def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
self.scandb = ScanDB()
self.instdb = InstrumentDB(self.scandb)
print("Connect ScanDB ", self.scandb.engine, self.instname)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def make_uscope_rotation(scandb,
offline_inst='IDE_Microscope',
offline_xyz=('13IDE:m1.VAL', '13IDE:m2.VAL',
'13IDE:m3.VAL'),
online_inst='IDE_SampleStage',
online_xyz=('13XRM:m4.VAL', '13XRM:m6.VAL',
'13XRM:m5.VAL')):
"""
Calculate and store the rotation maxtrix needed to convert
positions from the GSECARS offline microscope (OSCAR)
to the SampleStage in the microprobe station.
This calculates the rotation matrix based on all position
names that occur in the Position List for both instruments.
Note:
The result is saved as a json dictionary to the config table
"""
instdb = InstrumentDB(scandb)
pos_us = read_xyz(instdb, offline_inst, offline_xyz)
pos_ss = read_xyz(instdb, online_inst, online_xyz)
# calculate the rotation matrix
mat_us2ss, v1, v2 = calc_rotmatrix(pos_us, pos_ss)
if mat_us2ss is None:
return
#endif
uscope = instdb.get_instrument(offline_inst)
sample = instdb.get_instrument(online_inst)
uname = uscope.name.replace(' ', '_')
sname = sample.name.replace(' ', '_')
conf_us2ss = "CoordTrans:%s:%s" % (uname, sname)
us2ss = dict(source=offline_xyz,
dest=online_xyz,
rotmat=mat_us2ss.tolist())
scandb.set_config(conf_us2ss, json.dumps(us2ss))
# calculate the rotation matrix going the other way
mat_ss2us, v1, v2 = calc_rotmatrix(pos_ss, pos_us)
conf_ss2us = "CoordTrans:%s:%s" % (sname, uname)
ss2us = dict(source=online_xyz,
dest=offline_xyz,
rotmat=mat_ss2us.tolist())
print("Saving Calibration %s" % conf_ss2us)
scandb.set_config(conf_ss2us, json.dumps(ss2us))
scandb.commit()
def connect_scandb(dbname=None, server='postgresql', _larch=None, **kwargs):
if (_larch.symtable.has_symbol(SCANDB_NAME)
and _larch.symtable.get_symbol(SCANDB_NAME) is not None):
scandb = _larch.symtable.get_symbol(SCANDB_NAME)
else:
scandb = ScanDB(dbname=dbname, server=server, **kwargs)
_larch.symtable.set_symbol(SCANDB_NAME, scandb)
if (_larch.symtable.has_symbol(INSTDB_NAME)
and _larch.symtable.get_symbol(INSTDB_NAME) is not None):
instdb = _larch.symtable.get_symbol(INSTDB_NAME)
else:
instdb = InstrumentDB(scandb)
_larch.symtable.set_symbol(INSTDB_NAME, instdb)
return scandb
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
dbconn_dir = dbconn.get('dbconn_dir', '')
dbconn_file = dbconn.get('dbconn_file', '')
if os.path.exists(dbconn_dir) and len(dbconn_file) > 0:
sys.path.insert(0, dbconn_dir)
mod = __import__(dbconn_file)
conn = mod.conn
scandb = ScanDB(**mod.conn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def connect_scandb(scandb=None, dbname=None, _larch=None, **kwargs):
global _scandb, _instdb
if _scandb is not None:
return _scandb
if scandb is None:
scandb = ScanDB(dbname=dbname, **kwargs)
if scandb is not None:
_scandb = scandb
if _larch is not None:
_larch.symtable.set_symbol(SCANDB_NAME, _scandb)
if _instdb is None:
_instdb = InstrumentDB(_scandb)
if _larch is not None:
_larch.symtable.set_symbol(INSTDB_NAME, _instdb)
return _scandb
