def preLoopFunctions(self): self.dd = apDDprocess.initializeDDFrameprocess(self.params['sessionname'],self.params['wait']) self.dd.setUseGS(self.params['useGS']) self.dd.setRunDir(self.params['rundir']) self.dd.setTempDir(self.params['tempdir']) self.dd.setRawFrameType(self.getFrameType()) self.dd.setUseGPUFlat(True) self.dd.setSquareOutputShape(self.params['square']) self.dd.setTrimingEdge(self.params['trim']) self.dd.setDoseFDriftCorrOptions(self.params) self.dd.setGPUid(self.params['gpuid']) # keepstack is resolved for various cases in conflict check. There should be no ambiguity by now self.dd.setKeepStack(self.params['keepstack']) self.dd.setCycleReferenceChannels(self.params['cyclechannels']) if self.params['refimgid']: self.dd.setDefaultImageForReference(self.params['refimgid']) self.imageids = [] if self.params['stackid']: # create a list of unaligned imageids from the particle stack imageids_from_stack = apStack.getImageIdsFromStack(self.params['stackid']) self.imageids = self.getUnAlignedImageIds(imageids_from_stack) # Optimize AppionLoop wait time for this since the processing now takes longer than # image acquisition self.setWaitSleepMin(0.4) self.setProcessBatchCount(1)
def preLoopFunctions(self):
self.dd = apDDprocess.initializeDDFrameprocess(
self.params['sessionname'], self.params['wait'])
self.dd.setRunDir(self.params['rundir'])
self.dd.setDoseFDriftCorrOptions(self.params)
self.dd.setGPUid(self.params['gpuid'])
# keepstack is resolved for various cases in conflict check. There should be no ambiguity by now
self.dd.setKeepStack(self.params['keepstack'])
self.gain_corrected_ddproc = None
self.imageids = []
if self.params['stackid']:
# create a list of unaligned imageids from the particle stack
imageids_from_stack = apStack.getImageIdsFromStack(
self.params['stackid'])
self.imageids = self.getUnAlignedImageIds(imageids_from_stack)
if not self.params['ddstack']:
print 'This does not work yet. Need to create gain-corrected-ddstack first'
if self.params['ddstack']:
self.gain_corrected_ddproc = apDDprocess.DDStackProcessing()
self.gain_corrected_ddproc.setDDStackRun(
ddstackrunid=self.params['ddstack'])
# Optimize AppionLoop wait time for this since the processing now takes longer than
# image acquisition
self.setWaitSleepMin(0.4)
self.setProcessBatchCount(1)
def onInit(self):
if 'sessionname' not in self.params.keys():
self.params['sessionname'] = leginondata.SessionData(
).direct_query(self.params['expid'])['name']
self.dd = apDDprocess.initializeDDFrameprocess(
self.params['sessionname'], self.params['wait'])
self.dd.setRunDir(self.params['rundir'])
# The gain/dark corrected ddstack is unlikely to be on local disk
if 'tempdir' not in self.params.keys():
self.dd.setTempDir()
else:
self.dd.setTempDir(self.params['tempdir'])
self.dd.setNewBinning(self.rundata['params']['bin'])
# Get the unfinished ddstack run parameters to apply them here
jobdata = apDatabase.getJobDataFromPathAndType(
self.rundata['path']['path'], 'makeddrawframestack')
self.ddstack_script_params = apScriptLog.getScriptParamValuesFromRunname(
self.rundata['runname'], self.rundata['path'], jobdata)
if 'no-keepstack' in self.ddstack_script_params.keys():
self.dd.setKeepStack(False)
self.dd.setDoseFDriftCorrOptions(self.ddstack_script_params)
# Give an unique lockname
self.setLockname('ddalign')
self.success_count = 0
def preLoopFunctions(self):
self.is_dd_frame = False
self.is_dd_stack = False
self.is_dd = False
self.checkIsDD()
self.batchboxertimes = []
self.ctftimes = []
self.mergestacktimes = []
self.meanreadtimes = []
self.insertdbtimes = []
self.noimages = False
self.totalpart = 0
self.selectiondata = None
# Different class needed depending on if ddstack is specified or available
if self.is_dd:
from appionlib import apDDprocess
if self.is_dd_frame:
apDisplay.printMsg('DD Frame Processing')
self.dd = apDDprocess.initializeDDFrameprocess(
self.params['sessionname'])
self.dd.setUseGS(self.params['useGS'])
if self.is_dd_stack:
apDisplay.printMsg('DD Stack Processing')
self.dd = apDDprocess.DDStackProcessing()
if len(self.imgtree) == 0:
apDisplay.printWarning("No images were found to process")
self.noimages = True
# Still need to set attributes if waiting for more images
if not self.params['wait']:
return
if self.params['selectionid'] is not None:
self.selectiondata = apParticle.getSelectionRunDataFromID(
self.params['selectionid'])
if self.params['particlelabel'] == 'fromtrace':
if (not self.selectiondata['manparams']
or not self.selectiondata['manparams']['trace']):
apDisplay.printError(
"Can not use traced object center to extract boxed area without tracing"
)
else:
self.params['particlelabel'] = '_trace'
self.checkPixelSize()
self.existingParticleNumber = 0
self.setStartingParticleNumber()
apDisplay.printMsg("Starting at particle number: " +
str(self.particleNumber))
if self.params[
'partlimit'] is not None and self.particleNumber > self.params[
'partlimit']:
apDisplay.printError(
"Number of particles in existing stack already exceeds limit!")
