def _plot_inverse_isochron(self, po, plot, pid):
analyses = self.sorted_analyses
plot.padding_left = 75
refiso = analyses[0]
self._ref_constants = refiso.arar_constants
self._ref_j = refiso.j
self._ref_age_scalar = refiso.arar_constants.age_scalar
self._ref_age_units = refiso.arar_constants.age_units
try:
age, reg, data = calculate_isochron(analyses)
except TypeError:
return
xs, ys, xerrs, yerrs = data
self._cached_data = data
self._cached_reg = reg
self._age = age
graph = self.graph
graph.set_x_title('39Ar/40Ar')
graph.set_y_title('36Ar/40Ar')
graph.set_grid_traits(visible=False)
graph.set_grid_traits(visible=False, grid='y')
scatter, _p = graph.new_series(xs, ys,
xerror=ArrayDataSource(data=xerrs),
yerror=ArrayDataSource(data=yerrs),
type='scatter',
marker='circle',
bind_id=self.group_id,
#selection_marker_size=5,
#selection_color='green',
marker_size=2)
#self._scatter = scatter
graph.set_series_label('data{}'.format(self.group_id))
eo = ErrorEllipseOverlay(component=scatter)
scatter.overlays.append(eo)
mi, ma = graph.get_x_limits()
ma = max(ma, max(xs))
mi = min(mi, min(xs))
rxs = linspace(mi, ma)
rys = reg.predict(rxs)
graph.set_x_limits(min_=mi, max_=ma, pad='0.1')
graph.new_series(rxs, rys, color=scatter.color)
graph.set_series_label('fit{}'.format(self.group_id))
if po.show_labels:
self._add_point_labels(scatter)
self._add_scatter_inspector(scatter)
self._add_info(plot, reg, text_color=scatter.color)
def _calculate_isochron_age(self):
args = calculate_isochron(list(self.clean_analyses()))
if args:
age = args[0]
reg = args[1]
v, e = age.nominal_value, age.std_dev
e = self._modify_error(v, e, self.isochron_age_error_kind,
mswd=reg.mswd)
return ufloat(v, e)
def _make(self, ep):
opt = ep.doc(0)
db = self.db
with db.session_ctx():
ids = opt['identifiers']
progress = self.open_progress(n=len(ids), close_at_end=False)
editor = InverseIsochronEditor(processor=self)
editor.plotter_options_manager.set_plotter_options('Default')
p, _ = unique_path(
os.path.join(paths.dissertation, 'data', 'minnabluff'),
'compare_iso_spec')
wfile = open(p, 'w')
for i in ids:
hist = db.get_interpreted_age_histories((i, ))[-1]
li = db.get_labnumber(i)
ans = self._get_analyses(li)
if ans:
progress.change_message(
'Calculating isochron for {}'.format(i))
unks = self.make_analyses(ans,
use_progress=False,
use_cache=False)
age, reg, _ = calculate_isochron(unks)
# print self._calculate_intercept(reg)
iaage = hist.interpreted_age.age
iaerr = hist.interpreted_age.age_err
ii, ee = self._calculate_intercept(reg)
ee2 = 2 * ee * (reg.mswd**0.5 if reg.mswd > 1 else 1)
comp = 'EQ'
if ii - ee2 > 295.5:
comp = 'GT'
elif ii + ee2 < 295.5:
comp = 'LT'
t0 = 'Identifier: {}'.format(li.identifier)
t00 = 'Sample: {}'.format(li.sample.name)
t1 = 'InterpretedAge: {}+/-{}'.format(iaage, iaerr)
t2 = 'IsochronAge: {}'.format(age)
t3 = 'Dev: {} ({:0.2f}%)'.format(
age - iaage, (age - iaage) / iaage * 100)
t4 = 'TrappedComponent: {:0.2f}+/-{:0.3f}'.format(ii, ee)
t5 = 'TrappedComparison: {}'.format(comp)
t = '\n'.join((t0, t00, t1, t2, t3, t4, t5))
# print t
wfile.write(t + '\n---\n')
# editor.set_items(unks)
# editor.rebuild()
# print 'exception', editor.get_trapped_component()
wfile.close()
progress.close()
def _calculate_isochron_age(self):
args = calculate_isochron(list(self.clean_analyses()))
if args:
age = args[0]
reg = args[1]
v, e = age.nominal_value, age.std_dev
e = self._modify_error(v,
e,
self.isochron_age_error_kind,
mswd=reg.mswd)
return ufloat(v, e)
def _make(self, ep):
opt = ep.doc(0)
db = self.db
with db.session_ctx():
ids = opt['identifiers']
progress = self.open_progress(n=len(ids), close_at_end=False)
editor = InverseIsochronEditor(processor=self)
editor.plotter_options_manager.set_plotter_options('Default')
p, _ = unique_path(os.path.join(paths.dissertation, 'data', 'minnabluff'),
'compare_iso_spec')
