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 createSetOfParticles(self, setPartSqliteName, partFn,
doCtf=False):
# create a set of particles
self.partSet = SetOfParticles(filename=setPartSqliteName)
self.partSet.setAlignment(ALIGN_PROJ)
self.partSet.setAcquisition(Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
self.partSet.setSamplingRate(samplingRate)
self.partSet.setHasCTF(True)
aList = [np.array(m) for m in mList]
#defocus=15000 + 5000* random.random()
for i, a in enumerate(aList):
p = Particle()
if doCtf:
defocusU = defocusList[i]#+500.
defocusV = defocusList[i]
ctf = CTFModel(defocusU=defocusU,
defocusV=defocusV,
defocusAngle=defocusAngle[i])
ctf.standardize()
p.setCTF(ctf)
p.setLocation(i + 1, partFn)
p.setTransform(Transform(a))
self.partSet.append(p)
self.partSet.write()
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 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 eliminationStep(self, fnInputMd):
self.inputImages = self.inputParticles.get()
partsFile = self.inputImages.getFileName()
self.partsSet = SetOfParticles(filename=partsFile)
self.partsSet.loadAllProperties()
self.streamClosed = self.partsSet.isStreamClosed()
if self.check == None:
writeSetOfParticles(self.partsSet,
fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation')
else:
writeSetOfParticles(self.partsSet,
fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation>"' + str(self.check) + '"')
for p in self.partsSet.iterItems(orderBy='creation', direction='DESC'):
self.check = p.getObjCreation()
break
self.partsSet.close()
self.lenPartsSet = len(self.partsSet)
print("os.path.exists(fnInputMd)): %s" % os.path.exists(fnInputMd))
args = "-i %s -o %s -e %s -t %f" % (
fnInputMd, self.fnOutputMd, self.fnElimMd, self.threshold.get())
if self.addFeatures:
args += " --addFeatures"
if self.useDenoising:
args += " --useDenoising -d %f" % self.denoising.get()
self.runJob("xmipp_image_eliminate_empty_particles", args)
cleanPath(fnInputMd)
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(filename=self._getPath('micrographs_pairs.sqlite'))
print "self._dbName=%s" % self._dbName
modifiedSet = MicrographsTiltPair(filename=self._dbName, prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
outputU.append(untilted)
outputT.append(tilted)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output
def _createCluster(self):
""" Create the cluster with the selected particles
from the cluster. This method will be called when
the button 'Create Cluster' is pressed.
"""
# Write the particles
prot = self.protocol
project = prot.getProject()
inputSet = prot.getInputParticles()
fnSqlite = prot._getTmpPath('cluster_particles.sqlite')
cleanPath(fnSqlite)
partSet = SetOfParticles(filename=fnSqlite)
partSet.copyInfo(inputSet)
for point in self.getData():
if point.getState() == Point.SELECTED:
particle = inputSet[point.getId()]
partSet.append(particle)
partSet.write()
partSet.close()
from protocol_batch_cluster import BatchProtNMACluster
newProt = project.newProtocol(BatchProtNMACluster)
clusterName = self.clusterWindow.getClusterName()
if clusterName:
newProt.setObjLabel(clusterName)
newProt.inputNmaDimred.set(prot)
newProt.sqliteFile.set(fnSqlite)
project.launchProtocol(newProt)
def getParticles(self, protImport, classid):
dbPartSet = protImport._getPath("particles_class-%d.sqlite" % classid)
class3D = protImport.outputClasses[classid]
if os.path.exists(dbPartSet):
os.remove(dbPartSet)
partSet = SetOfParticles(filename=dbPartSet)
partSet.copyInfo(class3D)
for part in class3D:
partSet.append(part)
partSet.write()
partSet.close()
protImportCls1 = self.newProtocol(
ProtImportParticles,
objLabel='particles class-%d' % classid,
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=dbPartSet,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImportCls1)
self.assertIsNotNone(protImportCls1.outputParticles.getFileName(),
"There was a problem with the import")
return protImportCls1
def test_particlesToStar(self):
fnSqlite = self.getFile('particles')
partSet = SetOfParticles(filename=fnSqlite)
for i, img in enumerate(partSet):
img.printAll()
if i > 10:
break
partSet.printAll()
def _loadInput(self):
partsFile = self.inputParticles.get().getFileName()
inPartsSet = SetOfParticles(filename=partsFile)
inPartsSet.loadAllProperties()
if self.check == None:
writeSetOfParticles(inPartsSet,
self.fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation')
else:
writeSetOfParticles(inPartsSet,
self.fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation>"' + str(self.check) + '"')
writeSetOfParticles(inPartsSet,
self.fnInputOldMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation<"' + str(self.check) + '"')
for p in inPartsSet.iterItems(orderBy='creation', direction='DESC'):
self.check = p.getObjCreation()
break
streamClosed = inPartsSet.isStreamClosed()
inputSize = inPartsSet.getSize()
inPartsSet.close()
return inputSize, streamClosed
def _createCluster(self):
""" Create the cluster with the selected particles
from the cluster. This method will be called when
the button 'Create Cluster' is pressed.
"""
# Write the particles
prot = self.protocol
project = prot.getProject()
inputSet = prot.getInputParticles()
fnSqlite = prot._getTmpPath('cluster_particles.sqlite')
cleanPath(fnSqlite)
partSet = SetOfParticles(filename=fnSqlite)
partSet.copyInfo(inputSet)
for point in self.getData():
if point.getState() == Point.SELECTED:
particle = inputSet[point.getId()]
partSet.append(particle)
partSet.write()
partSet.close()
from protocol_batch_cluster import BatchProtNMACluster
newProt = project.newProtocol(BatchProtNMACluster)
clusterName = self.clusterWindow.getClusterName()
if clusterName:
newProt.setObjLabel(clusterName)
newProt.inputNmaDimred.set(prot)
newProt.sqliteFile.set(fnSqlite)
project.launchProtocol(newProt)
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 loadInputs(self):
micsFn = self.getInputMicrographs().getFileName()
micsSet = SetOfMicrographs(filename=micsFn)
micsSet.loadAllProperties()
availableMics = []
for mic in micsSet:
availableMics.append(mic.getObjId())
micsSetClosed = micsSet.isStreamClosed()
micsSet.close()
partsFn = self.getInputParticles().getFileName()
partsSet = SetOfParticles(filename=partsFn)
partsSet.loadAllProperties()
newParts = []
newMics = []
for item in partsSet:
micKey = item.getCoordinate().getMicId()
if micKey not in self.micsDone and micKey in availableMics:
newParts.append(item.getObjId())
if not micKey in self.micsDone:
newMics.append(micKey)
self.micsDone += newMics
self.inputSize = partsSet.getSize()
partSetClosed = partsSet.isStreamClosed()
partsSet.close()
return newParts, micsSetClosed and partSetClosed
def loadAcquisitionInfo(self):
""" Return a dictionary with acquisition values and
the sampling rate information.
