def readPartsFromMics(self, micList, outputParts): """ Read the particles extract for the given list of micrographs and update the outputParts set with new items. """ p = Particle() for mic in micList: # We need to make this dict because there is no ID in the .xmd file coordDict = {} for coord in self.coordDict[mic.getObjId()]: pos = self._getPos(coord) if pos in coordDict: print( "WARNING: Ignoring duplicated coordinate: %s, id=%s" % (coord.getObjId(), pos)) coordDict[pos] = coord added = set() # Keep track of added coords to avoid duplicates for row in md.iterRows(self._getMicXmd(mic)): pos = (row.getValue(md.MDL_XCOOR), row.getValue(md.MDL_YCOOR)) coord = coordDict.get(pos, None) if coord is not None and coord.getObjId() not in added: # scale the coordinates according to particles dimension. coord.scale(self.getBoxScale()) p.copyObjId(coord) p.setLocation(xmippToLocation(row.getValue(md.MDL_IMAGE))) p.setCoordinate(coord) p.setMicId(mic.getObjId()) p.setCTF(mic.getCTF()) # adding the variance and Gini coeff. value of the mic zone setXmippAttributes(p, row, md.MDL_SCORE_BY_VAR) setXmippAttributes(p, row, md.MDL_SCORE_BY_GINI) if row.containsLabel(md.MDL_ZSCORE_DEEPLEARNING1): setXmippAttributes(p, row, md.MDL_ZSCORE_DEEPLEARNING1) # disabled particles (in metadata) should not add to the # final set if row.getValue(md.MDL_ENABLED) > 0: outputParts.append(p) added.add(coord.getObjId()) # Release the list of coordinates for this micrograph since it # will not be longer needed del self.coordDict[mic.getObjId()]
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_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 _particlesFromEmx(protocol, emxData, emxFile, outputDir, acquisition, samplingRate, copyOrLink, alignType=ALIGN_NONE): """ Create the output SetOfCoordinates or SetOfParticles given an EMXData object. Add CTF information to the particles if present. """ emxParticle = emxData.getFirstObject(emxlib.PARTICLE) partDir = dirname(emxFile) micSet = getattr(protocol, 'outputMicrographs', None) if emxParticle is not None: # Check if there are particles or coordinates fn = emxParticle.get(emxlib.FILENAME) if exists(join( partDir, fn)): # if the particles has binary data, means particles case partSet = protocol._createSetOfParticles() partSet.setAcquisition( acquisition) # this adquisition is per project #we need one per particle part = Particle() if _hasCtfLabels(emxParticle) or _hasCtfLabels( emxParticle.getMicrograph()): part.setCTF(CTFModel()) partSet.setHasCTF(True) if emxParticle.has('centerCoord__X'): part.setCoordinate(Coordinate()) #if emxParticle.has('transformationMatrix__t11'): # _particleFromEmx(emxParticle, part) # #partSet.setAlignment3D() # partSet.setAlignment(alignType) #else: # partSet.setAlignment(alignType) partSet.setAlignment(alignType) if not samplingRate: samplingRate = part.getSamplingRate() partSet.setSamplingRate(samplingRate) partSet.setIsPhaseFlipped(protocol.haveDataBeenPhaseFlipped.get()) particles = True else: # if not binary data, the coordinate case if micSet is None: raise Exception( 'Could not import Coordinates from EMX, micrographs not imported.' ) partSet = protocol._createSetOfCoordinates(micSet) part = Coordinate() particles = False copiedFiles = {} # copied or linked for emxParticle in emxData.iterClasses(emxlib.PARTICLE): if particles: _particleFromEmx(emxParticle, part) i, fn = part.getLocation() partFn = join(partDir, fn) newFn = join(outputDir, basename(partFn)) newLoc = (i, newFn) if not partFn in copiedFiles: copyOrLink(partFn, newFn) copiedFiles[partFn] = newFn part.setLocation(newLoc) if partSet.hasAlignment(): transform = Transform() _transformFromEmx(emxParticle, part, transform, alignType) part.setTransform(transform) else: _coordinateFromEmx(emxParticle, part) partSet.append(part) part.cleanObjId() if particles: protocol._defineOutputs(outputParticles=partSet) else: protocol._defineOutputs(outputCoordinates=partSet) if micSet is not None: protocol._defineSourceRelation(protocol.outputMicrographs, partSet)
def _particlesFromEmx(protocol , emxData , emxFile , outputDir , acquisition , samplingRate , copyOrLink , alignType=ALIGN_NONE): """ Create the output SetOfCoordinates or SetOfParticles given an EMXData object. Add CTF information to the particles if present. """ emxParticle = emxData.getFirstObject(emxlib.PARTICLE) partDir = dirname(emxFile) micSet = getattr(protocol, 'outputMicrographs', None) if emxParticle is not None: # Check if there are particles or coordinates fn = emxParticle.get(emxlib.FILENAME) if exists(join(partDir, fn)): # if the particles has binary data, means particles case partSet = protocol._createSetOfParticles() partSet.setAcquisition(acquisition)# this adquisition is per project #we need one per particle part = Particle() if _hasCtfLabels(emxParticle) or _hasCtfLabels(emxParticle.getMicrograph()): part.setCTF(CTFModel()) partSet.setHasCTF(True) if emxParticle.has('centerCoord__X'): part.setCoordinate(Coordinate()) #if emxParticle.has('transformationMatrix__t11'): # _particleFromEmx(emxParticle, part) # #partSet.setAlignment3D() # partSet.setAlignment(alignType) #else: # partSet.setAlignment(alignType) partSet.setAlignment(alignType) if not samplingRate: samplingRate = part.getSamplingRate() partSet.setSamplingRate(samplingRate) partSet.setIsPhaseFlipped(protocol.haveDataBeenPhaseFlipped.get()) particles = True else: # if not binary data, the coordinate case if micSet is None: raise Exception('Could not import Coordinates from EMX, micrographs not imported.') partSet = protocol._createSetOfCoordinates(micSet) part = Coordinate() particles = False copiedFiles = {} # copied or linked for emxParticle in emxData.iterClasses(emxlib.PARTICLE): if particles: _particleFromEmx(emxParticle, part) i, fn = part.getLocation() partFn = join(partDir, fn) newFn = join(outputDir, basename(partFn)) newLoc = (i, newFn) if not partFn in copiedFiles: copyOrLink(partFn, newFn) copiedFiles[partFn] = newFn part.setLocation(newLoc) if partSet.hasAlignment(): transform = Transform() _transformFromEmx(emxParticle, part, transform, alignType) part.setTransform(transform) else: _coordinateFromEmx(emxParticle, part) partSet.append(part) part.cleanObjId() if particles: protocol._defineOutputs(outputParticles=partSet) else: protocol._defineOutputs(outputCoordinates=partSet) if micSet is not None: protocol._defineSourceRelation(protocol.outputMicrographs, partSet)