def loadInputs(self):
micsFn = self.getInputMicrographs().getFileName()
micsSet = SetOfMicrographs(filename=micsFn)
micsSet.loadAllProperties()
availableMics = []
for mic in micsSet:
availableMics.append(mic.getObjId())
micsSetClosed = micsSet.isStreamClosed()
micsSet.close()
partsFn = self.getInputParticles().getFileName()
partsSet = SetOfParticles(filename=partsFn)
partsSet.loadAllProperties()
newParts = []
newMics = []
for item in partsSet:
micKey = item.getCoordinate().getMicId()
if micKey not in self.micsDone and micKey in availableMics:
newParts.append(item.getObjId())
if not micKey in self.micsDone:
newMics.append(micKey)
self.micsDone += newMics
self.inputSize = partsSet.getSize()
partSetClosed = partsSet.isStreamClosed()
partsSet.close()
return newParts, micsSetClosed and partSetClosed
def _checkNewInput(self):
# Check if there are new micrographs to process from the input set
micsFile = self.inputMicrographs.get().getFileName()
micsSet = SetOfMicrographs(filename=micsFile)
micsSet.loadAllProperties()
self.SetOfMicrographs = [m.clone() for m in micsSet]
self.streamClosed = micsSet.isStreamClosed()
micsSet.close()
newMics = any(m.getObjId() not in self.insertedDict
for m in self.inputMics)
outputStep = self._getFirstJoinStep()
if newMics:
fDeps = self._insertNewMicsSteps(self.insertedDict, self.inputMics)
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def _stepsCheck(self):
# For now the streaming is not allowed for recalculate CTF
if self.recalculate:
return
# Check if there are new micrographs to process
micFn = self.inputMicrographs.get().getFileName()
micSet = SetOfMicrographs(filename=micFn)
micSet.loadAllProperties()
streamClosed = micSet.isStreamClosed()
outputStep = self._getFirstJoinStep()
self._checkNewMicrographs(micSet, outputStep)
ctfSet, newCTFs = self._checkNewCTFs(micSet)
if ctfSet is None:
return
endCTFs = streamClosed and micSet.getSize() == ctfSet.getSize()
if newCTFs:
# Check if it is the first time we are registering CTF to
# create the CTF_RELATION only once
firstTime = not self.hasAttribute('outputCTF')
ctfSet.setMicrographs(self.inputMics)
self._computeDefocusRange(ctfSet)
streamMode = ctfSet.STREAM_CLOSED if endCTFs else ctfSet.STREAM_OPEN
self._updateOutputSet('outputCTF', ctfSet, streamMode)
if firstTime: # define relation just once
self._defineCtfRelation(self.inputMics, ctfSet)
else:
ctfSet.close()
if outputStep and outputStep.isWaiting() and endCTFs:
outputStep.setStatus(STATUS_NEW)
micSet.close()