def parseFileForRunParameters(self):
''' PACKAGE-SPECIFIC FILE PARSER: if the parameters were not pickled, parse protocols script to determine ML3D params '''
### parameters can be found in python protocols
xmipp_protocol_ml3d = apXmipp.importProtocolPythonFile("xmipp_protocol_ml3d", self.params['rundir'])
packageparams = {}
packageparams['InSelFile'] = xmipp_protocol_ml3d.InSelFile
packageparams['InitialReference'] = xmipp_protocol_ml3d.InitialReference
packageparams['WorkingDir'] = xmipp_protocol_ml3d.WorkingDir
packageparams['DoDeleteWorkingDir'] = xmipp_protocol_ml3d.DoDeleteWorkingDir
# packageparams['ProjectDir'] = xmipp_protocol_ml3d.ProjectDir
# packageparams['LogDir'] = xmipp_protocol_ml3d.LogDir
packageparams['DoMlf'] = xmipp_protocol_ml3d.DoMlf
packageparams['DoCorrectAmplitudes'] = xmipp_protocol_ml3d.DoCorrectAmplitudes
packageparams['InCtfDatFile'] = xmipp_protocol_ml3d.InCtfDatFile
packageparams['HighResLimit'] = xmipp_protocol_ml3d.HighResLimit
packageparams['ImagesArePhaseFlipped'] = xmipp_protocol_ml3d.ImagesArePhaseFlipped
packageparams['InitialMapIsAmplitudeCorrected'] = xmipp_protocol_ml3d.InitialMapIsAmplitudeCorrected
packageparams['SeedsAreAmplitudeCorrected'] = xmipp_protocol_ml3d.SeedsAreAmplitudeCorrected
packageparams['DoCorrectGreyScale'] = xmipp_protocol_ml3d.DoCorrectGreyScale
packageparams['ProjMatchSampling'] = xmipp_protocol_ml3d.ProjMatchSampling
packageparams['DoLowPassFilterReference'] = xmipp_protocol_ml3d.DoLowPassFilterReference
packageparams['LowPassFilter'] = xmipp_protocol_ml3d.LowPassFilter
packageparams['PixelSize'] = xmipp_protocol_ml3d.PixelSize
packageparams['DoGenerateSeeds'] = xmipp_protocol_ml3d.DoGenerateSeeds
packageparams['NumberOfReferences'] = xmipp_protocol_ml3d.NumberOfReferences
packageparams['DoJustRefine'] = xmipp_protocol_ml3d.DoJustRefine
packageparams['SeedsSelfile'] = xmipp_protocol_ml3d.SeedsSelfile
packageparams['DoML3DClassification'] = xmipp_protocol_ml3d.DoML3DClassification
packageparams['AngularSampling'] = xmipp_protocol_ml3d.AngularSampling
packageparams['NumberOfIterations'] = xmipp_protocol_ml3d.NumberOfIterations
packageparams['Symmetry'] = xmipp_protocol_ml3d.Symmetry
packageparams['DoNorm'] = xmipp_protocol_ml3d.DoNorm
packageparams['DoFourier'] = xmipp_protocol_ml3d.DoFourier
packageparams['RestartIter'] = xmipp_protocol_ml3d.RestartIter
packageparams['ExtraParamsMLrefine3D'] = xmipp_protocol_ml3d.ExtraParamsMLrefine3D
# packageparams['NumberOfThreads'] = xmipp_protocol_ml3d.NumberOfThreads
# packageparams['DoParallel'] = xmipp_protocol_ml3d.DoParallel
# packageparams['NumberOfMpiProcesses'] = xmipp_protocol_ml3d.NumberOfMpiProcesses
# packageparams['SystemFlavour'] = xmipp_protocol_ml3d.SystemFlavour
# packageparams['AnalysisScript'] = xmipp_protocol_ml3d.AnalysisScript
if xmipp_protocol_ml3d.Symmetry[:1] == "i":
sym = "icos"
else:
sym = xmipp_protocol_ml3d.Symmetry
sym = sym.split()[0]
### set global parameters
runparams = {}
runparams['symmetry'] = apSymmetry.findSymmetry(sym)
runparams['apix'] = packageparams['PixelSize']
