def _load_tray_map(db, p, name):
from pychron.stage.maps.laser_stage_map import LaserStageMap
sm = LaserStageMap(file_path=p)
r = sm.g_dimension
# blob = ''.join([struct.pack('>fff', si.x, si.y, r)
# for si in sm.sample_holes])
# from pychron.canvas.utils import make_geom
blob = make_geom(((si.x, si.y, r) for si in sm.sample_holes))
db.add_load_holder(name, geometry=blob)
def _load_tray_map(db, p, name):
from pychron.stage.maps.laser_stage_map import LaserStageMap
sm = LaserStageMap(file_path=p)
r = sm.g_dimension
# blob = ''.join([struct.pack('>fff', si.x, si.y, r)
# for si in sm.sample_holes])
# from pychron.canvas.utils import make_geom
blob = make_geom(((si.x, si.y, r) for si in sm.sample_holes))
db.add_load_holder(name, geometry=blob)
def load_irradiation_map(db, p, name, overwrite_geometry=False):
holes = parse_irradiation_tray_map(p)
if holes is not None:
try:
# blob = ''.join([struct.pack('>fff', x, y, r) for x, y, r in holes])
blob = make_geom(holes)
name, _ = os.path.splitext(name)
h = db.add_irradiation_holder(name)
if overwrite_geometry or not h.geometry:
h.geometry = blob
except Exception as e:
print('load irradiation map', p, name, e)
db.session.rollback()
def load_irradiation_map(db, p, name, overwrite_geometry=False):
holes = parse_irradiation_tray_map(p)
if holes is not None:
try:
# blob = ''.join([struct.pack('>fff', x, y, r) for x, y, r in holes])
blob = make_geom(holes)
name, _ = os.path.splitext(name)
h = db.add_irradiation_holder(name)
if overwrite_geometry or not h.geometry:
h.geometry = blob
except Exception, e:
print 'load irradiation map', p, name, e
db.sess.rollback()
def _transfer_meta(self, dest, dban, monitor_mapping):
self.debug('transfer meta {}'.format(monitor_mapping))
dblab = dban.labnumber
if monitor_mapping is None:
dbsam = dblab.sample
project = dbsam.project.name
project_name = project.replace('/', '_').replace('\\', '_')
sample_name = dbsam.name
material_name = dbsam.material.name
else:
sample_name, material, project = monitor_mapping
sam = dest.get_sample(sample_name, project_name, material_name)
if not sam:
if not dest.get_material(material_name):
self.debug('add material {}'.format(material_name))
dest.add_material(material_name)
dest.flush()
if not dest.get_project(project_name):
self.debug('add project {}'.format(project_name))
dest.add_project(project_name)
dest.flush()
self.debug('add sample {}'.format(sample_name))
sam = dest.add_sample(sample_name, project_name, material_name)
dest.flush()
dbirradpos = dblab.irradiation_position
if not dbirradpos:
irradname = 'NoIrradiation'
levelname = 'A'
holder = 'Grid'
pos = None
identifier = dblab.identifier
doses = []
prod = None
prodname = 'NoIrradiation'
geom = make_geom([(0, 0, 0.0175),
(1, 0, 0.0175),
(2, 0, 0.0175),
(3, 0, 0.0175),
(4, 0, 0.0175),
(0, 1, 0.0175),
(1, 1, 0.0175),
(2, 1, 0.0175),
(3, 1, 0.0175),
(4, 1, 0.0175),
(0, 2, 0.0175),
(1, 2, 0.0175),
(2, 2, 0.0175),
(3, 2, 0.0175),
(4, 2, 0.0175),
(0, 3, 0.0175),
(1, 3, 0.0175),
(2, 3, 0.0175),
(3, 3, 0.0175),
(4, 3, 0.0175),
(0, 4, 0.0175),
(1, 4, 0.0175),
(2, 4, 0.0175),
(3, 4, 0.0175),
(4, 4, 0.0175)
])
else:
dblevel = dbirradpos.level
dbirrad = dblevel.irradiation
dbchron = dbirrad.chronology
irradname = dbirrad.name
levelname = dblevel.name
holder = dblevel.holder.name if dblevel.holder else ''
geom = dblevel.holder.geometry if dblevel.holder else ''
prodname = dblevel.production.name if dblevel.production else ''
prodname = prodname.replace(' ', '_')
pos = dbirradpos.position
doses = dbchron.get_doses()
meta_repo = self.dvc.meta_repo
# save db irradiation
if not dest.get_irradiation(irradname):
self.debug('Add irradiation {}'.format(irradname))
self.dvc.add_irradiation(irradname, doses)
dest.flush()
# meta_repo.add_irradiation(irradname)
# meta_repo.add_chronology(irradname, doses, add=False)
# meta_repo.commit('added irradiation {}'.format(irradname))
# save production name to db
if not dest.get_production(prodname):
self.debug('Add production {}'.format(prodname))
dest.add_production(prodname)
dest.flush()
# meta_repo.add_production(irradname, prodname, prod, add=False)
# meta_repo.commit('added production {}'.format(prodname))
# save db level
if not dest.get_irradiation_level(irradname, levelname):
self.debug('Add level irrad:{} level:{}'.format(irradname, levelname))
dest.add_irradiation_level(levelname, irradname, holder, prodname)
dest.flush()
meta_repo.add_irradiation_holder(holder, geom, add=False)
meta_repo.add_level(irradname, levelname, add=False)
meta_repo.update_level_production(irradname, levelname, prodname)
# meta_repo.commit('added empty level {}{}'.format(irradname, levelname))
if pos is None:
pos = self._get_irradpos(dest, irradname, levelname, identifier)
# save db irradiation position
if not dest.get_irradiation_position(irradname, levelname, pos):
self.debug('Add position irrad:{} level:{} pos:{}'.format(irradname, levelname, pos))
p = meta_repo.get_level_path(irradname, levelname)
with open(p, 'r') as rfile:
yd = json.load(rfile)
dd = dest.add_irradiation_position(irradname, levelname, pos)
dd.identifier = dblab.identifier
dd.sample = sam
dest.flush()
try:
f = dban.labnumber.selected_flux_history.flux
j, e = f.j, f.j_err
except AttributeError:
j, e = 0, 0
yd.append({'j': j, 'j_err': e, 'position': pos, 'decay_constants': {}})
dvc_dump(yd, p)
dest.commit()