def revertTargetListZ(self, targetlistdata):
'''use the z position of the target list parent image'''
imageref = targetlistdata.special_getitem('image', dereference=False)
imageid = imageref.dbid
imagedata = self.researchDBID(leginondata.AcquisitionImageData,
imageid,
readimages=False)
# look for a more recent version of this image
target = imagedata['target']
imquery = leginondata.AcquisitionImageData(target=target)
allversions = imquery.query(readimages=False)
imagedata = allversions[0]
scope = imagedata['scope']
z = scope['stage position']['z']
tem = scope['tem']
filename = imagedata['filename']
self.logger.info('returning %s to z=%.4e of parent image %s' % (
tem['name'],
z,
filename,
))
self.instrument.setTEM(tem['name'])
self.instrument.tem.StagePosition = {'z': z}
self.logger.info('z change done')
def insertAcquisitionImageData(self, imagedata):
acquisitionimagedata = leginondata.AcquisitionImageData(
initializer=imagedata, version=0)
self.setImageFilename(acquisitionimagedata)
acquisitionimagedata.attachPixelSize()
acquisitionimagedata.insert(force=True)
return acquisitionimagedata
def monitorDrift(self, driftdata=None):
self.setStatus('processing')
self.logger.info('DriftManager monitoring drift...')
if driftdata is not None:
## use driftdata to set up scope and camera
pname = driftdata['presetname']
emtarget = driftdata['emtarget']
threshold = driftdata['threshold']
target = emtarget['target']
self.presetsclient.toScope(pname, emtarget)
presetdata = self.presetsclient.getCurrentPreset()
else:
target = None
threshold = None
## acquire images, measure drift
self.abortevent.clear()
# extra pause to wait for image shift to stabilize
self.logger.info('pausing before loop')
time.sleep(self.settings['pause time'] / 2.0)
self.logger.info('paused before loop')
status, final, im = self.acquireLoop(target, threshold=threshold)
if status in ('drifted', 'timeout'):
## declare drift above threshold
self.declareDrift('threshold')
## Generate DriftMonitorResultData
## only output if this was called from another node
if driftdata is not None:
self.logger.info('Publishing final drift image...')
acqim = leginondata.AcquisitionImageData(initializer=im)
acqim['target'] = target
acqim['emtarget'] = emtarget
acqim['preset'] = presetdata
self.publish(acqim, pubevent=True)
self.logger.info('Publishing DriftMonitorResultData...')
result = leginondata.DriftMonitorResultData()
result['status'] = status
result['final'] = final
self.publish(result, pubevent=True, database=True, dbforce=True)
self.logger.info('DriftManager done monitoring drift')
self.setStatus('idle')
def fakeImage(self):
# need an existing image name
imageq = leginondata.AcquisitionImageData(
filename='08oct13d_00045ma_1')
results = imageq.query()
return results[0]