def _argsCtffind4(self):
# Avoid threads multiplication
# self._program = 'export OMP_NUM_THREADS=%d; ' % self.numberOfThreads.get()
self._program = 'export OMP_NUM_THREADS=1; '
self._program += CTFFIND4_PATH
self._args = """ << eof
%(micFn)s
%(ctffindPSD)s
%(sampling)f
%(voltage)f
%(sphericalAberration)f
%(ampContrast)f
%(windowSize)d
%(lowRes)f
%(highRes)f
%(minDefocus)f
%(maxDefocus)f
%(step_focus)f"""
if getVersion(CTFFIND4_APP) in ['4.1.5', '4.1.8', V4_1_10]:
if self.findPhaseShift:
self._args += """
no
%(slowSearch)s
yes
%(astigmatism)f
%(phaseShift)s
%(minPhaseShift)f
%(maxPhaseShift)f
%(stepPhaseShift)f
yes
%(resamplePix)s
eof
"""
else:
self._args += """
no
%(slowSearch)s
yes
%(astigmatism)f
%(phaseShift)s
yes
%(resamplePix)s
eof
"""
elif getVersion(CTFFIND4_APP) == V4_0_15:
if self.findPhaseShift:
self._args += """
%(astigmatism)f
%(phaseShift)s
%(minPhaseShift)f
%(maxPhaseShift)f
%(stepPhaseShift)f
eof
"""
else:
self._args += """
def _summary(self):
summary = em.ProtCTFMicrographs._summary(self)
if self.useCtffind4 and getVersion('CTFFIND4') == '4.1.5':
summary.append("NOTE: ctffind4.1.5 finishes correctly (all output "
"is generated properly), but returns an error code. "
"Disregard error messages until this is fixed."
"http://grigoriefflab.janelia.org/node/5421")
return summary
def _isNewUnblur(self):
return True if getVersion('UNBLUR') != '1.0.150529' else False
def _argsUnblur(self, movie, numberOfFrames):
""" Format argument for call unblur program. """
args = {
'movieName': self._getMovieFn(movie),
'numberOfFramesPerMovie': numberOfFrames,
'micFnName': self._getMicFn(movie),
'shiftFnName': self._getShiftsFn(movie),
'samplingRate': self.samplingRate,
'voltage': movie.getAcquisition().getVoltage(),
'frcFn': self._getFrcFn(movie),
'bfactor': self.bfactor.get(),
'minShiftInitSearch': self.minShiftInitSearch.get(),
'OutRadShiftLimit': self.OutRadShiftLimit.get(),
'HWVertFourMask': self.HWVertFourMask.get(),
'HWHoriFourMask': self.HWHoriFourMask.get(),
'terminShiftThreshold': self.terminShiftThreshold.get(),
'maximumNumberIterations': self.maximumNumberIterations.get(),
'doApplyDoseFilter': 'YES' if self.doApplyDoseFilter else 'NO',
'doRestoreNoisePwr': 'YES' if self.doRestoreNoisePwr else 'NO',
'doVerboseOutput': 'YES' if self.doVerboseOutput else 'NO',
'exposurePerFrame': movie.getAcquisition().getDosePerFrame() or 0.0
}
# Avoid threads multiplication
# self._program = 'export OMP_NUM_THREADS=%d; ' % self.numberOfThreads.get()
self._program = 'export OMP_NUM_THREADS=%d; ' % self.openmpThreads
self._program += UNBLUR_PATH
if getVersion('UNBLUR') != '1.0_150529':
args['preExposureAmount'] = movie.getAcquisition().getDoseInitial(
) or 0.0
self._args = """ << eof
%(movieName)s
%(numberOfFramesPerMovie)s
%(micFnName)s
%(shiftFnName)s
%(samplingRate)f
%(doApplyDoseFilter)s
%(exposurePerFrame)f
%(voltage)f
%(preExposureAmount)f
NO
YES
%(frcFn)s
%(minShiftInitSearch)f
%(OutRadShiftLimit)f
