def createOutputStep(self):
particles = self.inputParticles.get()
# Generate the SetOfAlignmet
alignedSet = self._createSetOfParticles()
alignedSet.copyInfo(particles)
inputMd = self._getPath('aligned_particles.xmd')
alignedSet.copyItems(particles,
updateItemCallback=self._updateItem,
itemDataIterator=md.iterRows(inputMd, sortByLabel=md.MDL_ITEM_ID))
# Remove alignment 2D
alignedSet.setAlignment(ALIGN_NONE)
# Define the output average
avgFile = self._getExtraPath("average.xmp")
imgh = ImageHandler()
avgImage = imgh.computeAverage(alignedSet)
avgImage.write(avgFile)
avg = Particle()
avg.setLocation(1, avgFile)
avg.copyInfo(alignedSet)
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputParticles, avg)
self._defineOutputs(outputParticles=alignedSet)
self._defineSourceRelation(self.inputParticles, alignedSet)
def createOutputStep(self):
subtomograms = self.inputSubtomograms.get()
alignedSet = self._createSetOfSubTomograms()
alignedSet.copyInfo(subtomograms)
inputMd = self._getPath('output_subtomograms.stk')
alignedSet.copyItems(subtomograms,
updateItemCallback=self._updateItem,
itemDataIterator=md.iterRows(
inputMd, sortByLabel=md.MDL_ITEM_ID))
alignedSet.setAlignment(pwem.ALIGN_NONE)
avgFile = self._getExtraPath("average.mrc")
imgh = ImageHandler()
avgImage = imgh.computeAverage(alignedSet)
avgImage.write(avgFile)
avg = AverageSubTomogram()
avg.setLocation(1, avgFile)
avg.copyInfo(alignedSet)
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputSubtomograms, avg)
self._defineOutputs(outputSubtomograms=alignedSet)
self._defineSourceRelation(self.inputSubtomograms, alignedSet)