def fromXML(self, xmlObj): """ fromXML : Assigns values to result attributes from XML object @param xmlObj: A xml object @author: Thomas Hrabe """ from lxml.etree import _Element if xmlObj.__class__ != _Element: from pytom.basic.exceptions import ParameterError raise ParameterError( 'Is not a lxml.etree._Element! You must provide a valid XML object.' ) from pytom.score.score import fromXML as fromXMLScore from pytom.angles.angle import AngleObject if xmlObj.tag == "Result": result = xmlObj else: result = xmlObj.xpath('Result') if len(result) == 0: raise PyTomClassError( "This XML is not an MaximisationResult. No Result provided." ) result = result[0] from pytom.basic.structures import Particle, Reference, Rotation, Shift particle_element = result.xpath('Particle')[0] p = Particle('') p.fromXML(particle_element) self._particle = p r = result.xpath('Reference') ref = Reference('') ref.fromXML(r[0]) self._reference = ref scoreXML = result.xpath('Score')[0] self._score = fromXMLScore(scoreXML) shiftXML = result.xpath('Shift')[0] self._shift = Shift() self._shift.fromXML(shiftXML) rotationXML = result.xpath('Rotation')[0] self._rotation = Rotation() self._rotation.fromXML(rotationXML) angleElement = result.xpath('Angles') ang = AngleObject() self._angleObject = ang.fromXML(angleElement[0])
def fromXML(self, xmlObj): from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "CTFCorrectionJob": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('CTFCorrectionJob') if len(jobDescription) == 0: raise Exception("This XML is not a CTFCorrectionJob.") jobDescription = jobDescription[0] from pytom.basic.structures import ParticleList, Reference, Mask, SampleInformation particleList_element = jobDescription.xpath('ParticleList')[0] pl = ParticleList('.') pl.fromXML(particleList_element) self.particleList = pl self.reference = [] r = jobDescription.xpath('Reference') for ref_obj in r: ref = Reference('') ref.fromXML(ref_obj) self.reference.append(ref) m = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(m) try: si = jobDescription.xpath('SampleInformation')[0] self.sampleInformation = SampleInformation() self.sampleInformation.fromXML(si) except: self._sampleInformation = SampleInformation() self.ctf_conv_pl = jobDescription.get('CTFConvolutedParticleList') self.peak_offset = int(jobDescription.get('PeakOffset')) self.bw_range = [ int(i) for i in jobDescription.get('BandwidthRange')[1:-1].split(',') ] self.freq = int(jobDescription.get('Frequency')) self.destination = jobDescription.get('Destination') self.max_iter = int(jobDescription.get('MaxIterations')) self.r_score = jobDescription.get('RScore') == 'True' self.weighting = jobDescription.get('WeightedAverage') == 'True' self.bfactor = jobDescription.get('BFactor') self.sum_ctf_sqr = jobDescription.get('CTFSquared')
class GrowingAverageInterimResult(PyTomClass): """ GrowingAverageInterimResult: """ def __init__(self,particle,reference,rotation,shift,score): self.particle = particle self.reference = reference self.rotation = rotation self.shift = shift self.score = score def getFilename(self): return self.particle.getFilename() def getWedgeInfo(self): return self.particle.getWedgeInfo() def getRotation(self): return self.rotation def getShift(self): return self.shift def toXML(self): """ toXML : Compiles a XML file from result object rtype : L{lxml.etree._Element} @author: Thomas Hrabe """ from lxml import etree result_element = etree.Element('GrowingAverageInterimResult') result_element.append(self.particle.toXML()) result_element.append(self.reference.toXML()) result_element.append(self.rotation.toXML()) result_element.append(self.shift.toXML()) result_element.append(self.score.toXML()) return result_element def fromXML(self,xmlObj): """ fromXML: @param xmlObj: A xml object @type xmlObj: L{lxml.etree._Element} @author: Thomas Hrabe """ from lxml.etree import _Element if xmlObj.__class__ != _Element : raise Exception('Is not a lxml.etree._Element! You must provide a valid XMLobject.') if xmlObj.tag == 'GrowingAverageInterimResult': result_element = xmlObj else: Exception('XML object is not a GrowingAverageInterimResult! You must provide a valid GrowingAverageInterimResultXML object.') from pytom.basic.structures import Particle,Reference particleXML = result_element.xpath('/GrowingAverageInterimResult/Particle')[0] self.particle = Particle('') self.particle.fromXML(particleXML) referenceXML = result_element.xpath('/GrowingAverageInterimResult/Result')[0] self.reference = Reference('') self.reference.fromXML(referenceXML)
