def createOutputStep(self):
if not self.realignMovieFrames:
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getExtraPath('relion_class001.mrc'))
vol.setSamplingRate(imgSet.getSamplingRate())
half1 = self._getFileName("final_half1_volume", ref3d=1)
half2 = self._getFileName("final_half2_volume", ref3d=1)
vol.setHalfMaps([half1, half2])
outImgSet = self._createSetOfParticles()
outImgSet.copyInfo(imgSet)
self._fillDataFromIter(outImgSet, self._lastIter())
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineOutputs(outputParticles=outImgSet)
self._defineTransformRelation(self.inputParticles, outImgSet)
fsc = FSC(objLabel=self.getRunName())
blockName = 'model_class_%d@' % 1
fn = blockName + self._getExtraPath("relion_model.star")
mData = md.MetaData(fn)
fsc.loadFromMd(mData, md.RLN_RESOLUTION,
md.RLN_MLMODEL_FSC_HALVES_REF)
self._defineOutputs(outputFSC=fsc)
self._defineSourceRelation(vol, fsc)
else:
movieSet = self.inputMovieParticles.get()
if self.movieIncludeRotSearch:
vol = Volume()
vol.setFileName(self._getExtraPath('relion_class001.mrc'))
vol.setSamplingRate(movieSet.getSamplingRate())
half1 = self._getFileName("final_half1_volume", ref3d=1)
half2 = self._getFileName("final_half2_volume", ref3d=1)
vol.setHalfMaps([half1, half2])
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineSourceRelation(self.inputMovieParticles, vol)
fnOut = self._getFileName('dataFinal')
outMovieSet = self._createSetOfMovieParticles()
outMovieSet.copyInfo(movieSet)
outMovieSet.setAlignmentProj()
# not using copyItems since input movie particle
# set is missing a lot of metadata (CTF, micName etc.)
# that was created in convertInputStep
readSetOfParticles(fnOut,
outMovieSet,
alignType=ALIGN_PROJ,
extraLabels=MOVIE_EXTRA_LABELS,
postprocessImageRow=self._updateParticle)
self._defineOutputs(outputParticles=outMovieSet)
self._defineTransformRelation(self.inputParticles, outMovieSet)
self._defineTransformRelation(self.inputMovieParticles,
outMovieSet)
def importParticles(self):
""" Import particles from a metadata 'images.xmd' """
self.ignoreIds = self.protocol.ignoreIdColumn.get()
self._imgDict = {} # store which images stack have been linked/copied and the new path
self._findImagesPath(label=md.RLN_IMAGE_NAME)
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.micSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol.fillAcquisition(self.micSet.getAcquisition())
partSet = self.protocol._createSetOfParticles()
partSet.setObjComment('Particles imported from Relion star file:\n%s' % self._starFile)
# 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._starFile' metadata
# but fixing the filenames with new ones (linked or copy to extraDir)
from convert import readSetOfParticles
readSetOfParticles(self._starFile, partSet,
preprocessImageRow=self._preprocessImageRow,
postprocessImageRow=self._postprocessImageRow,
readAcquisition=False, alignType=self.alignType)
if self._micIdOrName:
self.protocol._defineOutputs(outputMicrographs=self.micSet)
self.protocol._defineOutputs(outputParticles=partSet)
if self._classesFunc is not None:
self._createClasses(partSet)
def importParticles(self):
""" Import particles from Frealign.
Params:
parFile: the filename of the parameter file with the alignment in Frealign.
stackFile: single stack file with the images.
"""
partSet = self.protocol._createSetOfParticles()
partSet.setObjComment('Particles imported from Frealign parfile:\n%s' %
self.parFile)
# Create a local link to the input stack file
localStack = self.protocol._getExtraPath(
os.path.basename(self.stackFile))
pwutils.createLink(self.stackFile, localStack)
# Create a temporary set only with location
tmpSet = SetOfParticles(filename=':memory:')
tmpSet.readStack(localStack)
self._setupSet(tmpSet)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self._setupSet(partSet)
# Now read the alignment parameters from par file
readSetOfParticles(tmpSet, partSet, self.parFile)
partSet.setHasCTF(True)
# Register the output set of particles
self.protocol._defineOutputs(outputParticles=partSet)
def createOutputStep(self):
lastIter = self._getLastIter()
inputSet = self.inputParticles.get()
inputRef = self.input3DReference.get()
lastIterDir = self._iterWorkingDir(lastIter)
# Register output volume
volFn = join(lastIterDir, 'volume_iter_%03d.mrc' % lastIter)
vol = Volume()
vol.setSamplingRate(inputSet.getSamplingRate())
vol.setFileName(volFn)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(inputSet, vol)
self._defineSourceRelation(inputRef, vol)
# Register output Particles with their 3D alignment
#TODO: save alignment
#read last alignment file
file2 = self._getFileName('output_par', iter=lastIter)
partSet = self._createSetOfParticles()
partSet.copyInfo(inputSet)
readSetOfParticles(inputSet, partSet, file2)
self._defineOutputs(outputParticles=partSet)
self._defineTransformRelation(inputSet, partSet)
self._defineSourceRelation(inputRef, partSet)
def importParticles(self):
""" Import particles from Frealign.
