def _createMicsSubSetFromCTF(self, inputCTFs):
""" Create a subset of Micrographs and CTFs when analyzing the CTFs. """
outputMics = self._createSetOfMicrographs()
outputCtfs = self._createSetOfCTF()
setOfMics = inputCTFs.getMicrographs()
if setOfMics is None:
raise Exception('Could not create SetOfMicrographs subset from '
'this SetOfCTF, the micrographs were not set.')
outputMics.copyInfo(setOfMics)
modifiedSet = emobj.SetOfCTF(filename=self._dbName,
prefix=self._dbPrefix)
count = 0
for ctf in modifiedSet:
if ctf.isEnabled():
mic = ctf.getMicrograph()
outputMics.append(mic)
outputCtfs.append(ctf)
count += 1
# Register outputs
outputCtfs.setMicrographs(outputMics)
# NOTE: I've split the define output in 2 steps.
# It seems with python3 outputCTF was processed first and needs mics to be saved first.
self._defineOutputs(outputMicrographs=outputMics)
self._defineOutputs(outputCTF=outputCtfs)
self._defineTransformRelation(setOfMics, outputMics)
self._defineCtfRelation(outputMics, outputCtfs)
msg = 'From input %s of size %s created output ' % (
inputCTFs.getClassName(), inputCTFs.getSize())
msg += 'SetOfMicrographs and SetOfCTF of size %d' % count
self.summaryVar.set(msg)
return outputMics, outputCtfs
def getMicCTF(self, mic):
""" Retrieve the CTF associated to this micrograph. """
# The first time this function is called, the set of micrographs
# will be loaded from the given sqlite file
if not hasattr(self, 'ctfSet'):
self.ctfSet = emobj.SetOfCTF(filename=self._sqliteFile)
return self.ctfSet[mic.getObjId()]
def _insertRecalculateSteps(self):
recalDeps = []
# For each psd insert the steps to process it
self.recalculateSet = emobj.SetOfCTF(filename=self.sqliteFile.get(),
objDoStore=False)
inputMics = self.getInputMicrographs()
for ctf in self.recalculateSet:
line = ctf.getObjComment()
if ctf.isEnabled() and line:
# CTF Re-estimation
# Make estimation steps independent between them
objId = ctf.getObjId()
stepId = self._insertFunctionStep('reEstimateCtfStep',
objId,
prerequisites=[])
recalDeps.append(stepId)
self.micDict[objId] = inputMics[objId].clone()
return recalDeps
def checkOutputs(prot):
t0 = time.time()
while not (prot.isFinished() or prot.isFailed()):
# Time out 6 minutes, just in case
tdelta = time.time() - t0
if tdelta > 6*60:
break
time.sleep(10)
prot = self._updateProtocol(prot)
# Check if the protocol is still launched
if prot.isLaunched():
continue
elif prot.isScheduled():
continue
if prot.hasAttribute("outputCTF"):
ctfSet = emobj.SetOfCTF(filename=prot._getPath(CTF_SQLITE))
baseFn = prot._getPath(CTF_SQLITE)
self.assertTrue(os.path.isfile(baseFn))
counter = 0
if ctfSet.getSize() > counter:
counter += 1
for ctf in ctfSet:
self.assertNotEqual(ctf._resolution.get(), None)
self.assertNotEqual(ctf._fitQuality.get(), None)
self.assertNotEqual(ctf.isEnabled(), None)
self.assertNotEqual(ctf._defocusU.get(), None)
self.assertNotEqual(ctf._defocusV.get(), None)
self.assertNotEqual(ctf._defocusRatio.get(), None)
if ctf.getPhaseShift():
self.assertNotEqual(ctf.getPhaseShift(), None)
self.assertIsNotNone(prot.outputCTF,
"Error: outputCTF is not produced "
"in %s." % prot.getClassName())
self.assertEqual(prot.outputCTF.getSize(), MICS)