def load_measurement(self, an, ar):
j = self._get_j(an)
jf = 'NaN'
if j is not None:
jj = floatfmt(j.nominal_value, n=3, s=3)
jf = u'{} \u00b1{:0.2e}'.format(jj, j.std_dev)
a39 = ar.ar39decayfactor
a37 = ar.ar37decayfactor
#print ar, a39
ms = [
MeasurementValue(name='AnalysisID', value=self.analysis_id),
MeasurementValue(name='Spectrometer', value=an.mass_spectrometer),
MeasurementValue(name='Run Date',
value=an.rundate.strftime('%Y-%m-%d %H:%M:%S')),
MeasurementValue(name='Irradiation',
value=self._get_irradiation(an)),
MeasurementValue(name='J', value=jf),
MeasurementValue(name='Project', value=an.project),
MeasurementValue(name='Sample', value=an.sample),
MeasurementValue(name='Material', value=an.material),
MeasurementValue(name='Comment', value=an.comment),
MeasurementValue(name='Ar39Decay', value=floatfmt(a39)),
MeasurementValue(name='Ar37Decay', value=floatfmt(a37)),
]
self.measurement_values = ms
def _build_label_text(self, x, we, mswd, valid_mswd, n,
percent_error=False,
sig_figs=3):
display_n = True
display_mswd = n >= 2
if display_n:
n = 'n= {}'.format(n)
else:
n = ''
if display_mswd:
vd = '' if valid_mswd else '*'
mswd = '{}mswd= {:0.2f}'.format(vd, mswd)
else:
mswd = ''
sx = floatfmt(x, sig_figs)
swe = floatfmt(we, sig_figs)
if self.options.index_attr in ('uF', 'Ar40/Ar36'):
me = '{} +/-{}'.format(sx, swe)
else:
age_units = self._get_age_units()
pe = ''
if percent_error:
pe = '({})'.format(format_percent_error(x, we, include_percent_sign=True))
me = '{} +/-{}{} {}'.format(sx, swe, pe, age_units)
return u'{} {} {}'.format(me, mswd, n)
def test_hundreths(self):
x = 0.01
fx = floatfmt(x)
self.assertEqual(fx, '0.0100')
fx = floatfmt(x, n=2)
self.assertEqual(fx, '0.01')
def _load_air_computed(self, an, new_list):
if self.experiment_type == AR_AR:
if new_list:
c = an.arar_constants
ratios = [('40Ar/36Ar', 'Ar40/Ar36', nominal_value(c.atm4036)),
('40Ar/38Ar', 'Ar40/Ar38', nominal_value(c.atm4038))]
cv = self._make_ratios(ratios)
self.computed_values = cv
self._update_ratios()
try:
niso, diso = self._get_ratio('Ar40/Ar36')
if niso and diso:
noncorrected = self._get_non_corrected_ratio(niso, diso)
v, e = nominal_value(noncorrected), std_dev(noncorrected)
ref = 295.5
self.summary_str = u'Ar40/Ar36={} {}{}({}%) IC={:0.5f}'.format(
floatfmt(v), PLUSMINUS, floatfmt(e),
format_percent_error(v, e),
nominal_value(noncorrected / ref))
except:
pass
else:
# todo add ratios for other isotopes. e.g Ne
pass
def _make_tables(self, record):
age = record.age.nominal_value
age_error = record.age.std_dev
age_perror = calc_percent_error(age, age_error, n=3)
woj_age_error = record.age_error_wo_j
woj_age_perror = calc_percent_error(age, woj_age_error, n=3)
ar40_39 = record.Ar40_39.nominal_value
ar40_39_error = record.Ar40_39.std_dev
ar40_39_perror = calc_percent_error(ar40_39, ar40_39_error, n=3)
tt = TextTable(
HeaderRow(TextCell(''), TextCell('Value'),
TextCell(u'{}1{}'.format(PLUSMINUS, SIGMA)),
TextCell('% error')),
TextRow(
BoldCell('Age ({}):'.format(record.arar_constants.age_units)),
TextCell(floatfmt(age)), TextCell(floatfmt(age_error)),
TextCell(age_perror, n=2)),
TextRow(BoldCell('w/o J err:'), TextCell(''),
TextCell(floatfmt(woj_age_error)),
TextCell(woj_age_perror)),
TextRow(
BoldCell('40Ar*/39Ar:'),
TextCell(floatfmt(record.Ar40_39.nominal_value)),
TextCell(floatfmt(record.Ar40_39.std_dev)),
TextCell(ar40_39_perror),
# HtmlCell('<sup>40</sup>Ar*/<sup>39</sup>Ar',
# bold=True)
),
border=True)
return [tt]
def load_measurement(self, an, ar):
j = self._get_j(an)
jf = 'NaN'
if j is not None:
jj = floatfmt(j.nominal_value, n=7, s=5)
pe = format_percent_error(j.nominal_value,
j.std_dev,
include_percent_sign=True)
jf = u'{} \u00b1{:0.2e}({})'.format(jj, j.std_dev, pe)
a39 = ar.ar39decayfactor
a37 = ar.ar37decayfactor
ms = [