runparams['angularSamplingRate'] = packageparams['AngularSampling']
runparams['NumberOfReferences'] = packageparams['NumberOfReferences']
runparams['numiter'] = packageparams['NumberOfIterations']
runparams['package_params'] = packageparams
runparams['remoterundir'] = os.path.abspath(xmipp_protocol_ml3d.ProjectDir)
return runparams
def parseFileForRunParameters(self):
''' PACKAGE-SPECIFIC FILE PARSER: if the parameters were not pickled, parse protocols script to determine projection-matching params '''
### parameters can be found in python protocols
xmipp_protocol_projmatch = apXmipp.importProtocolPythonFile(
"xmipp_protocol_projmatch", self.params['rundir'])
packageparams = {}
packageparams[
'NumberofIterations'] = xmipp_protocol_projmatch.NumberofIterations
packageparams['MaskFileName'] = xmipp_protocol_projmatch.MaskFileName
packageparams['MaskRadius'] = xmipp_protocol_projmatch.MaskRadius
packageparams['InnerRadius'] = xmipp_protocol_projmatch.InnerRadius
packageparams['OuterRadius'] = xmipp_protocol_projmatch.OuterRadius
packageparams['SymmetryGroup'] = xmipp_protocol_projmatch.SymmetryGroup
packageparams[
'FourierMaxFrequencyOfInterest'] = xmipp_protocol_projmatch.FourierMaxFrequencyOfInterest
packageparams['SelFileName'] = xmipp_protocol_projmatch.SelFileName
packageparams['DocFileName'] = xmipp_protocol_projmatch.DocFileName
packageparams[
'ReferenceFileName'] = xmipp_protocol_projmatch.ReferenceFileName
packageparams['WorkingDir'] = xmipp_protocol_projmatch.WorkingDir
# packageparams['DoDeleteWorkingDir'] = xmipp_protocol_projmatch.DoDeleteWorkingDir
# packageparams['ContinueAtIteration'] = xmipp_protocol_projmatch.ContinueAtIteration
packageparams['CleanUpFiles'] = xmipp_protocol_projmatch.CleanUpFiles
# packageparams['ProjectDir'] = xmipp_protocol_projmatch.ProjectDir
# packageparams['LogDir'] = xmipp_protocol_projmatch.LogDir
packageparams[
'DoCtfCorrection'] = xmipp_protocol_projmatch.DoCtfCorrection
packageparams['CTFDatName'] = xmipp_protocol_projmatch.CTFDatName
packageparams[
'DoAutoCtfGroup'] = xmipp_protocol_projmatch.DoAutoCtfGroup
packageparams[
'CtfGroupMaxDiff'] = xmipp_protocol_projmatch.CtfGroupMaxDiff
packageparams[
'CtfGroupMaxResol'] = xmipp_protocol_projmatch.CtfGroupMaxResol
# packageparams['SplitDefocusDocFile'] = xmipp_protocol_projmatch.SplitDefocusDocFile
packageparams['PaddingFactor'] = xmipp_protocol_projmatch.PaddingFactor
packageparams[
'WienerConstant'] = xmipp_protocol_projmatch.WienerConstant
packageparams[
'DataArePhaseFlipped'] = xmipp_protocol_projmatch.DataArePhaseFlipped
packageparams[
'ReferenceIsCtfCorrected'] = xmipp_protocol_projmatch.ReferenceIsCtfCorrected
packageparams['DoMask'] = xmipp_protocol_projmatch.DoMask
packageparams[
'DoSphericalMask'] = xmipp_protocol_projmatch.DoSphericalMask
# packageparams['DoProjectionMatching'] = xmipp_protocol_projmatch.DoProjectionMatching
# packageparams['DisplayProjectionMatching'] = xmipp_protocol_projmatch.DisplayProjectionMatching
# packageparams['AvailableMemory'] = xmipp_protocol_projmatch.AvailableMemory
packageparams[