class FRMJob(PyTomClass): # i need to rename the class, but for now it works def __init__(self, pl=None, ref=None, mask=None, peak_offset=0, sample_info=None, bw_range=None, freq=None, dest='.', max_iter=10, r_score=False, weighting=False, bfactor=None, symmetries=None, adaptive_res=0.1, fsc_criterion=0.5, constraint=None, binning=1): """ initiate FRM job @param pl: particle list @type ps: L{pytom.basic.structures.ParticleList} @param ref: reference density @type ref: L{pytom.basic.structures.Reference} @param mask: mask @type ref: L{pytom.basic.structures.Mask} @param peak_offset: peak offset in voxel @type peak_offset: C{int} @param sample_info: ?? (Default: None) @type sample_info: ?? @param bw_range: bandwidth range in pixel (2-dim vector) @type bw_range: C{list} @param freq: frequency (default: None) @type: C{int} @param dest: distination directory (default: '.') @type: C{str} @param max_iter: maximum number of iterations @type max_iter: C{int} @param r_score: use r_score (??) (default: False) @type r_score: C{bool} @param weighting: weighting (default: False) @type weighting: C{bool} @param bfactor: B-factor (default: None) @type bfactor: C{float}? @param symmetries: symmetry (default: None) @type L{pytom.basic.structures.Symmetries} @param adaptive_res: adaptive resolution - add to resolution for filtering @type adaptive_res: C{float} @param fsc_criterion: FSC criterion (default: 0.5) @type fsc_criterion: C{float} @param constraint: Constraint on orientations (deafult: None) @type constraint: ?? @param binning: Perform binning (downscale) of subvolumes by factor. Default=1. @type binning C{float} """ self.particleList = pl self.reference = ref self.mask = mask self.peak_offset = peak_offset self.sampleInformation = sample_info self.bw_range = bw_range self.freq = freq self.destination = dest self.max_iter = max_iter self.r_score = r_score self.weighting = weighting self.bfactor = bfactor self.symmetries = symmetries self.adaptive_res = adaptive_res self.fsc_criterion = fsc_criterion self.constraint = constraint self.binning = binning def fromXML(self, xmlObj): """ read from xml file @param xmlObj: xml object @type xmlObj: L{lxml.etree.Element} """ from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "FRMJob": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('FRMJob') if len(jobDescription) == 0: raise Exception("This XML is not a FRMJob.") jobDescription = jobDescription[0] from pytom.basic.structures import ParticleList, Reference, Mask, SampleInformation, MultiSymmetries pl = ParticleList('.') particleList_element = jobDescription.xpath('ParticleList') if len(particleList_element) > 0: pl.fromXML(particleList_element[0]) else: list_elements = jobDescription.xpath('ParticleListLocation') for e in list_elements: sub_pl = ParticleList() sub_pl.fromXMLFile(e.get('Path')) pl += sub_pl self.particleList = pl r = jobDescription.xpath('Reference')[0] self.reference = Reference('') self.reference.fromXML(r) m = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(m) try: si = jobDescription.xpath('SampleInformation')[0] self.sampleInformation = SampleInformation() self.sampleInformation.fromXML(si) except: self.sampleInformation = SampleInformation() try: syms = jobDescription.xpath('MultiSymmetries')[0] self.symmetries = MultiSymmetries() self.symmetries.fromXML(syms) except: self.symmetries = MultiSymmetries() self.peak_offset = int(jobDescription.get('PeakOffset')) self.bw_range = [ int(i) for i in jobDescription.get('BandwidthRange')[1:-1].split(',') ] self.freq = int(jobDescription.get('Frequency')) self.destination = jobDescription.get('Destination') self.max_iter = int(jobDescription.get('MaxIterations')) self.r_score = jobDescription.get('RScore') == 'True' self.weighting = jobDescription.get('WeightedAverage') == 'True' self.bfactor = jobDescription.get('BFactor') self.binning = int(jobDescription.get('binning')) if jobDescription.get('AdaptiveResolution'): adaptive_resolution = jobDescription.get('AdaptiveResolution') if adaptive_resolution == '+1': self.adaptive_res = False # always increase by 1 else: self.adaptive_res = float(adaptive_resolution) else: self.adaptive_res = 0.0 # default, if not specified if jobDescription.get('FSC'): self.fsc_criterion = float(jobDescription.get('FSC')) else: self.fsc_criterion = 0.5 # default value # for the constraint try: from sh_alignment.constrained_frm import AngularConstraint con = jobDescription.xpath('AngularConstraint') if len(con) != 0: ac = AngularConstraint() c = ac.fromXML(con[0]) self.constraint = c else: self.constraint = None except: self.constraint = None def toXML(self): """ copy to xml structure @return: xml object for job @rtype L{lxml.etree.Element} """ from lxml import etree jobElement = etree.Element("FRMJob") jobElement.append(self.particleList.toXML()) jobElement.append(self.reference.toXML()) jobElement.append(self.mask.toXML()) jobElement.append(self.sampleInformation.toXML()) if self.symmetries is not None: jobElement.append(self.symmetries.toXML()) jobElement.set("PeakOffset", str(self.peak_offset)) jobElement.set("BandwidthRange", str(self.bw_range)) jobElement.set("Frequency", str(self.freq)) jobElement.set("Destination", self.destination) jobElement.set("MaxIterations", str(self.max_iter)) jobElement.set("RScore", str(self.r_score)) jobElement.set("WeightedAverage", str(self.weighting)) jobElement.set("BFactor", str(self.bfactor)) jobElement.set("binning", str(self.binning)) if self.adaptive_res is False: jobElement.set("AdaptiveResolution", '+1') else: jobElement.set("AdaptiveResolution", str(self.adaptive_res)) jobElement.set("FSC", str(self.fsc_criterion)) if self.constraint: jobElement.append(self.constraint.toXML()) return jobElement def check(self): from pytom.tools.files import checkDirExists self.particleList.check() self.reference.check() self.mask.check() if not checkDirExists(self.destination): raise RuntimeError('Destination path not found! ' + self.destination)
def fromXML(self, xmlObj): from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "FRMJob": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('FRMJob') if len(jobDescription) == 0: raise Exception("This XML is not a FRMJob.") jobDescription = jobDescription[0] from pytom.basic.structures import ParticleList, Reference, Mask, SampleInformation, MultiSymmetries pl = ParticleList('.') particleList_element = jobDescription.xpath('ParticleList') if len(particleList_element) > 0: pl.fromXML(particleList_element[0]) else: list_elements = jobDescription.xpath('ParticleListLocation') for e in list_elements: sub_pl = ParticleList() sub_pl.fromXMLFile(e.get('Path')) pl += sub_pl self.particleList = pl self.reference = [] r = jobDescription.xpath('Reference') for ref_obj in r: ref = Reference('') ref.fromXML(ref_obj) self.reference.append(ref) m = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(m) try: si = jobDescription.xpath('SampleInformation')[0] self.sampleInformation = SampleInformation() self.sampleInformation.fromXML(si) except: self.sampleInformation = SampleInformation() try: syms = jobDescription.xpath('MultiSymmetries')[0] self.symmetries = MultiSymmetries() self.symmetries.fromXML(syms) except: self.symmetries = MultiSymmetries() self.peak_offset = int(jobDescription.get('PeakOffset')) self.bw_range = [ int(i) for i in jobDescription.get('BandwidthRange')[1:-1].split(',') ] self.freq = int(jobDescription.get('Frequency')) self.destination = jobDescription.get('Destination') self.max_iter = int(jobDescription.get('MaxIterations')) self.r_score = jobDescription.get('RScore') == 'True' self.weighting = jobDescription.get('WeightedAverage') == 'True' self.bfactor = jobDescription.get('BFactor') if jobDescription.get('AdaptiveResolution'): adaptive_resolution = jobDescription.get('AdaptiveResolution') if adaptive_resolution == '+1': self.adaptive_res = False # always increase by 1 else: self.adaptive_res = float(adaptive_resolution) else: self.adaptive_res = 0.0 # default, if not specified if jobDescription.get('FSC'): self.fsc_criterion = float(jobDescription.get('FSC')) else: self.fsc_criterion = 0.5 # default value