%(bfactor)f
%(HWVertFourMask)d
%(HWHoriFourMask)d
%(terminShiftThreshold)f
%(maximumNumberIterations)d
%(doRestoreNoisePwr)s
%(doVerboseOutput)s
eof
""" % args
else:
self._args = """ << eof
%(movieName)s
%(numberOfFramesPerMovie)s
%(micFnName)s
%(shiftFnName)s
%(samplingRate)f
%(doApplyDoseFilter)s
%(exposurePerFrame)f
%(voltage)f
YES
%(frcFn)s
%(minShiftInitSearch)f
%(OutRadShiftLimit)f
%(bfactor)f
%(HWVertFourMask)d
%(HWHoriFourMask)d
%(terminShiftThreshold)f
%(maximumNumberIterations)d
%(doRestoreNoisePwr)s
%(doVerboseOutput)s
eof
""" % args
def _isNewCtffind4(self):
return self.useCtffind4 and getVersion('CTFFIND4') != V4_0_15
def _isNewUnblur(self):
return True if getVersion('UNBLUR') != '1.0.150529' else False
def _argsUnblur(self, movie, numberOfFrames):
""" Format argument for call unblur program. """
args = {'movieName': self._getMovieFn(movie),
'numberOfFramesPerMovie': numberOfFrames,
'micFnName': self._getMicFn(movie),
'shiftFnName': self._getShiftsFn(movie),
'samplingRate': self.samplingRate,
'voltage': movie.getAcquisition().getVoltage(),
'frcFn': self._getFrcFn(movie),
'bfactor': self.bfactor.get(),
'minShiftInitSearch': self.minShiftInitSearch.get(),
'OutRadShiftLimit': self.OutRadShiftLimit.get(),
'HWVertFourMask': self.HWVertFourMask.get(),
'HWHoriFourMask': self.HWHoriFourMask.get(),
'terminShiftThreshold': self.terminShiftThreshold.get(),
'maximumNumberIterations': self.maximumNumberIterations.get(),
'doApplyDoseFilter': 'YES' if self.doApplyDoseFilter else 'NO',
'doRestoreNoisePwr': 'YES' if self.doRestoreNoisePwr else 'NO',
'doVerboseOutput': 'YES' if self.doVerboseOutput else 'NO',
'exposurePerFrame': movie.getAcquisition().getDosePerFrame() or 0.0
}
# Avoid threads multiplication
# self._program = 'export OMP_NUM_THREADS=%d; ' % self.numberOfThreads.get()
self._program = 'export OMP_NUM_THREADS=%d; ' % self.openmpThreads
self._program += UNBLUR_PATH
if getVersion('UNBLUR') != '1.0_150529':
args['preExposureAmount'] = movie.getAcquisition().getDoseInitial() or 0.0
self._args = """ << eof
%(movieName)s
%(numberOfFramesPerMovie)s
%(micFnName)s
%(shiftFnName)s
%(samplingRate)f
%(doApplyDoseFilter)s
%(exposurePerFrame)f
%(voltage)f
%(preExposureAmount)f
NO
YES
%(frcFn)s
%(minShiftInitSearch)f
%(OutRadShiftLimit)f
%(bfactor)f
%(HWVertFourMask)d
%(HWHoriFourMask)d
%(terminShiftThreshold)f
%(maximumNumberIterations)d
%(doRestoreNoisePwr)s
%(doVerboseOutput)s
eof
""" % args
else:
self._args = """ << eof
%(movieName)s
%(numberOfFramesPerMovie)s
%(micFnName)s
%(shiftFnName)s
%(samplingRate)f
%(doApplyDoseFilter)s
%(exposurePerFrame)f
%(voltage)f
YES
%(frcFn)s
%(minShiftInitSearch)f
%(OutRadShiftLimit)f
%(bfactor)f
%(HWVertFourMask)d
%(HWHoriFourMask)d
%(terminShiftThreshold)f
%(maximumNumberIterations)d
%(doRestoreNoisePwr)s
%(doVerboseOutput)s
eof
""" % args
def _isNewCtffind4(self):
if self.useCtffind4 and getVersion('CTFFIND4') != '4.0.15':
return True
else:
return False