'AngSamplingRateDeg'] = xmipp_protocol_projmatch.AngSamplingRateDeg
packageparams[
'MaxChangeInAngles'] = xmipp_protocol_projmatch.MaxChangeInAngles
packageparams[
'PerturbProjectionDirections'] = xmipp_protocol_projmatch.PerturbProjectionDirections
packageparams[
'MaxChangeOffset'] = xmipp_protocol_projmatch.MaxChangeOffset
packageparams['Search5DShift'] = xmipp_protocol_projmatch.Search5DShift
packageparams['Search5DStep'] = xmipp_protocol_projmatch.Search5DStep
packageparams[
'DoRetricSearchbyTiltAngle'] = xmipp_protocol_projmatch.DoRetricSearchbyTiltAngle
packageparams['Tilt0'] = xmipp_protocol_projmatch.Tilt0
packageparams['TiltF'] = xmipp_protocol_projmatch.TiltF
packageparams[
'SymmetryGroupNeighbourhood'] = xmipp_protocol_projmatch.SymmetryGroupNeighbourhood
packageparams['OnlyWinner'] = xmipp_protocol_projmatch.OnlyWinner
packageparams[
'MinimumCrossCorrelation'] = xmipp_protocol_projmatch.MinimumCrossCorrelation
packageparams[
'DiscardPercentage'] = xmipp_protocol_projmatch.DiscardPercentage
packageparams[
'ProjMatchingExtra'] = xmipp_protocol_projmatch.ProjMatchingExtra
packageparams['DoAlign2D'] = xmipp_protocol_projmatch.DoAlign2D
packageparams['Align2DIterNr'] = xmipp_protocol_projmatch.Align2DIterNr
packageparams[
'Align2dMaxChangeOffset'] = xmipp_protocol_projmatch.Align2dMaxChangeOffset
packageparams[
'Align2dMaxChangeRot'] = xmipp_protocol_projmatch.Align2dMaxChangeRot
# packageparams['DoReconstruction'] = xmipp_protocol_projmatch.DoReconstruction
# packageparams['DisplayReconstruction'] = xmipp_protocol_projmatch.DisplayReconstruction
packageparams[
'ReconstructionMethod'] = xmipp_protocol_projmatch.ReconstructionMethod
packageparams['ARTLambda'] = xmipp_protocol_projmatch.ARTLambda
packageparams[
'ARTReconstructionExtraCommand'] = xmipp_protocol_projmatch.ARTReconstructionExtraCommand
packageparams[
'WBPReconstructionExtraCommand'] = xmipp_protocol_projmatch.WBPReconstructionExtraCommand
packageparams[
'FourierReconstructionExtraCommand'] = xmipp_protocol_projmatch.FourierReconstructionExtraCommand
# packageparams['DoSplitReferenceImages'] = xmipp_protocol_projmatch.DoSplitReferenceImages
packageparams['ResolSam'] = xmipp_protocol_projmatch.ResolSam
# packageparams['DisplayResolution'] = xmipp_protocol_projmatch.DisplayResolution
packageparams[
'ConstantToAddToFiltration'] = xmipp_protocol_projmatch.ConstantToAddToFiltration
# packageparams['NumberOfThreads'] = xmipp_protocol_projmatch.NumberOfThreads
# packageparams['DoParallel'] = xmipp_protocol_projmatch.DoParallel
# packageparams['NumberOfMpiProcesses'] = xmipp_protocol_projmatch.NumberOfMpiProcesses
# packageparams['MpiJobSize'] = xmipp_protocol_projmatch.MpiJobSize
# packageparams['SystemFlavour'] = xmipp_protocol_projmatch.SystemFlavour
# packageparams['AnalysisScript'] = xmipp_protocol_projmatch.AnalysisScript
if xmipp_protocol_projmatch.SymmetryGroup[:1] == "i":
sym = "icos"
else:
sym = xmipp_protocol_projmatch.SymmetryGroup
sym = sym.split()[0]
### set global parameters
runparams = {}
runparams['numiter'] = packageparams['NumberofIterations']
