def reseachCorrectorPlan(self, cameradata):
qcamera = leginondata.CameraEMData()
# Fix Me: Ignore gain index for now because camera setting does not have it when theplan is saved.
for key in ('ccdcamera','dimension','binning','offset'):
qcamera[key] = cameradata[key]
qplan = leginondata.CorrectorPlanData()
qplan['camera'] = qcamera
plandatalist = qplan.query()
if plandatalist:
return plandatalist[0]
else:
return None
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 storeCorrectorPlan(self, plan):
# import instrument here so that wx is not required unless Leginon is running
import instrument
camsettings = self.settings['camera settings']
ccdname = self.settings['instruments']['ccdcamera']
ccdcamera = self.instrument.getCCDCameraData(ccdname)
cameradata = leginondata.CameraEMData()
cameradata.update(self.settings['camera settings'])
cameradata['ccdcamera'] = ccdcamera
plandata = leginondata.CorrectorPlanData()
plandata['session'] = self.session
plandata['camera'] = cameradata
plandata['bad_rows'] = plan['rows']
plandata['bad_cols'] = plan['columns']
plandata['bad_pixels'] = plan['pixels']
plandata['despike'] = plan['despike']
plandata['despike size'] = plan['despike size']
plandata['despike threshold'] = plan['despike threshold']
plandata.insert(force=True)
self.stopTimer('Corrector.displayImage')
def storePlan(self, plan):
newcamstate = leginondata.CorrectorCamstateData()
newcamstate['session'] = self.session
if self.instrument is None or self.instrument.ccdcamera is None:
self.logger.error('Plan not saved: no camera to associate it with')
return
try:
self.instrument.ccdcamera.Settings = self.settings[
'camera settings']
newcamstate.friendly_update(self.instrument.ccdcamera.Geometry)
except Exception, e:
self.logger.error('Plan not saved: %s' % e)
return
plandata = leginondata.CorrectorPlanData()
plandata['session'] = self.session
plandata['camstate'] = newcamstate
plandata['bad_rows'] = plan['rows']
plandata['bad_cols'] = plan['columns']
plandata['bad_pixels'] = plan['pixels']
plandata['ccdcamera'] = self.instrument.getCCDCameraData()
self.publish(plandata, database=True, dbforce=True)
def acquireSeries(self, n):
series = []
for i in range(n):
self.logger.info('Acquiring reference image (%s of %s)' %
(i + 1, n))
image = self.instrument.ccdcamera.Image
series.append(image)