In the case of Xmipp, they are stored in files:
acquisition_info.xmd and microscope.xmd
"""
acquisitionDict = OrderedDict()
inputSet = SetOfParticles(filename=self._sqliteFile)
acquisitionDict['samplingRate'] = inputSet.getProperty('_samplingRate')
acquisitionDict['voltage'] = inputSet.getProperty('_acquisition._voltage')
acquisitionDict['amplitudeContrast'] = inputSet.getProperty('_acquisition._amplitudeContrast')
acquisitionDict['magnification'] = int(float(inputSet.getProperty('_acquisition._magnification')))
return acquisitionDict
def _checkProcessedData(self):
if self.setof == SET_OF_MOVIES:
objSet = SetOfMovies(filename=self._getPath('movies.sqlite'))
elif self.setof == SET_OF_MICROGRAPHS:
objSet = \
SetOfMicrographs(filename=self._getPath('micrographs.sqlite'))
elif self.setof == SET_OF_RANDOM_MICROGRAPHS:
objSet = \
SetOfMicrographs(filename=self._getPath('micrographs.sqlite'))
elif self.setof == SET_OF_PARTICLES:
objSet = SetOfParticles(filename=self._getPath('particles.sqlite'))
else:
raise Exception('Unknown data type')
newObjSet, newObj = self._checkNewItems(objSet)
if self.setof == SET_OF_MOVIES:
newObjSet.setFramesRange(self.inputMovies.get().getFramesRange())
# check if end ....
if self.setof != SET_OF_PARTICLES:
self.nDims = self.nDim.get()
endObjs = newObjSet.getSize() == self.nDims
if newObj:
if endObjs:
newObjSet.setStreamState(newObjSet.STREAM_CLOSED)
self._updateOutput(newObjSet)
newObjSet.close()
def retrieveTrainSets(self):
""" Retrieve, link and return a setOfParticles
corresponding to the NegativeTrain DeepConsensus trainning set
with certain extraction conditions (phaseFlip/invContrast)
"""
prefixYES = ''
prefixNO = 'no'
modelType = "negativeTrain_%sPhaseFlip_%sInvert.mrcs" % (
prefixYES if self.doInvert.get() else prefixNO,
prefixYES if self.ignoreCTF.get() else prefixNO)
modelPath = xmipp3.Plugin.getModel("deepConsensus", modelType)
print("Precompiled negative particles found at %s" % (modelPath))
modelFn = self._getTmpPath(modelType)
pwutils.createLink(modelPath, modelFn)
tmpSqliteSuff = "AddTrain"
partSet = self._createSetOfParticles(tmpSqliteSuff)
img = SetOfParticles.ITEM_TYPE()
imgh = ImageHandler()
_, _, _, n = imgh.getDimensions(modelFn)
if n > 1:
for index in range(1, n + 1):
img.cleanObjId()
img.setMicId(9999)
img.setFileName(modelFn)
img.setIndex(index)
partSet.append(img)
partSet.setAlignment(ALIGN_NONE)
cleanPath(self._getPath("particles%s.sqlite" % tmpSqliteSuff))
return partSet
def test_mrcsLink(self):
""" In this case just a link with .mrcs extension
should be created
"""
stackFile = self.dsEmx.getFile('particles/particles.mrc')
partSet = SetOfParticles(filename=':memory:')
for i in range(1, 10):
particle = Particle()
particle.setLocation(i, stackFile)
partSet.append(particle)
outputDir = self.getOutputPath()
filesDict = convertBinaryFiles(partSet, outputDir)
print filesDict
def test_mrcsLink(self):
""" In this case just a link with .mrcs extension
should be created
"""
stackFile = self.dsEmx.getFile('particles/particles.mrc')
partSet = SetOfParticles(filename=':memory:')
for i in range(1, 10):
particle = Particle()
particle.setLocation(i, stackFile)
partSet.append(particle)
outputDir = self.getOutputPath()
filesDict = convertBinaryFiles(partSet, outputDir)
print filesDict
def importParticles(self):
""" Import particles from a metadata 'images.xmd' """
inputSet = SetOfParticles(filename=self._sqliteFile)
inputSet.loadProperty('_alignment', ALIGN_NONE)
inputSet.loadProperty('_hasCtf', False)
self._findImagesPath(inputSet)
partSet = self.protocol._createSetOfParticles()
partSet.copyInfo(inputSet)
partSet.setObjComment('Particles imported from Scipion sqlite file:\n%s' % self._sqliteFile)
partSet.copyItems(inputSet, updateItemCallback=self._updateParticle)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self.protocol.setSamplingRate(partSet)
self.protocol.fillAcquisition(partSet.getAcquisition())
partSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol._defineOutputs(outputParticles=partSet)
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(
filename=self._getPath('micrographs_pairs.sqlite'))
modifiedSet = MicrographsTiltPair(filename=self._dbName,
prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(
filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
outputU.append(untilted)
outputT.append(tilted)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output
def test_particlesWithPhaseShiftToStar(self):
""" Write a SetOfParticles to Relion star input file. """
imgSet = SetOfParticles(filename=self.getOutputPath("particles_ph_sh.sqlite"))
n = 10
fn = self.getFile('particles_binary')
ctfs = [CTFModel(defocusU=10000, defocusV=15000,
defocusAngle=15, phaseShift=90),
CTFModel(defocusU=20000, defocusV=25000,
defocusAngle=25, phaseShift=60)
]
acquisition = Acquisition(magnification=60000, voltage=300,
sphericalAberration=2.,
amplitudeContrast=0.07)
imgSet.setAcquisition(acquisition)
coord = Coordinate()
coord.setMicId(1)
for i in range(n):
p = Particle()
p.setLocation(i + 1, fn)
ctf = ctfs[i % 2]
p.setCTF(ctf)
p.setAcquisition(acquisition)
p._xmipp_zScore = Float(i)
coord.setX(i * 10)
coord.setY(i * 10)
p.setCoordinate(coord)
imgSet.append(p)
fnStar = self.getOutputPath('particles_ph_sh.star')
fnStk = self.getOutputPath('particles.stk')
print (">>> Writing to file: %s" % fnStar)
relion.writeSetOfParticles(imgSet, fnStar, fnStk)
mdAll = md.MetaData(fnStar)
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_X))
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_Y))
self.assertFalse(mdAll.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE))
self.assertTrue(mdAll.containsLabel(md.RLN_CTF_PHASESHIFT))
def test_hdfToStk(self):
""" In this case the hdf stack files should be converted
to .stk spider files for Relion.
