoms=iq.atoms_at(date))
assert iq == iq3
def test_isotopequantity_ref_date_stable(stable_isotope, iq_date):
"""Test IsotopeQuantity.ref_date for a stable isotope"""
iq = IsotopeQuantity(stable_isotope, date=iq_date, atoms=1e24)
if isinstance(iq_date, datetime.datetime):
assert iq.ref_date == iq_date
elif isinstance(iq_date, string_types):
assert iq.ref_date == dateutil_parse(iq_date)
else:
assert (datetime.datetime.now() - iq.ref_date).total_seconds() < 5
def test_isotopequantity_ref_atoms_rad(radioisotope, iq_kwargs):
"""Test IsotopeQuantity.ref_atoms for a radioactive isotope"""
iq = IsotopeQuantity(radioisotope, **iq_kwargs)
if 'atoms' in iq_kwargs:
assert iq.ref_atoms == iq_kwargs['atoms']
elif 'g' in iq_kwargs:
assert iq.ref_atoms == (iq_kwargs['g'] / radioisotope.A * N_AV)
elif 'bq' in iq_kwargs:
assert iq.ref_atoms == iq_kwargs['bq'] / radioisotope.decay_const
else:
assert iq.ref_atoms == (iq_kwargs['uci'] * UCI_TO_BQ /
radioisotope.decay_const)
def test_isotopequantity_ref_atoms_rad(radioisotope, iq_kwargs):
"""Test IsotopeQuantity.ref_atoms for a radioactive isotope"""
iq = IsotopeQuantity(radioisotope, **iq_kwargs)
if "atoms" in iq_kwargs:
assert isclose(iq.ref_atoms, iq_kwargs["atoms"])
elif "g" in iq_kwargs:
assert isclose(iq.ref_atoms, (iq_kwargs["g"] / radioisotope.A * N_AV))
elif "bq" in iq_kwargs:
assert isclose(iq.ref_atoms,
iq_kwargs["bq"] / radioisotope.decay_const)
else:
assert isclose(iq.ref_atoms,
iq_kwargs["uci"] * UCI_TO_BQ / radioisotope.decay_const)
def test_irradiation_nan_g():
"""Regression test for https://github.com/lbl-anp/becquerel/issues/325.
From examples/isotopes.ipynb
"""
iso = Isotope("Na-23")
iso2 = Isotope("Na-24")
barns = 2.3 # making this up for now
irradiation_start = "2017-04-30 10:32:00"
irradiation_stop = "2017-04-30 11:32:00"
flux = 3.1e11
ni = NeutronIrradiation(irradiation_start, irradiation_stop, n_cm2_s=flux)
activated_qty = IsotopeQuantity(iso2, date="2017-05-01", bq=103.2)
na23_qty = ni.activate(barns, initial=iso, activated=activated_qty)
assert not np.isnan(na23_qty.g_at())
def test_irradiation_activate_pulse(activation_pair):
"""Test NeutronIrradiation.activate() for duration = 0"""
start = datetime.datetime.now()
stop = start
n_cm2 = 1e15
iso0, iso1 = activation_pair
barns = 1
iq0 = IsotopeQuantity(iso0, date=start, atoms=1e24)
expected_atoms = n_cm2 * barns * 1e-24 * iq0.ref_atoms
ni = NeutronIrradiation(start, stop, n_cm2=n_cm2)
# forward calculation
iq1 = ni.activate(barns, initial=iq0, activated=iso1)
assert iq1.ref_date == stop
assert np.isclose(iq1.ref_atoms, expected_atoms)
# backward calculation
iq0a = ni.activate(barns, activated=iq1, initial=iso0)
assert iq0a.ref_date == start
assert np.isclose(iq0a.ref_atoms, iq0.ref_atoms)
def iq(radioisotope):
"""An IsotopeQuantity object"""
date = datetime.datetime.now()
kwargs = {"uci": 10.047}
return IsotopeQuantity(radioisotope, date=date, **kwargs)
Na_22_spec = Spectrum.from_file('/Users/jackiegasca/Documents/Ca_sources/Na_22_flat_against_detector_531.Spe')
Mn_54_spec = Spectrum.from_file('/Users/jackiegasca/Documents/Ca_sources/Mn_54_flat_against_detector_1264-96-2.Spe')
Co_57_spec = Spectrum.from_file('/Users/jackiegasca/Documents/Ca_sources/Co_57_flat_against_detector_1264-96-3.Spe')
Cd_109_spec = Spectrum.from_file('/Users/jackiegasca/Documents/Ca_sources/Cd_109_flat_against_detector_1264-96-8.Spe')
Th_228_spec = Spectrum.from_file('/Users/jackiegasca/Documents/Ca_sources/Th_228_flat_against_detector_1415-83.Spe')
Eu_152_spec = Spectrum.from_file('/Users/jackiegasca/Documents/Ca_sources/Eu_152_flat_against_detector_1316-97-2.Spe')
Na_22_start = Na_22_spec.start_time
Mn_54_start = Mn_54_spec.start_time
Co_57_start = Co_57_spec.start_time
Cd_109_start = Cd_109_spec.start_time
Th_228_start = Th_228_spec.start_time
Eu_152_start = Eu_152_spec.start_time