MeasurementValue(name='DR Version', value=an.data_reduction_tag),
MeasurementValue(name='DAQ Version', value=an.collection_version),
MeasurementValue(name='AnalysisID', value=self.analysis_id),
MeasurementValue(name='Spectrometer', value=an.mass_spectrometer),
MeasurementValue(name='Run Date',
value=an.rundate.strftime('%Y-%m-%d %H:%M:%S')),
MeasurementValue(name='Irradiation',
value=self._get_irradiation(an)),
MeasurementValue(name='J', value=jf),
MeasurementValue(name='Project', value=an.project),
MeasurementValue(name='Sample', value=an.sample),
MeasurementValue(name='Material', value=an.material),
MeasurementValue(name='Comment', value=an.comment),
MeasurementValue(name='Ar39Decay', value=floatfmt(a39)),
MeasurementValue(name='Ar37Decay', value=floatfmt(a37)),
MeasurementValue(name='Sens.', value=floatfmt(an.sensitivity))
]
self.measurement_values = ms
def af(i, x, y, analysis):
v, e = self._get_interpolated_value(po, analysis)
return (u'Interpolated: {}{}{}'.format(floatfmt(v), PLUSMINUS,
floatfmt(e)),
'Run Date: {}'.format(
analysis.rundate.strftime('%m-%d-%Y %H:%M')),
'Rel. Time: {:0.4f}'.format(x))
def func(ai):
uv = ai.get_value(i_attr)
v = nominal_value(uv)
e = std_dev(uv)
pe = format_percent_error(v, e)
return '{}= {}+/-{}({}%)'.format(fi_attr, floatfmt(v), floatfmt(e),
pe)
def _build_label_text(self, x, we, n, total_n=None, mswd_args=None, percent_error=False, sig_figs=3):
display_n = True
display_mswd = n >= 2
if display_n:
if total_n and n != total_n:
n = "n= {}/{}".format(n, total_n)
else:
n = "n= {}".format(n)
else:
n = ""
if mswd_args and display_mswd:
mswd, valid_mswd, _ = mswd_args
vd = "" if valid_mswd else "*"
mswd = "{}mswd= {:0.2f}".format(vd, mswd)
else:
mswd = ""
sx = floatfmt(x, sig_figs)
swe = floatfmt(we, sig_figs)
if self.options.index_attr in ("uF", "Ar40/Ar36"):
me = u"{} {}{}".format(sx, PLUSMINUS, swe)
else:
age_units = self._get_age_units()
pe = ""
if percent_error:
pe = "({})".format(format_percent_error(x, we, include_percent_sign=True))
me = u"{} {}{}{} {}".format(sx, PLUSMINUS, swe, pe, age_units)
return u"{} {} {}".format(me, mswd, n)
def assemble_lines(self):
if self._cached_lines is None:
idx = self.current_position
comp = self.component
idx2 = idx * 2
e = comp.errors[idx2]
ys = comp.value.get_data()[::2]
v = ys[idx]
low_c = self.cumulative39s[idx2]
high_c = self.cumulative39s[idx2 + 1]
an = self.analyses[idx]
lines = [
'RunID={}'.format(an.record_id), 'Tag={}'.format(an.tag),
'Status={}'.format(an.status_text),
u'{}={} {}{} (1{})'.format(comp.container.y_axis.title,
floatfmt(v), PLUSMINUS, floatfmt(e),
SIGMA),
'Cumulative. Ar39={}-{}'.format(floatfmt(low_c),
floatfmt(high_c))
]
self._cached_lines = lines
return self._cached_lines
def test_hundreths(self):
x = 0.01
fx = floatfmt(x)
self.assertEqual(fx, '0.0100')
fx = floatfmt(x, n=2)
self.assertEqual(fx, '0.01')
def _get_discrimination_text(self):
ic = self.item.discrimination
if ic is None:
v, e = 1.0, 0
else:
v, e = nominal_value(ic), std_dev(ic)
return '{}+/-{}'.format(floatfmt(v, n=4), floatfmt(e, n=4))
def _get_discrimination_text(self):
ic = self.item.discrimination
if ic is None:
v, e = 1.0, 0
else:
v, e = nominal_value(ic), std_dev(ic)
return '{}+/-{}'.format(floatfmt(v, n=4), floatfmt(e, n=4))
def _load_unknown_computed(self, an, new_list):
attrs = (('Age', 'uage_w_j_err'),
# ('Age', 'age', None, None, 'age_err'),
('w/o J', 'wo_j', '', 'uage', 'age_err_wo_j'),
('K/Ca', 'kca'),
('K/Cl', 'kcl'),
('40Ar*', 'rad40_percent'),
('F', 'uF'),
('w/o Irrad', 'wo_irrad', '', 'uF', 'F_err_wo_irrad'))
if new_list:
def comp_factory(n, a, value=None, value_tag=None, error_tag=None):
if value is None:
value = getattr(an, a)
display_value = True
if value_tag:
value = getattr(an, value_tag)
display_value = False
if error_tag:
e = getattr(an, error_tag)
else:
e = std_dev(value)
