def convertInputStep(self, resetDeps):
""" Create the input file in STAR format as expected by Relion.
If the input particles comes from Relion, just link the file.
Params:
particlesId, volumesId: use this parameters just to force redo of
convert if either the input particles and/or input volumes are
changed.
"""
self._imgFnList = []
imgSet = self._getInputParticles()
imgStar = self._getFileName('input_star')
subset = em.SetOfParticles(filename=":memory:")
newIndex = 1
for img in imgSet.iterItems(orderBy='RANDOM()', direction='ASC'):
self._scaleImages(newIndex, img)
newIndex += 1
subset.append(img)
subsetSize = self.subsetSize.get()
minSize = min(subsetSize, imgSet.getSize())
if subsetSize > 0 and subset.getSize() == minSize:
break
writeSetOfParticles(subset,
imgStar,
self._getExtraPath(),
alignType=em.ALIGN_NONE,
postprocessImageRow=self._postprocessParticleRow)
self._convertInput(subset)
self._convertRef()
def _getIterData(self, it):
data_sqlite = self._getFileName('data_scipion', iter=it)
if not exists(data_sqlite):
iterImgSet = em.SetOfParticles(filename=data_sqlite)
iterImgSet.copyInfo(self._getInputParticles())
self._fillDataFromIter(iterImgSet, it)
iterImgSet.write()
iterImgSet.close()
return data_sqlite
def writeSqliteIterData(imgStar, imgSqlite, **kwargs):
""" Given a Relion images star file (from some iteration)
create the corresponding SetOfParticles (sqlite file)
for this iteration. This file can be visualized sorted
by the LogLikelihood.
"""
cleanPath(imgSqlite)
imgSet = em.SetOfParticles(filename=imgSqlite)
readSetOfParticles(imgStar, imgSet, **kwargs)
imgSet.write()
def _getIterData(self, it, **kwargs):
""" Sort the it??.data.star file by the maximum likelihood. """
data_sqlite = self._getFileName('data_scipion', iter=it)
if not exists(data_sqlite):
iterImgSet = em.SetOfParticles(filename=data_sqlite)
iterImgSet.copyInfo(self._getInputParticles())
self._fillDataFromIter(iterImgSet, it)
iterImgSet.write()
iterImgSet.close()
return data_sqlite
def _getIterParticles(self, it, clean=False):
import pyworkflow.em as em
""" Return a classes .sqlite file for this iteration.
If the file doesn't exists, it will be created by
converting from this iteration data.star file.
"""
dataParticles = self._getFileName('particlesScipion', iter=it)
if clean:
cleanPath(dataParticles)
if not exists(dataParticles):
partSet = em.SetOfParticles(filename=dataParticles)
self._fillParticlesFromIter(partSet, it)
partSet.write()
partSet.close()
else:
partSet = em.SetOfParticles(filename=dataParticles)
imgSet = self.inputParticles.get()
partSet.copyInfo(imgSet)
partSet.setAlignmentProj()
return partSet