# Mask should be in pixels of original stack. Xmipp returns pixels in terms of preped stack.
# so orig_pix = preped_pix * (orig_boxsize / preped_boxsize).
# This is needed in case the prepedatack was binned.
boxscale = self.runparams['original_boxsize'] / self.runparams[
'boxsize']
runparams['mask'] = packageparams['MaskRadius'] * boxscale
runparams[
'alignmentInnerRadius'] = packageparams['InnerRadius'] * boxscale
runparams[
'alignmentOuterRadius'] = packageparams['OuterRadius'] * boxscale
runparams['symmetry'] = apSymmetry.findSymmetry(sym)
runparams['angularSamplingRate'] = packageparams['AngSamplingRateDeg']
runparams['apix'] = packageparams['ResolSam']
runparams['package_params'] = packageparams
runparams['remoterundir'] = os.path.abspath(
xmipp_protocol_projmatch.ProjectDir)
runparams['rundir'] = self.params['rundir']
return runparams
def parseFileForRunParameters(self):
''' PACKAGE-SPECIFIC FILE PARSER: if the parameters were not pickled, parse protocols script to determine projection-matching params '''
### parameters can be found in python protocols
xmipp_protocol_projmatch = apXmipp.importProtocolPythonFile("xmipp_protocol_projmatch", self.params['rundir'])
packageparams = {}
packageparams['NumberofIterations'] = xmipp_protocol_projmatch.NumberofIterations
packageparams['MaskFileName'] = xmipp_protocol_projmatch.MaskFileName
packageparams['MaskRadius'] = xmipp_protocol_projmatch.MaskRadius
packageparams['InnerRadius'] = xmipp_protocol_projmatch.InnerRadius
packageparams['OuterRadius'] = xmipp_protocol_projmatch.OuterRadius
packageparams['SymmetryGroup'] = xmipp_protocol_projmatch.SymmetryGroup
packageparams['FourierMaxFrequencyOfInterest'] = xmipp_protocol_projmatch.FourierMaxFrequencyOfInterest
packageparams['SelFileName'] = xmipp_protocol_projmatch.SelFileName
packageparams['DocFileName'] = xmipp_protocol_projmatch.DocFileName
packageparams['ReferenceFileName'] = xmipp_protocol_projmatch.ReferenceFileName
packageparams['WorkingDir'] = xmipp_protocol_projmatch.WorkingDir
# packageparams['DoDeleteWorkingDir'] = xmipp_protocol_projmatch.DoDeleteWorkingDir
# packageparams['ContinueAtIteration'] = xmipp_protocol_projmatch.ContinueAtIteration
packageparams['CleanUpFiles'] = xmipp_protocol_projmatch.CleanUpFiles
# packageparams['ProjectDir'] = xmipp_protocol_projmatch.ProjectDir
# packageparams['LogDir'] = xmipp_protocol_projmatch.LogDir
packageparams['DoCtfCorrection'] = xmipp_protocol_projmatch.DoCtfCorrection
packageparams['CTFDatName'] = xmipp_protocol_projmatch.CTFDatName
packageparams['DoAutoCtfGroup'] = xmipp_protocol_projmatch.DoAutoCtfGroup
packageparams['CtfGroupMaxDiff'] = xmipp_protocol_projmatch.CtfGroupMaxDiff
packageparams['CtfGroupMaxResol'] = xmipp_protocol_projmatch.CtfGroupMaxResol
# packageparams['SplitDefocusDocFile'] = xmipp_protocol_projmatch.SplitDefocusDocFile
packageparams['PaddingFactor'] = xmipp_protocol_projmatch.PaddingFactor
packageparams['WienerConstant'] = xmipp_protocol_projmatch.WienerConstant
packageparams['DataArePhaseFlipped'] = xmipp_protocol_projmatch.DataArePhaseFlipped
packageparams['ReferenceIsCtfCorrected'] = xmipp_protocol_projmatch.ReferenceIsCtfCorrected
packageparams['DoMask'] = xmipp_protocol_projmatch.DoMask
packageparams['DoSphericalMask'] = xmipp_protocol_projmatch.DoSphericalMask
# packageparams['DoProjectionMatching'] = xmipp_protocol_projmatch.DoProjectionMatching
# packageparams['DisplayProjectionMatching'] = xmipp_protocol_projmatch.DisplayProjectionMatching
# packageparams['AvailableMemory'] = xmipp_protocol_projmatch.AvailableMemory
packageparams['AngSamplingRateDeg'] = xmipp_protocol_projmatch.AngSamplingRateDeg
packageparams['MaxChangeInAngles'] = xmipp_protocol_projmatch.MaxChangeInAngles
