def _set_age_values(self, f, include_decay_error=False):
arc = self.arar_constants
j = copy(self.j)
if j is None:
j = ufloat(1e-4, 1e-7)
j.tag = 'Position'
j.std_dev = self.position_jerr or 0
age = age_equation(j, f, include_decay_error=include_decay_error, arar_constants=arc)
self.uage_w_position_err = age
j = self.j
if j is None:
j = ufloat(1e-4, 1e-7, tag='J')
age = age_equation(j, f, include_decay_error=include_decay_error, arar_constants=arc)
self.uage_w_j_err = age
j = copy(self.j)
if j is None:
j = ufloat(1e-4, 1e-7, tag='J')
j.std_dev = 0
age = age_equation(j, f, include_decay_error=include_decay_error, arar_constants=arc)
self.uage = age
self.age = nominal_value(age)
self.age_err = std_dev(age)
self.age_err_wo_j = std_dev(age)
for iso in self.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
def _set_age_values(self, f, include_decay_error=False):
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
arc = self.arar_constants
age = age_equation(
j,
f,
include_decay_error=include_decay_error,
# lambda_k=self.lambda_k,
arar_constants=arc)
# age = ufloat((1, 0.1))
self.uage_w_j_err = age
# self.age = age.nominal_value
# self.age_err = age.std_dev
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
j.std_dev = 0
age = age_equation(
j,
f,
include_decay_error=include_decay_error,
# lambda_k=self.lambda_k,
arar_constants=arc)
self.age = nominal_value(age)
self.age_err = std_dev(age)
self.age_err_wo_j = float(age.std_dev)
self.uage = ufloat(self.age, self.age_err)
self.uage_wo_j_err = ufloat(self.age, self.age_err_wo_j)
# if self.j is not None:
# j = copy(self.j)
# else:
# j = ufloat(1e-4, 1e-7)
#
# age = age_equation(j, f_wo_irrad, include_decay_error=include_decay_error,
# arar_constants=arc)
#
# self.age_err_wo_irrad = age.std_dev
# j.std_dev = 0
# self.age_err_wo_j_irrad = age.std_dev
#
for iso in self.isotopes.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
def _calculate_integrated_age(self, ans, weighting):
ret = ufloat(0, 0)
if ans and all((not isinstance(a, InterpretedAgeGroup) for a in ans)):
rs = array([a.get_computed_value('rad40') for a in ans])
ks = array([a.get_computed_value('k39') for a in ans])
sks = ks.sum()
weights = None
if weighting == 'Volume':
weights = ks / sks
elif weighting == 'Variance':
weights = [1 / std_dev(k) ** 2 for k in rs/ks]
if weights is not None:
wmean, sum_weights = average([nominal_value(fi) for fi in rs / ks], weights=weights, returned=True)
werr = sum_weights ** -0.5
f = ufloat(wmean, werr)
else:
f = rs.sum() / sks
a = ans[0]
j = a.j
try:
ret = age_equation(f, j, a.arar_constants) # / self.age_scalar
except ZeroDivisionError:
pass
return ret
def _get_integrated_age(self):
rad40, k39 = zip(*[(a.get_computed_value('rad40'),
a.get_computed_value('k39')) for a in self.analyses])
rad40 = sum(rad40)
k39 = sum(k39)
j = a.j
return age_equation(rad40 / k39, j, a.arar_constants)
def _get_integrated_age(self):
rad40, k39 = zip(*[(a.get_computed_value('rad40'),
a.get_computed_value('k39'))
for a in self.analyses])
rad40 = sum(rad40)
k39 = sum(k39)
j = a.j
return age_equation(rad40 / k39, j, a.arar_constants)
def _set_age_values(self, f, include_decay_error=False):
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
arc = self.arar_constants
age = age_equation(j, f, include_decay_error=include_decay_error,
# lambda_k=self.lambda_k,
arar_constants=arc)
# age = ufloat((1, 0.1))
self.uage_w_j_err = age
# self.age = age.nominal_value
# self.age_err = age.std_dev
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
j.std_dev = 0
age = age_equation(j, f, include_decay_error=include_decay_error,
# lambda_k=self.lambda_k,
arar_constants=arc)
self.age = nominal_value(age)
self.age_err = std_dev(age)
self.age_err_wo_j = float(age.std_dev)
self.uage = ufloat(self.age, self.age_err)
