def getTomoDirs(WorkingDir, tomogram):
""" Give the tomogram filename, return the root and prefix
to store the result files. """
tomoBaseName = removeBasenameExt(tomogram)
tomoDir = join(WorkingDir, tomoBaseName)
tomoRoot = join(tomoDir, tomoBaseName)
return tomoBaseName, tomoDir, tomoRoot
def getTomograms(self):
''' Return a list with micrographs in WorkingDir'''
if self.Synchrotron == "Alba":
if self.ImportFrom == "single file":
return [self.Tomogram]
else:
return glob(join(self.DirTomograms, '*.hdf*'))
else:
return [self.DirBessyData]
def defineSteps(self):
md = self.getTomogramMd()
mdOut = xmipp.MetaData()
# for tomoName in blockList:
for objId in md:
# md.read('%s@%s' % (tomoName, TomogramsMd))
# objId = md.firstObject()
fnRootIn = removeFilenameExt(md.getValue(xmipp.MDL_TOMOGRAMMD, objId))
fnBaseName = basename(fnRootIn)
tomoDir = self.workingDirPath(fnBaseName)
fnRootOut = join(tomoDir, fnBaseName)
fnRootTmp = self.tmpPath(fnBaseName)
fnOut = fnRootOut + '.mrc'
self.insertStep('createDir', verifyfiles=[tomoDir], path=tomoDir)
tiltXcorrParams = {}
tiltXcorrParams['-input'] = '%(fnRootIn)s.mrc'
tiltXcorrParams['-output'] = '%(fnRootTmp)s.prexf'
tiltXcorrParams['-tiltfile'] = '%(fnRootIn)s.tlt'
tiltXcorrParams['-rotation'] = self.rotation
tiltXcorrParams['-sigma1'] = self.sigma1
tiltXcorrParams['-radius2'] = self.radius2
tiltXcorrParams['-sigma2'] = self.sigma2
params = ''
for k, v in tiltXcorrParams.iteritems():
params += " %s %s " % (k, str(v))
# params = '-input %(fnRootIn)s.mrc -output %(fnRootTmp)s.prexf -tiltfile %(fnRootIn)s.tlt '\
# '-rotation 0.0 -sigma1 0.03 -radius2 0.25 -sigma2 0.05'
self.insertRunJobStep('tiltxcorr', params=params % locals(), verifyFiles=[fnRootTmp + '.prexf'])
params = '-input %(fnRootTmp)s.prexf -nfit 0 -goutput %(fnRootTmp)s.prexg'
self.insertRunJobStep('xftoxg', params=params % locals(), verifyFiles=[fnRootTmp + '.prexg'])
params = '-input %(fnRootIn)s.mrc -output %(fnRootTmp)s.preali -mode 0 -xform %(fnRootTmp)s.prexg -float 2'
self.insertRunJobStep('newstack', params=params % locals(), verifyFiles=[fnRootTmp + '.preali'])
tiltXcorrParams['-input'] = '%(fnRootTmp)s.preali'
tiltXcorrParams['-output'] = '%(fnRootTmp)s.fid '
tiltXcorrParams['-tiltfile'] = '%(fnRootIn)s.tlt'
tiltXcorrParams['-prexf'] = '%(fnRootTmp)s.prexg'
tiltXcorrParams['-border'] = self.border
tiltXcorrParams['-size'] = self.size
tiltXcorrParams['-overlap'] = self.overlap
params = ''
for k, v in tiltXcorrParams.iteritems():
params += " %s %s " % (k, str(v))
# params = '-input %(fnRootTmp)s.preali -output %(fnRootTmp)s.fid -tiltfile %(fnRootIn)s.tlt '\
# '-prexf %(fnRootTmp)s.prexg -rotation 0.0 -sigma1 0.03 -radius2 0.25 -sigma2 0.05 -border 49,49 '\
# '-size 300,300 -overlap 0.33,0.33'
self.insertRunJobStep('tiltxcorr', params=params % locals(), verifyFiles=[fnRootTmp + '.fid'])
tiltAlignParams = {}
tiltAlignParams['-tiltfile'] = '%(fnRootIn)s.tlt'
tiltAlignParams['-ModelFile'] = '%(fnRootTmp)s.fid'
tiltAlignParams['-ImageFile'] = '%(fnRootTmp)s.preali'
tiltAlignParams['-OutputTransformFile'] = '%(fnRootTmp)s.tltxf'
tiltAlignParams['-OutputLocalFile'] = '%(fnRootTmp)s_local.xf'
tiltAlignParams['-OutputTiltFile'] = '%(fnRootOut)s.tlt'
