def setupXmippML3DProtocol(self):
''' sets up ML3D protocol parameters, pickles to file, etc.'''
protocolname = 'xmipp_protocol_ml3d'
### Locate protocol_ml3d
protocol_ml3d = apXmipp.locateXmippProtocol(protocolname)
### setup protocol parameters
protocolPrm = {}
### check for n input model dependencies
protocolPrm["InitialReference"] = self.params['modelnames'][0]
if len(self.params['modelnames']) > 1:
selfile = "reference_volumes.sel"
sf = open(selfile, "w")
for model in self.params['modelnames']:
sf.write("%s\t1\n" % os.path.join(self.params['rundir'], model))
sf.close()
protocolPrm["SeedsSelfile"] = os.path.join(self.params['rundir'], "reference_volumes.sel")
protocolPrm["DoGenerateSeeds"] = False
else:
protocolPrm["SeedsSelfile"] = ""
protocolPrm["DoGenerateSeeds"] = True
protocolPrm["InSelFile"] = "partlist.sel" ### this maybe should not be hardcoded
protocolPrm["WorkingDir"] = "ml3d"
protocolPrm["DoDeleteWorkingDir"] = False
protocolPrm["ProjectDir"] = self.params['recondir']
protocolPrm["LogDir"] = "Logs"
protocolPrm["DoMlf"] = self.params['DoMlf']
protocolPrm["DoCorrectAmplitudes"] = False
protocolPrm["InCtfDatFile"] = "all_images.ctfdat"
protocolPrm["HighResLimit"] = self.params['HighResLimit']
protocolPrm["ImagesArePhaseFlipped"] = self.params['ImagesArePhaseFlipped']
protocolPrm["InitialMapIsAmplitudeCorrected"] = False
protocolPrm["SeedsAreAmplitudeCorrected"] = False
protocolPrm["DoCorrectGreyScale"] = self.params['DoCorrectGreyScale']
protocolPrm["ProjMatchSampling"] = self.params['ProjMatchSampling']
if (self.params['LowPassFilter']>1) is True:
protocolPrm["DoLowPassFilterReference"] = True
protocolPrm["LowPassFilter"] = self.params['LowPassFilter']
else:
protocolPrm["DoLowPassFilterReference"] = False
protocolPrm["LowPassFilter"] = self.params['LowPassFilter']
protocolPrm["PixelSize"] = self.params['apix']
protocolPrm["NumberOfReferences"] = self.params['NumberOfReferences']
protocolPrm["DoJustRefine"] = False
protocolPrm["DoML3DClassification"] = True
protocolPrm["AngularSampling"] = self.params['AngularSampling']
protocolPrm["NumberOfIterations"] = self.params['numiter']
protocolPrm["Symmetry"] = self.params['symmetry'][0]
protocolPrm["DoNorm"] = False
protocolPrm["DoFourier"] = False
protocolPrm["RestartIter"] = 0
protocolPrm["ExtraParamsMLrefine3D"] = ""
protocolPrm["NumberOfThreads"] = 1
protocolPrm["DoParallel"] = self.params['nproc']>1
protocolPrm["NumberOfMpiProcesses"] = self.params['nproc']
protocolPrm["SystemFlavour"] = ""
protocolPrm["AnalysisScript"] = "visualize_ml3d.py"
### write out python protocol into run directory
protocolfile = os.path.join(self.params['remoterundir'],"%s.py" % protocolname)
apXmipp.particularizeProtocol(protocol_ml3d, protocolPrm, protocolfile)
os.chmod(os.path.join(self.params['rundir'], protocolfile), 0775)
### Write the parameters for posterior uploading, both generic and specific
self.runparams = {}
self.runparams['reconstruction_package'] = "xmipp_ml3d"
self.runparams['remoterundir'] = self.params['remoterundir']
# self.runparams['reconstruction_working_dir'] = protocolPrm["WorkingDir"]
self.runparams['reconstruction_working_dir'] = protocolPrm['WorkingDir']+"/RunML3D"
self.runparams['numiter'] = protocolPrm['NumberOfIterations']
self.runparams['NumberOfReferences'] = protocolPrm['NumberOfReferences']
self.runparams['symmetry'] = protocolPrm["Symmetry"]
self.runparams['package_params'] = protocolPrm