return ComputedValue(name=n,
tag=a,
value=nominal_value(value) or 0,
value_tag=value_tag or '',
display_value=display_value,
error=e or 0)
cv = [comp_factory(*args)
for args in attrs]
self.computed_values = cv
else:
age = an.uage
nage, sage = nominal_value(age), std_dev(age)
try:
self.summary_str = u'Age={} {}{}({}%)'.format(floatfmt(nage), PLUSMINUS,
floatfmt(sage), format_percent_error(nage, sage))
except:
pass
for ci in self.computed_values:
attr = ci.tag
if attr == 'wo_j':
ci.error = an.age_err_wo_j or 0
ci.value = nominal_value(getattr(an, ci.value_tag))
elif attr == 'wo_irrad':
ci.error = an.F_err_wo_irrad or 0
ci.value = nominal_value(getattr(an, ci.value_tag))
else:
v = getattr(an, attr)
if v is not None:
ci.value = nominal_value(v)
ci.error = std_dev(v)
def _load_unknown_computed(self, an, new_list):
attrs = (('Age', 'uage_w_j_err'), ('w/o J', 'wo_j', '', 'uage',
'age_err_wo_j'), ('K/Ca', 'kca'),
('K/Cl', 'kcl'), ('40Ar*', 'radiogenic_yield'), ('F', 'uF'),
('w/o Irrad', 'wo_irrad', '', 'uF', 'F_err_wo_irrad'))
if new_list:
def comp_factory(n, a, value=None, value_tag=None, error_tag=None):
if value is None:
value = getattr(an, a)
display_value = True
if value_tag:
value = getattr(an, value_tag)
display_value = False
if error_tag:
e = getattr(an, error_tag)
else:
e = std_dev(value)
return self._computed_value_factory(
name=n,
tag=a,
value=nominal_value(value) or 0,
value_tag=value_tag or '',
display_value=display_value,
error=e or 0)
cv = [comp_factory(*args) for args in attrs]
self.computed_values = cv
else:
age = an.uage
nage, sage = nominal_value(age), std_dev(age)
try:
self.summary_str = u'Age={} {}{}({}%)'.format(
floatfmt(nage), PLUSMINUS, floatfmt(sage),
format_percent_error(nage, sage))
except:
pass
for ci in self.computed_values:
ci.sig_figs = self.sig_figs
attr = ci.tag
if attr == 'wo_j':
ci.error = an.age_err_wo_j or 0
ci.value = nominal_value(getattr(an, ci.value_tag))
elif attr == 'wo_irrad':
ci.error = an.F_err_wo_irrad or 0
ci.value = nominal_value(getattr(an, ci.value_tag))
else:
v = getattr(an, attr)
if v is not None:
ci.value = nominal_value(v)
ci.error = std_dev(v)
def _make_flux_row(self, ans):
mR = sum(ai.R for ai in ans) / len(ans)
j, e = calculate_flux(mR, 1, self.monitor_age)
r = Row(fontsize=8)
r.add_item(value='<b>J</b>', span=5)
r.add_item(value='<b>{}</b>'.format(floatfmt(j)))
r.add_item(value='<b>{}</b>'.format(floatfmt(e)))
return r
def _make_flux_row(self, ans):
mR = sum(ai.R for ai in ans) / len(ans)
j, e = calculate_flux(mR, 1, self.monitor_age)
r = Row(fontsize=8)
r.add_item(value='<b>J</b>', span=5)
r.add_item(value='<b>{}</b>'.format(floatfmt(j)))
r.add_item(value='<b>{}</b>'.format(floatfmt(e)))
return r
def test_convert_to_scientific(self):
x = 0.001
fx = floatfmt(x, n=2)
self.assertEqual(fx, '1.00E-03')
fx = floatfmt(x, n=2, s=1)
self.assertEqual(fx, '1.0E-03')
x = 0.001
fx = floatfmt(x)
self.assertEqual(fx, '0.0010')
def calculate_width(self, txt):
if self.calculated_width is None:
self.calculated_width = self._calculate_label_width()
if isinstance(txt, float):
if self.nsigfigs:
txt = floatfmt(txt, self.nsigfigs, use_scientific=self.use_scientific)
else:
txt = floatfmt(txt)
self.calculated_width = max(self.calculated_width, len(str(txt))+5)
def _irradiation_changed(self):
if self.irradiation:
self.level = ''
chron = self.dvc.meta_repo.get_chronology(self.irradiation)
j = chron.duration * self.j_multiplier
self._estimated_j_value = j
self.estimated_j_value = u'{} {}{}'.format(floatfmt(j), PLUSMINUS,
floatfmt(j * 0.001))
items = [NeutronDose(*args) for args in chron.get_doses()]
self.chronology_items = items
def _update_ratios(self, an):
for ci in self.computed_values:
nd = ci.detectors
r = self._get_non_corrected_ratio(nd)
rr, ic = self._get_corrected_ratio(nd)
ci.trait_set(value=floatfmt(rr.nominal_value),
