def filter_volume(_log
, FourierMaxFrequencyOfInterest
, ReconstructedVolume
, ReconstructedFilteredVolume
, DoComputeResolution
, OuterRadius
, DoLowPassFilter
, UseFscForFilter
, ConstantToAddToFiltration
, ResolutionXmdPrevIterMax
, ResolSam
):
if (not DoLowPassFilter):
copyFile(_log, ReconstructedVolume, ReconstructedFilteredVolume)
else:
if (UseFscForFilter):
if (FourierMaxFrequencyOfInterest == -1):
md = MetaData(ResolutionXmdPrevIterMax)
id = md.firstObject()
FourierMaxFrequencyOfInterest = md.getValue(MDL_RESOLUTION_FREQREAL, id)
FourierMaxFrequencyOfInterest = ResolSam / FourierMaxFrequencyOfInterest
filter_in_pixels_at = float(FourierMaxFrequencyOfInterest) + float(ConstantToAddToFiltration)
else:
filter_in_pixels_at = float(ConstantToAddToFiltration)
if (filter_in_pixels_at > 0.5):
copyFile(_log, ReconstructedVolume, ReconstructedFilteredVolume)
else:
command = " -i " + ReconstructedVolume + \
" -o " + ReconstructedFilteredVolume + ' --fourier low_pass ' + \
str (filter_in_pixels_at)
runJob(_log, "xmipp_transform_filter", command)
def getBestVolumes(log,WorkingDir,NRansac,NumVolumes,UseAll):
volumes = []
inliers = []
for n in range(NRansac):
fnAngles = os.path.join(WorkingDir,"tmp/angles_ransac%05d"%n+".xmd")
md=MetaData("inliers@"+fnAngles)
numInliers=md.getValue(MDL_WEIGHT,md.firstObject())
volumes.append(fnAngles)
inliers.append(numInliers)
index = sorted(range(inliers.__len__()), key=lambda k: inliers[k])
fnBestAngles = ''
threshold=getCCThreshold(WorkingDir)
i=NRansac-1
indx = 0
while i>=0 and indx<NumVolumes:
fnBestAngles = volumes[index[i]]
fnBestAnglesOut=os.path.join(WorkingDir,"volumeProposed%05d"%indx+".xmd")
copyFile(log,fnBestAngles,fnBestAnglesOut)
print("Best volume "+str(indx)+" = "+fnBestAngles)
if not UseAll:
runJob(log,"xmipp_metadata_utilities","-i %s -o %s --query select \"maxCC>%f \" --mode append" %(fnBestAnglesOut,fnBestAnglesOut,threshold))
if getMdSize(fnBestAnglesOut) > 0:
indx += 1
else:
indx += 1
i -= 1
# Remove unnecessary files
for n in range(NRansac):
fnAngles = os.path.join(WorkingDir,"tmp/angles_ransac%05d"%n+".xmd")
deleteFile(log, fnAngles)
def executeMask(_log,
DoMask,
DoSphericalMask,
maskedFileName,
maskRadius,
ReconstructedFilteredVolume,
userSuppliedMask
):
_log.debug("executeMask")
print "executeMask", maskRadius
if DoMask:
command = ' -i ' + ReconstructedFilteredVolume + \
' -o ' + maskedFileName
if DoSphericalMask:
command += ' --mask circular -' + str(maskRadius)
else:
command += ' --mask binary_file ' + userSuppliedMask
runJob(_log, "xmipp_transform_mask", command)
else:
copyFile(_log, ReconstructedFilteredVolume, maskedFileName)
def gatherResults(log,
WorkingDir,
extraDir,
currProtMicrographClass,
currProtMicrograph,
currProtMicroscope,
currProtAcquisitionInfo,
prevProtMicrograph,
prevProtMicroscope,
prevProtAcquisitionInfo
):
import glob
#fnList=glob.glob(os.path.join(extraDir,'*_aligned.spi'))
copyFile(log,prevProtMicrograph,currProtMicrograph)
copyFile(log,prevProtMicroscope,currProtMicroscope)
copyFile(log,prevProtAcquisitionInfo,currProtAcquisitionInfo)
md=xmipp.MetaData(currProtMicrograph)
for id in md:
inputMovie = md.getValue(xmipp.MDL_MICROGRAPH, id)
movieNameList = os.path.basename(inputMovie)
movieName = os.path.splitext(movieNameList)[0]
file = _getFilename('movieAverage',movieDir=extraDir,baseName=movieName)
md.setValue(xmipp.MDL_MICROGRAPH,file,id)
if exists(file):
enabled = 1
else:
enabled = -1
md.setValue(xmipp.MDL_ENABLED,enabled)
md.sort(xmipp.MDL_MICROGRAPH)
md.write(currProtMicrographClass,xmipp.MD_APPEND)
def angular_project_library(_log
, AngSamplingRateDeg
, BlockWithAllExpImages
, ConstantToAddToFiltration
, CtfGroupSubsetFileName
, DoCtfCorrection
, DocFileInputAngles
, DoParallel
, DoRestricSearchbyTiltAngle
, FourierMaxFrequencyOfInterest
, KernelAngularProjection
, MaxChangeInAngles
, maskedFileNamesIter
, MpiJobSize
, NumberOfMpi
, NumberOfThreads
, OnlyWinner
, PaddingAngularProjection
, PerturbProjectionDirections
, ProjectLibraryRootName
, ProjectionMethod
, ResolSam
, ResolutionXmdPrevIterMax
, SymmetryGroup
, SymmetryGroupNeighbourhood
, Tilt0
, TiltF):
_log.debug("execute_projection_matching")
###need one block per reference
# Project all references
print '* Create projection library'
(Xdim, Ydim, Zdim, Ndim, _) = MetaDataInfo(maskedFileNamesIter)
memoryUsed=(Xdim*Xdim*Xdim*8.0)/pow(2,20)
parameters = ' -i ' + maskedFileNamesIter + \
' --experimental_images ' + BlockWithAllExpImages + '@' + DocFileInputAngles + \
' -o ' + ProjectLibraryRootName + \
' --sampling_rate ' + AngSamplingRateDeg + \
' --sym ' + SymmetryGroup + 'h' + \
' --compute_neighbors' + \
' --method ' + ProjectionMethod
if ProjectionMethod == 'fourier':
memoryUsed=memoryUsed*6
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
parameters += " " + str(PaddingAngularProjection)
parameters += " " + str(FourierMaxFrequencyOfInterest)
parameters += " " + str(KernelAngularProjection)
if (string.atof(MaxChangeInAngles) < 181.):
parameters += \
' --near_exp_data --angular_distance ' + str(MaxChangeInAngles)
else:
parameters += \
' --angular_distance -1'
if (PerturbProjectionDirections):
perturb = math.sin(math.radians(float(AngSamplingRateDeg))) / 4.