"""
stackFiles = ['BPV_1386_ptcls.hdf',
'BPV_1387_ptcls.hdf',
'BPV_1388_ptcls.hdf']
partSet = SetOfParticles(filename=':memory:')
for fn in stackFiles:
particle = Particle()
particle.setLocation(1, self.ds.getFile('particles/%s' % fn))
partSet.append(particle)
outputDir = self.getOutputPath()
filesDict = convertBinaryFiles(partSet, outputDir)
partSet.close()
print filesDict
def convertInputStep(self, imagesMd):
# It is unusual to create the output in the convertInputStep,
# but just to avoid reading twice the sqlite with particles
inputSet = self.inputNmaDimred.get().getInputParticles()
partSet = self._createSetOfParticles()
partSet.copyInfo(inputSet)
tmpSet = SetOfParticles(filename=self.sqliteFile.get())
partSet.appendFromImages(tmpSet)
# Register outputs
partSet.setAlignmentProj()
self._defineOutputs(outputParticles=partSet)
self._defineTransformRelation(inputSet, partSet)
writeSetOfParticles(partSet, imagesMd)
def loadAcquisitionInfo(self):
""" Return a dictionary with acquisition values and
the sampling rate information.
In the case of Scipion, these values will be read from the
'Properties' table of the particles.sqlite file.
"""
acq = OrderedDict()
inputSet = SetOfParticles(filename=self._sqliteFile)
def _get(key):
return inputSet.getProperty(key)
acq['samplingRate'] = _get('_samplingRate')
acq['voltage'] = _get('_acquisition._voltage')
acq['amplitudeContrast'] = _get('_acquisition._amplitudeContrast')
acq['sphericalAberration'] = float(
_get('_acquisition._sphericalAberration'))
return acq
def _checkNewInput(self):
# Check if there are new particles to process from the input set
partsFile = self.inputParticles.get().getFileName()
partsSet = SetOfParticles(filename=partsFile)
partsSet.loadAllProperties()
self.SetOfParticles = [m.clone() for m in partsSet]
self.streamClosed = partsSet.isStreamClosed()
partsSet.close()
partsSet = self._createSetOfParticles()
readSetOfParticles(self._getExtraPath("allDone.xmd"), partsSet)
newParts = any(m.getObjId() not in partsSet
for m in self.SetOfParticles)
outputStep = self._getFirstJoinStep()
if newParts:
fDeps = self._insertNewPartsSteps(self.insertedDict,
self.SetOfParticles)
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def _findPathAndCtf(self, warnings=True):
""" Find the relative path from which the micrographs exists
repect to the metadata location. Also check if it contains
CTF information and their relative root.
"""
inputSet = SetOfParticles(filename=self._sqliteFile)
inputSet.loadProperty('_alignment', ALIGN_NONE)
inputSet.loadProperty('_hasCtf', False)
particle = inputSet.getFirstItem()
self._imgPath = findRootFrom(self._sqliteFile, particle.getFileName())
if warnings and self._imgPath is None:
self.protocol.warning("Binary data was not found from metadata: %s" % self._sqliteFile)
return inputSet
def loadAcquisitionInfo(self):
""" Return a dictionary with acquisition values and
the sampling rate information.
In the case of Xmipp, they are stored in files:
acquisition_info.xmd and microscope.xmd
"""
acquisitionDict = OrderedDict()
inputSet = SetOfParticles(filename=self._sqliteFile)
acquisitionDict['samplingRate'] = inputSet.getProperty('_samplingRate')
acquisitionDict['voltage'] = inputSet.getProperty(
'_acquisition._voltage')
acquisitionDict['amplitudeContrast'] = inputSet.getProperty(
'_acquisition._amplitudeContrast')
acquisitionDict['magnification'] = int(
float(inputSet.getProperty('_acquisition._magnification')))
return acquisitionDict
def _allParticles(self, iterate=False):
# A handler function to iterate over the particles
inputSet = self.inputSet.get()
if self.isInputClasses():
iterParticles = inputSet.iterClassItems()
if iterate:
return iterParticles
else:
particles = SetOfParticles(filename=":memory:")
particles.copyInfo(inputSet.getFirstItem())
particles.copyItems(iterParticles)
return particles
else:
if iterate:
return inputSet.iterItems()
else:
return inputSet
def importParticles(self):
""" Import particles from a metadata 'images.xmd' """
inputSet = SetOfParticles(filename=self._sqliteFile)
inputSet.loadProperty('_alignment', ALIGN_NONE)
inputSet.loadProperty('_hasCtf', False)
self._findImagesPath(inputSet)
partSet = self.protocol._createSetOfParticles()
partSet.copyInfo(inputSet)
partSet.setObjComment(
'Particles imported from Scipion sqlite file:\n%s' %
self._sqliteFile)
partSet.copyItems(inputSet, updateItemCallback=self._updateParticle)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self.protocol.setSamplingRate(partSet)
self.protocol.fillAcquisition(partSet.getAcquisition())
partSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol._defineOutputs(outputParticles=partSet)
def aaatest_particlesToStar(self):
""" Write a SetOfParticles to Relion star input file. """
imgSet = SetOfParticles(
filename=self.getOutputPath("particles.sqlite"))
n = 10
fn = self.particles
ctfs = [
CTFModel(defocusU=10000, defocusV=15000, defocusAngle=15),
CTFModel(defocusU=20000, defocusV=25000, defocusAngle=25)
]
acquisition = Acquisition(magnification=60000,
voltage=300,
sphericalAberration=2.,
amplitudeContrast=0.07)
imgSet.setAcquisition(acquisition)
coord = Coordinate()
coord.setMicId(1)
for i in range(n):
p = Particle()
p.setLocation(i + 1, fn)
ctf = ctfs[i % 2]
p.setCTF(ctf)
p.setAcquisition(acquisition)
p._xmipp_zScore = Float(i)
coord.setX(i * 10)
coord.setY(i * 10)
p.setCoordinate(coord)
imgSet.append(p)
fnStar = self.getOutputPath('particles.star')
fnStk = self.getOutputPath('particles.stk')
print ">>> Writing to file: %s" % fnStar
relion.writeSetOfParticles(imgSet, fnStar, fnStk)
mdAll = md.MetaData(fnStar)
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_X))
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_Y))
self.assertFalse(mdAll.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE))
def test_hdfToStk(self):
""" In this case the hdf stack files should be converted
to .stk spider files for Relion.