error=floatfmt(rr.std_dev),
noncorrected_value=r.nominal_value,
noncorrected_error=r.std_dev,
ic_factor=nominal_value(ic))
def _update_ratios(self, an):
for ci in self.computed_values:
nd = ci.detectors
r = self._get_non_corrected_ratio(nd)
rr, ic = self._get_corrected_ratio(nd)
ci.trait_set(value=floatfmt(rr.nominal_value),
error=floatfmt(rr.std_dev),
noncorrected_value=r.nominal_value,
noncorrected_error=r.std_dev,
ic_factor=nominal_value(ic))
def _irradiation_changed(self):
if self.irradiation:
self.level = ''
chron = self.dvc.meta_repo.get_chronology(self.irradiation)
j = chron.duration * self.j_multiplier
self._estimated_j_value = j
self.estimated_j_value = u'{} {}{}'.format(floatfmt(j),
PLUSMINUS,
floatfmt(j * 0.001))
items = [NeutronDose(*args) for args in chron.get_doses()]
self.chronology_items = items
def traits_view(self):
def column(klass=ObjectColumn, editable=False, **kw):
return klass(text_font='arial 10', editable=editable, **kw)
cols = [
column(klass=CheckboxColumn,
name='use',
label='Use',
editable=True,
width=30),
column(name='hole_id', label='Hole'),
column(name='identifier', label='Identifier'),
column(name='sample', label='Sample', width=115),
column(name='x', label='X', format='%0.3f', width=50),
column(name='y', label='Y', format='%0.3f', width=50),
column(name='theta', label=u'\u03b8', format='%0.3f', width=50),
column(name='j',
label='J',
format_func=lambda x: floatfmt(x, n=7, s=3),
width=75),
column(name='jerr',
format_func=lambda x: floatfmt(x, n=8, s=3),
label=u'\u00b1\u03c3',
width=75),
column(name='dev', label='dev', format='%0.2f', width=70),
column(klass=CheckboxColumn,
name='save',
label='Save',
editable=True,
width=30)
]
editor = TableEditor(columns=cols, sortable=False, reorderable=False)
v = View(
VSplit(
UItem('graph',
style='custom',
editor=InstanceEditor(),
height=0.72),
VGroup(
HGroup(
spring,
icon_button_editor(
'save_unknowns_button',
'dialog-ok-5',
tooltip='Toggle "save" for unknown positions'),
icon_button_editor(
'save_all_button',
'dialog-ok-apply-5',
tooltip='Toggle "save" for all positions')),
UItem('positions', editor=editor, height=0.28))))
return v
def _permutate(self, ai, record_id, e, ici, prog, i, n):
if prog:
prog.change_message("Setting ic_factor to {}, {}".format(ici, e))
ai.set_ic_factor("CDD", ici, e)
ai.calculate_age(force=True)
r = PermutationRecord()
r.age = ai.uage
r.info_str = "{} (ic={},{})".format(record_id, floatfmt(ici), floatfmt(e))
r.identifier = ai.identifier
return r
def _permutate(self, ai, record_id, e, ici, prog, i, n):
if prog:
prog.change_message('Setting ic_factor to {}, {}'.format(ici, e))
ai.set_ic_factor('CDD', ici, e)
ai.calculate_age(force=True)
r = PermutationRecord()
r.age = ai.uage
r.info_str = '{} (ic={},{})'.format(record_id, floatfmt(ici), floatfmt(e))
r.identifier = ai.identifier
return r
def value_string(self, t):
if t == 'uF':
a, e = self.F, self.F_err
elif t == 'uage':
a, e = self.uage.nominal_value, self.uage.std_dev
else:
v = self.get_value(t)
if isinstance(v, Isotope):
v = v.get_intensity()
a, e = v.nominal_value, v.std_dev
pe = format_percent_error(a, e)
return u'{} {}{} ({}%)'.format(floatfmt(a), PLUSMINUS, floatfmt(e), pe)
def value_string(self, t):
if t == 'uF':
a, e = self.F, self.F_err
elif t == 'uage':
a, e = self.uage.nominal_value, self.uage.std_dev
else:
v = self.get_value(t)
if isinstance(v, Isotope):
v = v.get_intensity()
a, e = v.nominal_value, v.std_dev
pe = format_percent_error(a, e)
return u'{} {}{} ({}%)'.format(floatfmt(a), PLUSMINUS, floatfmt(e), pe)
def _make_weighted_mean_row(self, ans):
r = Row(fontsize=8)
ages, errors = zip(*[(ai.age.nominal_value, ai.age.std_dev)
for ai in ans])
wm, we = calculate_weighted_mean(ages, errors)
r.add_item(value='<b>weighted mean</b>', span=2)
r.add_blank_item(3)
