def upgradeLeginonDB(self):
if not self.leginon_dbupgrade.tableExists('EucentricFocusData'):
return
# EucentricFocusData
# initialize column by inserting the most recent data
last_data = leginondata.EucentricFocusData().query(results=1)[0]
q = leginondata.EucentricFocusData(initializer=last_data,
probe='micro')
q.insert()
# update as 'micro' as default
r = leginondata.EucentricFocusData().query()
r.reverse()
for data in r:
q = "UPDATE `EucentricFocusData` SET `probe` = 'micro' WHERE `DEF_id` =%d" % data.dbid
self.leginon_dbupgrade.executeCustomSQL(q)
# RotationCenterData
# initialize column by inserting the most recent data
last_data = leginondata.RotationCenterData().query(results=1)[0]
q = leginondata.RotationCenterData(initializer=last_data,
probe='micro')
q.insert()
# update as 'micro' as default
r = leginondata.RotationCenterData().query()
r.reverse()
for data in r:
q = "UPDATE `RotationCenterData` SET `probe` = 'micro' WHERE `DEF_id` =%d" % data.dbid
self.leginon_dbupgrade.executeCustomSQL(q)
# MatrixCalibrationData
# initialize column by inserting the most recent data
last_data = leginondata.MatrixCalibrationData().query(results=1)[0]
q = leginondata.MatrixCalibrationData(initializer=last_data,
probe='micro')
q.insert()
r = leginondata.MatrixCalibrationData().query()
r.reverse()
for data in r:
# update as 'micro' as default only on 'defocus' and 'stigx','stigy'
if data['type'] in ('defocus', 'stigx', 'stigy'):
q = "UPDATE `MatrixCalibrationData` SET `probe` = 'micro' WHERE `DEF_id` =%d" % data.dbid
self.leginon_dbupgrade.executeCustomSQL(q)
def getMatrix(self, tem, cam, ht, mag, type):
matdat = leginondata.MatrixCalibrationData()
matdat['tem'] = tem
matdat['ccdcamera'] = cam
matdat['type'] = type
matdat['magnification'] = mag
matdat['high tension'] = ht
caldatalist = self.node.research(datainstance=matdat, results=1)
if caldatalist:
return caldatalist[0]['matrix']
else:
excstr = 'No %s matrix for %s, %s, %seV, %sx' % (type, tem, cam, ht, mag)
raise RuntimeError(excstr)
def getMatrixCal(self, tem, ccd, ht, mag, timestamp, type):
qinst = leginondata.MatrixCalibrationData(type=type, magnification=mag)
qinst['high tension'] = ht
qinst['tem'] = tem
qinst['ccdcamera'] = ccd
caldatalist = dbdk.query(qinst)
# get the one that was valid at timestamp
caldata = None
for cal in caldatalist:
if cal.timestamp < timestamp:
caldata = cal['matrix']
break
if caldata is None:
if caldatalist:
caldata = caldatalist[0]['matrix']
else:
caldata = None
return caldata