"""
stackFiles = [
'BPV_1386_ptcls.hdf', 'BPV_1387_ptcls.hdf', 'BPV_1388_ptcls.hdf'
]
partSet = SetOfParticles(filename=':memory:')
for fn in stackFiles:
particle = Particle()
particle.setLocation(1, self.ds.getFile('particles/%s' % fn))
partSet.append(particle)
outputDir = self.getOutputPath()
filesDict = convertBinaryFiles(partSet, outputDir)
partSet.close()
print filesDict
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)
class TestSubProj(BaseTest):
@classmethod
def setUpClass(cls):
setupTestProject(cls)
def createSetOfParticles(self, setPartSqliteName, partFn,
doCtf=False):
# create a set of particles
self.partSet = SetOfParticles(filename=setPartSqliteName)
self.partSet.setAlignment(ALIGN_PROJ)
self.partSet.setAcquisition(Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
self.partSet.setSamplingRate(samplingRate)
self.partSet.setHasCTF(True)
aList = [np.array(m) for m in mList]
#defocus=15000 + 5000* random.random()
for i, a in enumerate(aList):
p = Particle()
if doCtf:
defocusU = defocusList[i]#+500.
defocusV = defocusList[i]
ctf = CTFModel(defocusU=defocusU,
defocusV=defocusV,
defocusAngle=defocusAngle[i])
ctf.standardize()
p.setCTF(ctf)
p.setLocation(i + 1, partFn)
p.setTransform(Transform(a))
self.partSet.append(p)
self.partSet.write()
def createProjection(self, proj, num, baseName):
img = xmipp.Image()
img.setDataType(xmipp.DT_FLOAT)
img.resize(projSize, projSize)
#img.initRandom(0., 1., xmipp.XMIPP_RND_GAUSSIAN)
img.initConstant(0.)
for coor in proj:
value = img.getPixel(coor[0], coor[1], coor[2], coor[3])
img.setPixel(coor[0], coor[1], coor[2], coor[3], coor[4]+value) # coor4 is the pixel value
img.write("%d@"%num + baseName)
def createVol(self, volume):
vol = xmipp.Image()
vol.setDataType(xmipp.DT_FLOAT)
vol.resize(projSize, projSize, projSize)
#vol.initRandom(0., .5, xmipp.XMIPP_RND_UNIFORM)
vol.initConstant(0.)
for coor in volume:
vol.setPixel(coor[0], coor[1], coor[2], coor[3], coor[4]) # coor4 is the pixel value
vol.write(self.volBaseFn)
def createMask(self, _maskName):
vol = xmipp.Image()
vol.setDataType(xmipp.DT_FLOAT)
vol.resize(projSize, projSize, projSize)
vol.initConstant(0.0)#ROB: not sure this is needed
halfDim = int(projSize/2)
maskRadius2 = maskRadius * maskRadius
for i in range(-halfDim,halfDim):
for j in range(-halfDim,halfDim):
for k in range(-halfDim,halfDim):
if(i*i+j*j+k*k) < maskRadius2:
vol.setPixel(0, k+halfDim, i+halfDim, j+halfDim, 1.) # coor4 is the pixel value
vol.write(_maskName)
def applyCTF(self, setPartMd):
writeSetOfParticles(self.partSet,setPartMd)
md1 = xmipp.MetaData()
md1.setColumnFormat(False)
idctf = md1.addObject()
_acquisition = self.partSet.getAcquisition()
for part in self.partSet:
baseFnCtf = self.proj.getTmpPath("kk")#self._getTmpPath("ctf_%d.param"%mic)
md1.setValue(xmipp.MDL_CTF_SAMPLING_RATE, samplingRate, idctf)
md1.setValue(xmipp.MDL_CTF_VOLTAGE, 200., idctf);
ctf = part.getCTF()
udefocus = ctf.getDefocusU()
vdefocus = ctf.getDefocusV()
angle = ctf.getDefocusAngle()
md1.setValue(xmipp.MDL_CTF_DEFOCUSU, udefocus, idctf);
md1.setValue(xmipp.MDL_CTF_DEFOCUSV, vdefocus, idctf);
md1.setValue(xmipp.MDL_CTF_DEFOCUS_ANGLE, 180.0 * random.random(), idctf);
md1.setValue(xmipp.MDL_CTF_CS, 2., idctf);
md1.setValue(xmipp.MDL_CTF_Q0, 0.07, idctf);
md1.setValue(xmipp.MDL_CTF_K, 1., idctf);
md1.write(baseFnCtf)
##writeSetOfParticles(self.partSet, setPartMd)
#apply ctf
args = " -i %s"%setPartMd
args += " -o %s"%self.proj.getTmpPath(setPartCtfName)
args += " -f ctf %s"%baseFnCtf
args += " --sampling %f"%samplingRate
runXmippProgram("xmipp_transform_filter", args)
args = " -i %s"%setPartMd
args += " -o %s"%self.proj.getTmpPath(setPartCtfPosName)
args += " -f ctfpos %s"%baseFnCtf
args += " --sampling %f"%samplingRate
runXmippProgram("xmipp_transform_filter", args)
def importData(self, baseFn, objLabel, protType, importFrom):
prot = self.newProtocol(protType,
objLabel=objLabel,
filesPath=baseFn,
maskPath=baseFn,
sqliteFile=baseFn,
haveDataBeenPhaseFlipped=False,
magnification=10000,
samplingRate=samplingRate,
importFrom=importFrom
)
self.launchProtocol(prot)
return prot
def test_pattern(self):
#1) create fake protocol so I have a place to save data
#prot = self.launchFakeProtocol()
#output stack
self.setPartName = self.proj.getTmpPath(setPartName)
self.setPartSqliteName = self.proj.getTmpPath(setPartSqliteName)
self.setPartSqliteCtfName = self.proj.getTmpPath(setPartSqliteCtfName)
self.setPartSqliteCTfPosName = self.proj.getTmpPath(setPartSqliteCTfPosName)
self.kksqlite = self.proj.getTmpPath("kk.sqlite")
self.setPartMd = self.proj.getTmpPath(setPartNameMd)
self.volBaseFn = self.proj.getTmpPath(volName)
self.maskName = self.proj.getTmpPath(maskName)
#2) create projections and sets of particles
self.createProjection(proj1, 1, self.setPartName)
self.createProjection(proj2, 2, self.setPartName)
self.createProjection(proj3, 3, self.setPartName)
self.createSetOfParticles(self.setPartSqliteCTfPosName, self.proj.getTmpPath(setPartCtfPosName), True)
self.createSetOfParticles(self.setPartSqliteCtfName, self.proj.getTmpPath(setPartCtfName), True)
self.createSetOfParticles(self.setPartSqliteName, self.setPartName, False)
#create auxiliary setofparticles