self.logpeaks = 2
def preLoopFunctions(self): self.dd = apDDprocess.initializeDDFrameprocess(self.params['sessionname'],self.params['wait']) self.dd.setRunDir(self.params['rundir']) self.dd.setRawFrameType(self.getFrameType()) self.dd.setDoseFDriftCorrOptions(self.params) self.exposurerate_is_default = self.params['radiationdamage_exposurerate'] == 1.0 self.imageids = [] # Optimize AppionLoop wait time for this since the processing now takes longer than # image acquisition self.setWaitSleepMin(0.4) self.setProcessBatchCount(1) self.params['output_fileformat'] = 'mrc'
def preLoopFunctions(self):
self.is_dd_frame = False
self.is_dd_stack = False
self.is_dd = False
self.checkIsDD()
self.batchboxertimes = []
self.ctftimes = []
self.mergestacktimes = []
self.meanreadtimes = []
self.insertdbtimes = []
self.noimages = False
self.totalpart = 0
self.selectiondata = None
# Different class needed depending on if ddstack is specified or available
if self.is_dd:
from appionlib import apDDprocess
if self.is_dd_frame:
apDisplay.printMsg('DD Frame Processing')
self.dd = apDDprocess.initializeDDFrameprocess(self.params['sessionname'])
self.dd.setUseGS(self.params['useGS'])
if self.is_dd_stack:
apDisplay.printMsg('DD Stack Processing')
self.dd = apDDprocess.DDStackProcessing()
if len(self.imgtree) == 0:
apDisplay.printWarning("No images were found to process")
self.noimages = True
# Still need to set attributes if waiting for more images
if not self.params['wait']:
return
if self.params['selectionid'] is not None:
self.selectiondata = apParticle.getSelectionRunDataFromID(self.params['selectionid'])
if self.params['particlelabel'] == 'fromtrace':
if (not self.selectiondata['manparams'] or not self.selectiondata['manparams']['trace']):
apDisplay.printError("Can not use traced object center to extract boxed area without tracing")
else:
self.params['particlelabel'] = '_trace'
self.checkPixelSize()
self.existingParticleNumber=0
self.setStartingParticleNumber()
apDisplay.printMsg("Starting at particle number: "+str(self.particleNumber))
if self.params['partlimit'] is not None and self.particleNumber > self.params['partlimit']:
apDisplay.printError("Number of particles in existing stack already exceeds limit!")
self.logpeaks = 2
def onInit(self):
if 'sessionname' not in self.params.keys():
self.params['sessionname'] = leginondata.SessionData().direct_query(self.params['expid'])['name']
self.dd = apDDprocess.initializeDDFrameprocess(self.params['sessionname'],self.params['wait'])
self.dd.setRunDir(self.params['rundir'])
# The gain/dark corrected ddstack is unlikely to be on local disk
if 'tempdir' not in self.params.keys():
self.dd.setTempDir()
else:
self.dd.setTempDir(self.params['tempdir'])
self.dd.setNewBinning(self.rundata['params']['bin'])
# Get the unfinished ddstack run parameters to apply them here
jobdata = apDatabase.getJobDataFromPathAndType(self.rundata['path']['path'], 'makeddrawframestack')
self.ddstack_script_params = apScriptLog.getScriptParamValuesFromRunname(self.rundata['runname'],self.rundata['path'],jobdata)
if 'no-keepstack' in self.ddstack_script_params.keys():
self.dd.setKeepStack(False)
# Give an unique lockname
self.setLockname('ddalign')
self.success_count = 0
def preLoopFunctions(self):
self.dd = apDDprocess.initializeDDFrameprocess(self.params['sessionname'],self.params['wait'])
self.dd.setUseGS(self.params['useGS'])
self.dd.setRunDir(self.params['rundir'])
self.dd.setTempDir(self.params['tempdir'])
self.dd.setRawFrameType(self.getFrameType())
self.dd.setUseGPUFlat(self.params['gpuflat'])
self.dd.setGPUid(self.params['gpuid'])
# keepstack is resolved for various cases in conflict check. There should be no ambiguity by now
self.dd.setKeepStack(self.params['keepstack'])
self.dd.setCycleReferenceChannels(self.params['cyclechannels'])
if self.params['refimgid']:
self.dd.setDefaultImageForReference(self.params['refimgid'])
self.imageids = []
if self.params['stackid']:
self.imageids = apStack.getImageIdsFromStack(self.params['stackid'])
# Optimize AppionLoop wait time for this since the processing now takes longer than
# image acquisition
self.setWaitSleepMin(0.4)
self.setProcessBatchCount(1)
def preLoopFunctions(self):
self.dd = apDDprocess.initializeDDFrameprocess(self.params["sessionname"], self.params["wait"])
self.dd.setRunDir(self.params["rundir"])
self.dd.setDoseFDriftCorrOptions(self.params)
self.dd.setGPUid(self.params["gpuid"])
# keepstack is resolved for various cases in conflict check. There should be no ambiguity by now
self.dd.setKeepStack(self.params["keepstack"])
self.gain_corrected_ddproc = None
self.imageids = []
if self.params["stackid"]:
# create a list of unaligned imageids from the particle stack
imageids_from_stack = apStack.getImageIdsFromStack(self.params["stackid"])
self.imageids = self.getUnAlignedImageIds(imageids_from_stack)
if not self.params["ddstack"]:
print "This does not work yet. Need to create gain-corrected-ddstack first"
if self.params["ddstack"]:
self.gain_corrected_ddproc = apDDprocess.DDStackProcessing()
self.gain_corrected_ddproc.setDDStackRun(ddstackrunid=self.params["ddstack"])
# Optimize AppionLoop wait time for this since the processing now takes longer than
# image acquisition
self.setWaitSleepMin(0.4)
self.setProcessBatchCount(1)
