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 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'])
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()
new_mags = j.getMagnifications()
answer = 'n'
while answer.lower() != 'y':
print new_mags
answer = format_input('O.K. to insert ? (Y/N) ')
if answer.lower()[0] != 'y':
mags_str = format_input('Enter all magnifications, separated by ",":')
new_mags = mags_str.split(',')
new_mags = map((lambda x: int(x)), new_mags)
q = leginondata.MagnificationsData(instrument=scopes[0],
magnifications=new_mags)
q.insert(force=True)
msgExit(ok_msg)
def importCalibrations(self, source_cam, source_tem, high_tension):
print "Importing calibrations...."
simumags = [50, 100, 500, 1000, 5000, 25000, 50000]
matrixtypes = ('image shift', 'stage position', 'defocus', 'stigx',
'stigy', 'beam shift', 'beam-tilt coma',
'image-shift coma')
sinedon.setConfig('leginondata', db=self.source_dbname)
#magnifications
# magnifications is not insession data
mags = leginondata.MagnificationsData(instrument=source_tem).query(
results=1)
if mags:
magnifications = mags[0]['magnifications']
else:
# simulator magnifications
magnifications = simumags
#camera sensitivity calibrations
senses = self.researchCalibration('CameraSensitivityCalibrationData',
tem=source_tem,
ccdcamera=source_cam,
high_tension=high_tension)
#beam size calibrations
beamsizes = []
for probe in ('micro', 'nano'):
beamsizes.extend(
self.researchCalibration('BeamSizeCalibrationData',
tem=source_tem,
probe_mode=probe))
#Modeled Stage calibrations
model = {}
for axis in ('x', 'y'):
model[axis] = self.researchCalibration('StageModelCalibrationData',
tem=source_tem,
ccdcamera=source_cam,
axis=axis)
pixel = {}
matrix = {}
modelmag = {}
ucenter = {}
rcenter = {}
for mag in magnifications:
#pixelsize calibrations
q = leginondata.PixelSizeCalibrationData(tem=source_tem,
ccdcamera=source_cam,
magnification=mag)
pixel[mag] = self.researchCalibration('PixelSizeCalibrationData',
tem=source_tem,
ccdcamera=source_cam,
magnification=mag)
#matrix calibrations
matrix[mag] = {}
for matrixtype in matrixtypes:
matrix[mag][matrixtype] = self.researchCalibration(
'MatrixCalibrationData',
tem=source_tem,
ccdcamera=source_cam,
magnification=mag,
type=matrixtype,
high_tension=high_tension)
#Modeled Mag Stage calibrations
modelmag[mag] = {}
for axis in ('x', 'y'):
modelmag[mag][axis] = self.researchCalibration(
'StageModelMagCalibrationData',
tem=source_tem,
ccdcamera=source_cam,
magnification=mag,
axis=axis,
high_tension=high_tension)
#eucenter focus calibrations
ucenter[mag] = {}
ucenter[mag] = self.researchCalibration('EucentricFocusData',
tem=source_tem,
magnification=mag)
#eucenter focus calibrations
rcenter[mag] = {}
rcenter[mag] = self.researchCalibration('RotationCenterData',
tem=source_tem,
magnification=mag)
sinedon.setConfig('leginondata', db=self.destination_dbname)
#magnifications
for m in mags:
m.insert(archive=True)
#camera sensitivity calibrations
for sense in senses:
sense.insert(archive=True)
#beam size calibrations
for beamsize in beamsizes:
beamsize.insert(archive=True)
#Modeled Stage calibrations
for axis in ('x', 'y'):
if model[axis]:
for m in model[axis]:
m.insert(archive=True)
for mag in magnifications:
#pixelsize calibrations
if pixel[mag]:
for p in pixel[mag]:
p.insert(archive=True)
#matrix calibrations
for matrixtype in matrixtypes:
if matrix[mag][matrixtype]:
for m in matrix[mag][matrixtype]:
m.insert(archive=True)
#Modeled Mag Stage calibrations
for axis in ('x', 'y'):
if modelmag[mag][axis]:
for m in modelmag[mag][axis]:
m.insert(archive=True)
#eucentric focus
if ucenter[mag]:
for u in ucenter[mag]:
u.insert(archive=True)
#rotation center
if rcenter[mag]:
for r in rcenter[mag]:
r.insert(archive=True)