# if self.j is not None:
# j = copy(self.j)
# else:
# j = ufloat(1e-4, 1e-7)
#
# age = age_equation(j, f_wo_irrad, include_decay_error=include_decay_error,
# arar_constants=arc)
#
# self.age_err_wo_irrad = age.std_dev
# j.std_dev = 0
# self.age_err_wo_j_irrad = age.std_dev
#
for iso in self.isotopes.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
def _set_age_values(self, f, include_decay_error=False):
arc = self.arar_constants
for iso in self.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
if self.j is None:
return
j = copy(self.j)
# if j is None:
# j = ufloat(1e-4, 1e-7)
j.tag = 'Position'
j.std_dev = self.position_jerr or 0
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
self.uage_w_position_err = age
j = self.j
# if j is None:
# j = ufloat(1e-4, 1e-7, tag='J')
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
self.uage_w_j_err = age
j = copy(self.j)
# if j is None:
# j = ufloat(1e-4, 1e-7, tag='J')
j.std_dev = 0
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
self.uage = age
self.age = nominal_value(age)
self.age_err = std_dev(age)
self.age_err_wo_j = std_dev(age)
def _get_integrated_age(self):
rad40, k39 = zip(*[(a.get_computed_value('rad40'),
a.get_computed_value('k39')) for a in self.clean_analyses()])
rad40 = sum(rad40)
k39 = sum(k39)
j = a.j
try:
return age_equation(rad40 / k39, j, a.arar_constants)
except ZeroDivisionError:
return nan
def _get_integrated_age(self):
rad40, k39 = zip(*[(a.get_computed_value('rad40'),
a.get_computed_value('k39'))
for a in self.clean_analyses()])
rad40 = sum(rad40)
k39 = sum(k39)
j = a.j
try:
return age_equation(rad40 / k39, j, a.arar_constants)
except ZeroDivisionError:
return nan
def _set_age_values(self, f, include_decay_error=False):
arc = self.arar_constants
for iso in self.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
if self.j is None:
return
j = copy(self.j)
j.tag = 'Position'
j.std_dev = self.position_jerr or 0
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
# new_monitor_age = None
# new_lambda_k = None
# age = convert_age(age, new_monitor_age, new_lambda_k)
self.uage_w_position_err = age
age = age_equation(self.j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
# age = convert_age(age, new_monitor_age, new_lambda_k)
self.uage_w_j_err = age
j = copy(self.j)
j.std_dev = 0
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
# age = convert_age(age, new_monitor_age, new_lambda_k)
self.uage = age
self.age = nominal_value(age)
self.age_err = std_dev(age)
self.age_err_wo_j = std_dev(age)
def _calculate_integrated_age(self, ans, weighting=None):
ret = ufloat(0, 0)
if ans and all((not isinstance(a, InterpretedAgeGroup) for a in ans)):
rs = array([a.get_computed_value('rad40') for a in ans])
ks = array([a.get_computed_value('k39') for a in ans])
# sks = ks.sum()
# fs = rs / ks
if weighting is None:
weighting = self.integrated_age_weighting
# if weighting == 'Volume':
# vpercent = array([nominal_value(v) for v in ks / sks])
# errs = array([std_dev(f) for f in fs])
# weights = (vpercent * errs) ** 2
#
# elif weighting == 'Variance':
# weights = [std_dev(f) ** -2 for f in fs]
#
# if weights is not None:
# wmean, sum_weights = average([nominal_value(fi) for fi in fs], weights=weights, returned=True)
# if weighting == 'Volume':
# werr = sum_weights ** 0.5
# else:
# werr = sum_weights ** -0.5
#
# f = ufloat(wmean, werr)
# else:
# f = rs.sum() / sks
f = self._calculate_integrated_mean_error(weighting, ks, rs)
j = self.j
if not self.include_j_error_in_integrated:
j = nominal_value(j)
try:
ret = age_equation(f, j, arar_constants=self.arar_constants)
except ZeroDivisionError:
pass
return ret
def _calculate_age(self, include_decay_error=None):
"""
approx 2/3 of the calculation time is in _assemble_ar_ar_isotopes.