self.createSetOfParticles(self.kksqlite, self.setPartName, True)
#4) apply CTF
self.applyCTF(self.setPartMd)
#5) create volume
self.createVol(vol1)
#6) create mask
self.createMask(self.maskName)
#import three projection datasets, volume and mask
protPlainProj = self.importData(self.setPartSqliteName, "plain projection",
ProtImportParticles,
ProtImportParticles.IMPORT_FROM_SCIPION)
protCTFProj = self.importData(self.setPartSqliteCtfName,"ctf projection",
ProtImportParticles,
ProtImportParticles.IMPORT_FROM_SCIPION)
protCTFposProj = self.importData(self.setPartSqliteCTfPosName, "pos ctf projection",
ProtImportParticles,
ProtImportParticles.IMPORT_FROM_SCIPION)
_protImportVol = self.importData(os.path.abspath(self.proj.getTmpPath(volName)), "3D reference",
ProtImportVolumes,
ProtImportParticles.IMPORT_FROM_FILES)
_protImportMask = self.importData(self.proj.getTmpPath(maskName), "3D mask",
ProtImportMask,
ProtImportParticles.IMPORT_FROM_FILES)
mask = VolumeMask()
mask.setFileName(self.proj.getTmpPath(maskName))
mask.setSamplingRate(samplingRate)
#launch substract protocol <<<<<<<<<<<<<<<<<<<<<<<<<<
protSubtract = self.newProtocol(XmippProtSubtractProjection)
protSubtract.inputParticles.set(protPlainProj.outputParticles)
protSubtract.inputVolume.set(_protImportVol.outputVolume)
protSubtract.refMask.set(_protImportMask.outputMask)
protSubtract.projType.set(XmippProtSubtractProjection.CORRECT_NONE)
self.launchProtocol(protSubtract)
protSubtractCTF = self.newProtocol(XmippProtSubtractProjection)
protSubtractCTF.inputParticles.set(protCTFProj.outputParticles)
protSubtractCTF.inputVolume.set(_protImportVol.outputVolume)
protSubtractCTF.refMask.set(_protImportMask.outputMask)
protSubtractCTF.projType.set(XmippProtSubtractProjection.CORRECT_FULL_CTF)
self.launchProtocol(protSubtractCTF)
protSubtractCTFpos = self.newProtocol(XmippProtSubtractProjection)
protSubtractCTFpos.inputParticles.set(protCTFposProj.outputParticles)
protSubtractCTFpos.inputVolume.set(_protImportVol.outputVolume)
protSubtractCTFpos.refMask.set(_protImportMask.outputMask)
protSubtractCTFpos.projType.set(XmippProtSubtractProjection.CORRECT_PHASE_FLIP)
self.launchProtocol(protSubtractCTFpos)
protSubtractCTFRelion = self.newProtocol(ProtRelionSubtract)
protSubtractCTFRelion.inputParticles.set(protCTFProj.outputParticles)
protSubtractCTFRelion.inputVolume.set(_protImportVol.outputVolume)
self.launchProtocol(protSubtractCTFRelion)
self.assertIsNotNone(protSubtract.outputParticles, "There was a problem with subtract projection")
self.assertTrue(True)
def testOrderBy(self):
""" create set of particles and orderby a given attribute
"""
# This function was written by Roberto. It does things
# differently, so let's keep it for reference.
#create set of particles
inFileNameMetadata = self.proj.getTmpPath('particlesOrderBy.sqlite')
inFileNameData = self.proj.getTmpPath('particlesOrderBy.stk')
imgSet = SetOfParticles(filename=inFileNameMetadata)
imgSet.setSamplingRate(1.5)
acq = Acquisition()
acq.setAmplitudeContrast(0.1)
acq.setMagnification(10000)
acq.setVoltage(200)
acq.setSphericalAberration(2.0)
imgSet.setAcquisition(acq)
img = Particle()
for i in range(1, 10):
img.setLocation(i, inFileNameData)
img.setMicId(i%3)
img.setClassId(i%5)
imgSet.append(img)
img.cleanObjId()
imgSet.write()
#now import the dataset
prot1 = self.newProtocol(ProtImportParticles,
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata,
magnification=10000,
samplingRate=1.5
)
prot1.setObjLabel('from sqlite (test-sets)')
self.launchProtocol(prot1)
if prot1.outputParticles is None:
raise Exception('Import of images: %s, failed. outputParticles is None.' % inFileNameMetadata)
protSplitSet = self.newProtocol(ProtSplitSet,
inputSet=prot1.outputParticles,
numberOfSets=2,
randomize=True)
self.launchProtocol(protSplitSet)
inputSets = [protSplitSet.outputParticles01,protSplitSet.outputParticles02]
outputSet = SetOfParticles(filename=self.proj.getTmpPath('gold.sqlite'))
for itemSet in inputSets:
for obj in itemSet:
outputSet.append(obj)
for item1, item2 in izip(imgSet, outputSet):
if not item1.equalAttributes(item2):
print "Items differ:"
prettyDict(item1.getObjDict())
prettyDict(item2.getObjDict())
self.assertTrue(item1.equalAttributes(item2), )
def testMergeDifferentAttrs(self):
""" Test merge from subsets with different attritubes.
That is, M1(a,b,c) U M2(a,b,c,d)"""
#create two set of particles
inFileNameMetadata1 = self.proj.getTmpPath('particles11.sqlite')
inFileNameMetadata2 = self.proj.getTmpPath('particles22.sqlite')
imgSet1 = SetOfParticles(filename=inFileNameMetadata1)
imgSet2 = SetOfParticles(filename=inFileNameMetadata2)
inFileNameData = self.proj.getTmpPath('particles.stk')
img1 = Particle()
img2 = Particle()
attrb1 = [11, 12, 13, 14]
attrb2 = [21, 22, 23, 24]
attrb3 = [31, 32]
counter = 0
for i in range(1, 3):
img1.cleanObjId()
img1.setLocation(i, inFileNameData)
img1.setMicId(i % 3)
img1.setClassId(i % 5)
img1.setSamplingRate(1.)
img1._attrb1 = Float(attrb1[counter])
img1._attrb2 = Float(attrb2[counter])
img1._attrb3 = Float(attrb3[counter])
imgSet1.append(img1)
counter += 1
for i in range(1, 3):
img2.cleanObjId()
img2.setLocation(i, inFileNameData)
img2.setClassId(i % 5)
img2.setMicId(i % 3)
img2.setSamplingRate(2.)
