def convertInputStep(self):
""" Generated the input particles metadata expected
by projection matching. And copy the generated file to be
used as initial docfile for further iterations.
"""
from pyworkflow.em.packages.xmipp3 import writeSetOfParticles
writeSetOfParticles(self.inputParticles.get(), self.selFileName,
blockName=self.blockWithAllExpImages)
def convertInputStep(self):
""" Generated the input particles metadata expected
by projection matching. And copy the generated file to be
used as initial docfile for further iterations.
"""
from pyworkflow.em.packages.xmipp3 import writeSetOfParticles
writeSetOfParticles(self.inputParticles.get(), self.selFileName,
blockName=self.blockWithAllExpImages)
def applyCTF(self, setPartMd):
writeSetOfParticles(self.partSet,setPartMd)
md1 = xmipp.MetaData()
md1.setColumnFormat(False)
idctf = md1.addObject()
_acquisition = self.partSet.getAcquisition()
for part in self.partSet:
baseFnCtf = self.proj.getTmpPath("kk")#self._getTmpPath("ctf_%d.param"%mic)
md1.setValue(xmipp.MDL_CTF_SAMPLING_RATE, samplingRate, idctf)
md1.setValue(xmipp.MDL_CTF_VOLTAGE, 200., idctf);
ctf = part.getCTF()
udefocus = ctf.getDefocusU()
vdefocus = ctf.getDefocusV()
angle = ctf.getDefocusAngle()
md1.setValue(xmipp.MDL_CTF_DEFOCUSU, udefocus, idctf);
md1.setValue(xmipp.MDL_CTF_DEFOCUSV, vdefocus, idctf);
md1.setValue(xmipp.MDL_CTF_DEFOCUS_ANGLE, 180.0 * random.random(), idctf);
md1.setValue(xmipp.MDL_CTF_CS, 2., idctf);
md1.setValue(xmipp.MDL_CTF_Q0, 0.07, idctf);
md1.setValue(xmipp.MDL_CTF_K, 1., idctf);
md1.write(baseFnCtf)
##writeSetOfParticles(self.partSet, setPartMd)
#apply ctf
args = " -i %s"%setPartMd
args += " -o %s"%self.proj.getTmpPath(setPartCtfName)
args += " -f ctf %s"%baseFnCtf
args += " --sampling %f"%samplingRate
runXmippProgram("xmipp_transform_filter", args)
args = " -i %s"%setPartMd
args += " -o %s"%self.proj.getTmpPath(setPartCtfPosName)
args += " -f ctfpos %s"%baseFnCtf
args += " --sampling %f"%samplingRate
runXmippProgram("xmipp_transform_filter", args)