def getCCDCameraData(self, name=None):
if name is None:
if self.ccdcamera is None:
return None
else:
name = self.ccdcamera._name
#dbtype = self.ccdcamera.DatabaseType
else:
if name not in self.ccdcameras:
raise RuntimeError('no CCD camera \'%s\' available' % name)
instrumentdata = leginondata.InstrumentData()
instrumentdata['name'] = name
#instrumentdata['type'] = dbtype
#print dbtype
try:
instrumentdata['hostname'] = self.ccdcameras[name].Hostname
except:
raise RuntimeError('unable to get TEM hostname')
results = instrumentdata.query(results=1)
## save in DB if not already there
if results:
dbinstrumentdata = results[0]
else:
dbinstrumentdata = instrumentdata
dbinstrumentdata.insert()
return dbinstrumentdata
def getRelatedFrameCameras(self,camdata): r = leginondata.InstrumentData(hostname=camdata['ccdcamera']['hostname']).query() k2cameras = [] for instrumentdata in r: if instrumentdata['name'] in VALID_CAMERA_NAMES: k2cameras.append(instrumentdata) return k2cameras
def importInstrument(self):
print "Importing instrument...."
self.is_upload = False
# guess instrument from the last image
sinedon.setConfig('leginondata', db=self.source_dbname)
q = leginondata.AcquisitionImageData(session=self.getSourceSession())
last_image = self.research(q, True)
# we know there are images for the session.
tem = last_image['scope']['tem']
camera = last_image['camera']['ccdcamera']
if tem is None:
# old uploaded session such as 12jun29b
self.is_upload = True
return None, None, 200000
high_tension = last_image['scope']['high tension']
q = leginondata.InstrumentData()
source_temdata = q.direct_query(tem.dbid)
source_cameradata = q.direct_query(camera.dbid)
if 'appion' in source_temdata['name'].lower():
self.is_upload = True
sinedon.setConfig('leginondata', db=self.destination_dbname)
tem.insert(archive=True)
camera.insert(archive=True)
return source_cameradata, source_temdata, high_tension
def querypoints(axis, label, hostname):
tem = leginondata.InstrumentData(hostname=hostname)
sm = leginondata.StageMeasurementData(label=label, axis=axis, tem=tem)
points = sm.query()
xy = []
for point in points:
x = point[axis]
y = math.hypot(point['imagex'], point['imagey']) / abs(point['delta'])
xy.append((x, y))
return xy
def querymodelmag(axis, label, hostname):
tem = leginondata.InstrumentData(hostname=hostname)
sm = leginondata.StageModelMagCalibrationData(axis=axis,
label=label,
tem=tem)
magcal = sm.query(results=1)
magcal = magcal[0]
print 'MAGCAL', magcal.timestamp
print magcal
mean = magcal['mean']
return 1.0 / mean
def saveMagnifications(self, instance, tem_name):
self.logger.info('Saving...')
instrumentdata = leginondata.InstrumentData()
instrumentdata['name'] = tem_name
instrumentdata['hostname'] = instance.getHostname()
instrumentdata['cs'] = instance.getCs()
magnificationsdata = leginondata.MagnificationsData()
magnificationsdata['instrument'] = instrumentdata
magnificationsdata['magnifications'] = instance.getMagnifications()
self.publish(magnificationsdata, database=True, dbforce=True)
self.logger.info('Magnifications saved.')
return magnificationsdata
def querymodel(axis, hostname, label=None):
tem = leginondata.InstrumentData(hostname=hostname)
sm = leginondata.StageModelCalibrationData(axis=axis, tem=tem, label=label)
model = sm.query(results=1)
if not model:
return None
model = model[0]
print 'MODEL', model.timestamp
print model
model['a'].shape = (-1, )
model['b'].shape = (-1, )
mod = gonmodel.GonModel()
mod.fromDict(model)
return mod
def upgradeLeginonDB(self):
if not self.leginon_dbupgrade.columnExists(
'AcquisitionImageData',
'REF|CorrectorPlanData|corrector plan'):
self.leginon_dbupgrade.addColumn(
'AcquisitionImageData', 'REF|CorrectorPlanData|corrector plan',
self.leginon_dbupgrade.int)
results = leginondata.InstrumentData(name='DE12').query(results=1)
if not results:
return
decameradata = results[0]
dim = {'x': 4096, 'y': 3072}
camq = leginondata.CameraEMData(ccdcamera=decameradata, dimension=dim)
plans = leginondata.CorrectorPlanData(camera=camq).query()
pairs = {}
ordered_keys = []
for i, plan in enumerate(plans):
if i == 0:
ordered_keys.append(i)
pairs[i] = (plan.timestamp.now(), plan.timestamp)
else:
ordered_keys.append(i)
pairs[i] = (plans[i - 1].timestamp, plan.timestamp)
camq = leginondata.CameraEMData(ccdcamera=decameradata, dimension=dim)
camq['save frames'] = True
imageq = leginondata.AcquisitionImageData(camera=camq)
print 'Query all DE12 images. This may take some time...'
