def validate(self):
errors = []
if not os.path.exists(self.VolumeList):
errors.append(self.VolumeList+" does not exist")
if self.MissingMd!="" and not os.path.exists(self.MissingMd):
errors.append(self.MissingMd+" does not exist")
if self.MaximumResolution>0.5:
errors.append("Maximum resolution must be smaller than 0.5")
AngSamplingList=getListFromVector(self.AngSampling)
AngLimitList=getListFromVector(self.AngLimit)
ShiftLimitList=getListFromVector(self.ShiftLimit)
NumberOfIterationsList=getListFromVector(self.NumberOfIterations)
if len(AngSamplingList)!=len(AngLimitList) or \
len(AngSamplingList)!=len(ShiftLimitList) or \
len(AngSamplingList)!=len(NumberOfIterationsList):
errors.append("You must supply the same number of parameters for Angular Sampling, Angular Limit, Shift Limit and Number of Iterations")
return errors
def defineSteps(self):
if self.MissingMd!="":
self.Db.insertStep("createLink",source=self.MissingMd,dest=self.getFilename("missingXmd"))
AngSamplingList=getListFromVector(self.AngSampling)
AngLimitList=getListFromVector(self.AngLimit)
ShiftLimitList=getListFromVector(self.ShiftLimit)
NumberOfIterationsList=getListFromVector(self.NumberOfIterations)
N=len(AngSamplingList)
for n in range(0,N):
workingDir=os.path.join(self.WorkingDir,"refinement_%02d"%n)
self.Db.insertStep("createDir",verifyfiles=[workingDir],path=workingDir)
fnIn=os.path.join(workingDir,'inputVolumeList.xmd')
fnRoot=os.path.join(workingDir,'mltomo')
if n==0:
self.Db.insertStep("createLink",verifyfiles=[fnIn],source=self.VolumeList,dest=fnIn)
else:
workingDir_1=os.path.join(self.WorkingDir,"refinement_%02d"%(n-1))
self.Db.insertStep("createLink",verifyfiles=[fnIn],source=os.path.join(workingDir_1,'mltomo_img.xmd'),dest=fnIn)
params= ' -i ' + fnIn + \
' --oroot ' + fnRoot + \
' --iter ' + NumberOfIterationsList[n] + \
' --sym ' + self.Symmetry +\
' --maxres ' + str(self.MaximumResolution)
# getComponentFromVector, getListFromVector
if self.MissingMd!="":
params+= ' --missing ' + self.getFilename("missingXmd")
if self.Dimension > 0:
params+= ' --dim ' + str(self.Dimension)
# Alignment parameters
params+= ' --ang ' + AngSamplingList[n]
if int(AngLimitList[n])<360:
params+= ' --ang_search ' + AngLimitList[n]
if self.DoPerturb:
params+= ' --perturb '
if int(ShiftLimitList[n])>0:
params+=" --limit_trans " + ShiftLimitList[n]
# Classification parameters
if self.DoGenerateReferences and n==0:
params+=' --nref ' + str(self.NumberOfReferences)
else:
if n==0:
params+=' --ref ' + self.RefMd
else:
params+=' --ref ' + os.path.join(workingDir_1,"mltomo_ref.xmd")
if self.InitialRegularization>0:
params+= ' --reg0 ' + str(self.InitialRegularization)
params+= ' --reg_steps ' + str(self.NumberRegularizationSteps)
# Extra parameters
if (len(self.ExtraParamsMLtomo) > 0):
params+=' ' + str (self.ExtraParamsMLtomo)
# Thread parallelization
if self.NumberOfThreads > 1:
params+=' --thr ' + str(self.NumberOfThreads)
verifyFiles=[fnRoot+"_img.xmd"]
self.insertRunJobStep("xmipp_ml_tomo", params, verifyFiles)
lastDir=os.path.join(self.WorkingDir,"refinement_%02d"%(N-1))
fnOut=self.workingDirPath("mltomo.fsc")
self.Db.insertStep("createLink",verifyfiles=[fnOut],source=os.path.join(lastDir,"mltomo.fsc"),dest=fnOut)
fnOut=self.workingDirPath("mltomo_img.xmd")
self.Db.insertStep("createLink",verifyfiles=[fnOut],source=os.path.join(lastDir,"mltomo_img.xmd"),dest=fnOut)
fnOut=self.workingDirPath("mltomo_ref.xmd")
self.Db.insertStep("createLink",verifyfiles=[fnOut],source=os.path.join(lastDir,"mltomo_ref.xmd"),dest=fnOut)
