def _loadClassesInfo(self, iteration):
""" Read some information about the produced Relion 3D classes
from the *model.star file.
"""
self._classesInfo = {} # store classes info, indexed by class id
modelFn = self._protocol._getFileName('model', iter=iteration)
modelIter = Table.iterRows('model_classes@' + modelFn)
for classNumber, row in enumerate(modelIter):
index, fn = relionToLocation(row.rlnReferenceImage)
# Store info indexed by id
self._classesInfo[classNumber + 1] = (index, fn, row)
def fillClassesFromIter(self, clsSet, iteration):
""" Create the SetOfClasses3D from a given iteration. """
prot = self._protocol # shortcut
self._loadClassesInfo(iteration)
tableName = 'particles@' # if Plugin.IS_GT30() else ''
dataStar = prot._getFileName('data', iter=iteration)
pixelSize = prot.inputParticles.get().getSamplingRate()
self._reader = createReader(alignType=self._alignType,
pixelSize=pixelSize)
mdIter = Table.iterRows(tableName + dataStar, key='rlnImageId')
clsSet.classifyItems(updateItemCallback=self._updateParticle,
updateClassCallback=self._updateClass,
itemDataIterator=mdIter,
doClone=False)
def _fillDataFromIter(self, subtomoClassesSet, iteration):
# tableName = 'particles@' if self.IS_GT30() else ''
dataStar = self._getFileName('data', iter=iteration)
# imgSet.setAlignmentProj()
for item in subtomoClassesSet:
item.setAlignmentProj()
# with open(dataStar) as fid:
# self.dataTable.readStar(fid)
self.reader = convert31.Reader(
alignType=ALIGN_PROJ,
pixelSize=subtomoClassesSet.getSamplingRate())
mdIter = Table.iterRows(dataStar, key='rlnImageName')
subtomoClassesSet.copyItems(self._getInputParticles(),
doClone=False,
updateItemCallback=self._updateParticle,
itemDataIterator=mdIter)