parameters += \
' --perturb ' + str(perturb)
if (DoRestricSearchbyTiltAngle):
parameters += \
' --min_tilt_angle ' + str(Tilt0) + \
' --max_tilt_angle ' + str(TiltF)
if (DoCtfCorrection):
parameters += \
' --groups ' + CtfGroupSubsetFileName
processorsToUse=NumberOfMpi * NumberOfThreads
if processorsToUse>1:
memoryAvailable=getMemoryAvailable()
processorsToUse=min(processorsToUse,floor(memoryAvailable/memoryUsed))
if (DoParallel and processorsToUse>1):
parameters = parameters + ' --mpi_job_size ' + str(MpiJobSize)
if (len(SymmetryGroupNeighbourhood) > 1):
parameters += \
' --sym_neigh ' + SymmetryGroupNeighbourhood + 'h'
if (OnlyWinner):
parameters += \
' --only_winner '
runJob(_log, 'xmipp_angular_project_library',
parameters,
processorsToUse)
if (not DoCtfCorrection):
src = ProjectLibraryRootName.replace(".stk", '_sampling.xmd')
dst = src.replace('sampling.xmd', 'group%06d_sampling.xmd' % 1)
copyFile(_log, src, dst)
def projection_matching(_log
, AvailableMemory
, CtfGroupRootName
, CtfGroupDirectory
, DocFileInputAngles
, DoComputeResolution
, DoCtfCorrection
, DoScale
, DoParallel
, InnerRadius
, MaxChangeOffset
, MpiJobSize
, NumberOfMpi
, NumberOfThreads
, OuterRadius
, PaddingFactor
, ProjectLibraryRootName
, ProjMatchRootName
, ReferenceIsCtfCorrected
, ScaleStep
, ScaleNumberOfSteps
, Search5DShift
, Search5DStep
):
# Loop over all CTF groups
# Use reverse order to have same order in add_to docfiles from angular_class_average
# get all ctf groups
_DoCtfCorrection = DoCtfCorrection
_ProjMatchRootName = ProjMatchRootName
refname = str(ProjectLibraryRootName)
file_name = join(CtfGroupDirectory, CtfGroupRootName) + 'Info.xmd'
if exists(file_name):
auxMD = MetaData("numberGroups@" + file_name)
NumberOfCtfGroups = auxMD.getValue(MDL_COUNT, auxMD.firstObject())
else:
NumberOfCtfGroups = 1
CtfGroupName = CtfGroupRootName #,ictf+1,'')
CtfGroupName = CtfGroupDirectory + '/' + CtfGroupName
#remove output metadata
if os.path.exists(_ProjMatchRootName):
os.remove(_ProjMatchRootName)
for ii in range(NumberOfCtfGroups):
if NumberOfCtfGroups > 1 :
print 'Focus Group: ', ii + 1, '/', NumberOfCtfGroups
ictf = NumberOfCtfGroups - ii
inputdocfile = CtfBlockName + str(ictf).zfill(FILENAMENUMBERLENGTH) + '@' + DocFileInputAngles
outputname = CtfBlockName + str(ictf).zfill(FILENAMENUMBERLENGTH) + '@' + _ProjMatchRootName
baseTxtFile = refname[:-len('.stk')]
neighbFile = baseTxtFile + '_sampling.xmd'
if (os.path.exists(neighbFile)):
os.remove(neighbFile)
neighbFileb = baseTxtFile + '_group' + str(ictf).zfill(FILENAMENUMBERLENGTH) + '_sampling.xmd'
print 'neighbFileb: ', neighbFileb
copyFile(_log, neighbFileb, neighbFile)
parameters = ' -i ' + inputdocfile + \
' -o ' + outputname + \
' --ref ' + refname + \
' --Ri ' + str(InnerRadius) + \
' --Ro ' + str(OuterRadius) + \
' --max_shift ' + str(MaxChangeOffset) + \
' --search5d_shift ' + str(Search5DShift) + \
' --search5d_step ' + str(Search5DStep) + \
' --mem ' + str(AvailableMemory * NumberOfThreads) + \
' --thr ' + str(NumberOfThreads) + \
' --append '
if (DoScale):
parameters += \
' --scale ' + str(ScaleStep) + ' ' + str(ScaleNumberOfSteps)
if (_DoCtfCorrection and ReferenceIsCtfCorrected):
ctffile = str(ictf).zfill(FILENAMENUMBERLENGTH) + '@' + CtfGroupName + '_ctf.stk'
parameters += \
' --pad ' + str(PaddingFactor) + \
' --ctf ' + ctffile
if (DoParallel):
parameters = parameters + ' --mpi_job_size ' + str(MpiJobSize)
runJob(_log, 'xmipp_angular_projection_matching',
parameters,
NumberOfMpi,
NumberOfThreads
)