Params:
parFile: the filename of the parameter file with the alignment in Frealing.
stackFile: single stack file with the images.
"""
partSet = self.protocol._createSetOfParticles()
partSet.setObjComment("Particles imported from Frealign parfile:\n%s" % self.parFile)
# Create a local link to the input stack file
localStack = self.protocol._getExtraPath(os.path.basename(self.stackFile))
pwutils.createLink(self.stackFile, localStack)
# Create a temporarly set only with location
tmpSet = SetOfParticles(filename=":memory:")
tmpSet.readStack(localStack)
self._setupSet(tmpSet)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self._setupSet(partSet)
# Now read the alignment parameters from par file
readSetOfParticles(tmpSet, partSet, self.parFile)
partSet.setHasCTF(True)
# Register the output set of particles
self.protocol._defineOutputs(outputParticles=partSet)
def importParticles(self):
""" Import particles from a metadata 'images.xmd' """
self.ignoreIds = self.protocol.ignoreIdColumn.get()
self._imgDict = {} # store which images stack have been linked/copied and the new path
self._findImagesPath(label=md.RLN_IMAGE_NAME)
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.micSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol.fillAcquisition(self.micSet.getAcquisition())
partSet = self.protocol._createSetOfParticles()
partSet.setObjComment('Particles imported from Relion star file:\n%s' % self._starFile)
# 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._starFile' metadata
# but fixing the filenames with new ones (linked or copy to extraDir)
from convert import readSetOfParticles
readSetOfParticles(self._starFile, partSet,
preprocessImageRow=self._preprocessImageRow,
postprocessImageRow=self._postprocessImageRow,
readAcquisition=False, alignType=self.alignType)
if self._micIdOrName:
self.protocol._defineOutputs(outputMicrographs=self.micSet)
self.protocol._defineOutputs(outputParticles=partSet)
if self._classesFunc is not None:
self._createClasses(partSet)
def createOutputStep(self):
if not self.realignMovieFrames:
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getExtraPath('relion_class001.mrc'))
vol.setSamplingRate(imgSet.getSamplingRate())
half1 = self._getFileName("final_half1_volume", ref3d=1)
half2 = self._getFileName("final_half2_volume", ref3d=1)
vol.setHalfMaps([half1, half2])
outImgSet = self._createSetOfParticles()
outImgSet.copyInfo(imgSet)
self._fillDataFromIter(outImgSet, self._lastIter())
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineOutputs(outputParticles=outImgSet)
self._defineTransformRelation(self.inputParticles, outImgSet)
fsc = FSC(objLabel=self.getRunName())
blockName = 'model_class_%d@' % 1
fn = blockName + self._getExtraPath("relion_model.star")
mData = md.MetaData(fn)
fsc.loadFromMd(mData,
md.RLN_RESOLUTION,
md.RLN_MLMODEL_FSC_HALVES_REF)
self._defineOutputs(outputFSC=fsc)
self._defineSourceRelation(vol, fsc)
else:
movieSet = self.inputMovieParticles.get()
if self.movieIncludeRotSearch:
vol = Volume()
vol.setFileName(self._getExtraPath('relion_class001.mrc'))
vol.setSamplingRate(movieSet.getSamplingRate())
half1 = self._getFileName("final_half1_volume", ref3d=1)
half2 = self._getFileName("final_half2_volume", ref3d=1)
vol.setHalfMaps([half1, half2])
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineSourceRelation(self.inputMovieParticles, vol)
fnOut = self._getFileName('dataFinal')
outMovieSet = self._createSetOfMovieParticles()
outMovieSet.copyInfo(movieSet)
outMovieSet.setAlignmentProj()
