def _mean_regress(self, r, x, y, ox, oy, index, fit, fod, apply_filter):
if r is None or not isinstance(r, MeanRegressor):
r = MeanRegressor()
r.trait_set(xs=x, ys=y, fit=fit)
if apply_filter:
r = self._apply_outlier_filter(r, ox, oy, index, fod)
return r
def _mean_regress(self, r, x, y, ox, oy, index,
fit, fod, apply_filter):
if r is None or not isinstance(r, MeanRegressor):
r = MeanRegressor()
r.trait_set(xs=x, ys=y, fit=fit)
if apply_filter:
r = self._apply_outlier_filter(r, ox, oy, index, fod)
return r
def _mean_regressor_factory(self):
from pychron.core.regression.mean_regressor import MeanRegressor
xs = self.offset_xs
reg = MeanRegressor(xs=xs, ys=self.ys,
filter_outliers_dict=self.filter_outliers_dict,
error_calc_type=self.error_type or 'SEM')
return reg
def _mean_regress(self, scatter, r, fit):
if hasattr(scatter, 'yerror'):
if r is None or not isinstance(r, WeightedMeanRegressor):
r = WeightedMeanRegressor()
else:
if r is None or not isinstance(r, MeanRegressor):
r = MeanRegressor()
self._set_regressor(scatter, r)
r.trait_set(fit=fit, trait_change_notify=False)
r.calculate()
self._set_excluded(scatter, r)
return r
def _mean_regress(self, scatter, r, fit):
from pychron.core.regression.mean_regressor import MeanRegressor, WeightedMeanRegressor
if hasattr(scatter, 'yerror') and fit == 'weighted mean':
if r is None or not isinstance(r, WeightedMeanRegressor):
r = WeightedMeanRegressor()
else:
if r is None or not isinstance(r, MeanRegressor):
r = MeanRegressor()
self._set_regressor(scatter, r)
# r.trait_setq(fit=fit)
r.calculate()
self._set_excluded(scatter, r)
return r
def setUp(self):
self.reg = MeanRegressor()
class TruncateRegressionTest(TestCase):
def setUp(self):
self.reg = MeanRegressor()
def test_pre_truncate(self):
xs, ys, sol = pre_truncated_data()
self.reg.trait_set(xs=xs, ys=ys)
self.solution = sol
self.reg.trait_set(xs=xs, ys=ys)
self.reg.set_truncate('x<5')
self.assertEqual(self.reg.mean, self.solution['pre_mean'])
def test_post_truncate(self):
xs, ys, sol = pre_truncated_data()
self.reg.trait_set(xs=xs, ys=ys)
self.solution = sol
self.reg.trait_set(xs=xs, ys=ys)
self.reg.set_truncate('x>=5')
self.assertEqual(self.reg.mean, self.solution['post_mean'])
def _test_fired(self):
import numpy as np
self.db.connect()
xbase = np.linspace(430, 580, 150)
# ybase = np.zeros(150)
# cddybase = np.zeros(150)
ybase = np.random.random(150)
cddybase = np.random.random(150) * 0.001
base = [
zip(xbase, ybase),
zip(xbase, ybase),
zip(xbase, ybase),
zip(xbase, ybase),
zip(xbase, cddybase),
]
xsig = np.linspace(20, 420, 410)
# y40 = np.ones(410) * 680
# y39 = np.ones(410) * 107
# y38 = np.zeros(410) * 1.36
# y37 = np.zeros(410) * 0.5
# y36 = np.ones(410) * 0.001
y40 = 680 - 0.1 * xsig
y39 = 107 - 0.1 * xsig
y38 = np.zeros(410) * 1.36
y37 = np.zeros(410) * 0.5
y36 = 1 + 0.1 * xsig
sig = [
zip(xsig, y40),
zip(xsig, y39),
zip(xsig, y38),
zip(xsig, y37),
zip(xsig, y36),
]
regbs = MeanRegressor(xs=xbase, ys=ybase)
cddregbs = MeanRegressor(xs=xbase, ys=cddybase)
reg = PolynomialRegressor(xs=xsig, ys=y40, fit='linear')
reg1 = PolynomialRegressor(xs=xsig, ys=y39, fit='linear')
reg2 = PolynomialRegressor(xs=xsig, ys=y38, fit='linear')
reg3 = PolynomialRegressor(xs=xsig, ys=y37, fit='linear')
reg4 = PolynomialRegressor(xs=xsig, ys=y36, fit='linear')
keys = [
('H1', 'Ar40'),
('AX', 'Ar39'),
('L1', 'Ar38'),
('L2', 'Ar37'),
('CDD', 'Ar36'),
