def createOutputStep(self):
inputParticles = self.inputParticles.get()
fnDeformedParticles = self._getExtraPath('deformed-particles.xmd')
outputSetOfParticles = self._createSetOfParticles()
readSetOfParticles(fnDeformedParticles, outputSetOfParticles)
outputSetOfParticles.copyInfo(inputParticles)
self._defineOutputs(outputParticles=outputSetOfParticles)
def createOutputStep(self):
inputParticles = self.inputParticles.get()
fnDeformedParticles = self._getExtraPath('deformed-particles.xmd')
outputSetOfParticles = self._createSetOfParticles()
readSetOfParticles(fnDeformedParticles, outputSetOfParticles)
outputSetOfParticles.copyInfo(inputParticles)
self._defineOutputs(outputParticles=outputSetOfParticles)
def createOutput(self):
imgSetOut = self._createSetOfAverages()
imgSetOut.setSamplingRate(self.inputVolume.get().getSamplingRate())
imgSetOut.setAlignmentProj()
readSetOfParticles(self._getPath("images.xmd"), imgSetOut)
self._defineOutputs(outputReprojections=imgSetOut)
self._defineSourceRelation(self.inputVolume, imgSetOut)
def createOutputStep(self):
inputSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
readSetOfParticles(self.imgsFn, partSet,
extraLabels=[xmipp.MDL_NMA, xmipp.MDL_COST])
partSet.copyInfo(inputSet)
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(self.getInputPdb(), partSet)
self._defineTransformRelation(inputSet, partSet)
def importParticles(self):
""" Import particles from a metadata 'images.xmd' """
self._imgDict = {} # store which images stack have been linked/copied and the new path
self._findPathAndCtf(label=md.MDL_IMAGE)
if self._micIdOrName:
# If MDL_MICROGRAPH_ID or MDL_MICROGRAPH then
# create a set to link from particles
self.micSet = self.protocol._createSetOfMicrographs()
self.protocol.setSamplingRate(self.micSet)
self.protocol.fillAcquisition(self.micSet.getAcquisition())
partSet = self.protocol._createSetOfParticles()
partSet.setObjComment('Particles imported from Xmipp metadata:\n%s' % self._mdFile)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self.protocol.setSamplingRate(partSet)
partSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol.fillAcquisition(partSet.getAcquisition())
# Read the micrographs from the 'self._mdFile' metadata
# but fixing the filenames with new ones (linked or copy to extraDir)
readSetOfParticles(self._mdFile, partSet,
preprocessImageRow=self._preprocessParticleRow,
readAcquisition=False)
if self._micIdOrName:
self.protocol._defineOutputs(outputMicrographs=self.micSet)
self.protocol._defineOutputs(outputParticles=partSet)
# Also create classes if MDL_REF or MDL_REF3D was found
if self._classFunc is not None:
clsSet = self._classFunc(partSet)
fillClasses(clsSet)
self.protocol._defineOutputs(outputClasses=clsSet)
self.protocol._defineSourceRelation(partSet, clsSet)