img2._attrb1 = Float(attrb1[counter])
img2._attrb2 = Float(attrb2[counter])
imgSet2.append(img2)
counter += 1
imgSet1.write()
imgSet2.write()
#import them
protImport1 = self.newProtocol(
ProtImportParticles,
objLabel='import set1',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata1,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImport1)
protImport2 = self.newProtocol(
ProtImportParticles,
objLabel='import set2',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata2,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImport2)
#create merge protocol
p_union = self.newProtocol(ProtUnionSet,
objLabel='join diff column order',
ignoreExtraAttributes=True)
p_union.inputSets.append(protImport1.outputParticles)
p_union.inputSets.append(protImport2.outputParticles)
self.proj.launchProtocol(p_union, wait=True)
#assert
counter = 0
for img in p_union.outputSet:
self.assertAlmostEqual(attrb1[counter], img._attrb1, 4)
self.assertAlmostEqual(attrb2[counter], img._attrb2, 4)
if hasattr(img, '_attrb3'):
self.assertTrue(False, "join should not have attrb3")
if not hasattr(img, '_attrb2'):
self.assertTrue(False, "join should have attrb2")
counter += 1
def testMergeAlternateColumn(self):
"""Test that the union operation works as expected.
Even if the order of the columns do not match.
That is, M1(a,b,c) U M2(a,c,b)"""
#create two set of particles
inFileNameMetadata1 = self.proj.getTmpPath('particles1.sqlite')
inFileNameMetadata2 = self.proj.getTmpPath('particles2.sqlite')
imgSet1 = SetOfParticles(filename=inFileNameMetadata1)
imgSet2 = SetOfParticles(filename=inFileNameMetadata2)
inFileNameData = self.proj.getTmpPath('particles.stk')
img1 = Particle()
img2 = Particle()
attrb1 = [11, 12, 13, 14]
attrb2 = [21, 22, 23, 24]
counter = 0
for i in range(1, 3):
img1.cleanObjId()
img1.setLocation(i, inFileNameData)
img1.setMicId(i % 3)
img1.setClassId(i % 5)
img1.setSamplingRate(1.)
img1._attrb1 = Float(attrb1[counter])
img1._attrb2 = Float(attrb2[counter])
imgSet1.append(img1)
counter +=1
for i in range(1, 3):
img2.cleanObjId()
img2.setLocation(i, inFileNameData)
img2.setClassId(i % 5)
img2.setMicId(i % 3)
img2.setSamplingRate(2.)
img2._attrb1= Float(attrb1[counter])
img2._attrb2= Float(attrb2[counter])
imgSet2.append(img2)
counter +=1
imgSet1.write()
imgSet2.write()
#import them
protImport1 = self.newProtocol(ProtImportParticles,
objLabel='import set1',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata1,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True
)
self.launchProtocol(protImport1)
protImport2 = self.newProtocol(ProtImportParticles,
objLabel='import set2',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata2,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True
)
self.launchProtocol(protImport2)
#create merge protocol
p_union = self.newProtocol(ProtUnionSet,
objLabel='join diff column order',
ignoreExtraAttributes=True)
p_union.inputSets.append(protImport1.outputParticles)
p_union.inputSets.append(protImport2.outputParticles)
self.proj.launchProtocol(p_union, wait=True)
#assert
counter=0
for img in p_union.outputSet:
self.assertAlmostEqual(attrb1[counter],img._attrb1,4)
self.assertAlmostEqual(attrb2[counter],img._attrb2,4)
counter += 1
def testOrderBy(self):
""" create set of particles and orderby a given attribute
"""
# This function was written by Roberto. It does things
# differently, so let's keep it for reference.
#create set of particles
inFileNameMetadata = self.proj.getTmpPath('particlesOrderBy.sqlite')
inFileNameData = self.proj.getTmpPath('particlesOrderBy.stk')
imgSet = SetOfParticles(filename=inFileNameMetadata)
imgSet.setSamplingRate(1.5)
acq = Acquisition()
acq.setAmplitudeContrast(0.1)
acq.setMagnification(10000)
acq.setVoltage(200)
acq.setSphericalAberration(2.0)
imgSet.setAcquisition(acq)
img = Particle()
for i in range(1, 10):
img.setLocation(i, inFileNameData)
img.setMicId(i % 3)
img.setClassId(i % 5)
imgSet.append(img)
img.cleanObjId()
imgSet.write()
#now import the dataset
prot1 = self.newProtocol(
ProtImportParticles,
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata,
magnification=10000,
samplingRate=1.5)
prot1.setObjLabel('from sqlite (test-sets)')
self.launchProtocol(prot1)
if prot1.outputParticles is None:
raise Exception(
'Import of images: %s, failed. outputParticles is None.' %
inFileNameMetadata)
protSplitSet = self.newProtocol(ProtSplitSet,
inputSet=prot1.outputParticles,
numberOfSets=2,
randomize=True)
self.launchProtocol(protSplitSet)
inputSets = [
protSplitSet.outputParticles01, protSplitSet.outputParticles02
]
outputSet = SetOfParticles(
filename=self.proj.getTmpPath('gold.sqlite'))
for itemSet in inputSets:
for obj in itemSet:
outputSet.append(obj)
for item1, item2 in izip(imgSet, outputSet):
if not item1.equalAttributes(item2):
print "Items differ:"
prettyDict(item1.getObjDict())
prettyDict(item2.getObjDict())
self.assertTrue(item1.equalAttributes(item2), )
def testMergeDifferentAttrs(self):
""" Test merge from subsets with different attritubes.