# not using copyItems since input movie particle
# set is missing a lot of metadata (CTF, micName etc.)
# that was created in convertInputStep
readSetOfParticles(fnOut, outMovieSet, alignType=ALIGN_PROJ,
extraLabels=MOVIE_EXTRA_LABELS,
postprocessImageRow=self._updateParticle)
self._defineOutputs(outputParticles=outMovieSet)
self._defineTransformRelation(self.inputParticles, outMovieSet)
self._defineTransformRelation(self.inputMovieParticles, outMovieSet)
def _getMetadataSqlite(self, fn, clean=False):
""" Read the classes from Xmipp metadata and write as sqlite file. """
fnSqlite = fn + '.sqlite'
if clean:
cleanPath(fnSqlite)
if not os.path.exists(fnSqlite):
imagesSet = SetOfParticles(filename=fnSqlite)
readSetOfParticles(fn+".xmd",imagesSet)
imagesSet.write()
imagesSet.close()
return fnSqlite
def createOutputStep(self):
# Create the SetOfImages object on the database
#imgSet = XmippSetOfParticles(self._getPath('images.xmd'))
fnImages = self._getOutputImgMd()
# Create output SetOfParticles
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputMics)
if self.doFlip:
# Check if self.inputMics are phase flipped.
if self.inputMics.isPhaseFlipped():
imgSet.setIsPhaseFlipped(False)
else:
imgSet.setIsPhaseFlipped(True)
#imgSet.setHasCTF(self.fnCTF is not None)
if self.downsampleType == OTHER:
imgSet.setSamplingRate(self.inputMics.getSamplingRate() *
self.downFactor.get())
imgSet.setCoordinates(self.inputCoords)
# Create a temporary set to read from the metadata file
# and later create the good one with the coordinates
# properly set. We need this because the .update is not
# working in the mapper when new attributes are added.
imgSet.setHasCTF(self.ctfRelations.hasValue())
auxSet = SetOfParticles(filename=':memory:')
auxSet.copyInfo(imgSet)
readSetOfParticles(fnImages, auxSet)
if self.downsampleType != SAME_AS_PICKING:
factor = self.samplingInput / self.samplingFinal
# For each particle retrieve micId from SetOFCoordinates and set it on the CTFModel
for img in auxSet:
#FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
coord = self.inputCoords[img.getObjId()]
if self.downsampleType != SAME_AS_PICKING:
x, y = coord.getPosition()
coord.setPosition(x * factor, y * factor)
ctfModel = img.getCTF()
if ctfModel is not None:
ctfModel.setObjId(coord.getMicId())
##img.setCTF(ctfModel)####JM
img.setMicId(coord.getMicId())
img.setCoordinate(coord)
imgSet.append(img)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=imgSet)
self._defineSourceRelation(self.inputCoordinates, imgSet)
if self.ctfRelations.hasValue():
self._defineSourceRelation(self.ctfRelations.get(), imgSet)
def createOutputStep(self):
# Create the SetOfImages object on the database
#imgSet = XmippSetOfParticles(self._getPath('images.xmd'))
fnImages = self._getOutputImgMd()
# Create output SetOfParticles
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputMics)
if self.doFlip:
# Check if self.inputMics are phase flipped.
if self.inputMics.isPhaseFlipped():
imgSet.setIsPhaseFlipped(False)
else:
imgSet.setIsPhaseFlipped(True)
#imgSet.setHasCTF(self.fnCTF is not None)
if self.downsampleType == OTHER:
imgSet.setSamplingRate(self.inputMics.getSamplingRate()*self.downFactor.get())
imgSet.setCoordinates(self.inputCoords)