]
regresults = (dict(
Ar40=ufloat(reg.predict(0), reg.predict_error(0)),
Ar39=ufloat(reg1.predict(0), reg1.predict_error(0)),
Ar38=ufloat(reg2.predict(0), reg2.predict_error(0)),
Ar37=ufloat(reg3.predict(0), reg3.predict_error(0)),
Ar36=ufloat(reg4.predict(0), reg4.predict_error(0)),
),
dict(Ar40=ufloat(regbs.predict(0),
regbs.predict_error(0)),
Ar39=ufloat(regbs.predict(0),
regbs.predict_error(0)),
Ar38=ufloat(regbs.predict(0),
regbs.predict_error(0)),
Ar37=ufloat(regbs.predict(0),
regbs.predict_error(0)),
Ar36=ufloat(cddregbs.predict(0),
cddregbs.predict_error(0))))
blanks = [
ufloat(0, 0.1),
ufloat(0.1, 0.001),
ufloat(0.01, 0.001),
ufloat(0.01, 0.001),
ufloat(0.00001, 0.0001),
]
fits = (dict(
zip(['Ar40', 'Ar39', 'Ar38', 'Ar37', 'Ar36'],
['Linear', 'Linear', 'Linear', 'Linear', 'Linear'])),
dict(
zip(['Ar40', 'Ar39', 'Ar38', 'Ar37', 'Ar36'], [
'Average Y', 'Average Y', 'Average Y', 'Average Y',
'Average Y'
])))
mass_spectrometer = 'obama'
extract_device = 'Laser Furnace'
extract_value = 10
position = 1
duration = 10
first_stage_delay = 0
second_stage_delay = 30
tray = '100-hole'
runscript_name = 'Foo'
runscript_text = 'this is a test script'
self.add_analysis(
'4318',
'500',
'',
'4318',
base,
sig,
blanks,
keys,
regresults,
fits,
mass_spectrometer,
extract_device,
tray,
position,
extract_value, # power requested
extract_value, # power achieved
duration, # total extraction
duration, # time at extract_value
first_stage_delay,
second_stage_delay,
runscript_name,
runscript_text,
)
def regressor(self):
fit = self.fit
if fit is None:
fit = 'linear'
self.fit = fit
lfit = fit.lower()
is_mean = 'average' in lfit
is_expo = lfit == 'exponential'
is_poly = not (is_mean or is_expo)
reg = self._regressor
if reg is None:
if is_mean:
reg = MeanRegressor()
elif is_expo:
reg = ExponentialRegressor()
else:
reg = PolynomialRegressor()
elif is_poly and not isinstance(reg, PolynomialRegressor):
reg = PolynomialRegressor()
elif is_mean and not isinstance(reg, MeanRegressor):
reg = MeanRegressor()
elif is_expo and not isinstance(reg, ExponentialRegressor):
reg = ExponentialRegressor()
if is_poly:
reg.set_degree(fit_to_degree(fit), refresh=False)
reg.trait_set(xs=self.offset_xs,
ys=self.ys,
error_calc_type=self.error_type or 'SEM',
filter_outliers_dict=self.filter_outliers_dict,
tag=self.name)
if self.truncate:
reg.set_truncate(self.truncate)
reg.calculate()
self._regressor = reg
return reg
def _test_fired(self):
import numpy as np
self.db.connect()
xbase = np.linspace(430, 580, 150)
# ybase = np.zeros(150)
# cddybase = np.zeros(150)
ybase = np.random.random(150)
cddybase = np.random.random(150) * 0.001
base = [zip(xbase, ybase), zip(xbase, ybase), zip(xbase, ybase), zip(xbase, ybase), zip(xbase, cddybase)]
xsig = np.linspace(20, 420, 410)
# y40 = np.ones(410) * 680
# y39 = np.ones(410) * 107
# y38 = np.zeros(410) * 1.36
# y37 = np.zeros(410) * 0.5
# y36 = np.ones(410) * 0.001
y40 = 680 - 0.1 * xsig
y39 = 107 - 0.1 * xsig
y38 = np.zeros(410) * 1.36
y37 = np.zeros(410) * 0.5
y36 = 1 + 0.1 * xsig
sig = [zip(xsig, y40), zip(xsig, y39), zip(xsig, y38), zip(xsig, y37), zip(xsig, y36)]
regbs = MeanRegressor(xs=xbase, ys=ybase)
cddregbs = MeanRegressor(xs=xbase, ys=cddybase)
reg = PolynomialRegressor(xs=xsig, ys=y40, fit="linear")
reg1 = PolynomialRegressor(xs=xsig, ys=y39, fit="linear")
reg2 = PolynomialRegressor(xs=xsig, ys=y38, fit="linear")