paramfile = os.path.join(self.params['remoterundir'], "xmipp_ml3d_"+self.timestamp+"-params.pickle")
apParam.dumpParameters(self.runparams, paramfile)
### finished setup of input files, now run xmipp_protocols_ml3d.py from jobfile
apDisplay.printMsg("finished setting up input files, now running xmipp_protocols_ml3d.py")
return protocolfile, protocolPrm
def setupXmippProtocol(self):
protocolname = 'xmipp_protocol_projmatch'
# Locate protocol_projmatch
protocol_projmatch=apXmipp.locateXmippProtocol(protocolname)
#make threads and mpi processes compatible with the xmipprequirement
self.params['alwaysone']=1
protocolPrm={}
protocolPrm["SelFileName"] = "partlist.sel"
protocolPrm["DocFileName"] = ""
protocolPrm["ReferenceFileName"] = self.params['modelnames'][0]
protocolPrm["WorkingDir"] = "ProjMatch"
protocolPrm["DoDeleteWorkingDir"] = True
protocolPrm["NumberofIterations"] = self.params['enditer']
protocolPrm["ContinueAtIteration"] = self.params['startiter']
protocolPrm["CleanUpFiles"] = False
protocolPrm["ProjectDir"] = self.params['recondir']
protocolPrm["LogDir"] = "Logs"
protocolPrm["DoCtfCorrection"] = False
protocolPrm["CTFDatName"] = ""
protocolPrm["DoAutoCtfGroup"] = False
protocolPrm["CtfGroupMaxDiff"] = 0.5
protocolPrm["CtfGroupMaxResol"] = 15
protocolPrm["SplitDefocusDocFile"] = ""
protocolPrm["PaddingFactor"] = 2
protocolPrm["WienerConstant"] = -1
protocolPrm["DataArePhaseFlipped"] = True
protocolPrm["ReferenceIsCtfCorrected"] = True
protocolPrm["DoMask"] = self.params['maskvol']>0
protocolPrm["DoSphericalMask"] = self.params['outerMaskRadius']>0
# split is needed because refineJob base class defines outMaskRadius as iteration parameter but xmipp can
# no accept such assignment
protocolPrm["MaskRadius"] = self.convertAngstromToPixel( self.params['outerMaskRadius'].split()[0] )
protocolPrm["MaskFileName"] = self.params['maskvol']
protocolPrm["DoProjectionMatching"] = True
protocolPrm["DisplayProjectionMatching"] = False
protocolPrm["InnerRadius"] = self.convertAngstromToPixel( self.params['innerAlignRadius'] )
protocolPrm["OuterRadius"] = self.convertAngstromToPixel( self.params['outerAlignRadius'] )
protocolPrm["AvailableMemory"] = self.calcRefineMem()
# protocolPrm["AngSamplingRateDeg"] = self.params['AngularSteps']
protocolPrm["AngSamplingRateDeg"] = self.params['angSampRate']
protocolPrm["MaxChangeInAngles"] = self.params['maxAngularChange']
protocolPrm["PerturbProjectionDirections"] = False
protocolPrm["MaxChangeOffset"] = self.params['maxChangeOffset']
protocolPrm["Search5DShift"] = self.params['search5DShift']
protocolPrm["Search5DStep"] = self.params['search5DStep']
protocolPrm["DoRetricSearchbyTiltAngle"] = False
protocolPrm["Tilt0"] = 0
protocolPrm["TiltF"] = 0
protocolPrm["SymmetryGroup"] = self.params['symmetry']
protocolPrm["SymmetryGroupNeighbourhood"] = ''
protocolPrm["OnlyWinner"] = False
protocolPrm["MinimumCrossCorrelation"] = '-1'
protocolPrm["DiscardPercentage"] = self.params['percentDiscard']
protocolPrm["ProjMatchingExtra"] = ''
protocolPrm["DoAlign2D"] = '0'
protocolPrm["Align2DIterNr"] = 4
protocolPrm["Align2dMaxChangeOffset"] = '1000'
protocolPrm["Align2dMaxChangeRot"] = '1000'
if not self.params['refineonly']:
protocolPrm["DoReconstruction"] = True
else:
protocolPrm["DoReconstruction"] = False
protocolPrm["DisplayReconstruction"] = False
protocolPrm["ARTLambda"] = self.params['ARTLambda']
protocolPrm["ARTReconstructionExtraCommand"]= ''
protocolPrm["FourierMaxFrequencyOfInterest"]= self.params['fouriermaxfrequencyofinterest']
