class ScanboxSBXView(object):
def __init__(self, path):
self.path = Path(path)
# def toDict(self):
# return dict(
# name = self.path.stem,
# user = '******',
# time = str(self.path.created_at),
# host = '2P',
# desc = '',
# mouse = self.path.size.str,
# package = 'package',
# )
def toDict(self):
return dict(
path=self.path.relative_to(opt.scanbox_root).str,
time=str(self.path.created_at),
size=self.path.size.str,
)
class ScanboxIO(object):
session = None
channel = None
def __init__(self, path):
self.path = Path(path).ensure_suffix('.io')
self.session = SessionBoundNamespace(self.db_session_factory(),
db.Workspace, db.ROI, db.Datatag,
db.Condition, db.Trial)
@property
def is_there(self):
return self.path.exists()
@property
def db_path(self):
return self.path.joinpath('db.sqlite3').absolute()
@property
def db_session_factory(self):
maker = db.get_sessionmaker(self.db_path)
# sessionmaker can configure without bind(engine)
# so setup event first. it's doable.
# event.remove(maker, 'before_attach', db.SQLite3Base.before_attach)
event.listen(maker, 'before_flush', db.before_flush)
event.listen(maker, 'after_commit', db.after_commit)
return maker
def set_workspace(self, id):
self.workspace_id = id
return self
@property
def workspace(self):
return self.session.Workspace.one_or_none(id=self.workspace_id)
@property
def mat(self):
return ScanboxMatView(self.path.with_suffix('.mat'))
@property
def sbx(self):
return ScanboxSBXView(self.path.with_suffix('.sbx'))
@property
def ephys(self):
return ScanboxEphysView(self, self.path.with_suffix('.txt'))
@property
def attributes(self):
error = None
try:
workspaces = self.session.Workspace.all()
except Exception as e:
notable = 'no such table' in str(e)
nocolumn = 'no such column' in str(e)
workspaces = []
error = dict(notable=notable,
nocolumn=nocolumn,
detail=str(e),
type=type(e).__name__)
return dict(hops=self.path.relative_to(opt.scanbox_root).parts,
path=self.path.str,
is_there=self.is_there,
mat=self.mat,
sbx=self.sbx,
error=error,
mode='uni' if self.mat.scanmode else 'bi',
workspaces=workspaces)
def get_channel(self, number):
return ScanboxChannel(self.path.joinpath('{}.chan'.format(number)))
def set_channel(self, number):
self.channel = self.get_channel(number)
return self
def remove_io(self):
self.path.rmtree()
self.session = SessionBoundNamespace( # unnecessary implementation
self.db_session_factory(), db.Workspace, db.ROI, db.Datatag,
db.Condition, db.Trial)
return self.attributes
def import_raw(self):
self.path.mkdir_if_none()
db.recreate(self.db_path)
self.session = SessionBoundNamespace(self.db_session_factory(),
db.Workspace, db.ROI, db.Datatag,
db.Condition, db.Trial)
self.import_exp_as_condition()
for chan in range(self.mat.nchannels):
self.get_channel(chan).import_with_io(self)
return self.attributes
def import_exp_as_condition(self):
s = glab()
entity = s.query(ExperimentV1).filter_by(
keyword=self.path.stem).one_or_none()
if entity:
print 'There is matching condition data in ED for {!r}'.format(
self.path.stem)
try:
session = self.session._session
with session.begin():
condition = db.Condition.from_expv1(entity)
condition.trials.extend([
db.Trial.init_and_update(**trial) for trial in entity
])
session.add(condition)
except Exception as e:
print 'Condition import failed with reason below,', str(e)
else:
print 'There is no matching condition data in ED for {!r}'.format(
self.path.stem)
def upgrade_db_schema(self):
db.upgrade(db.SQLite3Base.metadata,
self.db_session_factory.kw.get('bind'))
return self.attributes