Na_22_init_act = IsotopeQuantity('na22', date=ca.Na_22.date, uci=ca.Na_22.init_act)
Na_22_act = Na_22_init_act.bq_at(Na_22_start)
Mn_54_init_act = IsotopeQuantity('mn54', date=ca.Mn_54.date, uci=ca.Mn_54.init_act)
Mn_54_act = Mn_54_init_act.bq_at(Mn_54_start)
Co_57_init_act = IsotopeQuantity('co57', date=ca.Co_57.date, uci=ca.Co_57.init_act)
Co_57_act = Co_57_init_act.bq_at(Co_57_start)
Cd_109_init_act = IsotopeQuantity('cd109', date=ca.Cd_109.date, uci=ca.Cd_109.init_act)
Cd_109_act = Cd_109_init_act.bq_at(Cd_109_start)
Th_228_init_act = IsotopeQuantity('th229', date=ca.Th_228.date, uci=ca.Th_228.init_act)
Th_228_act = Th_228_init_act.bq_at(Th_228_start)
Eu_152_init_act = IsotopeQuantity('eu152', date=ca.Eu_152.date, uci=ca.Eu_152.init_act)
Eu_152_act = Eu_152_init_act.bq_at(Eu_152_start)
Na_22_ener_spec = Na_22_spec.energies_kev[0:len(Na_22_spec)]
Mn_54_ener_spec = Mn_54_spec.energies_kev[0:len(Mn_54_spec)]
Co_57_ener_spec = Co_57_spec.energies_kev[0:len(Co_57_spec)]
def test_isotopequantity_quantity_at(radioisotope, iq_kwargs):
"""Test IsotopeQuantity.quantity_at for a radioactive isotope"""
iq = IsotopeQuantity(radioisotope, **iq_kwargs)
key = next(iter(iq_kwargs))
assert iq_kwargs[key] == iq.quantity_at(key, iq.ref_date)
def test_isotopequantity_time_when_error(stable_isotope):
"""Test error for time_when on a stable isotope"""
iq = IsotopeQuantity(stable_isotope, g=10)
with pytest.raises(IsotopeQuantityError):
iq.time_when(g=5)
def test_isotopequantity_bad_init(iso, date, kwargs, error):
"""Test errors from Isotope.__init__()"""
with pytest.raises(error):
IsotopeQuantity(iso, date=date, **kwargs)
def Concentration():
conc = []
for i in range(len(iso_name)):
c = iso_name[i].split('_')
abb = c[0]
A = int(c[1])
A_0 = A - 1
iso_2 = '{0}-{1}'.format(abb, A_0)
iso_1 = '{0}-{1}'.format(abb, A)
nuclide = Isotope(iso_1)
def urlcreator(abb, A_0):
A_num = str(A_0)
if len(A_num) == 1:
A_num = '00' + A_num
elif len(A_num) == 2:
A_num = '0' + A_num
else:
A_num = A_num
url = 'http://wwwndc.jaea.go.jp/cgi-bin/Tab80WWW.cgi?/data' \
+ '/JENDL/JENDL-4-prc/intern/' + abb + A_num + '.intern'
html = urllib.request.urlopen(url)
bslink = BeautifulSoup(html, 'lxml')
return(bslink)
bslink = urlcreator(abb, A_0)
def tabledata(bslink):
'''extracts data from the jaea website'''
table = bslink.table
table_rows = table.find_all('tr')
for tr in table_rows:
td = tr.find_all('td')
row = [i.text for i in td]
if len(row) == 7:
if row[0] == 'total ':
x_sec = row[1]
x_sec_s = x_sec.split(' ')
x_val = float(x_sec_s[0])
barn = x_sec_s[1]
if barn[1] == 'k':
x_val = 10**(3) * x_val
return(x_val)
elif barn[1] == 'm':
x_val = 10**(-3) * x_val
return(x_val)
elif barn[1] == '&':
x_val = 10**(-6) * x_val
return(x_val)
else:
x_val = x_val
return(x_val)
else:
pass
else:
pass
return(x_val)
x_val = tabledata(bslink)
#print(x_val)
quantity = IsotopeQuantity(nuclide, date=spec_S1.start_time, bq=isotope_activities[i])
unc_quantity = IsotopeQuantity(nuclide, date=spec_S1.start_time, bq=stat_uncertainties[i])
irrad_quan = quantity.bq_at(irr_stop)
unc_irrad_quan = unc_quantity.bq_at(irr_stop)
irrad_act = IsotopeQuantity(nuclide, date=irr_stop, bq=irrad_quan)
unc_irrad_act = IsotopeQuantity(nuclide, date=irr_stop, bq=unc_irrad_quan)
ni = NeutronIrradiation(irr_start, irr_stop, n_cm2_s=flux)
init_comp = ni.activate(x_val, initial=Isotope(iso_2), activated=irrad_act)
unc_init_comp = ni.activate(x_val, initial=Isotope(iso_2), activated=unc_irrad_act)
init_comp.is_stable = True
unc_init_comp.is_stable = True
sinit_comp = str(init_comp)
sunc_init_comp = str(unc_init_comp)
#print(sinit_comp, sunc_init_comp)
s2 = sinit_comp.split(' ')
s0 = s2[0]
sunc2 = sunc_init_comp.split(' ')
sunc0 = sunc2[0]
isotope_type = ' ' + s2[1] + ' ' + s2[2] + ' ' + s2[3]
print(s0+' +/- '+sunc0 +isotope_type)
