def acquireEmptyCameraImageData(self):
imagedata = leginondata.CameraImageData()
imagedata['session'] = self.session
scopedata = self.instrument.getData(leginondata.ScopeEMData)
cameradata = self.instrument.getData(leginondata.CameraEMData)
imagedata['scope'] = scopedata
imagedata['camera'] = cameradata
return imagedata
def acquireCameraImageData(self, scopeclass=leginondata.ScopeEMData, allow_retracted=False, type='normal'):
'''Acquire a raw image from the currently configured CCD camera'''
## Retract the cameras that are above this one (higher zplane)
for name,cam in self.instrument.ccdcameras.items():
if cam.Zplane > self.instrument.ccdcamera.Zplane:
try:
if cam.Inserted:
cam.Inserted = False
self.logger.info('retracted camera: %s' % (name,))
except:
pass
## insert the current camera, unless allow_retracted
if not allow_retracted:
try:
inserted = self.instrument.ccdcamera.Inserted
except:
inserted = True
if not inserted:
camname = self.instrument.getCCDCameraName()
self.logger.info('inserting camera: %s' % (camname,))
self.instrument.ccdcamera.Inserted = True
## set type to normal or dark
self.instrument.ccdcamera.ExposureType = type
imagedata = leginondata.CameraImageData()
imagedata['session'] = self.session
## make sure shutter override is activated
try:
self.instrument.tem.ShutterControl = True
except:
# maybe tem has no such function
pass
## acquire image, get new scope/camera params
try:
scopedata = self.instrument.getData(scopeclass)
except:
raise
#cameradata_before = self.instrument.getData(leginondata.CameraEMData)
imagedata['scope'] = scopedata
self.startExposureTimer()
imagedata['image'] = self.instrument.ccdcamera.Image
cameradata_after = self.instrument.getData(leginondata.CameraEMData)
## only using cameradata_after, not cameradata_before
imagedata['camera'] = cameradata_after
## duplicating 'use frames' here because we may reuse same
## CameraEMData for multiple versions of AcquisitionImageData
imagedata['use frames'] = cameradata_after['use frames']
self.readout_done_event.set()
return imagedata
def calc_norm(self, refdata):
scopedata = refdata['scope']
cameradata = refdata['camera']
channel = refdata['channel']
if isinstance(refdata, leginondata.DarkImageData):
dark = refdata
bright = self.retrieveCorrectorImageData('bright', scopedata,
cameradata, channel)
if bright is None:
self.logger.warning(
'No bright reference image for normalization calculations')
return
if isinstance(refdata, leginondata.BrightImageData):
bright = refdata
dark = self.retrieveCorrectorImageData('dark', scopedata,
cameradata, channel)
if dark is None:
self.logger.warning(
'No dark reference image for normalization calculations')
return
try:
darkarray = self.prepareDark(dark, bright)
except:
self.logger.warning('Unable to load dark image from %s' %
dark['session']['image path'])
return
try:
brightarray = bright['image']
except:
self.logger.warning('Unable to load bright image from %s' %
bright['session']['image path'])
return
try:
normarray = brightarray - darkarray
except:
self.logger.error('dark subtraction failed.')
return
normarray = numpy.asarray(normarray, numpy.float32)
normavg = arraystats.mean(normarray)
# division may result infinity or zero division
# so make sure there are no zeros in norm
normarray = numpy.clip(normarray, 0.001, sys.maxint)
normarray = normavg / normarray
# Avoid over correcting dead pixels
normarray = numpy.ma.masked_greater(normarray, 20).filled(1)
# Saving normdata
normdata = leginondata.CameraImageData(initializer=refdata)
normdata['image'] = normarray
normdata['dark'] = dark
normdata['bright'] = bright
self.storeCorrectorImageData(normdata, 'norm', channel)
def acquire(self):
#This replaces the function of the same name in ManualAcquisition
#to pretend an image acquisition
self.logger.info('Loading image as if acquired...')
self.instrument.ccdcamera.Settings = self.uploadedInfo[
'camera settings']
try:
image = self.uploadedInfo['image']
scope = self.instrument.getData(leginondata.ScopeEMData)
camera = self.instrument.getData(leginondata.CameraEMData)
imagedata = leginondata.CameraImageData(image=image,
scope=scope,
camera=camera)
imagedata['session'] = self.session
except Exception, e:
self.logger.exception('Error loading image: %s' % e)
raise AcquireError
def acquireCameraImageData(self,
scopeclass=leginondata.ScopeEMData,
allow_retracted=False,
type='normal'):
'''Acquire a raw image from the currently configured CCD camera'''
self.prepareToAcquire(allow_retracted, exposure_type=type)
## set type to normal or dark
self.instrument.ccdcamera.ExposureType = type
imagedata = leginondata.CameraImageData()
imagedata['session'] = self.session
## make sure shutter override is activated
try:
self.instrument.tem.ShutterControl = True
except:
# maybe tem has no such function
pass
## acquire image, get new scope/camera params
try:
scopedata = self.instrument.getData(scopeclass)
except:
raise
#cameradata_before = self.instrument.getData(leginondata.CameraEMData)
imagedata['scope'] = scopedata
self.startExposureTimer()
imagedata['image'] = self.instrument.ccdcamera.Image
cameradata_after = self.instrument.getData(leginondata.CameraEMData)
## only using cameradata_after, not cameradata_before
imagedata['camera'] = cameradata_after
## duplicating 'use frames' here because we may reuse same
## CameraEMData for multiple versions of AcquisitionImageData
imagedata['use frames'] = cameradata_after['use frames']
self.readout_done_event.set()
return imagedata
(i + 1, n))
try:
imagedata = self.acquireCameraImageData(type=exposuretype)
except Exception, e:
self.logger.error('Error acquiring image: %s' % e)
raise
if self.settings['store series']:
self.storeCorrectorImageData(imagedata, type, channel)
imagearray = imagedata['image']
if i == 0:
avg = numpy.asarray(imagearray, numpy.float32)
else:
delta = imagearray - avg
avg = avg + delta / (i + 1)
## final image based on contents of last image in series
finaldata = leginondata.CameraImageData(initializer=imagedata)
finaldata['image'] = avg
finaldata = self.storeCorrectorImageData(finaldata, type, channel)
return finaldata
def acquireSeriesMedian(self, n, type, channel):
series = []
if type == 'dark':
exposuretype = 'dark'
else:
exposuretype = 'normal'
for i in range(n):
self.logger.info('Acquiring reference image (%s of %s)' %
(i + 1, n))
try:
imagedata = self.acquireCameraImageData(type=exposuretype)