That is, M1(a,b,c) U M2(a,b,c,d)"""
#create two set of particles
inFileNameMetadata1 = self.proj.getTmpPath('particles11.sqlite')
inFileNameMetadata2 = self.proj.getTmpPath('particles22.sqlite')
imgSet1 = SetOfParticles(filename=inFileNameMetadata1)
imgSet2 = SetOfParticles(filename=inFileNameMetadata2)
inFileNameData = self.proj.getTmpPath('particles.stk')
img1 = Particle()
img2 = Particle()
attrb1 = [11, 12, 13, 14]
attrb2 = [21, 22, 23, 24]
attrb3 = [31, 32]
counter = 0
# Test the join handles different attributes at a second level
ctf1 = CTFModel(defocusU=1000, defocusV=1000, defocusAngle=0)
ctf2 = CTFModel(defocusU=2000, defocusV=2000, defocusAngle=0)
ctf2._myOwnQuality = Float(1.)
img1.setCTF(ctf1)
img2.setCTF(ctf2)
for i in range(1, 3):
img1.cleanObjId()
img1.setLocation(i, inFileNameData)
img1.setMicId(i % 3)
img1.setClassId(i % 5)
img1.setSamplingRate(1.)
img1._attrb1 = Float(attrb1[counter])
img1._attrb2 = Float(attrb2[counter])
img1._attrb3 = Float(attrb3[counter])
imgSet1.append(img1)
counter += 1
for i in range(1, 3):
img2.cleanObjId()
img2.setLocation(i, inFileNameData)
img2.setClassId(i % 5)
img2.setMicId(i % 3)
img2.setSamplingRate(2.)
img2._attrb1 = Float(attrb1[counter])
img2._attrb2 = Float(attrb2[counter])
imgSet2.append(img2)
counter += 1
imgSet1.write()
imgSet2.write()
#import them
protImport1 = self.newProtocol(
ProtImportParticles,
objLabel='import set1',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata1,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImport1)
protImport2 = self.newProtocol(
ProtImportParticles,
objLabel='import set2',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata2,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImport2)
#create merge protocol
p_union = self.newProtocol(ProtUnionSet,
objLabel='join different attrs',
ignoreExtraAttributes=True)
p_union.inputSets.append(protImport1.outputParticles)
p_union.inputSets.append(protImport2.outputParticles)
self.proj.launchProtocol(p_union, wait=True)
counter = 0
for img in p_union.outputSet:
self.assertAlmostEqual(attrb1[counter], img._attrb1, 4)
self.assertAlmostEqual(attrb2[counter], img._attrb2, 4)
self.assertFalse(hasattr(img, '_attrb3'),
"join should not have attrb3")
self.assertTrue(hasattr(img, '_attrb2'), "join should have attrb2")
ctf = img.getCTF()
self.assertIsNotNone(ctf, "Image should have CTF after join")
self.assertFalse(hasattr(ctf, '_myOwnQuality'),
"CTF should not have non common attributes")
counter += 1
def testMergeAlternateColumn(self):
"""Test that the union operation works as expected.
Even if the order of the columns do not match.
That is, M1(a,b,c) U M2(a,c,b)"""
#create two set of particles
inFileNameMetadata1 = self.proj.getTmpPath('particles1.sqlite')
inFileNameMetadata2 = self.proj.getTmpPath('particles2.sqlite')
imgSet1 = SetOfParticles(filename=inFileNameMetadata1)
imgSet2 = SetOfParticles(filename=inFileNameMetadata2)
inFileNameData = self.proj.getTmpPath('particles.stk')
img1 = Particle()
img2 = Particle()
attrb1 = [11, 12, 13, 14]
attrb2 = [21, 22, 23, 24]
counter = 0
for i in range(1, 3):
img1.cleanObjId()
img1.setLocation(i, inFileNameData)
img1.setMicId(i % 3)
img1.setClassId(i % 5)
img1.setSamplingRate(1.)
img1._attrb1 = Float(attrb1[counter])
img1._attrb2 = Float(attrb2[counter])
imgSet1.append(img1)
counter += 1
for i in range(1, 3):
img2.cleanObjId()
img2.setLocation(i, inFileNameData)
img2.setClassId(i % 5)
img2.setMicId(i % 3)
img2.setSamplingRate(2.)
img2._attrb1 = Float(attrb1[counter])
img2._attrb2 = Float(attrb2[counter])
imgSet2.append(img2)
counter += 1
imgSet1.write()
imgSet2.write()
#import them
protImport1 = self.newProtocol(
ProtImportParticles,
objLabel='import set1',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata1,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImport1)
protImport2 = self.newProtocol(
ProtImportParticles,
objLabel='import set2',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata2,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImport2)
#create merge protocol
p_union = self.newProtocol(ProtUnionSet,
objLabel='join diff column order',
ignoreExtraAttributes=True)
p_union.inputSets.append(protImport1.outputParticles)
p_union.inputSets.append(protImport2.outputParticles)
self.proj.launchProtocol(p_union, wait=True)
#assert
counter = 0
for img in p_union.outputSet:
self.assertAlmostEqual(attrb1[counter], img._attrb1, 4)
self.assertAlmostEqual(attrb2[counter], img._attrb2, 4)
counter += 1
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 testMergeDifferentAttrs(self):
""" Test merge from subsets with different attritubes.
That is, M1(a,b,c) U M2(a,b,c,d)"""
#create two set of particles
inFileNameMetadata1 = self.proj.getTmpPath('particles11.sqlite')
inFileNameMetadata2 = self.proj.getTmpPath('particles22.sqlite')
imgSet1 = SetOfParticles(filename=inFileNameMetadata1)
imgSet2 = SetOfParticles(filename=inFileNameMetadata2)
inFileNameData = self.proj.getTmpPath('particles.stk')
img1 = Particle()
img2 = Particle()
attrb1 = [11, 12, 13, 14]
attrb2 = [21, 22, 23, 24]
attrb3 = [31, 32]
counter = 0
# Test the join handles different attributes at a second level
ctf1 = CTFModel(defocusU=1000, defocusV=1000, defocusAngle=0)
ctf2 = CTFModel(defocusU=2000, defocusV=2000, defocusAngle=0)
ctf2._myOwnQuality = Float(1.)
img1.setCTF(ctf1)
img2.setCTF(ctf2)
for i in range(1, 3):
img1.cleanObjId()
img1.setLocation(i, inFileNameData)
img1.setMicId(i % 3)
img1.setClassId(i % 5)
img1.setSamplingRate(1.)
img1._attrb1 = Float(attrb1[counter])
img1._attrb2 = Float(attrb2[counter])
img1._attrb3 = Float(attrb3[counter])
imgSet1.append(img1)
counter += 1
for i in range(1, 3):
img2.cleanObjId()
img2.setLocation(i, inFileNameData)
img2.setClassId(i % 5)
img2.setMicId(i % 3)
img2.setSamplingRate(2.)