class FRMJob(PyTomClass): # i need to rename the class, but for now it works def __init__(self, pl=None, ref=None, mask=None, peak_offset=0, sample_info=None, bw_range=None, freq=None, dest='.', max_iter=10, r_score=False, weighting=False, bfactor=None, symmetries=None, adaptive_res=0.1, fsc_criterion=0.5, constraint=None): self.particleList = pl self.reference = ref self.mask = mask self.peak_offset = peak_offset self.sampleInformation = sample_info self.bw_range = bw_range self.freq = freq self.destination = dest self.max_iter = max_iter self.r_score = r_score self.weighting = weighting self.bfactor = bfactor self.symmetries = symmetries self.adaptive_res = adaptive_res self.fsc_criterion = fsc_criterion self.constraint = constraint def fromXML(self, xmlObj): from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "FRMJob": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('FRMJob') if len(jobDescription) == 0: raise Exception("This XML is not a FRMJob.") jobDescription = jobDescription[0] from pytom.basic.structures import ParticleList, Reference, Mask, SampleInformation, MultiSymmetries pl = ParticleList('.') particleList_element = jobDescription.xpath('ParticleList') if len(particleList_element) > 0: pl.fromXML(particleList_element[0]) else: list_elements = jobDescription.xpath('ParticleListLocation') for e in list_elements: sub_pl = ParticleList() sub_pl.fromXMLFile(e.get('Path')) pl += sub_pl self.particleList = pl r = jobDescription.xpath('Reference')[0] self.reference = Reference('') self.reference.fromXML(r) m = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(m) try: si = jobDescription.xpath('SampleInformation')[0] self.sampleInformation = SampleInformation() self.sampleInformation.fromXML(si) except: self.sampleInformation = SampleInformation() try: syms = jobDescription.xpath('MultiSymmetries')[0] self.symmetries = MultiSymmetries() self.symmetries.fromXML(syms) except: self.symmetries = MultiSymmetries() self.peak_offset = int(jobDescription.get('PeakOffset')) self.bw_range = [ int(i) for i in jobDescription.get('BandwidthRange')[1:-1].split(',') ] self.freq = int(jobDescription.get('Frequency')) self.destination = jobDescription.get('Destination') self.max_iter = int(jobDescription.get('MaxIterations')) self.r_score = jobDescription.get('RScore') == 'True' self.weighting = jobDescription.get('WeightedAverage') == 'True' self.bfactor = jobDescription.get('BFactor') if jobDescription.get('AdaptiveResolution'): adaptive_resolution = jobDescription.get('AdaptiveResolution') if adaptive_resolution == '+1': self.adaptive_res = False # always increase by 1 else: self.adaptive_res = float(adaptive_resolution) else: self.adaptive_res = 0.0 # default, if not specified if jobDescription.get('FSC'): self.fsc_criterion = float(jobDescription.get('FSC')) else: self.fsc_criterion = 0.5 # default value # for the constraint try: from sh_alignment.constrained_frm import AngularConstraint con = jobDescription.xpath('AngularConstraint') if len(con) != 0: ac = AngularConstraint() c = ac.fromXML(con[0]) self.constraint = c else: self.constraint = None except: self.constraint = None def toXML(self): from lxml import etree jobElement = etree.Element("FRMJob") jobElement.append(self.particleList.toXML()) jobElement.append(self.reference.toXML()) jobElement.append(self.mask.toXML()) jobElement.append(self.sampleInformation.toXML()) if self.symmetries is not None: jobElement.append(self.symmetries.toXML()) jobElement.set("PeakOffset", str(self.peak_offset)) jobElement.set("BandwidthRange", str(self.bw_range)) jobElement.set("Frequency", str(self.freq)) jobElement.set("Destination", self.destination) jobElement.set("MaxIterations", str(self.max_iter)) jobElement.set("RScore", str(self.r_score)) jobElement.set("WeightedAverage", str(self.weighting)) jobElement.set("BFactor", str(self.bfactor)) if self.adaptive_res is False: jobElement.set("AdaptiveResolution", '+1') else: jobElement.set("AdaptiveResolution", str(self.adaptive_res)) jobElement.set("FSC", str(self.fsc_criterion)) if self.constraint: jobElement.append(self.constraint.toXML()) return jobElement def check(self): from pytom.tools.files import checkDirExists self.particleList.check() self.reference.check() self.mask.check() if not checkDirExists(self.destination): raise RuntimeError('Destination path not found! ' + self.destination)
