def load_molecular_weights(self):
import csv, yaml
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
yp = os.path.join(paths.spectrometer_dir, 'molecular_weights.yaml')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file. {}'.format(p))
with open(p, 'r') as f:
reader = csv.reader(f, delimiter='\t')
mws = {l[0]: float(l[1]) for l in reader}
elif os.path.isfile(yp):
self.info('loading "molecular_weights.yaml" file. {}'.format(yp))
with open(yp, 'r') as f:
mws = yaml.load(f)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mws
with open(p, 'U' if os.path.isfile(p) else 'w') as f:
writer = csv.writer(f, delimiter='\t')
# data = [a for a in six.itervalues(mws)]
data = [a for a in mws.values()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
self.debug('Mol weights {}'.format(mws))
self.molecular_weights = mws
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(self, db_mol_weights=True):
self.debug('******************************* LOAD Spec')
if db_mol_weights:
# get the molecular weights from the database
dbm = IsotopeDatabaseManager(application=self.application,
warn=False)
self.db = dbm
if dbm.isConnected():
self.info('loading molecular_weights from database')
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
self.spectrometer.molecular_weights = m
if not self.spectrometer.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, 'U') as f:
reader = csv.reader(f, delimiter='\t')
args = [[l[0], float(l[1])] for l in reader]
self.spectrometer.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, 'U') as f:
writer = csv.writer(f, delimiter='\t')
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
self.spectrometer.molecular_weights = mw
#config = self.get_configuration(path=os.path.join(paths.spectrometer_dir, 'detectors.cfg'))
#for name in config.sections():
# relative_position = self.config_get(config, name, 'relative_position', cast='float')
# color = self.config_get(config, name, 'color', default='black')
# default_state = self.config_get(config, name, 'default_state', default=True, cast='boolean')
# isotope = self.config_get(config, name, 'isotope')
# kind = self.config_get(config, name, 'kind', default='Faraday', optional=True)
# self.spectrometer.add_detector(name=name,
# relative_position=relative_position,
# color=color,
# active=default_state,
# isotope=isotope,
# kind=kind)
self.spectrometer.load()
return True
def load(self, db_mol_weights=True):
self.debug('******************************* LOAD Spec')
if db_mol_weights:
# get the molecular weights from the database
dbm = IsotopeDatabaseManager(application=self.application,
warn=False)
self.db = dbm
if dbm.isConnected():
self.info('loading molecular_weights from database')
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
self.spectrometer.molecular_weights = m
if not self.spectrometer.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, 'U') as f:
reader = csv.reader(f, delimiter='\t')
args = [[l[0], float(l[1])] for l in reader]
self.spectrometer.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, 'U') as f:
writer = csv.writer(f, delimiter='\t')
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
self.spectrometer.molecular_weights = mw
#config = self.get_configuration(path=os.path.join(paths.spectrometer_dir, 'detectors.cfg'))
#for name in config.sections():
# relative_position = self.config_get(config, name, 'relative_position', cast='float')
# color = self.config_get(config, name, 'color', default='black')
# default_state = self.config_get(config, name, 'default_state', default=True, cast='boolean')
# isotope = self.config_get(config, name, 'isotope')
# kind = self.config_get(config, name, 'kind', default='Faraday', optional=True)
# self.spectrometer.add_detector(name=name,
# relative_position=relative_position,
# color=color,
# active=default_state,
# isotope=isotope,
# kind=kind)
self.spectrometer.load()
return True
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 load(self, db_mol_weights=True):
spec = self.spectrometer
mftable = spec.magnet.mftable
self.debug('******************************* LOAD Spec')
if db_mol_weights:
# get the molecular weights from the database
# dbm = IsotopeDatabaseManager(application=self.application,
# warn=False)
dbm = self.application.get_service(
'pychron.database.isotope_database_manager.IsotopeDatabaseManager'
)
if dbm and dbm.is_connected():
self.info('loading molecular_weights from database')
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
spec.molecular_weights = m
mftable.db = dbm.db
if not spec.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, 'U') as f:
reader = csv.reader(f, delimiter='\t')
args = [[l[0], float(l[1])] for l in reader]
spec.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, 'U') as f:
writer = csv.writer(f, delimiter='\t')
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
spec.molecular_weights = mw
self.spectrometer.load()
mftable.spectrometer_name = self.spectrometer.name
return True
def load(self, db_mol_weights=True):
spec = self.spectrometer
mftable = spec.magnet.mftable
self.debug("******************************* LOAD Spec")
if db_mol_weights:
# get the molecular weights from the database
# dbm = IsotopeDatabaseManager(application=self.application,
# warn=False)
dbm = self.application.get_service("pychron.database.isotope_database_manager.IsotopeDatabaseManager")
if dbm and dbm.is_connected():
self.info("loading molecular_weights from database")
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
spec.molecular_weights = m
mftable.db = dbm.db
if not spec.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, "molecular_weights.csv")
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, "U") as f:
reader = csv.reader(f, delimiter="\t")
args = [[l[0], float(l[1])] for l in reader]
spec.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, "U") as f:
writer = csv.writer(f, delimiter="\t")
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
spec.molecular_weights = mw
self.spectrometer.load()
mftable.spectrometer_name = self.spectrometer.name
return True
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)
def load_molecular_weights(self):
import csv, yaml
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
yp = os.path.join(paths.spectrometer_dir, 'molecular_weights.yaml')
mws = None
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file. {}'.format(p))
with open(p, 'r') as f:
reader = csv.reader(f, delimiter='\t')
try:
mws = {l[0]: float(l[1]) for l in reader}
except BaseException:
mws = None
elif os.path.isfile(yp):
self.info('loading "molecular_weights.yaml" file. {}'.format(yp))
with open(yp, 'r') as f:
try:
mws = yaml.load(f)
except BaseException:
mws = None
if mws is None:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mws
with open(p, 'w') as f:
writer = csv.writer(f, delimiter='\t')
data = sorted(mws.items(), key=lambda x: x[1])
for row in data:
writer.writerow(row)
self.debug('Mol weights {}'.format(mws))
self.molecular_weights = mws