def _export_spec_factory(self):
# dc = self.collector
# fb = dc.get_fit_block(-1, self.fits)
# rs_name, rs_text = self._assemble_script_blob()
rid = self.per_spec.run_spec.runid
# blanks = self.get_previous_blanks()
# dkeys = [d.name for d in self._active_detectors]
# sf = dict(zip(dkeys, fb))
# p = self._current_data_frame
ic = self.per_spec.isotope_group.get_ic_factor('CDD')
exp = MassSpecExportSpec(runid=rid,
runscript_name=self.per_spec.runscript_name,
runscript_text=self.per_spec.runscript_blob,
# signal_fits=sf,
mass_spectrometer=self.per_spec.run_spec.mass_spectrometer.capitalize(),
# blanks=blanks,
# data_path=p,
isotopes=self.per_spec.isotope_group.isotopes,
# signal_intercepts=si,
# signal_intercepts=self._processed_signals_dict,
is_peak_hop=self.per_spec.save_as_peak_hop,
ic_factor_v=float(nominal_value(ic)),
ic_factor_e=float(std_dev(ic)))
exp.load_record(self.per_spec.run_spec)
return exp
def _export_spec_factory(self):
# dc = self.collector
# fb = dc.get_fit_block(-1, self.fits)
# rs_name, rs_text = self._assemble_script_blob()
rid = self.per_spec.run_spec.runid
# blanks = self.get_previous_blanks()
# dkeys = [d.name for d in self._active_detectors]
# sf = dict(zip(dkeys, fb))
# p = self._current_data_frame
ic = self.per_spec.isotope_group.get_ic_factor('CDD')
exp = MassSpecExportSpec(
runid=rid,
runscript_name=self.per_spec.runscript_name,
runscript_text=self.per_spec.runscript_blob,
# signal_fits=sf,
mass_spectrometer=self.per_spec.run_spec.mass_spectrometer.
capitalize(),
# blanks=blanks,
# data_path=p,
isotopes=self.per_spec.isotope_group.isotopes,
# signal_intercepts=si,
# signal_intercepts=self._processed_signals_dict,
is_peak_hop=self.per_spec.save_as_peak_hop,
ic_factor_v=float(nominal_value(ic)),
ic_factor_e=float(std_dev(ic)))
exp.load_record(self.per_spec.run_spec)
return exp
class ExportSpecTestCase(unittest.TestCase):
def setUp(self):
data_path = '/Users/ross/Sandbox/aaaa_isotope.h5'
self.spec = MassSpecExportSpec(data_path=data_path)
def test_sorted_iter_isotopes(self):
e = self.spec
with self.spec.open_file():
isotopes = list(e.iter_isotopes())
isotopes = sort_isotopes(isotopes, key=lambda x: x[0])
for (iso,
det), siso in zip(isotopes,
('Ar40', 'Ar39', 'Ar38', 'Ar37', 'Ar36')):
self.assertEqual(iso, siso)
def test_non_fool_massspec(self):
e = self.spec
with e.open_file():
det = e._get_baseline_detector('Ar40', 'H1')
self.assertEqual(det, 'H1')
def test_fool_massspec(self):
e = self.spec
with e.open_file():
e.is_peak_hop = True
det = e._get_baseline_detector('Ar40', 'H1')
self.assertEqual(det, e.peak_hop_detector)
def test_baseline(self):
e = self.spec
with e.open_file():
det = 'H1'
tb, vb = e.get_baseline_data('Ar40', det)
self.assertEqual(len(tb), 10)
def test_iter_isotopes(self):
with self.spec.open_file():
e = self.spec
gen = e.iter_isotopes()
iso, det = next(gen)
self.assertEqual(iso, 'Ar36')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar37')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar38')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar39')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar40')
self.assertEqual(det, 'CDD')
class ExportSpecTestCase(unittest.TestCase):
def setUp(self):
data_path = '/Users/ross/Sandbox/aaaa_isotope.h5'
self.spec = MassSpecExportSpec(data_path=data_path)
def test_sorted_iter_isotopes(self):
e = self.spec
with self.spec.open_file():
isotopes = list(e.iter_isotopes())
isotopes = sort_isotopes(isotopes, key=lambda x: x[0])
for (iso, det), siso in zip(isotopes, ('Ar40', 'Ar39',
'Ar38', 'Ar37', 'Ar36')):
self.assertEqual(iso, siso)
def test_non_fool_massspec(self):
e = self.spec
with e.open_file():
det = e._get_baseline_detector('Ar40', 'H1')
self.assertEqual(det, 'H1')
def test_fool_massspec(self):
e = self.spec
with e.open_file():
e.is_peak_hop = True
det = e._get_baseline_detector('Ar40', 'H1')
self.assertEqual(det, e.peak_hop_detector)
def test_baseline(self):
e = self.spec
with e.open_file():
det = 'H1'
tb, vb = e.get_baseline_data('Ar40', det)
self.assertEqual(len(tb), 10)
def test_iter_isotopes(self):
with self.spec.open_file():
e = self.spec
gen = e.iter_isotopes()
iso, det = next(gen)
self.assertEqual(iso, 'Ar36')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar37')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar38')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar39')
self.assertEqual(det, 'CDD')
iso, det = next(gen)
self.assertEqual(iso, 'Ar40')
self.assertEqual(det, 'CDD')
def _make_spec(self, ai):
rs_name, rs_text = '', ''
rid = ai.record_id
exp = MassSpecExportSpec(runid=rid,
runscript_name=rs_name,
runscript_text=rs_text,
mass_spectrometer=ai.mass_spectrometer.capitalize(),
isotopes=ai.isotopes)
exp.load_record(ai)
return exp
def _make_spec(self, ai):
rs_name, rs_text = '', ''
rid = ai.record_id
exp = MassSpecExportSpec(
runid=rid,
runscript_name=rs_name,
runscript_text=rs_text,
mass_spectrometer=ai.mass_spectrometer.capitalize(),
isotopes=ai.isotopes)
exp.load_record(ai)
return exp
def setUp(self):
data_path = '/Users/ross/Sandbox/aaaa_isotope.h5'
self.spec = MassSpecExportSpec(data_path=data_path)
def setUp(self):
data_path = '/Users/ross/Sandbox/aaaa_isotope.h5'
self.spec = MassSpecExportSpec(data_path=data_path)