images = imageq.query()
print 'Total of %d images' % (len(images), )
for image in images:
if image['corrector plan']:
continue
for key in ordered_keys:
if image.timestamp > pairs[key][1] and image.timestamp < pairs[
key][0]:
print key, image.dbid, image['filename'], image.timestamp
status = self.leginon_dbupgrade.updateColumn(
'AcquisitionImageData',
'REF|CorrectorPlanData|corrector plan',
'%d' % plans[key].dbid, '`DEF_id`=%d' % image.dbid,
True)
if not status:
print break_from_failed_update
def getMagnifications(self, name):
try:
instance = self.instruments[name]
except KeyError:
raise ValueError('no instrument %s' % name)
self.logger.info('Getting magnifications from the instrument...')
instance.findMagnifications()
self.logger.info('Saving...')
instrumentdata = leginondata.InstrumentData()
instrumentdata['name'] = name
instrumentdata['hostname'] = instance.getHostname()
instrumentdata['cs'] = instance.getCs()
magnificationsdata = leginondata.MagnificationsData()
magnificationsdata['instrument'] = instrumentdata
magnificationsdata['magnifications'] = instance.getMagnifications()
self.publish(magnificationsdata, database=True, dbforce=True)
self.logger.info('Magnifications saved.')
self.panel.onGetMagnificationsDone()
def initializeMagnifications(self, name):
try:
instance = self.instruments[name]
except KeyError:
raise ValueError('no instrument %s' % name)
if instance.getMagnificationsInitialized():
return
instrumentdata = leginondata.InstrumentData()
instrumentdata['name'] = name
instrumentdata['hostname'] = instance.getHostname()
queryinstance = leginondata.MagnificationsData()
queryinstance['instrument'] = instrumentdata
try:
result = self.research(queryinstance, results=1)[0]
except IndexError:
self.logger.warning('No magnifications saved for %s' % name)
return
instance.setMagnifications(result['magnifications'])
def getTEMData(self, name=None):
if name is None:
if self.tem is None:
return None
else:
name = self.tem._name
cs = self.tem.Cs
#dbtype = self.tem.DatabaseType
else:
if name not in self.tems:
raise RuntimeError('no TEM \'%s\' available' % name)
else:
cs = None
instrumentdata = leginondata.InstrumentData()
instrumentdata['name'] = name
#instrumentdata['type'] = dbtype
#print dbtype
try:
instrumentdata['hostname'] = self.tems[name].Hostname
except:
raise RuntimeError('unable to get TEM hostname')
results = instrumentdata.query(results=1)
## save in DB if not already there
if results:
dbinstrumentdata = results[0]
if dbinstrumentdata['cs'] is None:
raise RuntimeError(
'You must run db schema update script on existing TEMs before using this version of Leginon'
)
elif cs is not None and dbinstrumentdata['cs'] != cs:
raise RuntimeError(
'TEM Cs in instruments.cfg does not match database value. Correct either one to use it in Leginon'
)
else:
if cs is None:
cs = 2.0e-3
instrumentdata['cs'] = cs
dbinstrumentdata = instrumentdata
dbinstrumentdata.insert()
return dbinstrumentdata
def msgExit(msg=''):
if msg:
print msg
format_input('Hit Enter to exit')
if msg != ok_msg:
sys.exit(1)
def format_input(msg=''):
print ''
return raw_input(msg)
jeolcom_classname = format_input(
'Enter scope classname in instruments.cfg (Case sensitive): ')
scopes = leginondata.InstrumentData(name=jeolcom_classname).query()
if len(scopes) > 1:
print ''
print "There are more than one instrument using jeolcom class"
jeolcom_hostname = format_input(
'Enter the hostname where the magnifications need registering: ')
scopes = leginondata.InstrumentData(name=jeolcom_classname,
hostname=jeolcom_hostname).query()
if not scopes:
msg = "Error: Can not find a scope matching the description"
msgExit(msg)
# There should be only one scope now.
j = jeolcom.Jeol()
j.findMagnifications()
#!/usr/bin/env python
from leginon import leginondata
import sys
from sinedon import newdict
host = sys.argv[1]
i = leginondata.InstrumentData(hostname=host)
s = leginondata.StageModelCalibrationData(tem=i)
models = s.query()
labels = newdict.OrderedDict()
for model in models:
label = model['label']
labels[label] = None
for label in labels.keys():
print label