r.add_item(value='<b>{}</b>'.format(floatfmt(wm)))
r.add_item(value=u'<b>\u00b1{}</b>'.format(floatfmt(we)))
return r
def _make_weighted_mean_row(self, ans):
r = Row(fontsize=8)
ages, errors = zip(*[(ai.age.nominal_value, ai.age.std_dev)
for ai in ans])
wm, we = calculate_weighted_mean(ages, errors)
r.add_item(value='<b>weighted mean</b>', span=2)
r.add_blank_item(3)
r.add_item(value='<b>{}</b>'.format(floatfmt(wm)))
r.add_item(value=u'<b>\u00b1{}</b>'.format(floatfmt(we)))
return r
def calculate_width(self, txt):
if self.calculated_width is None:
self.calculated_width = self._calculate_label_width()
if isinstance(txt, float):
if self.nsigfigs:
txt = floatfmt(txt,
self.nsigfigs,
use_scientific=self.use_scientific)
else:
txt = floatfmt(txt)
self.calculated_width = max(self.calculated_width, len(str(txt)) + 5)
def comp_factory(n, a, value=None, error_tag=None):
if value is None:
aa = getattr(an, a)
value = floatfmt(nominal_value(aa))
if error_tag:
e = getattr(an, error_tag)
else:
e = std_dev(aa)
return ComputedValue(name=n,
tag=a,
value=value,
error=floatfmt(e))
def _air_ratio(self):
a4038 = self.isotope_group.get_ratio('Ar40/Ar38', non_ic_corr=True)
a4036 = self.isotope_group.get_ratio('Ar40/Ar36', non_ic_corr=True)
# e4038 = uformat_percent_error(a4038, include_percent_sign=True)
# e4036 = uformat_percent_error(a4036, include_percent_sign=True)
lines = [self._make_header('Ratios'),
'Ar40/Ar36= {} {}'.format(floatfmt(nominal_value(a4036)), errorfmt(nominal_value(a4036),
std_dev(a4036))),
'Ar40/Ar38= {} {}'.format(floatfmt(nominal_value(a4038)), errorfmt(nominal_value(a4038),
std_dev(a4038)))]
return self._make_lines(lines)
def _get_value(self, attr, n=3, **kw):
v = ''
item = self.item
if hasattr(item, attr):
v = getattr(self.item, attr)
if v:
v = floatfmt(nominal_value(v), n=n, **kw)
elif hasattr(item, 'isotopes'):
if attr in item.isotopes:
v = item.isotopes[attr].get_intensity()
v = floatfmt(nominal_value(v), n=n, **kw)
return v
def _get_value(self, attr, n=3, **kw):
v = ""
item = self.item
if hasattr(item, attr):
v = getattr(self.item, attr)
if v:
v = floatfmt(nominal_value(v), n=n, **kw)
elif hasattr(item, "isotopes"):
if attr in item.isotopes:
v = item.isotopes[attr].get_intensity()
v = floatfmt(nominal_value(v), n=n, **kw)
return v
def comp_factory(n, a, value=None, error_tag=None):
if value is None:
aa = getattr(an, a)
value = floatfmt(nominal_value(aa))
if error_tag:
e = getattr(an, error_tag)
else:
e = std_dev(aa)
return ComputedValue(name=n,
tag=a,
value=value,
error=floatfmt(e))
def ad(i, x, y, ai):
a = ai.isotopes['Ar39'].get_interference_corrected_value()
b = ai.isotopes['Ar40'].get_interference_corrected_value()
r = a / b
v = r.nominal_value
e = r.std_dev
try:
pe = '({:0.2f}%)'.format(e / v * 100)
except ZeroDivisionError:
pe = '(Inf%)'
return u'39Ar/40Ar = {} {}{} {}'.format(floatfmt(v, n=6), PLUSMINUS, floatfmt(e, n=7), pe)
def _irradiation_changed(self):
super(LabnumberEntry, self)._irradiation_changed()
if self.irradiation:
db = self.db
with db.session_ctx():
irrad = db.get_irradiation(self.irradiation)
j = irrad.chronology.duration
j *= self.j_multiplier
self.estimated_j_value = u'{} {}{}'.format(floatfmt(j),
PLUSMINUS,
floatfmt(j*0.001))
items = [NeutronDose(*args) for args in irrad.chronology.get_doses()]
self.chronology_items = items
def _update_ratios(self, an):
for ci in self.computed_values:
nd = ci.detectors
n, d = nd.split('/')
niso, diso = self._get_isotope(n), self._get_isotope(d)
noncorrected = self._get_non_corrected_ratio(niso, diso)
corrected, ic = self._get_corrected_ratio(niso, diso)
ci.trait_set(value=floatfmt(nominal_value(corrected)),
error=floatfmt(std_dev(corrected)),
noncorrected_value=nominal_value(noncorrected),
noncorrected_error=std_dev(noncorrected),
ic_factor=nominal_value(ic))
def load_measurement(self, an, ar):