# Create a temporary set to read from the metadata file
# and later create the good one with the coordinates
# properly set. We need this because the .update is not
# working in the mapper when new attributes are added.
imgSet.setHasCTF(self.ctfRelations.hasValue())
auxSet = SetOfParticles(filename=':memory:')
auxSet.copyInfo(imgSet)
readSetOfParticles(fnImages, auxSet)
if self.downsampleType != SAME_AS_PICKING:
factor = self.samplingInput / self.samplingFinal
# For each particle retrieve micId from SetOFCoordinates and set it on the CTFModel
for img in auxSet:
#FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
coord = self.inputCoords[img.getObjId()]
if self.downsampleType != SAME_AS_PICKING:
x, y = coord.getPosition()
coord.setPosition(x*factor, y*factor)
ctfModel = img.getCTF()
if ctfModel is not None:
ctfModel.setObjId(coord.getMicId())
##img.setCTF(ctfModel)####JM
img.setMicId(coord.getMicId())
img.setCoordinate(coord)
imgSet.append(img)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=imgSet)
self._defineSourceRelation(self.inputCoordinates, imgSet)
if self.ctfRelations.hasValue():
self._defineSourceRelation(self.ctfRelations.get(), imgSet)
def _getIterData(self, it, **kwargs):
from convert import readSetOfParticles
imgSqlite = self.protocol._getFileName('data_scipion', iter=it)
if not exists(imgSqlite):
imgPar = self.protocol._getFileName('output_par', iter=it)
cleanPath(imgSqlite)
imgSet = em.SetOfParticles(filename=imgSqlite)
readSetOfParticles(self.protocol.inputParticles.get(), imgSet, imgPar)
imgSet.write()
return imgSqlite
def createOutputStep(self):
imgSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
partSet.copyInfo(imgSet)
outImagesMd = self._getExtraPath('expanded_particles.star')
mdOut = md.MetaData(outImagesMd)
mdOut.removeLabel(md.RLN_IMAGE_ID) # remove repeating rlnImageId in mdOut
mdOut.write(outImagesMd, md.MD_OVERWRITE)
readSetOfParticles(outImagesMd, partSet, alignType=ALIGN_PROJ,
postprocessImageRow=self._postprocessImageRow)
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(imgSet, partSet)
def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getFileName('volume_shiny'))
vol.setSamplingRate(imgSet.getSamplingRate())
shinyPartSet = self._createSetOfParticles()
shinyPartSet.copyInfo(imgSet)
shinyPartSet.setAlignmentProj()
readSetOfParticles(self._getFileName('shiny'), shinyPartSet,
alignType=ALIGN_PROJ)
self._defineOutputs(outputParticles=shinyPartSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(imgSet, shinyPartSet)
self._defineSourceRelation(imgSet, vol)
def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getFileName('volume_shiny'))
vol.setSamplingRate(imgSet.getSamplingRate())
shinyPartSet = self._createSetOfParticles()
shinyPartSet.copyInfo(imgSet)
shinyPartSet.setAlignmentProj()
readSetOfParticles(self._getFileName('shiny'),
shinyPartSet,
alignType=ALIGN_PROJ)
self._defineOutputs(outputParticles=shinyPartSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(imgSet, shinyPartSet)
self._defineSourceRelation(imgSet, vol)
def createOutputStep(self):
""" Store the setOfParticles object
as result of the protocol.
"""
particles = self.inputParticles.get()
# Define the output average
avgFile = self._getExtraPath('level_00', 'class_classes.stk')
avg = Particle()
avg.setLocation(1, avgFile)
avg.copyInfo(particles)
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(particles, avg)
# Generate the Set of Particles with alignment
alignedSet = self._createSetOfParticles()
alignedSet.copyInfo(particles)
alignedSet.setRepresentative(avg)
readSetOfParticles(self.imgsFn, alignedSet)
