def createOutputStep(self):
# Create the SetOfImages object on the database
fnImages = self._getOutputImgMd()
# Create output SetOfParticles
self.imgSet = self._createSetOfParticles()
self.imgSet.copyInfo(self.inputMics)
# set coords from the input, will update later if needed
self.imgSet.setCoordinates(self.inputCoords)
coords2 = SetOfCoordinates()
if self.doFlip:
self.imgSet.setIsPhaseFlipped(not self.inputMics.isPhaseFlipped())
self.imgSet.setSamplingRate(self._getNewSampling())
self.imgSet.setHasCTF(self.ctfRelations.hasValue())
# a SetMdIterator is needed because in some cases, the number of
# items in SetOfCoordinates and in the metadata could be different.
iterator = md.SetMdIterator(fnImages, sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self.createParticles,
skipDisabled=True)
# THis use case is special, because copyItems method is designed to
# modified the same type of object of the input set. Here, a new type
# (SetOfParticles) is generated, and its needed an auxiliary set of
# coordinates and it not stored.
coordsAux = SetOfCoordinates()
coordsAux.copyItems(self.inputCoords,
updateItemCallback=iterator.updateItem,
copyDisabled=True)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=self.imgSet)
self._defineSourceRelation(self.inputCoordinates, self.imgSet)
if self.ctfRelations.hasValue():
self._defineSourceRelation(self.ctfRelations.get(), self.imgSet)
def createOutputStep(self):
self.mdClasses = xmipp.MetaData(self._getDirectionalClassesFn())
self.mdImages = xmipp.MetaData(self._getDirectionalImagesFn())
inputParticles = self.inputParticles.get()
classes2D = self._createSetOfClasses2D(inputParticles)
self.averageSet = self._createSetOfAverages()
self.averageSet.copyInfo(inputParticles)
self.averageSet.setAlignmentProj()
# Let's use a SetMdIterator because it could be less particles
# in the metadata produced than in the input set
iterator = md.SetMdIterator(self.mdImages,
sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
classes2D.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
self._defineOutputs(outputClasses=classes2D)
self._defineOutputs(outputAverages=self.averageSet)
self._defineSourceRelation(self.inputParticles, classes2D)
self._defineSourceRelation(self.inputParticles, self.averageSet)
def createOutputStep(self):
inputParticles = self.inputParticles.get()
if not self._useSeveralClasses():
newTs = inputParticles.getSamplingRate()
else:
newTs = self.readInfoField(self._getExtraPath(),"sampling",xmippLib.MDL_SAMPLINGRATE)
self.mdClasses = xmippLib.MetaData(self._getDirectionalClassesFn())
self.mdImages = xmippLib.MetaData(self._getDirectionalImagesFn())
classes2D = self._createSetOfClasses2D(inputParticles)
classes2D.getImages().setSamplingRate(newTs)
self.averageSet = self._createSetOfAverages()
self.averageSet.copyInfo(inputParticles)
self.averageSet.setAlignmentProj()
self.averageSet.setSamplingRate(newTs)
# Let's use a SetMdIterator because it should be less particles
# in the metadata produced than in the input set
iterator = md.SetMdIterator(self.mdImages, sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
fnHomogeneous = self._getExtraPath("images_homogeneous.xmd")
if exists(fnHomogeneous):
homogeneousSet = self._createSetOfParticles()
homogeneousSet.copyInfo(inputParticles)
homogeneousSet.setSamplingRate(newTs)
homogeneousSet.setAlignmentProj()
self.iterMd = md.iterRows(fnHomogeneous, md.MDL_PARTICLE_ID)
self.lastRow = next(self.iterMd)
homogeneousSet.copyItems(inputParticles,
updateItemCallback=self._updateHomogeneousItem)
self._defineOutputs(outputHomogeneous=homogeneousSet)
self._defineSourceRelation(self.inputParticles, homogeneousSet)
classes2D.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
self._defineOutputs(outputClasses=classes2D)
self._defineOutputs(outputAverages=self.averageSet)
self._defineSourceRelation(self.inputParticles, classes2D)
self._defineSourceRelation(self.inputParticles, self.averageSet)
if self.splitVolume and self.directionalClasses.get()>1:
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(newTs)
for i in range(2):
vol = Volume()
vol.setLocation(1, self._getExtraPath("split_v%d.vol"%(i+1)))
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(inputParticles, volumesSet)
def _fillClassesFromLevel(self, clsSet):
""" Create the SetOfClasses2D from a given iteration. """
myFileClasses = self._getExtraPath('last_classes.xmd')
myFileImages = self._getExtraPath('last_images.xmd')
self._loadClassesInfo(myFileClasses)
xmpMd = myFileImages
iterator = md.SetMdIterator(xmpMd, sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
clsSet.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
def _fillClassesFromLevel(self, clsSet):
""" Create the SetOfClasses2D from a given iteration. """
blocks = md.getBlocksInMetaDataFile(self._getExtraPath('output.xmd'))
for bId, b in enumerate(blocks):
if b.startswith('class0'):
