def createOutputStep(self):
""" Register the output (the alignment and the aligned particles.)
"""
outputStk = self._getFileName('particlesAligned')
if not exists(outputStk):
raise Exception('Ouptput stack %s not produced. ' % outputStk)
particles = self.inputParticles.get()
# Create the output average image
avg = Particle()
avg.copyInfo(self.inputParticles.get())
avg.setLocation(NO_INDEX, self.getAverage())
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputParticles, avg)
imgSet = self._createSetOfParticles()
imgSet.copyInfo(particles)
imgSet.setAlignment2D()
imgSet.copyItems(particles,
updateItemCallback=self._updateItem,
itemDataIterator=iter(
range(1,
particles.getSize() + 1)))
self._defineOutputs(outputParticles=imgSet)
self._defineTransformRelation(self.inputParticles, imgSet)
def createOutputStep(self):
""" Register the output (the alignment and the aligned particles.)
"""
particles = self.inputParticles.get()
# Create the output average image
avg = Particle()
avg.copyInfo(self.inputParticles.get())
avg.setLocation(NO_INDEX, self.getAverage())
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(particles, avg)
imgSet = self._createSetOfParticles()
imgSet.copyInfo(particles)
imgSet.setAlignment2D()
outputStk = self._getFileName('particlesAligned')
imgSet.readStack(outputStk,
postprocessImage=lambda img: img.setTransform(Transform()))
self._defineOutputs(outputParticles=imgSet)
self._defineTransformRelation(particles, imgSet)
def createOutputStep(self):
""" Register the output (the alignment and the aligned particles.)
"""
outputStk = self._getFileName('particlesAligned')
if not exists(outputStk):
raise Exception('Ouptput stack %s not produced. ' % outputStk)
particles = self.inputParticles.get()
# Create the output average image
avg = Particle()
avg.copyInfo(self.inputParticles.get())
avg.setLocation(NO_INDEX, self.getAverage())
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputParticles, avg)
imgSet = self._createSetOfParticles()
imgSet.copyInfo(particles)
imgSet.setAlignment2D()
imgSet.copyItems(particles,
updateItemCallback=self._updateItem,
itemDataIterator=iter(range(1, particles.getSize()+1)))
self._defineOutputs(outputParticles=imgSet)
self._defineTransformRelation(self.inputParticles, imgSet)