def defineSteps(self):
self.insertStep('createDir', verifyfiles=[self.ExtraDir], path=self.ExtraDir)
# launch relion program
self.insertRelionClassifyContinue()
#self.ImgStar = self.extraPath(replaceBasenameExt(tmpFileNameXMD, '.star'))
lastIteration = self.NumberOfIterations
NumberOfClasses=self.NumberOfClasses
firstIteration = self.ContinueFromIteration
ProtRelionBase.defineSteps2(self, firstIteration
, lastIteration
, NumberOfClasses)
def __init__(self, scriptname, project):
ProtRelionBase.__init__(self, protDict.relion_classify_continue.name, scriptname, project)
self.PrevRun=self.project.getProtocolFromFile(self.inputFileName)
#self.setPreviousRun(self.ImportRun)
self.Import = 'from protocol_relion_classify_continue import *'
self.relionType='classify'
#if optimizer has not been properly selected this will
#fail, let us go ahead and handle the situation in verify
try:
self.inputProperty('NumberOfClasses')
self.inputProperty('SamplingRate')
self.inputProperty('MaskRadiusA')
self.inputProperty('RegularisationParamT')
#self.lastIterationPrecRun=self.PrevRun.lastIter()
#self.NumberOfClasses = self.PrevRun.NumberOfClasses
#self.SamplingRate = self.PrevRun.SamplingRate
#self.MaskDiameterA = self.PrevRun.MaskDiameterA
#self.RegularisationParamT = self.PrevRun.RegularisationParamT
except:
print "Can not access the parameters from the original relion run"
def createFilenameTemplates(self):
myDict=ProtRelionBase.createFilenameTemplates(self)
#myDict['volume']=self.extraIter + "class%(ref3d)03d.spi"
#myDict['volumeMRC']=self.extraIter + "class%(ref3d)03d.mrc:mrc"
myDict['volume']=self.extraIter + "class%(ref3d)03d.mrc:mrc"
self.relionFiles += ['model']
#relionFiles=['data','model','optimiser','sampling']
for v in self.relionFiles:
myDict[v+'Re']=self.extraIter + v +'.star'
myDict[v+'Xm']=self.extraIter + v +'.xmd'
myDict['imagesAssignedToClass']='imagesAssignedToClass@'+self.ExtraDir+'/dataForVisualize.xmd'
extraIter = join('%(workingDir)s', 'extra', 'relion_it%(iter)03d_optimiser.star')
myDict['optimiserCont'] = extraIter
return myDict
def summary(self):
lines = ProtRelionBase.summary(self)
lastIteration = self.lastIter()
lines += ['Continuation from run: <%s>, iter: <%d>' % (self.PrevRunName, self.ContinueFromIteration)]
if (lastIteration - self.ContinueFromIteration) < 0 :
performedIteration=0
else:
performedIteration=lastIteration - self.ContinueFromIteration
lines += ['Performed <%d> iterations (number estimated from the files in working directory)' % performedIteration ]
lines += ['Input fileName = <%s>'%self.inputFileName]
#lines += ['test = <%s>'%self.getFilename('optimiserRe',iter=3)]
#lines += ['test = <%s>'%self.PrevRun.getFilename('optimiserRe',iter=3)]
#lines += ['WorkingDir = <%s>'%self.WorkingDir]
#lines += ['WorkingDir2 = <%s>'%self.PrevRun.WorkingDir]
#lines += ['lastIter = <%s>'%self.lastIter()]
#lines += ['lastIter2 = <%s>'%self.PrevRun.lastIter()]
return lines