img2._attrb1 = Float(attrb1[counter])
img2._attrb2 = Float(attrb2[counter])
imgSet2.append(img2)
counter +=1
imgSet1.write()
imgSet2.write()
#import them
protImport1 = self.newProtocol(ProtImportParticles,
objLabel='import set1',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata1,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True
)
self.launchProtocol(protImport1)
protImport2 = self.newProtocol(ProtImportParticles,
objLabel='import set2',
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=inFileNameMetadata2,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True
)
self.launchProtocol(protImport2)
#create merge protocol
p_union = self.newProtocol(ProtUnionSet,
objLabel='join different attrs',
ignoreExtraAttributes=True)
p_union.inputSets.append(protImport1.outputParticles)
p_union.inputSets.append(protImport2.outputParticles)
self.proj.launchProtocol(p_union, wait=True)
counter = 0
for img in p_union.outputSet:
self.assertAlmostEqual(attrb1[counter], img._attrb1, 4)
self.assertAlmostEqual(attrb2[counter], img._attrb2, 4)
self.assertFalse(hasattr(img, '_attrb3'),
"join should not have attrb3")
self.assertTrue(hasattr(img, '_attrb2'),
"join should have attrb2")
ctf = img.getCTF()
self.assertIsNotNone(ctf, "Image should have CTF after join")
self.assertFalse(hasattr(ctf, '_myOwnQuality'),
"CTF should not have non common attributes")
counter += 1
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
give the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print "\n"
print "*" * 80
print "* Launching test: ", fileKey
print "*" * 80
is2D = alignType == ALIGN_2D
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile(fileKey + '_Gold_output.vol')
if PRINT_FILES:
print "BINARY DATA: ", stackFn
print "SET1: ", partFn1
print " MD: ", mdFn
print "SET2: ", partFn2
print "OUTPUT: ", outputFn
print "GOLD: ", goldFn
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
partSet.setAcquisition(
Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [numpy.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print "Parset", partFn1
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.writeSetOfParticles(partSet,
mdFn,
"/tmp",
alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
relion.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
relion.readSetOfVolumes(mdFn, partSet2, alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print "-" * 5
print img.getFileName(), img.getIndex()
print 'm1:\n', m1, relion.geometryFromMatrix(m1, False)
print 'm2:\n', m2, relion.geometryFromMatrix(m2, False)
# self.assertTrue(numpy.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
give the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print ("\n")
print ("*" * 80)
print ("* Launching test: ", fileKey)
print ("*" * 80)
is2D = alignType == ALIGN_2D
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile(fileKey + '_Gold_output.vol')
if PRINT_FILES:
print("BINARY DATA: ", stackFn)
print("SET1: ", partFn1)
print(" MD: ", mdFn)
print("SET2: ", partFn2)
print("OUTPUT: ", outputFn)
print("GOLD: ", goldFn)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
partSet.setAcquisition(Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [numpy.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print ("Parset", partFn1)
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.writeSetOfParticles(partSet, mdFn,"/tmp", alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
relion.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
relion.readSetOfVolumes(mdFn, partSet2, alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print ("-" * 5)
print (img.getFileName(), img.getIndex())
print ('m1:\n', m1, relion.geometryFromMatrix(m1, False))
print ('m2:\n', m2, relion.geometryFromMatrix(m2, False))
# self.assertTrue(numpy.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))
class XmippProtEliminateEmptyParticles(XmippProtEliminateEmptyBase):
""" Takes a set of particles and using statistical methods
(variance of variances of sub-parts of input image) eliminates those samples,
where there is no object/particle (only noise is presented there).
Threshold parameter can be used for fine-tuning the algorithm for type of data.
"""
_label = 'eliminate empty particles'
def __init__(self, **args):
XmippProtEliminateEmptyBase.__init__(self, **args)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label=Message.LABEL_INPUT)
# - - - F O R P A R T I C L E S - - -
form.addParam('inputParticles',
param.PointerParam,
important=True,
label="Input particles",
pointerClass='SetOfParticles',
help='Select the input particles to be classified.')
form.addParam('threshold',
param.FloatParam,
default=1.1,
label='Threshold used in elimination:',
help='Higher threshold => more particles will be '
'eliminated. Set to -1 for no elimination, even so '
'the "xmipp_scoreEmptiness" value will be attached to '
'every paricle for a posterior inspection.')
self.addAdvancedParams(form)
# --------------------------- INSERT steps functions ----------------------
def _checkNewInput(self):
# Check if there are new particles to process from the input set
partsFile = self.inputParticles.get().getFileName()
self.lastCheck = getattr(self, 'lastCheck', datetime.now())
mTime = datetime.fromtimestamp(os.path.getmtime(partsFile))
# If the input movies.sqlite have not changed since our last check,
# it does not make sense to check for new input data
if self.lastCheck > mTime:
return None
self.lastCheck = datetime.now()
outputStep = self._getFirstJoinStep()
fDeps = self._insertNewPartsSteps()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def eliminationStep(self, fnInputMd):
self.inputImages = self.inputParticles.get()
partsFile = self.inputImages.getFileName()
self.partsSet = SetOfParticles(filename=partsFile)
self.partsSet.loadAllProperties()
self.streamClosed = self.partsSet.isStreamClosed()
if self.check == None:
writeSetOfParticles(self.partsSet,
fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation')
else:
writeSetOfParticles(self.partsSet,
fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation>"' + str(self.check) + '"')
for p in self.partsSet.iterItems(orderBy='creation', direction='DESC'):
self.check = p.getObjCreation()
break
self.partsSet.close()
self.lenPartsSet = len(self.partsSet)
print("os.path.exists(fnInputMd)): %s" % os.path.exists(fnInputMd))
args = "-i %s -o %s -e %s -t %f" % (
fnInputMd, self.fnOutputMd, self.fnElimMd, self.threshold.get())
if self.addFeatures:
args += " --addFeatures"
if self.useDenoising:
args += " --useDenoising -d %f" % self.denoising.get()
self.runJob("xmipp_image_eliminate_empty_particles", args)
cleanPath(fnInputMd)
def createOutputs(self):
streamMode = Set.STREAM_CLOSED if getattr(self, 'finished', False) \
else Set.STREAM_OPEN
def updateOutputs(mdFn, suffix):
newData = os.path.exists(mdFn)
lastToClose = getattr(self, 'finished', False) and \
hasattr(self, '%sParticles'%suffix)
if newData or lastToClose:
outSet = self._loadOutputSet(em.SetOfParticles,
'%sParticles.sqlite' % suffix)
if newData:
partsSet = self._createSetOfParticles("AUX")
readSetOfParticles(mdFn, partsSet)
outSet.copyItems(partsSet,
updateItemCallback=self._updateParticle,
itemDataIterator=md.iterRows(
mdFn, sortByLabel=md.MDL_ITEM_ID))
self.outputSize = self.outputSize + len(partsSet)
self._updateOutputSet('%sParticles' % suffix, outSet,
streamMode)
cleanPath(mdFn)
updateOutputs(self.fnOutMdTmp, 'output')
updateOutputs(self.fnElimMdTmp, 'eliminated')
def getInput(self):
return self.inputParticles.get()
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 _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