def _checkNewCTFs(self, micSet):
""" Check for already computed CTF and update the output set. """
newCTFs = []
ctfDict = {}
ctfSet = SetOfCTF(filename=self._getPath('ctfs.sqlite'))
ctfSet.setMicrographs(self.inputMicrographs.get())
for ctf in ctfSet:
ctfDict[ctf.getObjId()] = True
if ctfDict: # it means there are previous ctfs computed
ctfSet.loadAllProperties()
if ctfSet.getSize():
ctfSet.enableAppend()
else:
ctfSet.setStreamState(ctfSet.STREAM_OPEN)
for micFn, micDir, mic in self._iterMicrographs(micSet):
if (exists(self._getMicrographDone(micDir))
and not mic.getObjId() in ctfDict):
ctf = self._createCtfModel(mic)
ctfSet.append(ctf)
newCTFs.append(mic.getObjId())
return ctfSet, newCTFs
def _checkNewInput(self):
if self.calculateConsensus:
# Check if there are new ctf to process from the input set
ctfsFile1 = self.inputCTF.get().getFileName()
ctfsFile2 = self.inputCTF2.get().getFileName()
self.lastCheck = getattr(self, 'lastCheck', datetime.now())
mTime = max(datetime.fromtimestamp(os.path.getmtime(ctfsFile1)),
datetime.fromtimestamp(os.path.getmtime(ctfsFile2)))
# If the input movies.sqlite have not changed since our last check,
# it does not make sense to check for new input data
if self.lastCheck > mTime and hasattr(self, 'SetOfCtf1'):
return None
ctfsSet1 = SetOfCTF(filename=ctfsFile1)
ctfsSet2 = SetOfCTF(filename=ctfsFile2)
ctfsSet1.loadAllProperties()
ctfsSet2.loadAllProperties()
if len(self.allCtf1) > 0:
newCtf1 = [ctf.clone() for ctf in
ctfsSet1.iterItems(orderBy='creation',
where='creation>"' + str(
self.checkCtf1) + '"')]
else:
newCtf1 = [ctf.clone() for ctf in ctfsSet1]
self.allCtf1 = self.allCtf1 + newCtf1
if len(newCtf1) > 0:
for ctf in ctfsSet1.iterItems(orderBy='creation',
direction='DESC'):
self.checkCtf1 = ctf.getObjCreation()
break
if len(self.allCtf2) > 0:
newCtf2 = [ctf.clone() for ctf in
ctfsSet2.iterItems(orderBy='creation',
where='creation>"' + str(
self.checkCtf2) + '"')]
else:
newCtf2 = [ctf.clone() for ctf in ctfsSet2]
self.allCtf2 = self.allCtf2 + newCtf2
if len(newCtf2) > 0:
for ctf in ctfsSet2.iterItems(orderBy='creation',
direction='DESC'):
self.checkCtf2 = ctf.getObjCreation()
break
self.lastCheck = datetime.now()
self.isStreamClosed = ctfsSet1.isStreamClosed() and \
ctfsSet2.isStreamClosed()
ctfsSet1.close()
ctfsSet2.close()
outputStep = self._getFirstJoinStep()
if len(set(self.allCtf1)) > len(set(self.processedDict)) and \
len(set(self.allCtf2)) > len(set(self.processedDict)):
fDeps = self._insertNewCtfsSteps(ctfsSet1, ctfsSet2,
self.insertedDict)
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
else:
ctfFile = self.inputCTF.get().getFileName()
now = datetime.now()
self.lastCheck = getattr(self, 'lastCheck', now)
mTime = datetime.fromtimestamp(os.path.getmtime(ctfFile))
self.debug('Last check: %s, modification: %s'
% (pwutils.prettyTime(self.lastCheck),
pwutils.prettyTime(mTime)))
# Open input ctfs.sqlite and close it as soon as possible
ctfSet = self._loadInputCtfSet()
self.isStreamClosed = ctfSet.isStreamClosed()
self.allCtf1 = [m.clone() for m in ctfSet]
ctfSet.close()
# If the input ctfs.sqlite have not changed since our last check,
# it does not make sense to check for new input data
if self.lastCheck > mTime and hasattr(self, 'allCtf1'):
return None
self.lastCheck = now
newCtf = any(ctf.getObjId() not in
self.insertedDict for ctf in self.allCtf1)
outputStep = self._getFirstJoinStep()
if newCtf:
fDeps = self._insertNewSelectionSteps(self.insertedDict,
self.allCtf1)
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()