# j = self._get_j(an)
j = ar.j
jf = 'NaN'
if j is not None:
jj = floatfmt(nominal_value(j), n=7, s=5)
pe = format_percent_error(nominal_value(j), std_dev(j), include_percent_sign=True)
jf = u'{} \u00b1{:0.2e}({})'.format(jj, std_dev(j), pe)
a39 = ar.ar39decayfactor
a37 = ar.ar37decayfactor
ms = [MeasurementValue(name='Branch',
value=an.branch),
MeasurementValue(name='DAQ Version',
value=an.collection_version),
MeasurementValue(name='UUID',
value=an.uuid),
MeasurementValue(name='RepositoryID',
value=an.repository_identifier),
MeasurementValue(name='Spectrometer',
value=an.mass_spectrometer),
MeasurementValue(name='Run Date',
value=an.rundate.strftime('%Y-%m-%d %H:%M:%S')),
MeasurementValue(name='Irradiation',
value=self._get_irradiation(an)),
MeasurementValue(name='J',
value=jf),
MeasurementValue(name='Position Error',
value=floatfmt(an.position_jerr, use_scientific=True)),
MeasurementValue(name='Lambda K',
value=nominal_value(ar.arar_constants.lambda_k),
units='1/a'),
MeasurementValue(name='Project',
value=an.project),
MeasurementValue(name='Sample',
value=an.sample),
MeasurementValue(name='Material',
value=an.material),
MeasurementValue(name='Comment',
value=an.comment),
MeasurementValue(name='Ar39Decay',
value=floatfmt(a39)),
MeasurementValue(name='Ar37Decay',
value=floatfmt(a37)),
MeasurementValue(name='Sens.',
value=floatfmt(an.sensitivity, use_scientific=True),
units=an.sensitivity_units)]
self.measurement_values = ms
def _update_ratios(self, an):
for ci in self.computed_values:
nd = ci.detectors
n, d = nd.split('/')
niso, diso = self._get_isotope(n), self._get_isotope(d)
noncorrected = self._get_non_corrected_ratio(niso, diso)
corrected, ic = self._get_corrected_ratio(niso, diso)
ci.trait_set(value=floatfmt(nominal_value(corrected)),
error=floatfmt(std_dev(corrected)),
noncorrected_value=nominal_value(noncorrected),
noncorrected_error=std_dev(noncorrected),
ic_factor=nominal_value(ic))
def assemble_lines(self):
pt = self.current_position
if pt:
# x, y = self.component.map_data(pt)
comp = self.component
inds = self.get_selected_index()
lines = []
convert_index = self.convert_index
if inds is not None and len(inds):
he = hasattr(self.component, 'yerror')
ys = comp.value.get_data()[inds]
xs = comp.index.get_data()[inds]
for i, x, y in zip(inds, xs, ys):
if he:
ye = comp.yerror.get_data()[i]
pe = self.percent_error(y, ye)
ye = floatfmt(ye, n=6, s=3)
sy = u'{} {}{} ({})'.format(y, PLUSMINUS, ye, pe)
else:
sy = floatfmt(y, n=6, s=3)
if convert_index:
x = convert_index(x)
else:
x = '{:0.5f}'.format(x)
lines.extend(
[u'pt={:03d}, x= {}, y= {}'.format(i + 1, x, sy)])
if hasattr(comp, 'display_index'):
x = comp.display_index.get_data()[i]
lines.append('{}'.format(x))
if self.additional_info is not None:
try:
ad = self.additional_info(i, self.id)
except BaseException:
ad = self.additional_info(i)
if isinstance(ad, (list, tuple)):
lines.extend(ad)
else:
lines.append(ad)
return lines
# delim_n = max([len(li) for li in lines])
# return intersperse(lines, '-' * delim_n)
else:
return []
def assemble_lines(self):
pt = self.current_position
if pt:
# x, y = self.component.map_data(pt)
comp = self.component
inds = self.get_selected_index()
lines = []
convert_index = self.convert_index
if inds is not None and len(inds):
he = hasattr(self.component, 'yerror')
ys = comp.value.get_data()[inds]
xs = comp.index.get_data()[inds]
for i, x, y in zip(inds, xs, ys):
if he:
ye = comp.yerror.get_data()[i]
pe = self.percent_error(y, ye)
ye = floatfmt(ye, n=6, s=3)
sy = u'{} {}{} ({})'.format(y, PLUSMINUS, ye, pe)
else:
sy = floatfmt(y, n=6, s=3)
if convert_index:
x = convert_index(x)
else:
x = '{:0.5f}'.format(x)
lines.extend([u'pt={:03d}, x= {}, y= {}'.format(i + 1, x, sy)])
if hasattr(comp, 'display_index'):
x = comp.display_index.get_data()[i]