self._defineOutputs(outputParticles=alignedSet)
self._defineSourceRelation(particles, alignedSet)
def createOutputStep(self):
lastIter = self._getLastIter()
inputSet = self._getInputParticles()
# Register output volume
volFn = self._getFileName('iter_vol', iter=lastIter)
vol = em.Volume()
vol.setFileName(volFn)
vol.setSamplingRate(inputSet.getSamplingRate())
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
# Register output Particles with their 3D alignment
file2 = self._getFileName('output_par', iter=lastIter)
partSet = self._createSetOfParticles()
partSet.copyInfo(inputSet)
readSetOfParticles(inputSet, partSet, file2)
self._defineOutputs(outputParticles=partSet)
self._defineTransformRelation(self._getInputParticlesPointer(), partSet)
if not self.doContinue:
self._defineSourceRelation(self.input3DReference, vol)
self._defineSourceRelation(self.input3DReference, partSet)
def createOutputStep(self):
# Create the SetOfImages objects on the database and the ImagesTiltPair
mdUntilted = xmipp.MetaData()
mdTilted = xmipp.MetaData()
#for objId in mdPairs:
for uMic, tMic in izip(self.uMics, self.tMics):
umicName = removeBaseExt(uMic.getFileName())
fnMicU = self._getExtraPath(umicName + ".xmd")
fnPosU = self._getExtraPath(umicName + ".pos")
# Check if there are picked particles in this micrographs
if exists(fnMicU):
mdMicU = xmipp.MetaData(fnMicU)
mdPosU = xmipp.MetaData('particles@%s' % fnPosU)
mdPosU.merge(mdMicU)
mdUntilted.unionAll(mdPosU)
tmicName = removeBaseExt(tMic.getFileName())
fnMicT = self._getExtraPath(tmicName + ".xmd")
fnPosT = self._getExtraPath(tmicName + ".pos")
mdMicT = xmipp.MetaData(fnMicT)
mdPosT = xmipp.MetaData('particles@%s' % fnPosT)
mdPosT.merge(mdMicT)
mdTilted.unionAll(mdPosT)
# Write image metadatas (check if it is really necessary)
fnTilted = self._getExtraPath("images_tilted.xmd")
fnUntilted = self._getExtraPath("images_untilted.xmd")
mdUntilted.write(fnUntilted)
mdTilted.write(fnTilted)
# Create outputs SetOfParticles both for tilted and untilted
imgSetU = self._createSetOfParticles(suffix="Untilted")
imgSetU.copyInfo(self.uMics)
imgSetT = self._createSetOfParticles(suffix="Tilted")
imgSetT.copyInfo(self.tMics)
if self.downsampleType == OTHER:
imgSetU.setSamplingRate(self.samplingFinal)
imgSetT.setSamplingRate(self.samplingFinal)
imgSetU.setCoordinates(self.inputCoordinatesTiltedPairs.get().getUntilted())
imgSetT.setCoordinates(self.inputCoordinatesTiltedPairs.get().getTilted())
#Read untilted and tilted particles on a temporary object (also disabled particles)
imgSetAuxU = self._createSetOfParticles('auxU')
imgSetAuxU.copyInfo(imgSetU)
readSetOfParticles(fnUntilted, imgSetAuxU, removeDisabled=False)
imgSetAuxU.write()
imgSetAuxT = self._createSetOfParticles('auxT')
imgSetAuxT.copyInfo(imgSetT)
readSetOfParticles(fnTilted, imgSetAuxT, removeDisabled=False)
imgSetAuxT.write()
coordsT = self.inputCoordinatesTiltedPairs.get().getTilted()
# For each untilted particle retrieve micId from SetOFCoordinates untilted
for imgU, coordU in izip(imgSetAuxU, self.inputCoordinatesTiltedPairs.get().getUntilted()):
#FIXME: REmove this check when sure that objIds are equal
id = imgU.getObjId()
if id != coordU.getObjId():
raise Exception('ObjId in untilted is not equal!!!!')
imgT = imgSetAuxT[id]
coordT = coordsT[id]
#If both particles are enabled append them
if imgU.isEnabled() and imgT.isEnabled():
imgU.setCoordinate(coordU)
imgSetU.append(imgU)
imgT.setCoordinate(coordT)
imgSetT.append(imgT)
# For each untilted particle retrieve micId from SetOFCoordinates tilted
#for img in imgSetAuxU:
