def reconstruction(_log
, ARTReconstructionExtraCommand
, WBPReconstructionExtraCommand
, FourierReconstructionExtraCommand
, Iteration_number
, DoParallel
, maskedFileNamesIter
, MpiJobSize
, NumberOfMpi
, NumberOfThreads
, ReconstructionMethod
, FourierMaxFrequencyOfInterest
, ARTLambda
, SymmetryGroup
, ReconstructionXmd
, ReconstructedVolume
, ResolSam
, ResolutionXmdPrevIterMax
, PaddingFactor
, ConstantToAddToFiltration
):
#if inout metadata is empty create a Blanck image
if emptyMd(ReconstructionXmd):
from protlib_utils import printLog
img = Image()
img.read(maskedFileNamesIter, DATA)
#(x,y,z,n) = img.getDimensions()
printLog("Metadata %s is empty. Creating a Black file named %s" % (ReconstructionXmd, ReconstructedVolume))
#createEmptyFile(ReconstructedVolume,x,y,z,n)
img.initRandom()
img.write(ReconstructedVolume)
return
print '*********************************************************************'
print '* Reconstruct volume using '
if ReconstructionMethod == 'wbp':
program = 'xmipp_reconstruct_wbp'
parameters = ' -i ' + ReconstructionXmd + \
' --doc ' + ReconstructionXmd + \
' -o ' + ReconstructedVolume + \
' --sym ' + SymmetryGroup + \
' --weight --use_each_image '
parameters = parameters + WBPReconstructionExtraCommand
elif ReconstructionMethod == 'art':
program = 'xmipp_reconstruct_art'
parameters = ' -i ' + ReconstructionXmd + \
' -o ' + ReconstructedVolume + ' ' + \
' --sym ' + SymmetryGroup + \
' --thr ' + str(NumberOfThreads) + \
' --WLS '
if len(ARTLambda) > 1:
parameters = parameters + ' -l ' + ARTLambda + ' '
parameters = parameters + ARTReconstructionExtraCommand
NumberOfMpi = 1
NumberOfThreads = 1
DoParallel = False
elif ReconstructionMethod == 'fourier':
if FourierMaxFrequencyOfInterest == -1:
md = MetaData(ResolutionXmdPrevIterMax)
id = md.firstObject()
FourierMaxFrequencyOfInterest = md.getValue(MDL_RESOLUTION_FREQREAL, id)
FourierMaxFrequencyOfInterest = ResolSam / FourierMaxFrequencyOfInterest + float(ConstantToAddToFiltration)
if FourierMaxFrequencyOfInterest > 0.5:
FourierMaxFrequencyOfInterest = 0.5
elif FourierMaxFrequencyOfInterest < 0.:
FourierMaxFrequencyOfInterest = 0.001
program = 'xmipp_reconstruct_fourier'
parameters = ' -i ' + ReconstructionXmd + \
' -o ' + ReconstructedVolume + \
' --sym ' + SymmetryGroup + \
' --thr ' + str(NumberOfThreads) + \
' --weight ' + \
' --max_resolution ' + str(FourierMaxFrequencyOfInterest) + \
' --padding ' + str(PaddingFactor) + ' ' + str(PaddingFactor)
if (DoParallel):
parameters = parameters + ' --mpi_job_size ' + str(MpiJobSize)
runJob(_log
, program
, parameters
, NumberOfMpi
, NumberOfThreads
)
def angular_class_average(_log
, Align2DIterNr
, Align2dMaxChangeOffset
, Align2dMaxChangeRot
, CtfGroupDirectory
, CtfGroupRootName
, DiscardImages
, DiscardPercentage
, DiscardPercentagePerClass
, DoAlign2D
, DoComputeResolution
, DoCtfCorrection
, DocFileInputAngles
, DoParallel
, DoSaveImagesAssignedToClasses
, DoSplitReferenceImages
, InnerRadius
, MaxChangeOffset
, MinimumCrossCorrelation
, MpiJobSize
, NumberOfMpi
, NumberOfThreads
, OutClasses
, PaddingFactor
, ProjectLibraryRootName
):
CtfGroupName = CtfGroupDirectory + '/' + CtfGroupRootName
refname = str(ProjectLibraryRootName)
baseTxtFile = refname[:-len('.stk')]
neighbFile = baseTxtFile + '.xmd'
if emptyMd(DocFileInputAngles):
print "Empty metadata file: %s" % DocFileInputAngles
return
parameters = ' -i ctfGroup[0-9][0-9][0-9][0-9][0-9][0-9]\$@' + DocFileInputAngles + \
' --lib ' + refname.replace(".stk", ".doc") + \
' -o ' + OutClasses
if(DoSaveImagesAssignedToClasses):
parameters += ' --save_images_assigned_to_classes'
if(DiscardImages == 'maxCC'):
parameters += ' --limit0 ' + MinimumCrossCorrelation
elif(DiscardImages == 'percentage'):
parameters += ' --limitRper ' + DiscardPercentage
elif(DiscardImages == 'classPercentage'):
parameters += ' --limitRclass ' + DiscardPercentagePerClass
#else 'none'
# On-the fly apply Wiener-filter correction and add all CTF groups together
if (DoCtfCorrection):
parameters += \
' --wien ' + CtfGroupName + '_wien.stk' + \
' --pad ' + str(PaddingFactor)
if (DoAlign2D == '1'):
parameters += \
' --iter ' + Align2DIterNr + \
' --Ri ' + str(InnerRadius) + \
' --Ro ' + str(OuterRadius)
if (DoComputeResolution and DoSplitReferenceImages):
parameters += ' --split '
if (DoParallel):
parameters = parameters + ' --mpi_job_size ' + str(MpiJobSize)
runJob(_log,
'xmipp_angular_class_average',
parameters,
NumberOfMpi * NumberOfThreads
)