lines.append('{}'.format(x))
if self.additional_info is not None:
try:
ad = self.additional_info(i, self.id)
except BaseException:
ad = self.additional_info(i)
if isinstance(ad, (list, tuple)):
lines.extend(ad)
else:
lines.append(ad)
return lines
# delim_n = max([len(li) for li in lines])
# return intersperse(lines, '-' * delim_n)
else:
return []
def traits_view(self):
return View(HGroup(Item('age_kind',
style='readonly', show_label=False),
Item('display_age', format_func=lambda x: floatfmt(x, 3),
label='Age',
style='readonly'),
Item('display_age_err',
label=u'\u00b11\u03c3',
format_func=lambda x: floatfmt(x, 4),
style='readonly'),
Item('display_age_units',
style='readonly', show_label=False),
Item('mswd',
format_func=lambda x: floatfmt(x, 2),
style='readonly', label='MSWD')))
def overlay(self, other_component, gc, view_bounds=None, mode="normal"):
tool = self.tool
y, y2 = other_component.y, other_component.y2
x, x2 = other_component.x, other_component.x2
if tool.ruler_pos:
a, b = tool.ruler_pos
if tool.orientation == 'x':
x, x2 = a, a
self.label.sx = x
self.label.sy = b + 10
else:
y, y2 = b, b
self.label.sx = a + 20
self.label.sy = y
with gc:
gc.set_stroke_color(self.color_)
gc.set_line_width(2)
gc.lines([(x, y), (x2, y2)])
gc.stroke_path()
if tool.entered_value:
self.label.bgcolor = self.label_manual_color
v = tool.entered_value
else:
self.label.bgcolor = self.label_bgcolor
v = floatfmt(tool.ruler_data_pos)
self.label.text = '{}: {}'.format(tool.orientation.upper(), v)
self.label.overlay(other_component, gc, view_bounds=None, mode="normal")
def make_items(isotopes):
items = []
for det in DETECTOR_ORDER:
ai = next((ai for ai in isotopes.values() if ai.detector.upper() == det), None)
if ai:
rv = ai.get_non_detector_corrected_value()
r = RatioItem(name=ai.detector,
refvalue=rv,
intensity=floatfmt(nominal_value(rv)),
intensity_err=floatfmt(std_dev(rv)))
r.add_ratio(ai)
for bi in isotopes.values():
r.add_ratio(bi)
items.append(r)
return items
def run(self):
self._alive = True
st = self._start_time
p = self.period
rd = self.response_device
rds = self.response_device_secondary
od = self.output_device
dm = self.data_manager
odata = self.output_data
rdata = self.response_data
while self._alive:
to = time.time()
t = to - st
out = od.get_output()
odata = vstack((odata, (t, out)))
r = rd.get_response(force=True)
rdata = vstack((rdata, (t, r)))
r2 = rds.get_response(force=True)
datum = (t, out, r, r2)
datum = map(lambda x: floatfmt(x, n=3), datum)
dm.write_to_frame(datum)
et = time.time() - to
slt = p - et - 0.001
if slt > 0:
time.sleep(slt)
self.output_data = odata
self.response_data = rdata
def _air_ratio(self):
a4038 = self.isotope_group.get_ratio('Ar40/Ar38', non_ic_corr=True)
a4036 = self.isotope_group.get_ratio('Ar40/Ar36', non_ic_corr=True)
# e4038 = uformat_percent_error(a4038, include_percent_sign=True)
# e4036 = uformat_percent_error(a4036, include_percent_sign=True)
lines = [
self._make_header('Ratios'), 'Ar40/Ar36= {} {}'.format(
floatfmt(nominal_value(a4036)),
errorfmt(nominal_value(a4036), std_dev(a4036))),
'Ar40/Ar38= {} {}'.format(
floatfmt(nominal_value(a4038)),
errorfmt(nominal_value(a4038), std_dev(a4038)))
]
return self._make_lines(lines)
def _add_peak_labels(self, line):
opt = self.options
xs = line.index.get_data()
ys = line.value.get_data()
if xs.shape[0]:
xp, yp = fast_find_peaks(ys, xs)
self.peaks = xp
if opt.label_all_peaks:
border = opt.peak_label_border
border_color = opt.peak_label_border_color
bgcolor = opt.peak_label_bgcolor if opt.peak_label_bgcolor_enabled else 'transparent'
for xi, yi in zip(xp, yp):
label = PeakLabel(line,
data_point=(xi, yi),
label_text=floatfmt(
xi, n=opt.peak_label_sigfigs),
border_visible=bool(border),
border_width=border,
border_color=border_color,
bgcolor=bgcolor)
line.overlays.append(label)