# for img, coord in izip(imgSetAuxT, self.inputCoordinatesTiltedPairs.get().getTilted()):
# #FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
# #FIXME: REmove this check when sure that objIds are equal
# if img.getObjId() != coord.getObjId():
# raise Exception('ObjId is not equal!!!!')
# #coord = self.inputCoordinatesTiltedPairs.get().getTilted()[img.getObjId()]
# img.setCoordinate(coord)
# #img.cleanObjId()
# imgSetT.append(img)
imgSetU.write()
imgSetT.write()
self._storeMethodsInfo(fnUntilted)
# Define output ParticlesTiltPair
outputset = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
outputset.setTilted(imgSetT)
outputset.setUntilted(imgSetU)
for imgU, imgT in izip(imgSetU, imgSetT):
outputset.append(TiltPair(imgU, imgT))
outputset.setCoordsPair(self.inputCoordinatesTiltedPairs.get())
self._defineOutputs(outputParticlesTiltPair=outputset)
self._defineSourceRelation(self.inputCoordinatesTiltedPairs, outputset)
def createOutputStep(self):
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputParticles.get())
readSetOfParticles(self.outputMd.get(), imgSet)
self._defineOutputs(outputParticles=imgSet)
def createOutputStep(self):
# Create the SetOfImages object on the database
#imgSet = XmippSetOfParticles(self._getPath('images.xmd'))
#Create images.xmd metadata
fnImages = self._getPath('images.xmd')
imgsXmd = xmipp.MetaData()
posFiles = glob(self._getExtraPath('*.pos'))
for posFn in posFiles:
xmdFn = self._getExtraPath(replaceBaseExt(posFn, "xmd"))
if exists(xmdFn):
md = xmipp.MetaData(xmdFn)
mdPos = xmipp.MetaData('particles@%s' % posFn)
mdPos.merge(md)
#imgSet.appendFromMd(mdPos)
imgsXmd.unionAll(mdPos)
else:
self.warning("The coord file %s wasn't used to extract! Maybe you are extracting over a subset of micrographs" % basename(posFn))
imgsXmd.write(fnImages)
# IF selected run xmipp_image_sort_by_statistics to add zscore info to images.xmd
if self.doSort:
args="-i %(fnImages)s --addToInput"
if self.rejectionMethod == REJECT_MAXZSCORE:
maxZscore = self.maxZscore.get()
args += " --zcut " + str(maxZscore)
elif self.rejectionMethod == REJECT_PERCENTAGE:
percentage = self.percentage.get()
args += " --percent " + str(percentage)
self.runJob("xmipp_image_sort_by_statistics", args % locals())
# Create output SetOfParticles
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputMics)
if self.doFlip:
# Check if self.inputMics are phase flipped.
if self.inputMics.isPhaseFlipped():
imgSet.setIsPhaseFlipped(False)
else:
imgSet.setIsPhaseFlipped(True)
#imgSet.setHasCTF(self.fnCTF is not None)
if self.downsampleType == OTHER:
imgSet.setSamplingRate(self.inputMics.getSamplingRate()*self.downFactor.get())
imgSet.setCoordinates(self.inputCoords)
# Create a temporary set to read from the metadata file
# and later create the good one with the coordinates
# properly set. We need this because the .update is not
# working in the mapper when new attributes are added.
imgSet.setHasCTF(self.ctfRelations.hasValue())
auxSet = SetOfParticles(filename=':memory:')
auxSet.copyInfo(imgSet)
readSetOfParticles(fnImages, auxSet)
# For each particle retrieve micId from SetOFCoordinates and set it on the CTFModel
for img in auxSet:
#FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
coord = self.inputCoords[img.getObjId()]
ctfModel = img.getCTF()
if ctfModel is not None:
ctfModel.setObjId(coord.getMicId())
##img.setCTF(ctfModel)####JM
img.setMicId(coord.getMicId())
img.setCoordinate(coord)
imgSet.append(img)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=imgSet)
self._defineSourceRelation(self.inputCoords, imgSet)
def createOutputStep(self):
fnTilted = self._getExtraPath("images_tilted.xmd")
fnUntilted = self._getExtraPath("images_untilted.xmd")
# Create outputs SetOfParticles both for tilted and untilted
imgSetU = self._createSetOfParticles(suffix="Untilted")
imgSetU.copyInfo(self.uMics)
imgSetT = self._createSetOfParticles(suffix="Tilted")
imgSetT.copyInfo(self.tMics)
sampling = self.samplingMics if self._micsOther(
) else self.samplingInput
if self._doDownsample():
sampling *= self.downFactor.get()
imgSetU.setSamplingRate(sampling)
imgSetT.setSamplingRate(sampling)
# set coords from the input, will update later if needed
imgSetU.setCoordinates(
self.inputCoordinatesTiltedPairs.get().getUntilted())
imgSetT.setCoordinates(
self.inputCoordinatesTiltedPairs.get().getTilted())
# Read untilted and tilted particles on a temporary object (also disabled particles)
imgSetAuxU = SetOfParticles(filename=':memory:')
imgSetAuxU.copyInfo(imgSetU)
readSetOfParticles(fnUntilted, imgSetAuxU, removeDisabled=False)
imgSetAuxT = SetOfParticles(filename=':memory:')
imgSetAuxT.copyInfo(imgSetT)
readSetOfParticles(fnTilted, imgSetAuxT, removeDisabled=False)
# calculate factor for coords scaling
factor = 1 / self.samplingFactor
if self._doDownsample():
factor /= self.downFactor.get()
coordsT = self.inputCoordinatesTiltedPairs.get().getTilted()
# For each untilted particle retrieve micId from SetOfCoordinates untilted
for imgU, coordU in izip(
imgSetAuxU,
self.inputCoordinatesTiltedPairs.get().getUntilted()):
# FIXME: Remove this check when sure that objIds are equal
id = imgU.getObjId()
if id != coordU.getObjId():
raise Exception(
'ObjIds in untilted img and coord are not the same!!!!')
