def convertImagesStep(self):
from pyworkflow.em.packages.eman2.convert import writeSetOfParticles
strFn = ""
partSet = self.inputParticles.get()
partAlign = partSet.getAlignment()
storePath = self._getExtraPath("particles")
makePath(storePath)
writeSetOfParticles(partSet, storePath, alignType=em.ALIGN_PROJ)
if partSet.hasCTF():
program = getEmanProgram('e2ctf.py')
acq = partSet.getAcquisition()
args = " --voltage %3d" % acq.getVoltage()
args += " --cs %f" % acq.getSphericalAberration()
args += " --ac %f" % (100 * acq.getAmplitudeContrast())
if not partSet.isPhaseFlipped():
args += " --phaseflip"
args += " --computesf --apix %f --allparticles --autofit --curdefocusfix --storeparm -v 8" % (
partSet.getSamplingRate())
self.runJob(program, args, cwd=self._getExtraPath())
program = getEmanProgram('e2buildsets.py')
args = " --setname=inputSet --allparticles --minhisnr=-1"
self.runJob(program, args, cwd=self._getExtraPath())
def convertImagesStep(self):
from pyworkflow.em.packages.eman2.convert import writeSetOfParticles
partSet = self._getInputParticles()
partAlign = partSet.getAlignment()
storePath = self._getExtraPath("particles")
makePath(storePath)
writeSetOfParticles(partSet, storePath, alignType=partAlign)
if partSet.hasCTF():
program = getEmanProgram('e2ctf.py')
acq = partSet.getAcquisition()
args = " --voltage %3d" % acq.getVoltage()
args += " --cs %f" % acq.getSphericalAberration()
args += " --ac %f" % (100 * acq.getAmplitudeContrast())
if not partSet.isPhaseFlipped():
args += " --phaseflip"
args += " --computesf --apix %f --allparticles --autofit --curdefocusfix --storeparm -v 8" % (partSet.getSamplingRate())
self.runJob(program, args, cwd=self._getExtraPath())
program = getEmanProgram('e2buildsets.py')
args = " --setname=inputSet --allparticles --minhisnr=-1"
self.runJob(program, args, cwd=self._getExtraPath())
def refineStep(self, args):
""" Run the EMAN program to refine a volume. """
if not self.doContinue:
cleanPattern(self._getExtraPath('refine_01'))
program = getEmanProgram('e2refine_easy.py')
self.runJob(program, args, cwd=self._getExtraPath())
def refineStep(self, args):
""" Run the EMAN program to refine a volume. """
if not self.doContinue:
cleanPattern(self._getExtraPath('refine_01'))
program = getEmanProgram('e2refine_easy.py')
self.runJob(program, args, cwd=self._getExtraPath())
def reconstructVolumeStep(self, args):
""" Run the EMAN program to reconstruct a volume. """
cleanPattern(self._getFileName("volume"))
program = getEmanProgram('e2make3d.py')
self.runJob(program, args, cwd=self._getExtraPath())