def _stepsCheck(self):
setOfMicFn = self._getPath('micrographs.sqlite')
micSet = SetOfMicrographs(filename=setOfMicFn)
micSet, newMic = self._checkNewMics(micSet)
#check if end ....
endMics = micSet.getSize() == self.nDim.get()
if newMic:
if endMics:
micSet.setStreamState(micSet.STREAM_CLOSED)
self._updateOutput(micSet)
micSet.close()
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()
def test_pattern(self):
""" Import several Particles from a given pattern.
"""
kwargs = {'xDim': 1024,
'yDim': 1024,
'nDim': MICS,
'samplingRate': 1.25,
'creationInterval': 5,
'delay': 0,
'setof': SET_OF_RANDOM_MICROGRAPHS # SetOfMicrographs
}
# create input micrographs
protStream = self.newProtocol(ProtCreateStreamData, **kwargs)
protStream.setObjLabel('create Stream Mic')
self.proj.launchProtocol(protStream, wait=False)
counter = 1
while not protStream.hasAttribute('outputMicrographs'):
time.sleep(2)
protStream = self._updateProtocol(protStream)
if counter > 100:
break
counter += 1
# then introduce monitor, checking all the time ctf and
# saving to database
protCTF = ProtCTFFind(useCftfind4=True)
protCTF.inputMicrographs.set(protStream.outputMicrographs)
protCTF.ctfDownFactor.set(2)
protCTF.highRes.set(0.4)
protCTF.lowRes.set(0.05)
protCTF.numberOfThreads.set(4)
self.proj.launchProtocol(protCTF, wait=False)
counter = 1
while not protCTF.hasAttribute('outputCTF'):
time.sleep(2)
protCTF = self._updateProtocol(protCTF)
if counter > 100:
break
counter += 1
kwargs = {
'maxDefocus': 28000,
'minDefocus': 1000,
'astigmatism': 1000,
'resolution': 7
}
protCTFSel = self.newProtocol(XmippProtCTFSelection, **kwargs)
protCTFSel.inputCTF.set(protCTF.outputCTF)
self.proj.launchProtocol(protCTFSel, wait=False)
counter = 1
while not protCTFSel.hasAttribute('outputCTF'):
time.sleep(2)
protCTFSel = self._updateProtocol(protCTFSel)
if counter > 100:
break
counter += 1
kwargs = {
'maxDefocus': 40000,
'minDefocus': 1000,
'astigmatism': 1000,
'resolution': 3.7,
}
protCTFSel2 = self.newProtocol(XmippProtCTFSelection, **kwargs)
protCTFSel2.inputCTF.set(protCTFSel.outputCTF)
self.proj.launchProtocol(protCTFSel2)
counter = 1
while not (protCTFSel2.hasAttribute('outputCTF') and
protCTFSel2.hasAttribute('outputMicrographs')):
time.sleep(2)
protCTFSel2 = self._updateProtocol(protCTFSel2)
if counter > 100:
self.assertTrue(False)
counter += 1
# AJ the number of micrographs discarded and selected in the first CTF
# selection protocol must be equal to the number of mics in the
# CTF estimation protocol
micSetDiscarded1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_DISCARDED_SQLITE))
micSet1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_SQLITE))
counter = 1
while not ((micSetDiscarded1.getSize() + micSet1.getSize()) == 10):
time.sleep(2)
micSetDiscarded1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_DISCARDED_SQLITE))
micSet1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_SQLITE))
if counter > 100:
self.assertTrue(False)
counter += 1
# AJ the number of micrographs discarded and selected in the second CTF
# selection protocol must be equal to the number of ctfs in the first
# CTF selection protocol
micSetDiscarded2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_DISCARDED_SQLITE))
micSet2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_SQLITE))
ctfSet1 = SetOfCTF(filename=protCTFSel._getPath(CTF_SQLITE))
counter = 1
while not (ctfSet1.getSize() == (micSetDiscarded2.getSize() +
micSet2.getSize())):
time.sleep(2)
micSetDiscarded2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_DISCARDED_SQLITE))
micSet2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_SQLITE))
ctfSet1 = SetOfCTF(filename=protCTFSel._getPath(CTF_SQLITE))
if counter > 100:
self.assertTrue(False)
counter += 1
ctfSet = SetOfCTF(filename=protCTFSel2._getPath(CTF_SQLITE))
for ctf in ctfSet:
defocusU = ctf.getDefocusU()
defocusV = ctf.getDefocusV()
astigm = defocusU - defocusV
resol = ctf.getResolution() # TODO
if defocusU < 1000 \
or defocusU > 28000 \
or defocusV < 1000 \
or defocusV > 28000 \
or astigm > 1000 or resol > 3.7:
self.assertTrue(False, "A CTF without the correct parameters"
" is included in the output set")
def test_pattern(self):
""" Import several Particles from a given pattern.
