def fromXML(self,xmlObj):
"""
@param xmlObj: A xml object
@type xmlObj: L{lxml.etree._Element}
@author: chen
"""
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-Volume object.')
if xmlObj.tag == 'Volume':
e = xmlObj
else:
e = xmlObj.xpath('Volume')
e = e[0]
self._filename = e.get('Filename')
s = e.get('Subregion')
if s != None and s!= 'None':
s = s[1:-1]
self.subregion = [int(float(i)) for i in s.split(',')]
s = e.get('Sampling')
if s != None and s!= 'None':
s = s[1:-1]
self.sampling = [int(i) for i in s.split(',')]
s = e.get('Binning')
if s != None and s!= 'None':
s = s[1:-1]
self.binning = [int(i) for i in s.split(',')]
def fromXML(self, xmlObj):
from lxml.etree import _Element
if xmlObj.__class__ != _Element:
from pytom.basic.exceptions import ParameterError
raise ParameterError('You must provide a valid XML object.')
if xmlObj.tag == "FoundParticle":
main = xmlObj
else:
main = xmlObj.xpath('FoundParticle')
if len(main) == 0:
from pytom.basic.exceptions import PyTomClassError
raise PyTomClassError("This XML is not a FoundParticle.")
main = main[0]
from pytom.basic.structures import PickPosition, Rotation
from pytom.score.score import fromXML as fromXMLScore
self.filename = main.get('Filename')
p = main.xpath('PickPosition')[0]
self.pos = PickPosition()
self.pos.fromXML(p)
o = main.xpath('Rotation')[0]
self.orient = Rotation()
self.orient.fromXML(o)
s = main.xpath('Score')[0]
self.score = fromXMLScore(s)
def FSFWrapper(self, volume, reference):
from pytom.tompy.correlation import weightedXCF
if self.numberOfBands == 0:
from pytom.basic.exceptions import ParameterError
raise ParameterError('Bands attribute is empty. Abort.')
return weightedXCF(volume, reference, self.bands, self.wedgeAngle)
def __init__(self,particle=None,particleList=None,mask=None,particleIndex = None,applyWedge = True,binningFactor=0,lowestFrequency=-1,highestFrequency=-1):
"""
__init__:
@param particle: Particle
@type particle: pytom.alignment.structures.Particle
@param particleList: ParticleList of all particles will be correlated with self._particle
@type particleList: pytom.alignment.structures.ParticleList
@param mask: Mask used for correlation
@type mask: str
@param applyWedge: Apply wedge during correlation. True by default, disable for rotation classification.
@type applyWedge: Bool
@param binningFactor: Binning factor accroding to libtomc definition. 0 by default.
@type binningFactor: unsigned int
@param lowestFrequency: Lowest frequency for bandpass in nyquist
@type lowestFrequency: float
@param highestFrequency: Highest frequency for bandpass in nyquist
@type highestFrequency: float
"""
from pytom.basic.structures import Particle,ParticleList,Mask
if particle and particle.__class__ != Particle:
raise ParameterError('You must provide a Particle object.')
if particleList and particleList.__class__ != ParticleList:
raise ParameterError('You must provide a ParticleList object.')
self._particle = particle
self._particleList = particleList
if not mask:
mask = Mask()
elif mask.__class__ == str:
mask = Mask(mask)
elif mask.__class__ != Mask:
from pytom.basic.exceptions import ParameterError
raise ParameterError('Mask must be a string or Mask object!')
self._mask = mask
self._particleIndex = particleIndex
self._applyWedge = applyWedge
self._binningFactor = binningFactor
self._lowestFrequency = lowestFrequency
self._highestFrequency = highestFrequency
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 __init__(self,particleList=None,mask='',resultMatrixName='',applyWedge = True,binningFactor=0,lowestFrequency=-1,highestFrequency=-1):
"""
__init__:
@param particleList: ParticleList of all particles that will be correlated
@type particleList: L{pytom.basic.structures.ParticleList}
@param mask: Mask used for correlation
@type mask: str or L{pytom.basic.structures.Mask}
@param resultMatrixName: Result filename
@type resultMatrixName: str
@param applyWedge: Apply wedge weighting if available?
@type applyWedge: boolean, False by default
@param binningFactor: Binning factor accroding to libtomc definition. 0 by default.