def _format_number(self, attr, **kw):
if self.item.record_id:
v = getattr(self.item, attr)
r = floatfmt(v, **kw)
else:
r = ''
return r
def _irradiation_changed(self):
super(LabnumberEntry, self)._irradiation_changed()
if self.irradiation:
db = self.db
with db.session_ctx():
irrad = db.get_irradiation(self.irradiation)
j = irrad.chronology.duration
j *= self.j_multiplier
self.estimated_j_value = u'{} {}{}'.format(
floatfmt(j), PLUSMINUS, floatfmt(j * 0.001))
items = [
NeutronDose(*args)
for args in irrad.chronology.get_doses()
]
self.chronology_items = items
def assemble_lines(self):
idx = self.current_position
comp = self.component
e = comp.errors[idx]
ys = comp.value.get_data()[::2]
v = ys[idx]
low_c = 0 if idx == 0 else self.cumulative39s[idx - 1]
return ['Step={}'.format(ALPHAS[idx]),
'{}={} +/- {} (1s)'.format(comp.container.y_axis.title, floatfmt(v),
floatfmt(e)
),
'Cumulative. Ar39={}-{}'.format(floatfmt(low_c),
floatfmt(self.cumulative39s[idx]))]
def _rebuild_hole_vs_j(self, x, y, r, reg):
g = Graph()
self.graph = g
p = g.new_plot(xtitle='Hole (Theta)',
ytitle='J',
padding=[90, 5, 5, 40])
p.y_axis.tick_label_formatter = lambda x: floatfmt(x, n=2, s=3)
xs = arctan2(x, y)
ys = reg.ys
yserr = reg.yserr
scatter, _ = g.new_series(xs, ys,
yerror=yserr,
type='scatter', marker='circle')
ebo = ErrorBarOverlay(component=scatter,
orientation='y')
scatter.overlays.append(ebo)
self._add_inspector(scatter)
a = max((abs(min(xs)), abs(max(xs))))
fxs = linspace(-a, a)
a = r * sin(fxs)
b = r * cos(fxs)
pts = vstack((a, b)).T
fys = reg.predict(pts)
g.new_series(fxs, fys)
g.set_x_limits(-3.2, 3.2)
def _format_number(self, attr, **kw):
if self.item.record_id:
v = getattr(self.item, attr)
r = floatfmt(v, **kw)
else:
r = ''
return r
def run(self):
self._alive = True
st = self._start_time
p = self.period
rd = self.response_device
rds = self.response_device_secondary
od = self.output_device
dm = self.data_manager
odata = self.output_data
rdata = self.response_data
while self._alive:
to = time.time()
t = to - st
out = od.get_output()
odata = vstack((odata, (t, out)))
r = rd.get_response(force=True)
rdata = vstack((rdata, (t, r)))
r2 = rds.get_response(force=True)
datum = (t, out, r, r2)
datum = map(lambda x: floatfmt(x, n=3), datum)
dm.write_to_frame(datum)
et = time.time() - to
slt = p - et - 0.001
if slt > 0:
time.sleep(slt)
self.output_data = odata
self.response_data = rdata
def overlay(self, other_component, gc, view_bounds=None, mode="normal"):
tool = self.tool
y, y2 = other_component.y, other_component.y2
x, x2 = other_component.x, other_component.x2
if tool.ruler_pos:
a, b = tool.ruler_pos
if tool.orientation == 'x':
x, x2 = a, a
self.label.sx = x
self.label.sy = b + 10
else:
y, y2 = b, b
self.label.sx = a + 20
self.label.sy = y
with gc:
gc.set_stroke_color(self.color_)
gc.set_line_width(2)
gc.lines([(x, y), (x2, y2)])
gc.stroke_path()
if tool.entered_value:
self.label.bgcolor = self.label_manual_color
v = tool.entered_value
else:
self.label.bgcolor = self.label_bgcolor
v = floatfmt(tool.ruler_data_pos)
self.label.text = '{}: {}'.format(tool.orientation.upper(), v)
self.label.overlay(other_component, gc, view_bounds=None, mode="normal")
def assemble_lines(self):
reg = self.component.regressor
v, e = reg.predict(0), reg.predict_error(0)
lines = [reg.make_equation(),
'x=0, y={} +/-{}({}%)'.format(floatfmt(v, n=5),
floatfmt(e, n=5),
format_percent_error(v, e))]
if not reg.mswd in ('NaN', None):
valid = '' if reg.valid_mswd else '*'
lines.append('MSWD= {}{}, n={}'.format(valid,
floatfmt(reg.mswd, n=3), reg.n))
lines.extend(map(unicode.strip, map(unicode, reg.tostring().split(','))))
return lines
def _get_diff_text(self):
v = self.item.diff
if isinstance(v, float):
v = floatfmt(v, n=8, use_scientific=True)
elif isinstance(v, bool):
v = '---' if v else ''
return v