def load_isotopedb_defaults(db):
with db.session_ctx() as sess:
for name, mass in MOLECULAR_WEIGHTS.iteritems():
db.add_molecular_weight(name, mass)
for at in ['blank_air',
'blank_cocktail',
'blank_unknown',
'background', 'air', 'cocktail', 'unknown']:
# blank', 'air', 'cocktail', 'background', 'unknown']:
db.add_analysis_type(at)
for mi in ['obama', 'jan', 'nmgrl map']:
db.add_mass_spectrometer(mi)
project = db.add_project('references')
#print project
for i, di in enumerate(['blank_air',
'blank_cocktail',
'blank_unknown',
'background', 'air', 'cocktail']):
samp = db.add_sample(di, project=project)
#print samp.id, samp, project.id
# samp.project = project
#samp.project_id=project.id
#print samp.project_id
db.add_labnumber(i + 1, sample=samp)
sess.commit()
for hi, kind, make in [('Fusions CO2', '10.6um co2', 'photon machines'),
('Fusions Diode', '810nm diode', 'photon machines'),
('Fusions UV', '193nm eximer', 'photon machines')
]:
db.add_extraction_device(name=hi,
kind=kind,
make=make,
)
mdir = os.path.join(paths.setup_dir, 'irradiation_tray_maps')
mdir=paths.irradiation_tray_maps_dir
# if not os.path.isdir(mdir):
# if information(None, 'No irradiation_tray_maps directory. add to .../setupfiles'):
# try:
# os.mkdir(mdir)
# except OSError,e:
# warning(None, 'Failed making {}: error={}'.format(mdir, e))
#
# else:
for p, name in iterdir(mdir, exclude=('.zip',)):
load_irradiation_map(db, p, name)
mdir = paths.map_dir
for p, name in iterdir(mdir):
_load_tray_map(db, p, name)
for t in ('ok', 'invalid'):
db.add_tag(t, user='******')
def map_dac_to_isotope(self, dac=None, det=None, current=True):
if dac is None:
dac = self._dac
if det is None:
det = self.detector
if det:
dac = self.spectrometer.uncorrect_dac(det, dac, current=current)
m = self.map_dac_to_mass(dac, det.name)
molweights = self.spectrometer.molecular_weights
return next((k for k, v in molweights.iteritems() if abs(v - m) < 0.001), None)
def load_isotopedb_defaults(db):
with db.session_ctx() as sess:
for name, mass in MOLECULAR_WEIGHTS.iteritems():
db.add_molecular_weight(name, mass)
populate_isotopes(db)
for at in ['blank_air',
'blank_cocktail',
'blank_unknown',
'background', 'air', 'cocktail', 'unknown']:
# blank', 'air', 'cocktail', 'background', 'unknown']:
db.add_analysis_type(at)
# for mi in ['obama', 'jan', 'nmgrl map']:
# db.add_mass_spectrometer(mi)
project = db.add_project('REFERENCES')
# print project
for i, di in enumerate(['blank_air',
'blank_cocktail',
'blank_unknown',
'background', 'air', 'cocktail']):
samp = db.add_sample(di, project=project)
# print samp.id, samp, project.id
# samp.project = project
# samp.project_id=project.id
# print samp.project_id
# db.add_labnumber(i + 1, sample=samp)
sess.commit()
# for hi, kind, make in [('Fusions CO2', '10.6um co2', 'photon machines'),
# ('Fusions Diode', '810nm diode', 'photon machines'),
# ('Fusions UV', '193nm eximer', 'photon machines')]:
# db.add_extraction_device(name=hi,
# kind=kind,
# make=make)
mdir = paths.irradiation_tray_maps_dir
for p, name in iterdir(mdir, exclude=('.zip',)):
og = False
load_irradiation_map(db, p, name, overwrite_geometry=og)
mdir = paths.map_dir
for p, name in iterdir(mdir):
try:
_load_tray_map(db, p, name)
except BaseException:
print 'failed loading tray map "{}", "{}"'.format(p, name)
for t in ('ok', 'invalid'):
db.add_tag(t, user='******')
def map_dac_to_isotope(self, dac=None, det=None, current=True):
"""
convert a dac voltage to isotope name for a given detector
:param dac: float, voltage
:param det: str, detector name
:param current: bool, get current hv
:return: str, e.g Ar40
"""
if dac is None:
dac = self._dac
if det is None:
det = self.detector
if det:
dac = self.spectrometer.uncorrect_dac(det, dac, current=current)
m = self.map_dac_to_mass(dac, det.name)
if m is not None:
molweights = self.spectrometer.molecular_weights
return next((k for k, v in molweights.iteritems() if abs(v - m) < 0.001), None)
def map_dac_to_isotope(self, dac=None, det=None, current=True):
"""
convert a dac voltage to isotope name for a given detector
:param dac: float, voltage
:param det: str, detector name
:param current: bool, get current hv
:return: str, e.g Ar40
"""
if dac is None:
dac = self._dac
if det is None:
det = self.detector
if det:
dac = self.spectrometer.uncorrect_dac(det, dac, current=current)
m = self.map_dac_to_mass(dac, det.name)
if m is not None:
molweights = self.spectrometer.molecular_weights
return next((k for k, v in molweights.iteritems() if abs(v - m) < 0.001), None)