コード例 #1
0
ファイル: test_data_eman.py プロジェクト: josegutab/scipion
 def testConvert(self):
     micSet = SetOfMicrographs(filename=self.dbGold)
     
     
     # Test writing micrgraphs to an hdf        
     filename = self.getOutputPath('micrographs.hdf')
     e2convert.writeSetOfParticles(micSet, filename, self.dataset.getPath())
コード例 #2
0
    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())
コード例 #3
0
ファイル: protocol_refineasy.py プロジェクト: I2PC/scipion
 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())