Isotope.get_intensity takes about 5ms.
"""
isos = self._assemble_ar_ar_isotopes()
if not isos:
return
arc = self.arar_constants
isos = abundance_sensitivity_correction(isos, arc.abundance_sensitivity)
isos[1] *= self.ar39decayfactor
isos[3] *= self.ar37decayfactor
f, f_wo_irrad, non_ar, computed, interference_corrected = calculate_F(
isos,
decay_time=self.decay_days,
interferences=self.interference_corrections,
arar_constants=self.arar_constants,
)
self.non_ar_isotopes = non_ar
self.computed = computed
self.rad40_percent = computed["rad40_percent"]
for k, v in interference_corrected.iteritems():
self.isotopes[k].interference_corrected_value = v
self.uF = f
self.F = f.nominal_value
self.F_err = f.std_dev
self.F_err_wo_irrad = f_wo_irrad.std_dev
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
age = age_equation(j, f, include_decay_error=include_decay_error, arar_constants=self.arar_constants)
self.uage = age
self.age = float(age.nominal_value)
self.age_err = float(age.std_dev)
j.std_dev = 0
self.age_err_wo_j = float(age.std_dev)
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
age = age_equation(j, f_wo_irrad, include_decay_error=include_decay_error, arar_constants=self.arar_constants)
self.age_err_wo_irrad = float(age.std_dev)
j.std_dev = 0
self.age_err_wo_j_irrad = float(age.std_dev)
# print 'asddsadf'
# print self.age_err
# print self.age_err_wo_j
# print self.age_err_wo_j_irrad
for iso in self.isotopes.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
def _calculate_age(self, include_decay_error=None):
"""
approx 2/3 of the calculation time is in _assemble_ar_ar_isotopes.
Isotope.get_intensity takes about 5ms.
"""
isos = self._assemble_ar_ar_isotopes()
if not isos:
return
arc = self.arar_constants
isos = abundance_sensitivity_correction(isos, arc.abundance_sensitivity)
isos[1] *= self.ar39decayfactor
isos[3] *= self.ar37decayfactor
f, f_wo_irrad, non_ar, computed, interference_corrected = calculate_F(isos,
decay_time=self.decay_days,
interferences=self.interference_corrections,
arar_constants=self.arar_constants)
self.non_ar_isotopes = non_ar
self.computed = computed
self.rad40_percent = computed['rad40_percent']
for k, v in interference_corrected.iteritems():
self.isotopes[k].interference_corrected_value = v
self.uF = f
self.F = f.nominal_value
self.F_err = f.std_dev
self.F_err_wo_irrad = f_wo_irrad.std_dev
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4,1e-7)
age = age_equation(j, f, include_decay_error=include_decay_error,
arar_constants=self.arar_constants)
self.uage = age
self.age = float(age.nominal_value)
self.age_err = float(age.std_dev)
j.std_dev = 0
self.age_err_wo_j = float(age.std_dev)
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
age = age_equation(j, f_wo_irrad, include_decay_error=include_decay_error,
arar_constants=self.arar_constants)
self.age_err_wo_irrad = float(age.std_dev)
j.std_dev = 0
self.age_err_wo_j_irrad = float(age.std_dev)
#print 'asddsadf'
#print self.age_err