packageparams['PerturbProjectionDirections'] = xmipp_protocol_projmatch.PerturbProjectionDirections
packageparams['MaxChangeOffset'] = xmipp_protocol_projmatch.MaxChangeOffset
packageparams['Search5DShift'] = xmipp_protocol_projmatch.Search5DShift
packageparams['Search5DStep'] = xmipp_protocol_projmatch.Search5DStep
packageparams['DoRetricSearchbyTiltAngle'] = xmipp_protocol_projmatch.DoRetricSearchbyTiltAngle
packageparams['Tilt0'] = xmipp_protocol_projmatch.Tilt0
packageparams['TiltF'] = xmipp_protocol_projmatch.TiltF
packageparams['SymmetryGroupNeighbourhood'] = xmipp_protocol_projmatch.SymmetryGroupNeighbourhood
packageparams['OnlyWinner'] = xmipp_protocol_projmatch.OnlyWinner
packageparams['MinimumCrossCorrelation'] = xmipp_protocol_projmatch.MinimumCrossCorrelation
packageparams['DiscardPercentage'] = xmipp_protocol_projmatch.DiscardPercentage
packageparams['ProjMatchingExtra'] = xmipp_protocol_projmatch.ProjMatchingExtra
packageparams['DoAlign2D'] = xmipp_protocol_projmatch.DoAlign2D
packageparams['Align2DIterNr'] = xmipp_protocol_projmatch.Align2DIterNr
packageparams['Align2dMaxChangeOffset'] = xmipp_protocol_projmatch.Align2dMaxChangeOffset
packageparams['Align2dMaxChangeRot'] = xmipp_protocol_projmatch.Align2dMaxChangeRot
# packageparams['DoReconstruction'] = xmipp_protocol_projmatch.DoReconstruction
# packageparams['DisplayReconstruction'] = xmipp_protocol_projmatch.DisplayReconstruction
packageparams['ReconstructionMethod'] = xmipp_protocol_projmatch.ReconstructionMethod
packageparams['ARTLambda'] = xmipp_protocol_projmatch.ARTLambda
packageparams['ARTReconstructionExtraCommand'] = xmipp_protocol_projmatch.ARTReconstructionExtraCommand
packageparams['WBPReconstructionExtraCommand'] = xmipp_protocol_projmatch.WBPReconstructionExtraCommand
packageparams['FourierReconstructionExtraCommand'] = xmipp_protocol_projmatch.FourierReconstructionExtraCommand
# packageparams['DoSplitReferenceImages'] = xmipp_protocol_projmatch.DoSplitReferenceImages
packageparams['ResolSam'] = xmipp_protocol_projmatch.ResolSam
# packageparams['DisplayResolution'] = xmipp_protocol_projmatch.DisplayResolution
packageparams['ConstantToAddToFiltration'] = xmipp_protocol_projmatch.ConstantToAddToFiltration
# packageparams['NumberOfThreads'] = xmipp_protocol_projmatch.NumberOfThreads
# packageparams['DoParallel'] = xmipp_protocol_projmatch.DoParallel
# packageparams['NumberOfMpiProcesses'] = xmipp_protocol_projmatch.NumberOfMpiProcesses
# packageparams['MpiJobSize'] = xmipp_protocol_projmatch.MpiJobSize
# packageparams['SystemFlavour'] = xmipp_protocol_projmatch.SystemFlavour
# packageparams['AnalysisScript'] = xmipp_protocol_projmatch.AnalysisScript
if xmipp_protocol_projmatch.SymmetryGroup[:1] == "i":
sym = "icos"
else:
sym = xmipp_protocol_projmatch.SymmetryGroup
sym = sym.split()[0]
### set global parameters
runparams = {}
runparams['numiter'] = packageparams['NumberofIterations']
# Mask should be in pixels of original stack. Xmipp returns pixels in terms of preped stack.
# so orig_pix = preped_pix * (orig_boxsize / preped_boxsize).
# This is needed in case the prepedatack was binned.
boxscale = self.runparams['original_boxsize'] / self.runparams['boxsize']
runparams['mask'] = packageparams['MaskRadius'] * boxscale
runparams['alignmentInnerRadius'] = packageparams['InnerRadius'] * boxscale
runparams['alignmentOuterRadius'] = packageparams['OuterRadius'] * boxscale
runparams['symmetry'] = apSymmetry.findSymmetry(sym)
runparams['angularSamplingRate'] = packageparams['AngSamplingRateDeg']
runparams['apix'] = packageparams['ResolSam']
runparams['package_params'] = packageparams
runparams['remoterundir'] = os.path.abspath(xmipp_protocol_projmatch.ProjectDir)
runparams['rundir'] = self.params['rundir']
return runparams