protocolPrm["WBPReconstructionExtraCommand"]=''
protocolPrm["FourierReconstructionExtraCommand"]=''
if not self.params['refineonly']:
protocolPrm["ReconstructionMethod"] = self.params['reconMethod']
protocolPrm["DoComputeResolution"] = self.params['docomputeresolution']
protocolPrm["DoSplitReferenceImages"] = True
protocolPrm["DoLowPassFilter"] = self.params['dolowpassfilter']
protocolPrm["UseFscForFilter"] = self.params['usefscforfilter']
else:
#Xmipp does not allow False SplitReferenceImage except the exact syntex of 'fourier' in ReconstructionMethod
protocolPrm["ReconstructionMethod"] = 'fourier'
#These should never be used if reconstruction is not done
protocolPrm["DoComputeResolution"] = False
protocolPrm["DoSplitReferenceImages"] = False
protocolPrm["DoLowPassFilter"] = False
protocolPrm["UseFscForFilter"] = False
protocolPrm["ResolSam"] = self.params['apix']
protocolPrm["DisplayResolution"] = False
if self.params['usefscforfilter'] is False and self.params['filterResolution']:
protocolPrm["ConstantToAddToFiltration"] = str(self.params['apix'] / self.params['filterResolution'])
else:
protocolPrm["ConstantToAddToFiltration"] = str(self.params['filterConstant'])
print protocolPrm["ConstantToAddToFiltration"]
protocolPrm["NumberOfThreads"] = self.params['alwaysone']
protocolPrm["DoParallel"] = self.params['nproc']>1
protocolPrm["NumberOfMpiProcesses"] = self.params['nproc']
protocolPrm["MpiJobSize"] = '10'
protocolPrm["SystemFlavour"] = ''
protocolPrm["AnalysisScript"] = 'visualize_projmatch.py'
### write out python protocol into run directory
protocolfile = os.path.join(self.params['remoterundir'],"%s.py" % protocolname)
if self.params['refineonly']:
tempprotocolfile = os.path.join(self.params['remoterundir'],"%s.temp" % protocolname)
apXmipp.fixRefineOnlyProtocol(protocol_projmatch,tempprotocolfile)
apXmipp.particularizeProtocol(tempprotocolfile, protocolPrm, protocolfile)
os.remove(tempprotocolfile)
else:
apXmipp.particularizeProtocol(protocol_projmatch, protocolPrm, protocolfile)
os.chmod(os.path.join(self.params['rundir'], protocolfile), 0775)
### Write the parameters for posterior uploading, both generic and specific
self.runparams = {} ### these are generic params that includes a dictionary entry for package-specific params
# self.runparams['symmetry'] = apSymmetry.getSymmetryDataFromName(self.params['symmetry'])
#sym = apSymmetry.getSymmetryDataFromID(self.params['symmetry'])
#sym2 = self.convertSymmetryNameForPackage(sym)
sym = protocolPrm["SymmetryGroup"][0]
if sym in ('i','I'):
self.runparams['symmetry'] = "Icos (2 3 5) Viper/3DEM"
else:
self.runparams['symmetry'] = protocolPrm["SymmetryGroup"]
self.runparams['numiter'] = protocolPrm['NumberofIterations']
self.runparams['mask'] = protocolPrm["MaskRadius"]
self.runparams['imask'] = None
self.runparams['alignmentInnerRadius'] = protocolPrm["InnerRadius"]
self.runparams['alignmentOuterRadius'] = protocolPrm["OuterRadius"]
self.runparams['reconstruction_package'] = "Xmipp"
self.runparams['remoterundir'] = self.params['remoterundir']
self.runparams['reconstruction_working_dir'] = protocolPrm["WorkingDir"]
self.runparams['package_params'] = protocolPrm
self.picklefile = os.path.join(self.params['remoterundir'], "xmipp_projection_matching_"+self.timestamp+"-params.pickle")
apParam.dumpParameters(self.runparams, self.picklefile)
### finished setup of input files, now run xmipp_protocols_ml3d.py from jobfile
apDisplay.printMsg("finished setting up input files, now ready to run protocol")