def fromXML(self, xmlObj): """ fromXML : Assigns values to job attributes from XML object @param xmlObj: A xml object @author: Thomas Hrabe """ from lxml.etree import _Element if xmlObj.__class__ != _Element: from pytom.basic.exceptions import ParameterError raise ParameterError( 'You must provide a valid XML-MaximisationJob object.') if xmlObj.tag == "JobDescription": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('JobDescription') if len(jobDescription) == 0: from pytom.basic.structures import PyTomClassError raise PyTomClassError("This XML is not an JobDescription.") jobDescription = jobDescription[0] from pytom.angles.angle import AngleObject from pytom.score.score import fromXML as fromXMLScore from pytom.alignment.preprocessing import Preprocessing from pytom.basic.structures import Mask, Particle, Reference, ReferenceList self.binning = int(jobDescription.get('Binning')) particle_element = jobDescription.xpath('Particle')[0] p = Particle('') p.fromXML(particle_element) self.particle = p r = jobDescription.xpath('Reference') if len(r) > 0: ref = Reference('') ref.fromXML(r[0]) self.reference = ref else: r = jobDescription.xpath('ReferenceList') ref = ReferenceList() ref.fromXML(r[0]) self.reference = ref mask = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(mask) self.numberRefinementRounds = jobDescription.get( 'NumberRefinementRounds') self.numberRefinementRounds = int(self.numberRefinementRounds) score = jobDescription.xpath('Score') self.score = fromXMLScore(score[0]) angles = jobDescription.xpath('Angles') ang = AngleObject() self.rotations = ang.fromXML(angles[0]) preObj = xmlObj.xpath('Preprocessing') if len(preObj) == 0: self.preprocessing = Preprocessing() else: p = Preprocessing() p.fromXML(preObj[0]) self.preprocessing = p
class PeakJob(PyTomClass): """ PeakJob: stores all the infos needed for calculation of the peak score """ def __init__(self, volume='', reference='', mask='', wedge='', rotations='', score='', jobID=0, members=1, dstDir='./', bandpass=None): """ @param volume: target volume @type volume: L{pytom.localization.structures.Volume} @param reference: reference volume @type reference: L{pytom.basic.structures.Reference} @param mask: mask volume @type mask: L{pytom.basic.structures.Mask} @param wedge: wedge information @type wedge: L{pytom.basic.structures.WedgeInfo} @param rotations: rotation list @type rotations: L{pytom.angles.angle} @param score: score function @type score: L{pytom.score.score} @param jobID: job identification @type jobID: integer @param members: how many members are there available to accomplish this job (1 means only itself) @type members: integer @param dstDir: destination directory where the result is written to @type dstDir: string @param bandpass: bandpass object that will be applied to the reference @type bandpass: L{pytom.basic.structure.BandPassFilter} """ self.volume = volume self.reference = reference self.mask = mask self.wedge = wedge self.rotations = rotations self.score = score self.jobID = jobID self.members = members if dstDir[-1] == '/': self.dstDir = dstDir else: self.dstDir = dstDir + '/' self.bandpass = bandpass def copy(self, fromJob): self.volume = fromJob.volume self.reference = fromJob.reference self.mask = fromJob.mask self.wedge = fromJob.wedge self.rotations = fromJob.rotations self.score = fromJob.score self.jobID = fromJob.jobID self.members = fromJob.members self.dstDir = fromJob.dstDir self.bandpass = fromJob.bandpass def fromXML(self, xmlObj): """ fromXML : Assigns values to job attributes from XML object @param xmlObj: A xml object @author: chen """ from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "JobDescription": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('JobDescription') if len(jobDescription) == 0: raise Exception("This XML is not an JobDescription.") jobDescription = jobDescription[0] id = jobDescription.get('ID') if id != None and id != 'None': self.jobID = int(id) members = jobDescription.get('Members') if