def _createSubSetFromParticlesTiltPair(self, particlesTiltPair):
print 'create subset from particles tilt pair'
""" Create a subset of Micrographs Tilt Pair. """
output = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
inputU = particlesTiltPair.getUntilted()
inputT = particlesTiltPair.getTilted()
outputU = SetOfParticles(filename=self._getPath('particles_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('particles_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
modifiedSet = ParticlesTiltPair(filename=self._dbName, prefix=self._dbPrefix)
for pair, u, t in izip(modifiedSet, inputU, inputT):
if pair.isEnabled():
output.append(pair)
outputU.append(u)
outputT.append(t)
# Register outputs
output.setUntilted(outputU)
output.setTilted(outputT)
outputDict = {'outputParticlesTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(particlesTiltPair, output)
return output
def _createSubSetFromParticlesTiltPair(self, particlesTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = ParticlesTiltPair(
filename=self._getPath('particles_pairs.sqlite'))
inputU = particlesTiltPair.getUntilted()
inputT = particlesTiltPair.getTilted()
outputU = SetOfParticles(
filename=self._getPath('particles_untilted.sqlite'))
outputT = SetOfParticles(
filename=self._getPath('particles_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
modifiedSet = ParticlesTiltPair(filename=self._dbName,
prefix=self._dbPrefix)
for pair, u, t in izip(modifiedSet, inputU, inputT):
if pair.isEnabled():
output.append(pair)
outputU.append(u)
outputT.append(t)
# Register outputs
output.setUntilted(outputU)
output.setTilted(outputT)
outputDict = {'outputParticlesTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(particlesTiltPair, output)
return output
def _createSubSetFromParticlesTiltPair(self, particlesTiltPair):
print 'create subset from particles tilt pair'
""" Create a subset of Micrographs Tilt Pair. """
output = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
print "self._dbName=%s" % self._dbName
modifiedSet = ParticlesTiltPair(filename=self._dbName, prefix=self._dbPrefix)
for particlePairI in modifiedSet:
untilted = particlePairI.getUntilted()
tilted = particlePairI.getTilted()
if particlePairI.isEnabled():
micPairO = ParticlesTiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
# Register outputs
outputDict = {'outputParticlesTiltPair': output}
self._defineOutputs(**outputDict)
return output
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.getMicSampling() if self._micsOther(
) else self.getCoordSampling()
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.getCoords().getTilted()
# For each untilted particle retrieve micId from SetOfCoordinates untilted
for imgU, coordU in izip(imgSetAuxU, self.getCoords().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)
if self.doFlip:
imgSetU.setIsPhaseFlipped(self.ctfUntilt.hasValue())
imgSetU.setHasCTF(self.ctfUntilt.hasValue())
imgSetT.setIsPhaseFlipped(self.ctfTilt.hasValue())
imgSetT.setHasCTF(self.ctfTilt.hasValue())
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)
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)