return protocolfile, protocolPrm
def setupXmippProtocol(self):
protocolname = 'xmipp_protocol_projmatch'
# Locate protocol_projmatch
protocol_projmatch = apXmipp.locateXmippProtocol(protocolname)
#make threads and mpi processes compatible with the xmipprequirement
self.params['alwaysone'] = 1
protocolPrm = {}
protocolPrm["SelFileName"] = "partlist.sel"
protocolPrm["DocFileName"] = ""
protocolPrm["ReferenceFileName"] = self.params['modelnames'][0]
protocolPrm["WorkingDir"] = "ProjMatch"
protocolPrm["DoDeleteWorkingDir"] = True
protocolPrm["NumberofIterations"] = self.params['enditer']
protocolPrm["ContinueAtIteration"] = self.params['startiter']
protocolPrm["CleanUpFiles"] = False
protocolPrm["ProjectDir"] = self.params['recondir']
protocolPrm["LogDir"] = "Logs"
protocolPrm["DoCtfCorrection"] = False
protocolPrm["CTFDatName"] = ""
protocolPrm["DoAutoCtfGroup"] = False
protocolPrm["CtfGroupMaxDiff"] = 0.5
protocolPrm["CtfGroupMaxResol"] = 15
protocolPrm["SplitDefocusDocFile"] = ""
protocolPrm["PaddingFactor"] = 2
protocolPrm["WienerConstant"] = -1
protocolPrm["DataArePhaseFlipped"] = True
protocolPrm["ReferenceIsCtfCorrected"] = True
protocolPrm["DoMask"] = self.params['maskvol'] > 0
protocolPrm["DoSphericalMask"] = self.params['outerMaskRadius'] > 0
# split is needed because refineJob base class defines outMaskRadius as iteration parameter but xmipp can
# no accept such assignment
protocolPrm["MaskRadius"] = self.convertAngstromToPixel(
self.params['outerMaskRadius'].split()[0])
protocolPrm["MaskFileName"] = self.params['maskvol']
protocolPrm["DoProjectionMatching"] = True
protocolPrm["DisplayProjectionMatching"] = False
protocolPrm["InnerRadius"] = self.convertAngstromToPixel(
self.params['innerAlignRadius'])
protocolPrm["OuterRadius"] = self.convertAngstromToPixel(
self.params['outerAlignRadius'])
protocolPrm["AvailableMemory"] = self.calcRefineMem()
# protocolPrm["AngSamplingRateDeg"] = self.params['AngularSteps']
protocolPrm["AngSamplingRateDeg"] = self.params['angSampRate']
protocolPrm["MaxChangeInAngles"] = self.params['maxAngularChange']
protocolPrm["PerturbProjectionDirections"] = False
protocolPrm["MaxChangeOffset"] = self.params['maxChangeOffset']
protocolPrm["Search5DShift"] = self.params['search5DShift']
protocolPrm["Search5DStep"] = self.params['search5DStep']
protocolPrm["DoRetricSearchbyTiltAngle"] = False
protocolPrm["Tilt0"] = 0
protocolPrm["TiltF"] = 0
protocolPrm["SymmetryGroup"] = self.params['symmetry']
protocolPrm["SymmetryGroupNeighbourhood"] = ''
protocolPrm["OnlyWinner"] = False
protocolPrm["MinimumCrossCorrelation"] = '-1'
protocolPrm["DiscardPercentage"] = self.params['percentDiscard']
protocolPrm["ProjMatchingExtra"] = ''
protocolPrm["DoAlign2D"] = '0'
protocolPrm["Align2DIterNr"] = 4
protocolPrm["Align2dMaxChangeOffset"] = '1000'
protocolPrm["Align2dMaxChangeRot"] = '1000'
if not self.params['refineonly']:
protocolPrm["DoReconstruction"] = True
else:
protocolPrm["DoReconstruction"] = False
protocolPrm["DisplayReconstruction"] = False
protocolPrm["ARTLambda"] = self.params['ARTLambda']
protocolPrm["ARTReconstructionExtraCommand"] = ''
protocolPrm["FourierMaxFrequencyOfInterest"] = self.params[
'fouriermaxfrequencyofinterest']
protocolPrm["WBPReconstructionExtraCommand"] = ''
protocolPrm["FourierReconstructionExtraCommand"] = ''
if not self.params['refineonly']:
protocolPrm["ReconstructionMethod"] = self.params['reconMethod']
