def createOutputStep(self):
from convert import readSetOfClasses3D
numberOfClasses = self.numberOfRef
imgSet = self.inputParticles.get()
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(imgSet.getSamplingRate())
fileparList = []
volumeList = []
for ref in range(1, numberOfClasses + 1):
vol = Volume()
filepar = self._getBaseName('output_par_class', iter=self._getLastIter(), ref=ref)
volFn = self._getFileName('iter_vol_class', iter=self._getLastIter(), ref=ref)
vol.setFileName(volFn)
volumes.append(vol)
fileparList.append(filepar)
volumeList.append(volFn)
classes = self._createSetOfClasses3D(imgSet)
readSetOfClasses3D(classes, fileparList, volumeList)
# Define the outputs and relations
self._defineOutputs(outputClasses=classes)
self._defineOutputs(outputVolumes=volumes)
#TODO: save alignment
self._defineSourceRelation(imgSet, classes)
self._defineSourceRelation(self.input3DReference.get(), classes)
self._defineSourceRelation(imgSet, volumes)
self._defineSourceRelation(self.input3DReference.get(), volumes)
def _getIterClasses(self, it, clean=False):
""" Return the file with the classes for this iteration.
If the file doesn't exists, it will be created.
"""
from convert import readSetOfClasses3D
dataClasses = self.protocol._getFileName('classes_scipion', iter=it)
if clean:
cleanPath(dataClasses)
if not exists(dataClasses):
fileparList = []
volumeList = []
for ref in self._refsList:
filepar = self.protocol._getFileName('output_par_class', iter=it, ref=ref)
volFn = self.protocol._getFileName('iter_vol_class', iter=it, ref=ref)
fileparList.append(filepar)
volumeList.append(volFn)
clsSet = em.SetOfClasses3D(filename=dataClasses)
clsSet.setImages(self.inputParticles.get())
readSetOfClasses3D(clsSet, fileparList, volumeList)
clsSet.write()
clsSet.close()
return dataClasses