#print self.age_err_wo_j
#print self.age_err_wo_j_irrad
for iso in self.isotopes.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
def _rebuild_graph(self):
g = self.graph
g.clear()
plot1 = g.new_plot(ytitle='Delta Age (ka)',
xtitle='Time (s)',
padding_left=70,
padding_right=25
)
plot2 = g.new_plot(ytitle='Ar39 (fA)',
padding_left=70,
padding_right=25
)
plot3 = g.new_plot(ytitle='Ar40 (fA)',
padding_left=70,
padding_right=25
)
Ar40 = self.Ar40.intensity
Ar39 = self.Ar39.intensity
if not (Ar40 and Ar39):
return
plot2.value_range.low_setting = Ar39 * .95
plot2.value_range.high_setting = Ar39 * 1.05
plot3.value_range.low_setting = Ar40 * .95
plot3.value_range.high_setting = Ar40 * 1.01
R = Ar40 / Ar39
xma = self.max_time
rs = []
ns = []
ds = []
if self.vary_time_zero:
posts = (15,)
xs = list(range(0, 15))
index = xs
else:
posts = list(range(5, 30))
xs = (0,)
index = posts
for pi in posts:
for ti in xs:
# subplot(311)
n = self.calc_intercept(Ar40, pi,
self.Ar40.equil_rate,
self.Ar40.static_rate,
xma, 2,
time_zero=ti
)
# subplot(312)
d = self.calc_intercept(Ar39, pi,
self.Ar39.equil_rate,
self.Ar39.static_rate,
xma, 1,
time_zero=ti)
ns.append(n)
ds.append(d)
# rs.append(((n / d) - R) / R * 100)
rs.append((n / d))
# print ns
# g.new_series(xs, ns, plotid=2)
# g.new_series(xs, ds, plotid=1)
# g.new_series(to, rs, plotid=0)
mon_age = 28
j = calculate_flux((Ar40, 0), (Ar39, 0), mon_age)
ages = [(age_equation(j[0], abs(ri)) - mon_age) * 1000 for ri in rs]
g.new_series(index, ages, plotid=0)
def _rebuild_graph(self):
g = self.graph
g.clear()
plot1 = g.new_plot(ytitle='Delta Age (ka)',
xtitle='Time (s)',
padding_left=70,
padding_right=25)
plot2 = g.new_plot(ytitle='Ar39 (fA)',
padding_left=70,
padding_right=25)
plot3 = g.new_plot(ytitle='Ar40 (fA)',
padding_left=70,
padding_right=25)
Ar40 = self.Ar40.intensity
Ar39 = self.Ar39.intensity
if not (Ar40 and Ar39):
return
plot2.value_range.low_setting = Ar39 * .95
plot2.value_range.high_setting = Ar39 * 1.05
plot3.value_range.low_setting = Ar40 * .95
plot3.value_range.high_setting = Ar40 * 1.01
R = Ar40 / Ar39
xma = self.max_time
rs = []
ns = []
ds = []
if self.vary_time_zero:
posts = (15, )
xs = range(0, 15)
index = xs
else:
posts = range(5, 30)
xs = (0, )
index = posts
for pi in posts:
for ti in xs:
# subplot(311)
n = self.calc_intercept(Ar40,
pi,
self.Ar40.equil_rate,
self.Ar40.static_rate,
xma,
2,
time_zero=ti)
# subplot(312)
d = self.calc_intercept(Ar39,
pi,
self.Ar39.equil_rate,
self.Ar39.static_rate,
xma,
1,
time_zero=ti)
ns.append(n)
ds.append(d)
# rs.append(((n / d) - R) / R * 100)
rs.append((n / d))
# print ns
# g.new_series(xs, ns, plotid=2)
# g.new_series(xs, ds, plotid=1)
# g.new_series(to, rs, plotid=0)
mon_age = 28
j = calculate_flux((Ar40, 0), (Ar39, 0), mon_age)
ages = [(age_equation(j[0], abs(ri)) - mon_age) * 1000 for ri in rs]
g.new_series(index, ages, plotid=0)
def _calculate_age(self, include_decay_error=None):
"""
approx 2/3 of the calculation time is in _assemble_ar_ar_isotopes.