self._loadClassesInfo(
self._getExtraPath("level_00/%s_classes.stk" % b), bId)
xmpMd = b + "@" + self._getExtraPath('output.xmd')
iterator = md.SetMdIterator(
xmpMd,
sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
clsSet.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
def _fillClassesFromLevel(self, clsSet, level, subset):
""" Create the SetOfClasses2D from a given iteration. """
self._loadClassesInfo(self._getLevelMdClasses(lev=level,
subset=subset))
if subset == '' and level == "last":
xmpMd = self._getFileName('output_particles')
if not exists(xmpMd):
xmpMd = self._getLevelMdImages(level, subset)
else:
xmpMd = self._getLevelMdImages(level, subset)
iterator = md.SetMdIterator(xmpMd,
sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
# itemDataIterator is not neccesary because, the class SetMdIterator
# contain all the information about the metadata
clsSet.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
def createOutputStep(self):
inputParticles = self.inputParticles.get()
# if not self._useSeveralClasses():
# newTs = inputParticles.getSamplingRate()
# else:
# newTs = self.readInfoField(self._getExtraPath(), "sampling",
# xmipp.MDL_SAMPLINGRATE)
self.mdClasses = xmippLib.MetaData(self._getDirectionalClassesFn())
self.mdImages = xmippLib.MetaData(self._getDirectionalImagesFn())
origTs = inputParticles.getSamplingRate()
lastTs = self.readInfoField(self._getExtraPath(), "sampling",
xmippLib.MDL_SAMPLINGRATE)
if origTs!=lastTs:
newXdim=inputParticles.getXDim()
self.runJob("xmipp_image_resize", "-i %s -o %s --save_metadata_stack %s --fourier %d"
% (self._getDirectionalClassesFn(),
self._getPath("aux_directional_local_classes.stk"),
self._getPath("aux_directional_classes.xmd"),
newXdim), numberOfMpi=1)
from shutil import copy
copy(self._getPath("aux_directional_local_classes.stk"),
self._getPath("directional_local_classes.stk"))
copy(self._getPath("aux_directional_classes.xmd"),
self._getPath("directional_classes.xmd"))
cleanPattern(self._getPath("aux_directional*"))
classes2D = self._createSetOfClasses2D(inputParticles)
#classes2D.getImages().setSamplingRate(newTs)
classes2D.getImages().setSamplingRate(origTs)
self.averageSet = self._createSetOfAverages()
self.averageSet.copyInfo(inputParticles)
self.averageSet.setAlignmentProj()
#self.averageSet.setSamplingRate(newTs)
self.averageSet.setSamplingRate(origTs)
# Let's use a SetMdIterator because it should be less particles
# in the metadata produced than in the input set
iterator = md.SetMdIterator(self.mdImages, sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
fnHomogeneous = self._getExtraPath("images_homogeneous.xmd")
if exists(fnHomogeneous):
if origTs != lastTs:
newXdim = inputParticles.getXDim()
self.runJob("xmipp_image_resize", "-i %s --dim %d"
% (fnHomogeneous, newXdim), numberOfMpi=1)
homogeneousSet = self._createSetOfParticles()
homogeneousSet.copyInfo(inputParticles)
#homogeneousSet.getImages().setSamplingRate(newTs)
homogeneousSet.getImages().setSamplingRate(origTs)
homogeneousSet.setAlignmentProj()
self.iterMd = md.iterRows(fnHomogeneous, md.MDL_PARTICLE_ID)
self.lastRow = next(self.iterMd)
homogeneousSet.copyItems(inputParticles,
updateItemCallback=self._updateHomogeneousItem)
self._defineOutputs(outputHomogeneous=homogeneousSet)
self._defineSourceRelation(self.inputParticles, homogeneousSet)
#AJ testing
#AJ por que desaparece una clase que tiene imagenes asignadas
listRefId=[]
for row in md.iterRows(self.mdClasses, xmippLib.MDL_REF2):
refId = row.getValue(xmippLib.MDL_REF2, row.getObjId())
if len(listRefId)>0 and refId != listRefId[-1]+1:
whereEnd = listRefId[-1]+1
for i in range(refId-whereEnd):
rowNew = row
rowNew.setValue(xmippLib.MDL_REF2, listRefId[-1]+i+1)
rowNew.setValue(xmippLib.MDL_IMAGE, 'None')
rowNew.setValue(xmippLib.MDL_IMAGE1, 'None')
rowNew.addToMd(self.mdClasses)
listRefId.append(listRefId[-1]+i+1)
listRefId.append(refId)
else:
listRefId.append(refId)
self.mdClasses.write(self._getDirectionalClassesFn())
self.mdClasses = xmippLib.MetaData(self._getDirectionalClassesFn())
#END AJ
classes2D.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
self._defineOutputs(outputClasses=classes2D)
self._defineOutputs(outputAverages=self.averageSet)
self._defineSourceRelation(self.inputParticles, classes2D)
self._defineSourceRelation(self.inputParticles, self.averageSet)
if self.splitVolume and self.directionalClasses.get() > 1:
volumesSet = self._createSetOfVolumes()
#volumesSet.setSamplingRate(newTs)
volumesSet.setSamplingRate(origTs)
for i in range(2):
vol = Volume()
if origTs != lastTs:
newXdim = inputParticles.getXDim()
self.runJob("xmipp_image_resize", "-i %s --dim %d"
% (self._getExtraPath("split%d.vol" % (i + 1)),
newXdim), numberOfMpi=1)
vol.setLocation(1, self._getExtraPath("split%d.vol" % (i + 1)))
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(inputParticles, volumesSet)