protocolPrm["DoComputeResolution"] = self.params[
'docomputeresolution']
protocolPrm["DoSplitReferenceImages"] = True
protocolPrm["DoLowPassFilter"] = self.params['dolowpassfilter']
protocolPrm["UseFscForFilter"] = self.params['usefscforfilter']
else:
#Xmipp does not allow False SplitReferenceImage except the exact syntex of 'fourier' in ReconstructionMethod
protocolPrm["ReconstructionMethod"] = 'fourier'
#These should never be used if reconstruction is not done
protocolPrm["DoComputeResolution"] = False
protocolPrm["DoSplitReferenceImages"] = False
protocolPrm["DoLowPassFilter"] = False
protocolPrm["UseFscForFilter"] = False
protocolPrm["ResolSam"] = self.params['apix']
protocolPrm["DisplayResolution"] = False
if self.params['usefscforfilter'] is False and self.params[
'filterResolution']:
protocolPrm["ConstantToAddToFiltration"] = str(
self.params['apix'] / self.params['filterResolution'])
else:
protocolPrm["ConstantToAddToFiltration"] = str(
self.params['filterConstant'])
print protocolPrm["ConstantToAddToFiltration"]
protocolPrm["NumberOfThreads"] = self.params['alwaysone']
protocolPrm["DoParallel"] = self.params['nproc'] > 1
protocolPrm["NumberOfMpiProcesses"] = self.params['nproc']
protocolPrm["MpiJobSize"] = '10'
protocolPrm["SystemFlavour"] = ''
protocolPrm["AnalysisScript"] = 'visualize_projmatch.py'
### write out python protocol into run directory
protocolfile = os.path.join(self.params['remoterundir'],
"%s.py" % protocolname)
if self.params['refineonly']:
tempprotocolfile = os.path.join(self.params['remoterundir'],
"%s.temp" % protocolname)
apXmipp.fixRefineOnlyProtocol(protocol_projmatch, tempprotocolfile)
apXmipp.particularizeProtocol(tempprotocolfile, protocolPrm,
protocolfile)
os.remove(tempprotocolfile)
else:
apXmipp.particularizeProtocol(protocol_projmatch, protocolPrm,
protocolfile)
os.chmod(os.path.join(self.params['rundir'], protocolfile), 0775)
### Write the parameters for posterior uploading, both generic and specific
self.runparams = {
} ### these are generic params that includes a dictionary entry for package-specific params
# self.runparams['symmetry'] = apSymmetry.getSymmetryDataFromName(self.params['symmetry'])
#sym = apSymmetry.getSymmetryDataFromID(self.params['symmetry'])
#sym2 = self.convertSymmetryNameForPackage(sym)
sym = protocolPrm["SymmetryGroup"][0]
if sym in ('i', 'I'):
self.runparams['symmetry'] = "Icos (2 3 5) Viper/3DEM"
else:
self.runparams['symmetry'] = protocolPrm["SymmetryGroup"]
self.runparams['numiter'] = protocolPrm['NumberofIterations']
self.runparams['mask'] = protocolPrm["MaskRadius"]
self.runparams['imask'] = None
self.runparams['alignmentInnerRadius'] = protocolPrm["InnerRadius"]
self.runparams['alignmentOuterRadius'] = protocolPrm["OuterRadius"]
self.runparams['reconstruction_package'] = "Xmipp"
self.runparams['remoterundir'] = self.params['remoterundir']
self.runparams['reconstruction_working_dir'] = protocolPrm[
"WorkingDir"]
self.runparams['package_params'] = protocolPrm
self.picklefile = os.path.join(
self.params['remoterundir'],
"xmipp_projection_matching_" + self.timestamp + "-params.pickle")
apParam.dumpParameters(self.runparams, self.picklefile)
### finished setup of input files, now run xmipp_protocols_ml3d.py from jobfile
apDisplay.printMsg(
"finished setting up input files, now ready to run protocol")
return protocolfile, protocolPrm
def setupXmippML3DProtocol(self):
''' sets up ML3D protocol parameters, pickles to file, etc.'''
