def _getIterClasses(self, it, clean=False):
""" 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.
"""
data_classes = self._getFileName('classes_scipion', iter=it)
if clean:
cleanPath(data_classes)
if not exists(data_classes):
clsSet = em.SetOfClasses2D(filename=data_classes)
clsSet.setImages(self._getInputParticles())
self._fillClassesFromIter(clsSet, it)
clsSet.write()
clsSet.close()
return data_classes
def _getLevelClasses(self, lev, suffix, clean=False):
""" Return a classes .sqlite file for this level.
If the file doesn't exists, it will be created by
converting from this level level_images.xmd file.
"""
dataClasses = self._getFileName('classes_scipion',
level=lev,
sub=suffix)
if clean:
cleanPath(dataClasses)
if not exists(dataClasses):
clsSet = em.SetOfClasses2D(filename=dataClasses)
clsSet.setImages(self.inputParticles.get())
self._fillClassesFromLevel(clsSet, level=lev, subset=suffix)
clsSet.write()
clsSet.close()
return dataClasses
def createOutputClasses(self, suffix, streamingState, fillCls):
baseName = '%sClasses.sqlite' % suffix
setFile = self._getPath(baseName)
if os.path.exists(setFile):
outputSet = em.SetOfClasses2D(filename=setFile)
outputSet.loadAllProperties()
outputSet.enableAppend()
else:
outputSet = em.SetOfClasses2D(filename=setFile)
outputSet.setStreamState(streamingState)
outputSet.copyInfo(self.inputClasses.get()) # if fails, delete
if fillCls:
# FIXME: Review this !!!
decision = ACCEPTED if suffix == 'output' else DISCARDED
print("in createOutput... %s" %
('ACCEPTED' if suffix == 'output' else 'DISCARDED'))
desiredIds = [
ids for ids, enable in self.enableCls.iteritems()
if enable == decision
]
print("self.enableCls: %s" % self.enableCls)
print("desiredIds: %s" % desiredIds)
for cls in self.inputClasses.get():
repId = cls.getObjId()
if repId in desiredIds:
representative = cls.getRepresentative()
newClass = em.Class2D(objId=repId)
newClass.setAlignment2D()
newClass.copyInfo(self.inputImages)
newClass.setAcquisition(self.inputImages.getAcquisition())
newClass.setRepresentative(representative)
newClass.setStreamState(streamingState)
outputSet.append(newClass)
for cls in self.inputClasses.get():
repId = cls.getObjId()
if repId in desiredIds:
newClass = outputSet[repId]
for img in cls:
newClass.append(img)
outputSet.update(newClass)
self.enableCls.update({idItem: ATTACHED for idItem in desiredIds})
outputSet.setStreamState(streamingState)
outputName = '%sClasses' % suffix
if self.hasAttribute(outputName):
outputSet.write() # Write to commit changes
outputAttr = getattr(self, outputName)
# Copy the properties to the object contained in the protocol
outputAttr.copy(outputSet, copyId=False)
# Persist changes
self._store(outputAttr)
else:
# FIXME: no outputClasses are generated because they are corrupted.
# self._defineOutputs(**{outputName: outputSet})
# self._defineSourceRelation(self.inputClasses, outputSet)
self._store(outputSet)
# Close set databaset to avoid locking it
outputSet.close()