Isotope.get_intensity takes about 5ms.
"""
# self.debug('calculate age')
iso_intensities = self._assemble_isotope_intensities()
if not iso_intensities:
return
self.Ar39_decay_corrected = iso_intensities[1]
self.Ar37_decay_corrected = iso_intensities[3]
self.isotopes["Ar37"].decay_corrected = self.Ar37_decay_corrected
self.isotopes["Ar39"].decay_corrected = self.Ar39_decay_corrected
# self.debug('allow_negative ca correction {}'.format(arc.allow_negative_ca_correction))
self.corrected_intensities = dict(
Ar40=iso_intensities[0],
Ar39=iso_intensities[1],
Ar38=iso_intensities[2],
Ar37=iso_intensities[3],
Ar36=iso_intensities[4],
)
f, f_wo_irrad, non_ar, computed, interference_corrected = self._calculate_F(iso_intensities)
self.non_ar_isotopes = non_ar
self.computed = computed
self.rad40_percent = computed["rad40_percent"]
isotopes = self.isotopes
for k, v in interference_corrected.iteritems():
isotopes[k].interference_corrected_value = v
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
arc = self.arar_constants
age = age_equation(j, f, include_decay_error=include_decay_error, arar_constants=arc)
self.uage = age
self.age = age.nominal_value
self.age_err = age.std_dev
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
j.std_dev = 0
age = age_equation(j, f, include_decay_error=include_decay_error, arar_constants=arc)
self.age_err_wo_j = float(age.std_dev)
self.uage_wo_j_err = ufloat(self.age, self.age_err_wo_j)
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
age = age_equation(j, f_wo_irrad, include_decay_error=include_decay_error, arar_constants=arc)
self.age_err_wo_irrad = age.std_dev
j.std_dev = 0
self.age_err_wo_j_irrad = age.std_dev
for iso in isotopes.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
def _calculate_age(self, include_decay_error=None):
"""
approx 2/3 of the calculation time is in _assemble_ar_ar_isotopes.
Isotope.get_intensity takes about 5ms.
"""
# self.debug('calculate age')
iso_intensities = self._assemble_isotope_intensities()
if not iso_intensities:
return
self.Ar39_decay_corrected = iso_intensities[1]
self.Ar37_decay_corrected = iso_intensities[3]
self.isotopes['Ar37'].decay_corrected = self.Ar37_decay_corrected
self.isotopes['Ar39'].decay_corrected = self.Ar39_decay_corrected
# self.debug('allow_negative ca correction {}'.format(arc.allow_negative_ca_correction))
self.corrected_intensities = dict(Ar40=iso_intensities[0],
Ar39=iso_intensities[1],
Ar38=iso_intensities[2],
Ar37=iso_intensities[3],
Ar36=iso_intensities[4])
f, f_wo_irrad, non_ar, computed, interference_corrected = self._calculate_F(
iso_intensities)
self.non_ar_isotopes = non_ar
self.computed = computed
self.rad40_percent = computed['rad40_percent']
isotopes = self.isotopes
for k, v in interference_corrected.iteritems():
isotopes[k].interference_corrected_value = v
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
arc = self.arar_constants
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
self.uage = age
self.age = age.nominal_value
self.age_err = age.std_dev
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
j.std_dev = 0
age = age_equation(j,
f,
include_decay_error=include_decay_error,
arar_constants=arc)
self.age_err_wo_j = float(age.std_dev)
self.uage_wo_j_err = ufloat(self.age, self.age_err_wo_j)
if self.j is not None:
j = copy(self.j)
else:
j = ufloat(1e-4, 1e-7)
age = age_equation(j,
f_wo_irrad,
include_decay_error=include_decay_error,
arar_constants=arc)
self.age_err_wo_irrad = age.std_dev
j.std_dev = 0
self.age_err_wo_j_irrad = age.std_dev
for iso in isotopes.itervalues():
iso.age_error_component = self.get_error_component(iso.name)
