def runCLTomo(self):
fnVols=self._getPath('input_volumes.xmd')
writeSetOfVolumes(self.inputVolumes.get(), fnVols)
params= ' -i ' + fnVols + \
' --oroot ' + self._getExtraPath("results") + \
' --iter ' + str(self.numberOfIterations.get()) + \
' --nref ' + str(self.numberOfReferences.get()) + \
' --sym ' + self.symmetry.get() + \
' --maxFreq ' + str(self.maximumResolution.get()) + \
' --sparsity ' + str(self.sparsity.get()/100.0) + \
' --DWTsparsity ' + str(self.dwtSparsity.get()/100.0) + \
' --maxShiftX ' + str(self.maxShiftX.get()) + \
' --maxShiftY ' + str(self.maxShiftY.get()) + \
' --maxShiftZ ' + str(self.maxShiftZ.get()) + \
' --maxRot ' + str(self.maxRot.get()) + \
' --maxTilt ' + str(self.maxTilt.get()) + \
' --maxPsi ' + str(self.maxPsi.get())
if self.doGenerateInitial.get():
params+=' --nref0 '+str(self.numberOfReferences0.get())
if self.randomizeOrientation.get():
params+=' --randomizeStartingOrientation'
else:
fnInitialVols=self._getExtraPath('intial_volumes.xmd')
writeSetOfVolumes(self.referenceList.get(), fnInitialVols)
params+=' --ref0 '+fnInitialVols
if self.inputMask.hasValue():
params+=' --mask binary_file '+self.inputMask.get().getLocation()
if self.generateAligned.get():
params+=" --generateAlignedVolumes"
if not self.align:
params+=" --dontAlign"
self.runJob('xmipp_mpi_classify_CLTomo','%d %s'%(self.numberOfMpi.get(),params),env=self.getCLTomoEnviron(),numberOfMpi=1)
def runCLTomo(self):
fnVols = self._getPath("input_volumes.xmd")
writeSetOfVolumes(self.inputVolumes.get(), fnVols)
params = (
" -i "
+ fnVols
+ " --oroot "
+ self._getExtraPath("results")
+ " --iter "
+ str(self.numberOfIterations.get())
+ " --nref "
+ str(self.numberOfReferences.get())
+ " --sym "
+ self.symmetry.get()
+ " --maxFreq "
+ str(self.maximumResolution.get())
+ " --sparsity "
+ str(self.sparsity.get() / 100.0)
+ " --DWTsparsity "
+ str(self.dwtSparsity.get() / 100.0)
+ " --maxShiftX "
+ str(self.maxShiftX.get())
+ " --maxShiftY "
+ str(self.maxShiftY.get())
+ " --maxShiftZ "
+ str(self.maxShiftZ.get())
+ " --maxRot "
+ str(self.maxRot.get())
+ " --maxTilt "
+ str(self.maxTilt.get())
+ " --maxPsi "
+ str(self.maxPsi.get())
)
if self.doGenerateInitial.get():
params += " --nref0 " + str(self.numberOfReferences0.get())
if self.randomizeOrientation.get():
params += " --randomizeStartingOrientation"
else:
fnInitialVols = self._getExtraPath("intial_volumes.xmd")
writeSetOfVolumes(self.referenceList.get(), fnInitialVols)
params += " --ref0 " + fnInitialVols
if self.inputMask.hasValue():
params += " --mask binary_file " + self.inputMask.get().getLocation()
if self.generateAligned.get():
params += " --generateAlignedVolumes"
if self.dontAlign.get():
params += " --dontAlign"
self.runJob(
"xmipp_mpi_classify_CLTomo",
"%d %s" % (self.numberOfMpi.get(), params),
env=self.getCLTomoEnviron(),
numberOfMpi=1,
)
def convertInputStep(self):
printLicense()
self.info('Wrinting pytom xml file: ' + self.volXml)
volsDir = self._getExtraPath('inputVolumes')
pwutils.makePath(volsDir)
writeSetOfVolumes(self.inputVolumes.get(), self.volXml, volsDir)
if self.provideReferences:
ih = em.ImageHandler()
self.info('Converting input references')
for r, vol in enumerate(self.inputReferences.get()):
refFn = self._getExtraPath('reference_%02d.mrc' % (r+1))
ih.convert(vol, refFn)
def convertInputStep(self):
printLicense()
self.info('Writing pytom xml file: ' + self.volXml)
volsDir = self._getExtraPath('inputVolumes')
pwutils.makePath(volsDir)
writeSetOfVolumes(self.inputVolumes.get(), self.volXml, volsDir)
ih = em.ImageHandler()
self.info('Converting input reference to: ' + self.refVol)
ih.convert(self.inputReference.get(), self.refVol)
self.info('Converting input mask to: ' + self.maskVol)
ih.convert(self.alignmentMask.get(), self.maskVol)
def runCLTomo(self):
fnVols = self._getPath('input_volumes.xmd')
writeSetOfVolumes(self.inputVolumes.get(), fnVols)
params= ' -i ' + fnVols + \
' --oroot ' + self._getExtraPath("results") + \
' --iter ' + str(self.numberOfIterations.get()) + \
' --nref ' + str(self.numberOfReferences.get()) + \
' --sym ' + self.symmetry.get() + \
' --maxFreq ' + str(self.maximumResolution.get()) + \
' --sparsity ' + str(self.sparsity.get()/100.0) + \
' --DWTsparsity ' + str(self.dwtSparsity.get()/100.0) + \
' --maxShiftX ' + str(self.maxShiftX.get()) + \
' --maxShiftY ' + str(self.maxShiftY.get()) + \
' --maxShiftZ ' + str(self.maxShiftZ.get()) + \
' --maxRot ' + str(self.maxRot.get()) + \
' --maxTilt ' + str(self.maxTilt.get()) + \
' --maxPsi ' + str(self.maxPsi.get())
if self.doGenerateInitial.get():
params += ' --nref0 ' + str(self.numberOfReferences0.get())
if self.randomizeOrientation.get():
params += ' --randomizeStartingOrientation'
else:
fnInitialVols = self._getExtraPath('intial_volumes.xmd')
writeSetOfVolumes(self.referenceList.get(), fnInitialVols)
params += ' --ref0 ' + fnInitialVols
if self.inputMask.hasValue():
params += ' --mask binary_file ' + self.inputMask.get(
).getLocation()
if self.generateAligned.get():
params += " --generateAlignedVolumes"
if not self.align:
params += " --dontAlign"
self.runJob('xmipp_mpi_classify_CLTomo',
'%d %s' % (self.numberOfMpi.get(), params),
env=self.getCLTomoEnviron(),
numberOfMpi=1)
