def _updateItem(self, particle, row):
self.reader.setParticleTransform(particle, row)
# FIXME: check if other attrs need saving
particle._rlnImageOriginalName = String(row.rlnImageOriginalName)
particle._rlnRandomSubset = Integer(row.rlnRandomSubset)
newLoc = convert.relionToLocation(row.rlnImageName)
particle.setLocation(newLoc)
def _setFileName(self, item, row):
relionFn = row.getValue(md.RLN_IMAGE_NAME)
indx, fn = convert.relionToLocation(relionFn)
item.setLocation(indx, self._getPath(fn))
invFactor = 1 / self._getScaleFactor(item)
if invFactor != 1.0:
if item.hasCoordinate():
item.scaleCoordinate(invFactor)
if item.hasTransform():
item.getTransform().scaleShifts(invFactor)
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 _updatePtcl(self, particle, row):
newLoc = convert.relionToLocation(row.getValue('rlnImageName'))
particle.setLocation(newLoc)
def _updateItem(self, item, row):
newFn = row.getValue(md.RLN_IMAGE_NAME)
newLoc = convert.relionToLocation(newFn)
item.setLocation(newLoc)