reg3 = PolynomialRegressor(xs=xsig, ys=y37, fit="linear")
reg4 = PolynomialRegressor(xs=xsig, ys=y36, fit="linear")
keys = [("H1", "Ar40"), ("AX", "Ar39"), ("L1", "Ar38"), ("L2", "Ar37"), ("CDD", "Ar36")]
regresults = (
dict(
Ar40=ufloat(reg.predict(0), reg.predict_error(0)),
Ar39=ufloat(reg1.predict(0), reg1.predict_error(0)),
Ar38=ufloat(reg2.predict(0), reg2.predict_error(0)),
Ar37=ufloat(reg3.predict(0), reg3.predict_error(0)),
Ar36=ufloat(reg4.predict(0), reg4.predict_error(0)),
),
dict(
Ar40=ufloat(regbs.predict(0), regbs.predict_error(0)),
Ar39=ufloat(regbs.predict(0), regbs.predict_error(0)),
Ar38=ufloat(regbs.predict(0), regbs.predict_error(0)),
Ar37=ufloat(regbs.predict(0), regbs.predict_error(0)),
Ar36=ufloat(cddregbs.predict(0), cddregbs.predict_error(0)),
),
)
blanks = [ufloat(0, 0.1), ufloat(0.1, 0.001), ufloat(0.01, 0.001), ufloat(0.01, 0.001), ufloat(0.00001, 0.0001)]
fits = (
dict(zip(["Ar40", "Ar39", "Ar38", "Ar37", "Ar36"], ["Linear", "Linear", "Linear", "Linear", "Linear"])),
dict(
zip(
["Ar40", "Ar39", "Ar38", "Ar37", "Ar36"],
["Average Y", "Average Y", "Average Y", "Average Y", "Average Y"],
)
),
)
mass_spectrometer = "obama"
extract_device = "Laser Furnace"
extract_value = 10
position = 1
duration = 10
first_stage_delay = 0
second_stage_delay = 30
tray = "100-hole"
runscript_name = "Foo"
runscript_text = "this is a test script"
self.add_analysis(
"4318",
"500",
"",
"4318",
base,
sig,
blanks,
keys,
regresults,
fits,
mass_spectrometer,
extract_device,
tray,
position,
extract_value, # power requested
extract_value, # power achieved
duration, # total extraction
duration, # time at extract_value
first_stage_delay,
second_stage_delay,
runscript_name,
runscript_text,
)
def _mean_regressor_factory(self):
reg = MeanRegressor(xs=self.xs, ys=self.ys,
filter_outliers_dict=self.filter_outliers_dict,
error_type=self.error_type)
return reg
def regressor(self):
fit = self.fit
if fit is None:
fit = 'linear'
self.fit = fit
lfit = fit.lower()
is_mean = 'average' in lfit
is_expo = lfit == 'exponential'
is_poly = not (is_mean or is_expo)
reg = self._regressor
if reg is None:
if is_mean:
reg = MeanRegressor()
elif is_expo:
reg = ExponentialRegressor()
else:
reg = PolynomialRegressor()
elif is_poly and not isinstance(reg, PolynomialRegressor):
reg = PolynomialRegressor()
elif is_mean and not isinstance(reg, MeanRegressor):
reg = MeanRegressor()
elif is_expo and not isinstance(reg, ExponentialRegressor):
reg = ExponentialRegressor()
if is_poly:
reg.set_degree(fit_to_degree(fit), refresh=False)
reg.trait_set(xs=self.offset_xs, ys=self.ys,
error_calc_type=self.error_type or 'SEM',
filter_outliers_dict=self.filter_outliers_dict,
tag=self.name)
if self.truncate:
reg.set_truncate(self.truncate)
reg.calculate()
self._regressor = reg
return reg
def setUp(self):
self.reg = MeanRegressor()
class TruncateRegressionTest(TestCase):
def setUp(self):
self.reg = MeanRegressor()
def test_pre_truncate(self):
xs, ys, sol = pre_truncated_data()
self.reg.trait_set(xs=xs, ys=ys)
self.solution = sol
self.reg.trait_set(xs=xs, ys=ys)
self.reg.set_truncate('x<5')
self.assertEqual(self.reg.mean, self.solution['pre_mean'])
def test_post_truncate(self):
xs, ys, sol = pre_truncated_data()
self.reg.trait_set(xs=xs, ys=ys)
self.solution = sol
self.reg.trait_set(xs=xs, ys=ys)
self.reg.set_truncate('x>=5')
self.assertEqual(self.reg.mean, self.solution['post_mean'])