tiltAlignParams['-RotationAngle'] = self.RotationAngle
tiltAlignParams['-AngleOffset'] = self.AngleOffset
tiltAlignParams['-RotOption'] = self.RotOption
tiltAlignParams['-RotDefaultGrouping'] = self.RotDefaultGrouping
tiltAlignParams['-TiltOption'] = self.TiltOption
tiltAlignParams['-MagReferenceView'] = self.MagReferenceView
tiltAlignParams['-MagOption'] = self.MagOption
tiltAlignParams['-MagDefaultGrouping'] = self.MagDefaultGrouping
tiltAlignParams['-XStretchOption'] = self.XStretchOption
tiltAlignParams['-XStretchDefaultGrouping'] = self.XStretchDefaultGrouping
tiltAlignParams['-SkewOption'] = self.SkewOption
tiltAlignParams['-SkewDefaultGrouping'] = self.SkewDefaultGrouping
tiltAlignParams['-ResidualReportCriterion'] = self.ResidualReportCriterion
tiltAlignParams['-SurfacesToAnalyze'] = self.SurfacesToAnalyze
tiltAlignParams['-MetroFactor'] = self.MetroFactor
tiltAlignParams['-MaximumCycles'] = self.MaximumCycles
tiltAlignParams['-AxisZShift'] = self.AxisZShift
tiltAlignParams['-LocalAlignments'] = self.LocalAlignments
tiltAlignParams['-MinFidsTotalAndEachSurface'] = self.MinFidsTotalAndEachSurface
tiltAlignParams['-LocalOutputOptions'] = self.LocalOutputOptions
tiltAlignParams['-LocalRotOption'] = self.LocalRotOption
tiltAlignParams['-LocalRotDefaultGrouping'] = self.LocalRotDefaultGrouping
tiltAlignParams['-LocalTiltOption'] = self.LocalTiltOption
tiltAlignParams['-LocalTiltDefaultGrouping'] = self.LocalTiltDefaultGrouping
tiltAlignParams['-LocalMagReferenceView'] = self.LocalMagReferenceView
tiltAlignParams['-LocalMagOption'] = self.LocalMagOption
tiltAlignParams['-LocalMagDefaultGrouping'] = self.LocalMagDefaultGrouping
tiltAlignParams['-LocalXStretchOption'] = self.LocalXStretchOption
tiltAlignParams['-LocalXStretchDefaultGrouping'] = self.LocalXStretchDefaultGrouping
tiltAlignParams['-LocalSkewOption'] = self.LocalSkewOption
tiltAlignParams['-LocalSkewDefaultGrouping'] = self.LocalSkewDefaultGrouping
tiltAlignParams['-BeamTiltOption'] = self.BeamTiltOption
params = ''
for k, v in tiltAlignParams.iteritems():
params += " %s %s " % (k, str(v))
self.insertRunJobStep('tiltalign', params=params % locals(), verifyFiles=[fnRootTmp + '.tltxf', fnRootTmp + '_local.xf', fnRootOut + '.tlt'])
params = '-in1 %(fnRootTmp)s.prexg -in2 %(fnRootTmp)s.tltxf -output %(fnRootTmp)s_fid.xf'
self.insertRunJobStep('xfproduct', params=params % locals(), verifyFiles=[fnRootTmp + '_fid.xf'])
self.insertStep('copyFile', source=fnRootTmp + '_fid.xf', dest=fnRootTmp + '.xf', verifyfiles=[fnRootTmp + '.xf'])
params = '-input %(fnRootIn)s.mrc -output %(fnOut)s -offset 0,0 -xform %(fnRootTmp)s_fid.xf -origin -taper 1,0'
self.insertRunJobStep('newstack', params=params % locals(), verifyFiles=[fnOut])
# Create metadata
self.insertStep('createtMd', tomoOut=fnOut, tomoRoot=fnRootOut, fnTiltIn=fnRootIn + '.tlt', fnTiltOut=fnRootOut + '.tlt', verifyfiles=[fnRootOut + '.xmd'])
# Add aligned tomo to list
self.tomoAlignedList.append(fnRootOut)
self.insertStep('createResultMd', TomogramList=self.tomoAlignedList, resultMd=self.TomogramsMd, verifyfiles=[self.TomogramsMd])
# Removing temporary files
self.insertDeleteTmpDir()