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 *'