imgT = imgSetAuxT[id]
coordT = coordsT[id]
# If both particles are enabled append them
if imgU.isEnabled() and imgT.isEnabled():
if self._micsOther() or self._doDownsample():
coordU.scale(factor)
coordT.scale(factor)
imgU.setCoordinate(coordU)
imgSetU.append(imgU)
imgT.setCoordinate(coordT)
imgSetT.append(imgT)
imgSetU.write()
imgSetT.write()
# Define output ParticlesTiltPair
outputset = ParticlesTiltPair(
filename=self._getPath('particles_pairs.sqlite'))
outputset.setTilted(imgSetT)
outputset.setUntilted(imgSetU)
for imgU, imgT in izip(imgSetU, imgSetT):
outputset.append(TiltPair(imgU, imgT))
outputset.setCoordsPair(self.inputCoordinatesTiltedPairs.get())
self._defineOutputs(outputParticlesTiltPair=outputset)
self._defineSourceRelation(self.inputCoordinatesTiltedPairs, outputset)
def createOutputStep(self):
fnTilted = self._getExtraPath("images_tilted.xmd")
fnUntilted = self._getExtraPath("images_untilted.xmd")
# Create outputs SetOfParticles both for tilted and untilted
imgSetU = self._createSetOfParticles(suffix="Untilted")
imgSetU.copyInfo(self.uMics)
imgSetT = self._createSetOfParticles(suffix="Tilted")
imgSetT.copyInfo(self.tMics)
sampling = self.samplingMics if self._micsOther() else self.samplingInput
if self._doDownsample():
sampling *= self.downFactor.get()
imgSetU.setSamplingRate(sampling)
imgSetT.setSamplingRate(sampling)
# set coords from the input, will update later if needed
imgSetU.setCoordinates(self.inputCoordinatesTiltedPairs.get().getUntilted())
imgSetT.setCoordinates(self.inputCoordinatesTiltedPairs.get().getTilted())
# Read untilted and tilted particles on a temporary object (also disabled particles)
imgSetAuxU = SetOfParticles(filename=':memory:')
imgSetAuxU.copyInfo(imgSetU)
readSetOfParticles(fnUntilted, imgSetAuxU, removeDisabled=False)
imgSetAuxT = SetOfParticles(filename=':memory:')
imgSetAuxT.copyInfo(imgSetT)
readSetOfParticles(fnTilted, imgSetAuxT, removeDisabled=False)
# calculate factor for coords scaling
factor = 1 / self.samplingFactor
if self._doDownsample():
factor /= self.downFactor.get()
coordsT = self.inputCoordinatesTiltedPairs.get().getTilted()
# For each untilted particle retrieve micId from SetOfCoordinates untilted
for imgU, coordU in izip(imgSetAuxU, self.inputCoordinatesTiltedPairs.get().getUntilted()):
# FIXME: Remove this check when sure that objIds are equal
id = imgU.getObjId()
if id != coordU.getObjId():
raise Exception('ObjIds in untilted img and coord are not the same!!!!')
