def evaluateSingleMicrograph(self, micFn, micDir):
mdCTFparam = xmipp.MetaData(
self._getFileName('ctfparam', micDir=micDir))
ctfDownFactor = mdCTFparam.getValue(xmipp.MDL_CTF_DOWNSAMPLE_PERFORMED,
mdCTFparam.firstObject())
mdEval = md.MetaData()
objId = mdEval.addObject()
# Check what happen with movies
# if md.MDL_TYPE == md.MDL_MICROGRAPH_MOVIE:
# mdEval.setValue(md.MDL_MICROGRAPH_MOVIE, micFn, objId)
# mdEval.setValue(md.MDL_MICROGRAPH,('%05d@%s'%(1, micFn)), objId)
# else:
mdEval.setValue(md.MDL_MICROGRAPH, micFn, objId)
mdEval.setValue(md.MDL_PSD,
str(self._getFileName('psd', micDir=micDir)), objId)
mdEval.setValue(md.MDL_PSD_ENHANCED,
str(self._getFileName('enhanced_psd', micDir=micDir)),
objId)
mdEval.setValue(md.MDL_CTF_MODEL,
str(self._getFileName('ctfparam', micDir=micDir)),
objId)
mdEval.setValue(
md.MDL_IMAGE1,
str(self._getFileName('ctfmodel_quadrant', micDir=micDir)), objId)
mdEval.setValue(
md.MDL_IMAGE2,
str(self._getFileName('ctfmodel_halfplane', micDir=micDir)), objId)
mdEval.setValue(md.MDL_CTF_DOWNSAMPLE_PERFORMED, float(ctfDownFactor),
objId)
fnEval = self._getFileName('ctf', micDir=micDir)
mdEval.write(fnEval)
# Evaluate if estimated ctf is good enough
# self.runJob("xmipp_ctf_sort_psds","-i %s --downsampling %f"%(fnEval,ctfDownFactor))
try:
self.runJob("xmipp_ctf_sort_psds", "-i %s" % (fnEval))
except Exception:
pass
# print >> sys.stderr, "xmipp_ctf_sort_psds has been Failed!"
# raise ex
# Check if it is a good micrograph
fnRejected = self._getTmpPath(basename(micFn + "_rejected.xmd"))
self.runJob(
"xmipp_metadata_utilities", '-i %s --query select "%s" -o %s' %
(fnEval, self._criterion, fnRejected))
retval = True
if not isMdEmpty(fnRejected):
mdCTF = md.MetaData(fnEval)
mdCTF.setValue(md.MDL_ENABLED, -1, mdCTF.firstObject())
mdCTF.write(fnEval)
retval = False
cleanPath(fnRejected)
return retval
def runReconstructionStep(self, iterN, refN, program, method, args, suffix,
**kwargs):
#if input metadata is empty create a Blanck image
reconsXmd = 'reconstructionXmd' + suffix
reconsVol = 'reconstructedFileNamesIters' + suffix
mdFn = self._getFileName(reconsXmd, iter=iterN, ref=refN)
volFn = self._getFileName(reconsVol, iter=iterN, ref=refN)
maskFn = self._getFileName('maskedFileNamesIters', iter=iterN, ref=refN)
if method == "art":
mpi = 1
threads = 1
else:
mpi = self.numberOfMpi.get()
threads = self.numberOfThreads.get()
args += ' --thr %d' % threads
if isMdEmpty(mdFn):
img = xmipp.Image()
img.read(maskFn)
#(x,y,z,n) = img.getDimensions()
self._log.warning(
"Metadata '%s' is empty. \n Creating a random volume file '%s'" %
(mdFn, volFn))
#createEmptyFile(ReconstructedVolume,x,y,z,n)
img.initRandom()
img.write(volFn)
else:
if method == 'fourier':
if self._fourierMaxFrequencyOfInterest[iterN] == -1:
fourierMaxFrequencyOfInterest = self._getFourierMaxFrequencyOfInterest(
iterN - 1, refN)
fourierMaxFrequencyOfInterest = self.resolSam / fourierMaxFrequencyOfInterest + self._constantToAddToMaxReconstructionFrequency[
iterN]
if fourierMaxFrequencyOfInterest > 0.5:
fourierMaxFrequencyOfInterest = 0.5
elif fourierMaxFrequencyOfInterest < 0.:
fourierMaxFrequencyOfInterest = 0.001
else:
fourierMaxFrequencyOfInterest = self._fourierMaxFrequencyOfInterest[
iterN]
args += ' --max_resolution %s' % fourierMaxFrequencyOfInterest
if mpi > 1:
args += ' --mpi_job_size %s' % self.mpiJobSize.get()
self._log.info(
'*********************************************************************'
)
self._log.info('* Reconstruct volume using %s' % method)
self.runJob(program,
args,
numberOfMpi=mpi,
numberOfThreads=threads,
**kwargs)
def evaluateSingleMicrograph(self, micFn, micDir):
fnCTF = self._getFileName('ctfparam', micDir=micDir)
mdCTFparam = md.MetaData(fnCTF)
objId = mdCTFparam.firstObject()
mdCTFparam.setValue(md.MDL_MICROGRAPH, micFn, objId)
mdCTFparam.setValue(md.MDL_PSD,
str(self._getFileName('psd', micDir=micDir)), objId)
mdCTFparam.setValue(md.MDL_PSD_ENHANCED,
str(self._getFileName('enhanced_psd',
micDir=micDir)), objId)
mdCTFparam.setValue(md.MDL_CTF_MODEL,
str(self._getFileName('ctfparam',
micDir=micDir)), objId)
mdCTFparam.setValue(md.MDL_IMAGE1,
str(self._getFileName('ctfmodel_quadrant',
micDir=micDir)), objId)
mdCTFparam.setValue(md.MDL_IMAGE2,
