def __init__(self, scriptname, project): XmippProtocol.__init__(self, protDict.ml2d.name, scriptname, project) self.Import = 'from protocol_ml2d import *' self.acquisionInfo = self.findAcquisitionInfo(self.ImgMd) if not self.acquisionInfo is None: md = MetaData(self.acquisionInfo) self.SamplingRate = md.getValue(MDL_SAMPLINGRATE, md.firstObject())
def __init__(self, protDictName, scriptname, project): self.FileKeys = ['data', 'optimiser', 'sampling'] self.ClassLabel = MDL_REF # by default 3d self.ClassFnTemplate = '%(rootDir)s/relion_it%(iter)03d_class%(ref)03d.mrc:mrc' self.outputClasses = 'classes_ref3D.xmd' self.outputVols = 'volumes.xmd' XmippProtocol.__init__(self, protDictName, scriptname, project) self.ParamsStr = '' program = 'relion_refine' if self.NumberOfMpi > 1: program += '_mpi' if self.DoContinue: if os.path.exists(self.optimiserFileName): if not self.optimiserFileName.startswith(self.WorkingDir): self.setPreviousRunFromFile(self.optimiserFileName) try: self.inputProperty('ImgMd') except: print "Cannot find the input file with experimental images in protocol %s" % self.PrevRunName self.addParam('program', program) self.addParam('ORoot', self.WorkingDir + '/') self.addParam('SamplingRate', getSampling(self.ImgMd, 0.))
def __init__(self, scriptname, project): XmippProtocol.__init__(self, protDict.xmipp.name, scriptname, project) self.Import = 'from protocol_program import *'
def __init__(self, scriptname, project): XmippProtocol.__init__(self, protDict.relion_postprocess.name, scriptname, project) self.Import = 'from protocol_relion_postprocess import *'