imgT = imgSetAuxT[id]
coordT = coordsT[id]
# If both particles are enabled append them
if imgU.isEnabled() and imgT.isEnabled():
if self._micsOther() or self._doDownsample():
coordU.scale(factor)
coordT.scale(factor)
imgU.setCoordinate(coordU)
imgSetU.append(imgU)
imgT.setCoordinate(coordT)
imgSetT.append(imgT)
imgSetU.write()
imgSetT.write()
# Define output ParticlesTiltPair
outputset = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
outputset.setTilted(imgSetT)
outputset.setUntilted(imgSetU)
for imgU, imgT in izip(imgSetU, imgSetT):
outputset.append(TiltPair(imgU, imgT))
outputset.setCoordsPair(self.inputCoordinatesTiltedPairs.get())
self._defineOutputs(outputParticlesTiltPair=outputset)
self._defineSourceRelation(self.inputCoordinatesTiltedPairs, outputset)
def createOutputStep(self):
# Create the SetOfImages objects on the database and the ImagesTiltPair
mdUntilted = xmipp.MetaData()
mdTilted = xmipp.MetaData()
#for objId in mdPairs:
for uMic, tMic in izip(self.uMics, self.tMics):
umicName = removeBaseExt(uMic.getFileName())
fnMicU = self._getExtraPath(umicName + ".xmd")
fnPosU = self._getExtraPath(umicName + ".pos")
# Check if there are picked particles in this micrographs
if exists(fnMicU):
mdMicU = xmipp.MetaData(fnMicU)
mdPosU = xmipp.MetaData('particles@%s' % fnPosU)
mdPosU.merge(mdMicU)
mdUntilted.unionAll(mdPosU)
tmicName = removeBaseExt(tMic.getFileName())
fnMicT = self._getExtraPath(tmicName + ".xmd")
fnPosT = self._getExtraPath(tmicName + ".pos")
mdMicT = xmipp.MetaData(fnMicT)
mdPosT = xmipp.MetaData('particles@%s' % fnPosT)
mdPosT.merge(mdMicT)
mdTilted.unionAll(mdPosT)
# Write image metadatas (check if it is really necessary)
fnTilted = self._getExtraPath("images_tilted.xmd")
fnUntilted = self._getExtraPath("images_untilted.xmd")
mdUntilted.write(fnUntilted)
mdTilted.write(fnTilted)
# Create outputs SetOfParticles both for tilted and untilted
imgSetU = self._createSetOfParticles(suffix="Untilted")
imgSetU.copyInfo(self.uMics)
imgSetT = self._createSetOfParticles(suffix="Tilted")
imgSetT.copyInfo(self.tMics)
if self.downsampleType == OTHER:
imgSetU.setSamplingRate(self.samplingFinal)
imgSetT.setSamplingRate(self.samplingFinal)
imgSetU.setCoordinates(self.inputCoordinatesTiltedPairs.get().getUntilted())
imgSetT.setCoordinates(self.inputCoordinatesTiltedPairs.get().getTilted())
#Read untilted and tilted particles on a temporary object (also disabled particles)
imgSetAuxU = self._createSetOfParticles('auxU')
imgSetAuxU.copyInfo(imgSetU)
readSetOfParticles(fnUntilted, imgSetAuxU, removeDisabled=False)
imgSetAuxU.write()
imgSetAuxT = self._createSetOfParticles('auxT')
imgSetAuxT.copyInfo(imgSetT)
readSetOfParticles(fnTilted, imgSetAuxT, removeDisabled=False)
imgSetAuxT.write()
coordsT = self.inputCoordinatesTiltedPairs.get().getTilted()
# For each untilted particle retrieve micId from SetOFCoordinates untilted
for imgU, coordU in izip(imgSetAuxU, self.inputCoordinatesTiltedPairs.get().getUntilted()):
#FIXME: REmove this check when sure that objIds are equal
id = imgU.getObjId()
if id != coordU.getObjId():
raise Exception('ObjId in untilted is not equal!!!!')
imgT = imgSetAuxT[id]
coordT = coordsT[id]
#If both particles are enabled append them
if imgU.isEnabled() and imgT.isEnabled():
imgU.setCoordinate(coordU)
imgSetU.append(imgU)
imgT.setCoordinate(coordT)
imgSetT.append(imgT)
# For each untilted particle retrieve micId from SetOFCoordinates tilted
#for img in imgSetAuxU:
# for img, coord in izip(imgSetAuxT, self.inputCoordinatesTiltedPairs.get().getTilted()):
# #FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
# #FIXME: REmove this check when sure that objIds are equal
# if img.getObjId() != coord.getObjId():
# raise Exception('ObjId is not equal!!!!')
# #coord = self.inputCoordinatesTiltedPairs.get().getTilted()[img.getObjId()]
# img.setCoordinate(coord)
# #img.cleanObjId()
# imgSetT.append(img)
imgSetU.write()
imgSetT.write()
self._storeMethodsInfo(fnUntilted)
# Define output ParticlesTiltPair
outputset = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
outputset.setTilted(imgSetT)
outputset.setUntilted(imgSetU)
for imgU, imgT in izip(imgSetU, imgSetT):
outputset.append(TiltPair(imgU, imgT))
outputset.setCoordsPair(self.inputCoordinatesTiltedPairs.get())
self._defineOutputs(outputParticlesTiltPair=outputset)
self._defineSourceRelation(self.inputCoordinatesTiltedPairs, outputset)