@type binningFactor: unsigned int
@param lowestFrequency: Lowest frequency for bandpass in nyquist
@type lowestFrequency: float
@param highestFrequency: Highest frequency for bandpass in nyquist
@type highestFrequency: float
"""
from pytom.basic.structures import ParticleList,Mask
from pytom.tools.files import checkFileExists
if not particleList:
particleList = ParticleList('/')
elif particleList.__class__ != ParticleList:
raise ParameterError('You must provide a ParticleList object!')
self._particleList = particleList
if mask.__class__ == str:
mask = Mask(mask)
elif mask.__class__ != Mask:
raise ParameterError('Mask must be a string or Mask object!')
self._mask = mask
self._resultMatrixName = resultMatrixName
self._applyWedge = applyWedge
self._binningFactor = binningFactor
self._lowestFrequency = lowestFrequency
self._highestFrequency = highestFrequency
def fromXML(self, xmlObj):
"""
fromXML: Sets attributes of self to those defined by xmlObj
@param xmlObj: A XML attribute as generated by toXML
@author: Thomas Hrabe
"""
from lxml.etree import _Element
if xmlObj.__class__ != _Element:
raise ParameterError(
'You must provide a valid XML-GlobalSampling object.')
if xmlObj.tag == 'Angles':
angles = xmlObj
else:
angles = xmlObj.xpath('Angles')
if len(angles) == 0:
from pytom.basic.exceptions import ParameterError
raise ParameterError("This XML is not an GlobalSampling DOM.")
angles = angles[0]
self._currentIndex = 0
parameters = angles.xpath('RefinementParameters')
self._refinementParameters = []
if len(parameters) == 1:
parameters = parameters[0]
self._refinementParameters.append(float(parameters.get('Shells')))
self._refinementParameters.append(
float(parameters.get('Increment')))
else:
self._refinementParameters.append(self._defaultShells)
self._refinementParameters.append(self._defaultIncrement)
self._filename = angles.get('File')
self.readRotationsFromEMFile(self._filename)
def fromXML(self, xmlObj):
"""
fromXML : Assigns values to job attributes from XML object
@param xmlObj: A xml object
@type xmlObj: L{lxml.etree._Element}
@author: Thomas Hrabe
"""
from lxml import etree
from lxml.etree import _Element
from pytom.basic.structures import ParticleList
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.'
)
if not xmlObj.tag == 'ExpectationJob':
jobElement = xmlObj.xpath('ExpectationJob')
if len(jobElement) == 0:
from pytom.basic.exceptions import ParameterError
raise ParameterError(
'You must provide a valid XML-ExpectationJob object.')
else:
jobElement = jobElement[0]
else:
jobElement = xmlObj
self._newAverageName = jobElement.get('AverageName').__str__()
particleListXML = xmlObj.xpath('ParticleList')
self._particleList = ParticleList('/')
if len(particleListXML) > 0:
self._particleList.fromXML(particleListXML[0])
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, tostring
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.'
)
self.resultFileName = xmlObj.get('ResultFileName')
self.wedgeSumName = xmlObj.get('WedgeSumName')
def fromXML(self, xmlObj):
from lxml.etree import _Element
if xmlObj.__class__ != _Element:
from pytom.basic.exceptions import ParameterError
raise ParameterError('You must provide a valid XML object.')
if xmlObj.tag == "ParticleList":
main = xmlObj
else:
main = xmlObj.xpath('ParticleList')
if len(main) == 0:
from pytom.basic.exceptions import PyTomClassError
raise PyTomClassError("This XML is not a ParticleList.")
main = main[0]
for p in main.xpath('FoundParticle'):
particle = FoundParticle()
particle.fromXML(p)
self.pl.append(particle)
for p in main.xpath('ClassifiedParticle'):
particle = ClassifiedParticle()
particle.fromXML(p)
self.pl.append(particle)
for p in main.xpath('SimulatedParticle'):
from pytom.localization.simulation import SimulatedParticle
particle = SimulatedParticle()
particle.fromXML(p)
self.pl.append(particle)
for p in main.xpath('IdentifiedParticle'):
from pytom.localization.simulation import IdentifiedParticle
particle = IdentifiedParticle()
particle.fromXML(p)
self.pl.append(particle)
for p in main.xpath('Particle'): # now also support reading class Particle, but will convert to FoundParticle
from pytom.basic.structures import Particle
pp = Particle()
pp.fromXML(p)
# convert to FoundParticle
particle = FoundParticle()
particle.fromParticle(pp)
self.pl.append(particle)
def fromXML(self, xmlObj):
from lxml.etree import _Element
if xmlObj.__class__ != _Element:
from pytom.basic.exceptions import ParameterError
raise ParameterError('You must provide a valid XML object.')
if xmlObj.tag == "ClassifiedParticle":
main = xmlObj
else:
main = xmlObj.xpath('ClassifiedParticle')
if len(main) == 0:
from pytom.basic.exceptions import PyTomClassError
raise PyTomClassError("This XML is not a IdentifiedParticle.")
main = main[0]
self.classified = main.get('Classified')
correct = main.get('Correct')
if correct == 'True':
self.correct = True
elif correct == 'False':
self.correct = False
else:
self.correct = None
f_particle = main.xpath('FoundParticle')
if len(f_particle) > 0:
self.particle = FoundParticle()
self.particle.fromXML(f_particle[0])
s_particle = main.xpath('SimulatedParticle')
if len(s_particle) > 0:
from pytom.localization.simulation import SimulatedParticle
self.particle = SimulatedParticle()
self.particle.fromXML(s_particle[0])
i_particle = main.xpath('IdentifiedParticle')
if len(i_particle) > 0:
from pytom.localization.simulation import IdentifiedParticle
self.particle = IdentifiedParticle()
self.particle.fromXML(i_particle[0])
def fromJob(self,job):
"""
fromJob: Initializes this object.