"""
kwargs = {
'xDim': 1024,
'yDim': 1024,
'nDim': MICS,
'samplingRate': 1.25,
'creationInterval': 5,
'delay': 0,
'setof': SET_OF_RANDOM_MICROGRAPHS # SetOfMicrographs
}
# create input micrographs
protStream = self.newProtocol(ProtCreateStreamData, **kwargs)
protStream.setObjLabel('create Stream Mic')
self.proj.launchProtocol(protStream, wait=False)
counter = 1
while not protStream.hasAttribute('outputMicrographs'):
time.sleep(2)
protStream = self._updateProtocol(protStream)
if counter > 100:
break
counter += 1
# then introduce monitor, checking all the time ctf and
# saving to database
protCTF = ProtCTFFind(useCftfind4=True)
protCTF.inputMicrographs.set(protStream.outputMicrographs)
protCTF.ctfDownFactor.set(2)
protCTF.highRes.set(0.4)
protCTF.lowRes.set(0.05)
protCTF.numberOfThreads.set(4)
self.proj.launchProtocol(protCTF, wait=False)
counter = 1
while not protCTF.hasAttribute('outputCTF'):
time.sleep(2)
protCTF = self._updateProtocol(protCTF)
if counter > 100:
break
counter += 1
kwargs = {
'maxDefocus': 28000,
'minDefocus': 1000,
'astigmatism': 1000,
'resolution': 7
}
protCTFSel = self.newProtocol(XmippProtCTFSelection, **kwargs)
protCTFSel.inputCTF.set(protCTF.outputCTF)
self.proj.launchProtocol(protCTFSel, wait=False)
counter = 1
while not protCTFSel.hasAttribute('outputCTF'):
time.sleep(2)
protCTFSel = self._updateProtocol(protCTFSel)
if counter > 100:
break
counter += 1
kwargs = {
'maxDefocus': 40000,
'minDefocus': 1000,
'astigmatism': 1000,
'resolution': 3.7,
}
protCTFSel2 = self.newProtocol(XmippProtCTFSelection, **kwargs)
protCTFSel2.inputCTF.set(protCTFSel.outputCTF)
self.proj.launchProtocol(protCTFSel2)
counter = 1
while not (protCTFSel2.hasAttribute('outputCTF')
and protCTFSel2.hasAttribute('outputMicrographs')):
time.sleep(2)
protCTFSel2 = self._updateProtocol(protCTFSel2)
if counter > 100:
self.assertTrue(False)
counter += 1
# AJ the number of micrographs discarded and selected in the first CTF
# selection protocol must be equal to the number of mics in the
# CTF estimation protocol
micSetDiscarded1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_DISCARDED_SQLITE))
micSet1 = SetOfMicrographs(filename=protCTFSel._getPath(MIC_SQLITE))
counter = 1
while not ((micSetDiscarded1.getSize() + micSet1.getSize()) == 10):
time.sleep(2)
micSetDiscarded1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_DISCARDED_SQLITE))
micSet1 = SetOfMicrographs(
filename=protCTFSel._getPath(MIC_SQLITE))
if counter > 100:
self.assertTrue(False)
counter += 1
# AJ the number of micrographs discarded and selected in the second CTF
# selection protocol must be equal to the number of ctfs in the first
# CTF selection protocol
micSetDiscarded2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_DISCARDED_SQLITE))
micSet2 = SetOfMicrographs(filename=protCTFSel2._getPath(MIC_SQLITE))
ctfSet1 = SetOfCTF(filename=protCTFSel._getPath(CTF_SQLITE))
counter = 1
while not (ctfSet1.getSize()
== (micSetDiscarded2.getSize() + micSet2.getSize())):
time.sleep(2)
micSetDiscarded2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_DISCARDED_SQLITE))
micSet2 = SetOfMicrographs(
filename=protCTFSel2._getPath(MIC_SQLITE))
ctfSet1 = SetOfCTF(filename=protCTFSel._getPath(CTF_SQLITE))
if counter > 100:
self.assertTrue(False)
counter += 1
ctfSet = SetOfCTF(filename=protCTFSel2._getPath(CTF_SQLITE))
for ctf in ctfSet:
defocusU = ctf.getDefocusU()
defocusV = ctf.getDefocusV()
astigm = defocusU - defocusV
resol = ctf.getResolution() # TODO
if defocusU < 1000 \
or defocusU > 28000 \
or defocusV < 1000 \
or defocusV > 28000 \
or astigm > 1000 or resol > 3.7:
self.assertTrue(
False, "A CTF without the correct parameters"
" is included in the output set")