str(self._getFileName('ctfmodel_halfplane',
micDir=micDir)), objId)
fnEval = self._getFileName('ctf', micDir=micDir)
mdCTFparam.write(fnEval)
# Evaluate if estimated ctf is good enough
try:
self.runJob("xmipp_ctf_sort_psds", "-i %s" % (fnEval))
except Exception:
pass
# Check if it is a good micrograph
fnRejected = self._getTmpPath(pwutils.path.basename(micFn +
"_rejected.xmd"))
self.runJob("xmipp_metadata_utilities",
'-i %s --query select "%s" -o %s'
% (fnEval, self._criterion, fnRejected))
retval = True
if not isMdEmpty(fnRejected):
mdCTFparam = md.MetaData(fnEval)
mdCTFparam.setValue(md.MDL_ENABLED, -1, mdCTFparam.firstObject())
mdCTFparam.write(fnEval)
retval = False
pwutils.path.cleanPath(fnRejected)
return retval
def runReconstructionStep(self, iterN, refN, program, method, args, suffix, **kwargs):
#if input metadata is empty create a Blanck image
reconsXmd = 'reconstructionXmd' + suffix
reconsVol = 'reconstructedFileNamesIters' + suffix
mdFn = self._getFileName(reconsXmd, iter=iterN, ref=refN)
volFn = self._getFileName(reconsVol, iter=iterN, ref=refN)
maskFn = self._getFileName('maskedFileNamesIters', iter=iterN, ref=refN)
if method=="art":
mpi = 1
threads = 1
else:
mpi = self.numberOfMpi.get()
threads = self.numberOfThreads.get()
args += ' --thr %d' % threads
if isMdEmpty(mdFn):
img = xmipp.Image()
img.read(maskFn)
#(x,y,z,n) = img.getDimensions()
self._log.warning("Metadata '%s' is empty. \n Creating a random volume file '%s'" % (mdFn, volFn))
#createEmptyFile(ReconstructedVolume,x,y,z,n)
img.initRandom()
img.write(volFn)
else:
if method == 'fourier':
if self._fourierMaxFrequencyOfInterest[iterN] == -1:
fourierMaxFrequencyOfInterest = self._getFourierMaxFrequencyOfInterest(iterN-1, refN)
fourierMaxFrequencyOfInterest = self.resolSam / fourierMaxFrequencyOfInterest + self._constantToAddToMaxReconstructionFrequency[iterN]
if fourierMaxFrequencyOfInterest > 0.5:
fourierMaxFrequencyOfInterest = 0.5
elif fourierMaxFrequencyOfInterest < 0.:
fourierMaxFrequencyOfInterest = 0.001
else:
fourierMaxFrequencyOfInterest = self._fourierMaxFrequencyOfInterest[iterN]
args += ' --max_resolution %s' % fourierMaxFrequencyOfInterest
if mpi > 1:
args += ' --mpi_job_size %s' % self.mpiJobSize.get()
self._log.info('*********************************************************************')
self._log.info('* Reconstruct volume using %s' % method)
self.runJob( program, args, numberOfMpi=mpi, numberOfThreads=threads, **kwargs)
def evaluateSingleMicrograph(self,micFn,micDir):
mdCTFparam=xmipp.MetaData(self._getFileName('ctfparam', micDir=micDir))
ctfDownFactor=mdCTFparam.getValue(xmipp.MDL_CTF_DOWNSAMPLE_PERFORMED,mdCTFparam.firstObject())
mdEval = md.MetaData()
id = mdEval.addObject()
# Check what happen with movies
# if md.MDL_TYPE == md.MDL_MICROGRAPH_MOVIE:
# mdEval.setValue(md.MDL_MICROGRAPH_MOVIE, micFn, id)
# mdEval.setValue(md.MDL_MICROGRAPH,('%05d@%s'%(1, micFn)), id)
# else:
mdEval.setValue(md.MDL_MICROGRAPH, micFn, id)
mdEval.setValue(md.MDL_PSD, str(self._getFileName('psd', micDir=micDir)), id)
mdEval.setValue(md.MDL_PSD_ENHANCED, str(self._getFileName('enhanced_psd', micDir=micDir)), id)
mdEval.setValue(md.MDL_CTF_MODEL, str(self._getFileName('ctfparam', micDir=micDir)), id)
mdEval.setValue(md.MDL_IMAGE1, str(self._getFileName('ctfmodel_quadrant', micDir=micDir)), id)
mdEval.setValue(md.MDL_IMAGE2, str(self._getFileName('ctfmodel_halfplane', micDir=micDir)), id)
mdEval.setValue(md.MDL_CTF_DOWNSAMPLE_PERFORMED,float(ctfDownFactor), id)
fnEval = self._getFileName('ctf', micDir=micDir)
mdEval.write(fnEval)
# Evaluate if estimated ctf is good enough
# self.runJob("xmipp_ctf_sort_psds","-i %s --downsampling %f"%(fnEval,ctfDownFactor))
try:
self.runJob("xmipp_ctf_sort_psds","-i %s"%(fnEval))
except Exception:
pass
# print >> sys.stderr, "xmipp_ctf_sort_psds has been Failed!"
# raise ex
# Check if it is a good micrograph
fnRejected = self._getTmpPath(basename(micFn +"_rejected.xmd"))
self.runJob("xmipp_metadata_utilities",'-i %s --query select "%s" -o %s' % (fnEval, self._criterion, fnRejected))
retval=True
if not isMdEmpty(fnRejected):
mdCTF = md.MetaData(fnEval)
mdCTF.setValue(md.MDL_ENABLED, -1, mdCTF.firstObject())
mdCTF.write(fnEval)
retval=False
cleanPath(fnRejected)
return retval