protocolname = 'xmipp_protocol_ml3d'
### Locate protocol_ml3d
protocol_ml3d = apXmipp.locateXmippProtocol(protocolname)
### setup protocol parameters
protocolPrm = {}
### check for n input model dependencies
protocolPrm["InitialReference"] = self.params['modelnames'][0]
if len(self.params['modelnames']) > 1:
selfile = "reference_volumes.sel"
sf = open(selfile, "w")
for model in self.params['modelnames']:
sf.write("%s\t1\n" %
os.path.join(self.params['rundir'], model))
sf.close()
protocolPrm["SeedsSelfile"] = os.path.join(
self.params['rundir'], "reference_volumes.sel")
protocolPrm["DoGenerateSeeds"] = False
else:
protocolPrm["SeedsSelfile"] = ""
protocolPrm["DoGenerateSeeds"] = True
protocolPrm[
"InSelFile"] = "partlist.sel" ### this maybe should not be hardcoded
protocolPrm["WorkingDir"] = "ml3d"
protocolPrm["DoDeleteWorkingDir"] = False
protocolPrm["ProjectDir"] = self.params['recondir']
protocolPrm["LogDir"] = "Logs"
protocolPrm["DoMlf"] = self.params['DoMlf']
protocolPrm["DoCorrectAmplitudes"] = False
protocolPrm["InCtfDatFile"] = "all_images.ctfdat"
protocolPrm["HighResLimit"] = self.params['HighResLimit']
protocolPrm["ImagesArePhaseFlipped"] = self.params[
'ImagesArePhaseFlipped']
protocolPrm["InitialMapIsAmplitudeCorrected"] = False
protocolPrm["SeedsAreAmplitudeCorrected"] = False
protocolPrm["DoCorrectGreyScale"] = self.params['DoCorrectGreyScale']
protocolPrm["ProjMatchSampling"] = self.params['ProjMatchSampling']
if (self.params['LowPassFilter'] > 1) is True:
protocolPrm["DoLowPassFilterReference"] = True
protocolPrm["LowPassFilter"] = self.params['LowPassFilter']
else:
protocolPrm["DoLowPassFilterReference"] = False
protocolPrm["LowPassFilter"] = self.params['LowPassFilter']
protocolPrm["PixelSize"] = self.params['apix']
protocolPrm["NumberOfReferences"] = self.params['NumberOfReferences']
protocolPrm["DoJustRefine"] = False
protocolPrm["DoML3DClassification"] = True
protocolPrm["AngularSampling"] = self.params['AngularSampling']
protocolPrm["NumberOfIterations"] = self.params['numiter']
protocolPrm["Symmetry"] = self.params['symmetry'][0]
protocolPrm["DoNorm"] = False
protocolPrm["DoFourier"] = False
protocolPrm["RestartIter"] = 0
protocolPrm["ExtraParamsMLrefine3D"] = ""
protocolPrm["NumberOfThreads"] = 1
protocolPrm["DoParallel"] = self.params['nproc'] > 1
protocolPrm["NumberOfMpiProcesses"] = self.params['nproc']
protocolPrm["SystemFlavour"] = ""
protocolPrm["AnalysisScript"] = "visualize_ml3d.py"
### write out python protocol into run directory
protocolfile = os.path.join(self.params['remoterundir'],
"%s.py" % protocolname)
apXmipp.particularizeProtocol(protocol_ml3d, protocolPrm, protocolfile)
os.chmod(os.path.join(self.params['rundir'], protocolfile), 0775)
### Write the parameters for posterior uploading, both generic and specific
self.runparams = {}
self.runparams['reconstruction_package'] = "xmipp_ml3d"
self.runparams['remoterundir'] = self.params['remoterundir']
# self.runparams['reconstruction_working_dir'] = protocolPrm["WorkingDir"]
self.runparams['reconstruction_working_dir'] = protocolPrm[
'WorkingDir'] + "/RunML3D"
self.runparams['numiter'] = protocolPrm['NumberOfIterations']
self.runparams['NumberOfReferences'] = protocolPrm[
'NumberOfReferences']
self.runparams['symmetry'] = protocolPrm["Symmetry"]
self.runparams['package_params'] = protocolPrm
paramfile = os.path.join(
self.params['remoterundir'],
"xmipp_ml3d_" + self.timestamp + "-params.pickle")
apParam.dumpParameters(self.runparams, paramfile)
### finished setup of input files, now run xmipp_protocols_ml3d.py from jobfile
apDisplay.printMsg(
"finished setting up input files, now running xmipp_protocols_ml3d.py"
)
return protocolfile, protocolPrm