members != None and members != 'None': self.members = int(members) dstDir = jobDescription.get('Destination') if dstDir != None: if dstDir[-1] == '/': self.dstDir = dstDir else: self.dstDir = dstDir + '/' from pytom.score.score import fromXML as fromXMLScore from pytom.basic.structures import Mask, Reference, Wedge # from pytom.angles.angleList import AngleList from pytom.localization.structures import Volume e = jobDescription.xpath('Volume')[0] v = Volume() v.fromXML(e) self.volume = v ref = jobDescription.xpath('Reference')[0] self.reference = Reference('') self.reference.fromXML(ref) wedgeXML = jobDescription.xpath('Wedge') if len(wedgeXML) == 0: wedgeXML = jobDescription.xpath('SingleTiltWedge') if len(wedgeXML) == 0: wedgeXML = jobDescription.xpath('WedgeInfo') if len(wedgeXML) == 0: wedgeXML = jobDescription.xpath('DoubleTiltWedge') assert len(wedgeXML) > 0 self.wedge = Wedge() self.wedge.fromXML(wedgeXML[0]) mask = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(mask) score = jobDescription.xpath('Score') self.score = fromXMLScore(score[0]) rot = jobDescription.xpath('Angles')[0] from pytom.angles.angle import AngleObject ang = AngleObject() self.rotations = ang.fromXML(rot) # self.rotations = AngleList() # self.rotations.fromXML(rot) bp = jobDescription.xpath('BandPassFilter') if bp != []: bp = bp[0] from pytom.basic.structures import BandPassFilter self.bandpass = BandPassFilter(0, 0, 0) self.bandpass.fromXML(bp) else: self.bandpass = None def toXML(self): """ toXML : Compiles a XML file from job object @author: chen """ from lxml import etree jobElement = etree.Element("JobDescription", ID=str(self.jobID), Members=str(self.members), Destination=str(self.dstDir)) jobElement.append(self.volume.toXML()) jobElement.append(self.reference.toXML()) jobElement.append(self.mask.toXML()) jobElement.append(self.wedge.toXML()) jobElement.append(self.rotations.toXML()) jobElement.append(self.score.toXML()) if self.bandpass: jobElement.append(self.bandpass.toXML()) return jobElement def check(self): """ check: Performs check whether all settings are valid. Paths and Files exist @author: chen """ from pytom.tools.files import checkFileExists, checkDirExists returnValue = checkFileExists(self.volume.getFilename()) if not returnValue: raise IOError('File: ' + str(self.volume) + ' not found!') returnValue = checkFileExists(self.reference.getReferenceFilename()) if not returnValue: raise IOError('File: ' + str(self.reference) + ' not found!') returnValue = checkFileExists(self.mask.getFilename()) if not returnValue: raise IOError('File: ' + str(self.mask) + ' not found!') returnValue = checkDirExists(self.dstDir[:-1]) if not returnValue: raise IOError('Directory: ' + str(self.dstDir) + ' not found!') return returnValue def send(self, source, destination): """ send: Send the job-relevant message from source to destination @param source: source machine id gained from pytom_mpi @type source: int @param destination: destination machine id @type destination: int @author: chen """ from pytom.localization.peak_job_msg import PeakJobMsg # self.check() msg = PeakJobMsg(str(source), str(destination)) msg.setJob(self) import pytom_mpi print(f'destination: {destination}\ntype: {type(destination)}') pytom_mpi.send(str(msg), int(destination))
class CTFCorrectionJob(PyTomClass): """For the worker to actually run. """ def __init__(self, pl=None, ctf_conv_pl=None, ref=None, mask=None, peak_offset=0, sample_info=None, bw_range=None, freq=None, dest='.', max_iter=10, r_score=False, weighting=False, bfactor=None, sum_ctf_sqr=None): self.particleList = pl self.ctf_conv_pl = ctf_conv_pl self.reference = ref self.mask = mask self.peak_offset = peak_offset self.sampleInformation = sample_info self.bw_range = bw_range self.freq = freq self.destination = dest self.max_iter = max_iter self.r_score = r_score self.weighting = weighting self.bfactor = bfactor self.sum_ctf_sqr = sum_ctf_sqr def fromXML(self, xmlObj): from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "CTFCorrectionJob": jobDescription = xmlObj else: jobDescription = xmlObj.xpath('CTFCorrectionJob') if len(jobDescription) == 0: raise Exception("This XML is not a CTFCorrectionJob.") jobDescription = jobDescription[0] from pytom.basic.structures import ParticleList, Reference, Mask, SampleInformation particleList_element = jobDescription.xpath('ParticleList')[0] pl = ParticleList('.') pl.fromXML(particleList_element) self.particleList = pl r = jobDescription.xpath('Reference')[0] self.reference = Reference('') self.reference.fromXML(r) m = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(m) try: si = jobDescription.xpath('SampleInformation')[0] self.sampleInformation = SampleInformation() self.sampleInformation.fromXML(si) except: self._sampleInformation = SampleInformation() self.ctf_conv_pl = jobDescription.get('CTFConvolutedParticleList') self.peak_offset = int(jobDescription.get('PeakOffset')) self.bw_range = [int(i) for i in jobDescription.get('BandwidthRange')[1:-1].split(',')] self.freq = int(jobDescription.get('Frequency')) self.destination = jobDescription.get('Destination') self.max_iter = int(jobDescription.get('MaxIterations')) self.r_score = jobDescription.get('RScore')=='True' self.weighting = jobDescription.get('WeightedAverage')=='True' self.bfactor = jobDescription.get('BFactor') self.sum_ctf_sqr = jobDescription.get('CTFSquared') def toXML(self): from lxml import etree jobElement = etree.Element("CTFCorrectionJob") jobElement.append(self.particleList.toXML()) jobElement.append(self.reference.toXML()) jobElement.append(self.mask.toXML()) jobElement.append(self.sampleInformation.toXML()) jobElement.set("CTFConvolutedParticleList", self.ctf_conv_pl) jobElement.set("PeakOffset", str(self.peak_offset)) jobElement.set("BandwidthRange", str(self.bw_range)) jobElement.set("Frequency", str(self.freq)) jobElement.set("Destination", self.destination) jobElement.set("MaxIterations", str(self.max_iter)) jobElement.set("RScore", str(self.r_score)) jobElement.set("WeightedAverage", str(self.weighting)) jobElement.set("BFactor", str(self.bfactor)) jobElement.set("CTFSquared", str(self.sum_ctf_sqr)) return jobElement
class MultiDefocusJob(FRMJob): """For the entry of the whole procedure. """ def fromXML(self, xmlObj): # only rewrite this function from lxml.etree import _Element if xmlObj.__class__ != _Element: raise Exception('You must provide a valid XML object.') if xmlObj.tag == "FRMJob": # the name is not changed here! jobDescription = xmlObj else: jobDescription = xmlObj.xpath('FRMJob') if len(jobDescription) == 0: raise Exception("This XML is not a FRMJob.") jobDescription = jobDescription[0] from pytom.basic.structures import Reference, Mask, SampleInformation, MultiSymmetries particleList_element = jobDescription.xpath('ParticleListSet')[0] pl = ParticleListSet() pl.fromXML(particleList_element) self.particleList = pl # here i still use the original name! r = jobDescription.xpath('Reference')[0] self.reference = Reference('') self.reference.fromXML(r) m = jobDescription.xpath('Mask')[0] self.mask = Mask('') self.mask.fromXML(m) try: si = jobDescription.xpath('SampleInformation')[0] self.sampleInformation = SampleInformation() self.sampleInformation.fromXML(si) except: self.sampleInformation = SampleInformation() try: syms = jobDescription.xpath('MultiSymmetries')[0] self.symmetries = MultiSymmetries() self.symmetries.fromXML(syms) except: self.symmetries = MultiSymmetries() self.peak_offset = int(jobDescription.get('PeakOffset')) self.bw_range = [int(i) for i in jobDescription.get('BandwidthRange')[1:-1].split(',')] self.freq = int(jobDescription.get('Frequency')) self.destination = jobDescription.get('Destination') self.max_iter = int(jobDescription.get('MaxIterations')) self.r_score = jobDescription.get('RScore')=='True' self.weighting = jobDescription.get('WeightedAverage')=='True' self.bfactor = jobDescription.get('BFactor') if jobDescription.get('AdaptiveResolution'): adaptive_resolution = jobDescription.get('AdaptiveResolution') if adaptive_resolution == '+1': self.adaptive_res = False # always increase by 1 else: self.adaptive_res = float(adaptive_resolution) else: self.adaptive_res = 0.0 # default, if not specified if jobDescription.get('FSC'): self.fsc_criterion = float(jobDescription.get('FSC')) else: self.fsc_criterion = 0.5 # default value def check(self): for p in self.particleList.pairs: p.check()