fp = open(p, 'w')
for i in ids:
hist = db.get_interpreted_age_histories((i,))[-1]
li = db.get_labnumber(i)
ans = self._get_analyses(li)
if ans:
progress.change_message('Calculating isochron for {}'.format(i))
unks = self.make_analyses(ans,
use_progress=False,
use_cache=False)
age, reg, _ = calculate_isochron(unks)
# print self._calculate_intercept(reg)
iaage = hist.interpreted_age.age
iaerr = hist.interpreted_age.age_err
ii, ee = self._calculate_intercept(reg)
ee2 = 2 * ee * (reg.mswd ** 0.5 if reg.mswd > 1 else 1)
comp = 'EQ'
if ii - ee2 > 295.5:
comp = 'GT'
elif ii + ee2 < 295.5:
comp = 'LT'
t0 = 'Identifier: {}'.format(li.identifier)
t00 = 'Sample: {}'.format(li.sample.name)
t1 = 'InterpretedAge: {}+/-{}'.format(iaage, iaerr)
t2 = 'IsochronAge: {}'.format(age)
t3 = 'Dev: {} ({:0.2f}%)'.format(age - iaage, (age - iaage) / iaage * 100)
t4 = 'TrappedComponent: {:0.2f}+/-{:0.3f}'.format(ii, ee)
t5 = 'TrappedComparison: {}'.format(comp)
t = '\n'.join((t0, t00, t1, t2, t3, t4, t5))
# print t
fp.write(t + '\n---\n')
# editor.set_items(unks)
# editor.rebuild()
# print editor.get_trapped_component()
fp.close()
progress.close()
def get_isochron_data(self, exclude_non_plateau=False):
ans = [a for a in self.analyses if isinstance(a, ArArAge)]
if exclude_non_plateau and hasattr(self, 'get_is_plateau_step'):
def test(ai):
a = ai.is_omitted()
b = not self.get_is_plateau_step(ai)
return a or b
else:
def test(ai):
return ai.is_omitted()
exclude = [i for i, x in enumerate(ans) if test(x)]
if ans:
return calculate_isochron(ans,
self.isochron_age_error_kind,
exclude=exclude)
def get_isochron_data(self):
return calculate_isochron(list(self.clean_analyses()))
def _plot_inverse_isochron(self, po, plot, pid):
analyses = self.sorted_analyses
plot.padding_left = 75
refiso = analyses[0]
self._ref_constants = refiso.arar_constants
self._ref_j = refiso.j
self._ref_age_scalar = refiso.arar_constants.age_scalar
self._ref_age_units = refiso.arar_constants.age_units
try:
age, reg, data = calculate_isochron(analyses)
except TypeError:
return
xs, ys, xerrs, yerrs = data
self._cached_data = data
self._cached_reg = reg
self._age = age
graph = self.graph
graph.set_x_title('39Ar/40Ar')
graph.set_y_title('36Ar/40Ar')
graph.set_grid_traits(visible=False)
graph.set_grid_traits(visible=False, grid='y')
scatter, _p = graph.new_series(
xs,
ys,
xerror=ArrayDataSource(data=xerrs),
yerror=ArrayDataSource(data=yerrs),
type='scatter',
marker='circle',
bind_id=self.group_id,
#selection_marker_size=5,
#selection_color='green',
marker_size=2)
#self._scatter = scatter
graph.set_series_label('data{}'.format(self.group_id))
eo = ErrorEllipseOverlay(component=scatter)
scatter.overlays.append(eo)
mi, ma = graph.get_x_limits()
ma = max(ma, max(xs))
mi = min(mi, min(xs))
rxs = linspace(mi, ma)
rys = reg.predict(rxs)
graph.set_x_limits(min_=mi, max_=ma, pad='0.1')
graph.new_series(rxs, rys, color=scatter.color)
graph.set_series_label('fit{}'.format(self.group_id))
if po.show_labels:
self._add_point_labels(scatter)
self._add_scatter_inspector(scatter)
self._add_info(plot, reg, text_color=scatter.color)
def get_isochron_data(self):
return calculate_isochron(list(self.clean_analyses()))
def get_isochron_data(self):
ans = [a for a in self.analyses if isinstance(a, ArArAge)]
exclude = [i for i, x in enumerate(ans) if x.is_omitted()]
if ans:
return calculate_isochron(ans, self.isochron_age_error_kind, exclude=exclude)
def _calculate_isochron_age(self):
args = calculate_isochron(self.analyses)
if args:
return args[0]
def get_isochron_data(self):
return calculate_isochron(list(self.clean_analyses()), self.isochron_age_error_kind)
def _calculate_isochron_age(self):
args = calculate_isochron(self.analyses)
if args:
return args[0]
def get_isochron_data(self):
return calculate_isochron(list(self.clean_analyses()),
self.isochron_age_error_kind)
