def __init__(self, protDictName, scriptname, project):
self.FileKeys = ['data', 'optimiser', 'sampling']
self.ClassLabel = MDL_REF # by default 3d
self.ClassFnTemplate = '%(rootDir)s/relion_it%(iter)03d_class%(ref)03d.mrc:mrc'
self.outputClasses = 'classes_ref3D.xmd'
self.outputVols = 'volumes.xmd'
XmippProtocol.__init__(self, protDictName, scriptname, project)
self.ParamsStr = ''
program = 'relion_refine'
if self.NumberOfMpi > 1:
program += '_mpi'
if self.DoContinue:
if os.path.exists(self.optimiserFileName):
if not self.optimiserFileName.startswith(self.WorkingDir):
self.setPreviousRunFromFile(self.optimiserFileName)
try:
self.inputProperty('ImgMd')
except:
print "Cannot find the input file with experimental images in protocol %s" % self.PrevRunName
self.addParam('program', program)
self.addParam('ORoot', self.WorkingDir + '/')
self.addParam('SamplingRate', getSampling(self.ImgMd, 0.))
def wizardChooseBandPassFilter(gui, var):
'''Wizard dialog to help choosing Bandpass filter parameters (used in protocol_preprocess_particles) '''
sampling = getSampling(gui.getVarValue('InSelFile'))
vList = ['Freq_low','Freq_high','Freq_decay']
from protlib_gui_ext import XmippBrowserBandpassFilter
results = wizardHelperFilter(gui, XmippBrowserBandpassFilter, "Bandpass Filter",
freqs=gui.getVarlistValue(vList), sampling=sampling)
if results:
gui.setVarlistValue(vList, results)
def wizardChooseLowPassFilter(gui, var):
'''Wizard dialog to help choosing Lowpass filter parameters (used in protocol_relion...) '''
sampling = getSampling(gui.getVarValue('ImgMd'))
vList = [0,var.getTkValue(),0.02]#this 0.02 is a value in Fourier space in px ^-1
from protlib_gui_ext import XmippBrowserBandpassFilter
results = wizardHelperFilter(gui, XmippBrowserBandpassFilter, "Lowpass Filter", freqs=vList,
varName='Ref3D', showDecay=False, showLowFreq=False, unit='angstrom',
sampling=sampling )
if results:
var.setTkValue(1./results[1])
def defineSteps(self):
samplingRate = getSampling(self.ModelStar)
args = ""
args += " --i %s/relion" % dirname(self.ModelStar)
args += " --angpix %f" % samplingRate
args += " --o %s/relion_postprocess" % self.WorkingDir
if self.AutoMask:
args += ' --auto_mask'
else:
args += ' --inimask_threshold %f' % self.InimaskThreshold
args += ' --extend_inimask %f' % self.ExtendInimask
args += ' --width_mask_edge %f' % self.WidthMaskEdge
args += ' --mask %s' % self.Mask
mtfFile = self.Mtf.strip()
if mtfFile:
args += ' --mtf %s' % mtfFile
if self.AutoBfac:
args += ' --auto_bfac'
args += ' --autob_lowres %f' % self.AutobLowres
args += ' --autob_highres %f' % self.AutobHighres
else:
args += ' --adhoc_bfac %f' % self.AdhocBfac
if not self.UseFscWeighting:
args += ' --skip_fsc_weighting'
if self.LowPass > 0.:
args += ' --low_pass %f' % self.LowPass
# Expert params
args += ' --filter_edge_width %d' % self.FilterEdgeWidth
args += ' --randomize_at_fsc %f' % self.RandomizeAtFsc
args += ' --verb %d' % self.Verb
outputs = [self.workingDirPath('relion_postprocess%s.mrc' % s)
for s in ['', '_masked', '_automask']]
self.insertRunJobStep('relion_postprocess', args, verifyFiles=outputs)
self.insertStep('createVolumesMd',
verifyfiles=[self.workingDirPath(VOLUMES)],
volumeList=outputs)
def wizardSetMaskRadiusRelion(gui, var):
fnSel = gui.getVarValue('ImgMd')
wizardHelperSetRadii(gui, 'ImgMd','MaskRadiusA', unit='angstrom', sampling=getSampling(fnSel))
def getTs(InputVol):
return getSampling(InputVol,1.)