@param job:
@type job: L{pytom.alignment.structures.GrowingAverageJob}
"""
from pytom.alignment.structures import GrowingAverageJob
if not job.__class__ == GrowingAverageJob:
from pytom.basic.exceptions import ParameterError
raise ParameterError('You must provide a GrowingAverageJob object to initialize GrowingAverage.')
self._particleList = job.particleList
self._angleObject = job.angleObject
self._startParticleNumber = job.startParticleNumber
self._maskFile = job.maskFile
self._score = job.score
self._destinationDirectory = job.destinationDirectory
self._preprocessing = job.preprocessing
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,tostring
if xmlObj.__class__ != _Element :
from pytom.basic.exceptions import ParameterError
raise ParameterError('Is not a lxml.etree._Element! You must provide a valid XML-MaximisationJobMsg object.')
main = xmlObj.xpath('/GrowingAverageResultMsg')
message = main[0].xpath('Message')
message = message[0]
self._sender = int(message.get('Sender'))
self._recipient = int(message.get('Recipient'))
self._timestamp = message.get('Timestamp')
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,tostring
if xmlObj.__class__ != _Element :
from pytom.basic.exceptions import ParameterError
raise ParameterError('Is not a lxml.etree._Element! You must provide a valid XML-StatusMessage object.')
message = xmlObj.xpath('Message')
message = message[0]
self._sender = message.get('Sender')
self._recipient = message.get('Recipient')
self._timestamp = message.get('Timestamp')
status = xmlObj.xpath('Status')
status = status[0]
self._status = status.get('Value')
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:
from pytom.basic.exceptions import ParameterError
raise ParameterError(
'Is not a lxml.etree._Element! You must provide a valid XML-PeakJobMsg object.'
)
from pytom.localization.peak_job import PeakJob
main = xmlObj.xpath('/PeakJobMsg')
if len(main) == 0:
from pytom.parallel.messages import MessageError
raise MessageError("This message is not a PeakJobMsg")
main = main[0]
message = main.xpath('Message')
message = message[0]
# jobDescription = main.xpath('JobDescription')
# jobDescription = jobDescription[0]
self._sender = message.get('Sender')
self._recipient = message.get('Recipient')
self._timestamp = message.get('Timestamp')
jobDescription = main.xpath('/*/JobDescription')
j = PeakJob()
j.fromXML(jobDescription[0])
self.setJob(j)
def fromXML(self, xmlObj):
"""
fromXML : Assigns values to result attributes from XML object
@param xmlObj: A xml object
@author: chen
"""
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-PeakResultMsg object.'
)
from pytom.localization.peak_job import PeakResult
if xmlObj.tag == "PeakResultMsg":
main = xmlObj
else:
main = xmlObj.xpath('PeakResultMsg')
if len(main) == 0:
from pytom.parallel.messages import MessageError
raise MessageError("This message is not a PeakResultMsg")
main = main[0]
message = main.xpath('Message')
message = message[0]
self._sender = message.get('Sender')
self._recipient = message.get('Recipient')
self._timestamp = message.get('Timestamp')
res = main.xpath('Result')[0]
self.result = PeakResult()
self.result.fromXML(res)
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
def calculate_averages(pl, binning, mask, outdir='./'):
"""
calcuate averages for particle lists
@param pl: particle list
@type pl: L{pytom.basic.structures.ParticleList}
@param binning: binning factor
@type binning: C{int}
last change: Jan 18 2020: error message for too few processes, FF
"""
import os
from pytom_volume import complexDiv, vol, pasteCenter
from pytom.basic.fourier import fft, ifft
from pytom.basic.correlation import FSC, determineResolution
from pytom_fftplan import fftShift
from pytom_volume import reducedToFull
pls = pl.copy().splitByClass()
res = {}
freqs = {}
wedgeSum = {}
for pp in pls:
# ignore the -1 class, which is used for storing the trash class
class_label = pp[0].getClass()
if class_label != '-1':
assert len(pp) > 3
if len(pp) >= 4 * mpi.size:
spp = mpi._split_seq(pp, mpi.size)
else: # not enough particle to do averaging on one node
spp = [None] * 2
spp[0] = pp[:len(pp) // 2]
spp[1] = pp[len(pp) // 2:]
args = list(
zip(spp, [True] * len(spp), [binning] * len(spp),
[False] * len(spp), [outdir] * len(spp)))
avgs = mpi.parfor(paverage, args)
even_a, even_w, odd_a, odd_w = None, None, None, None
even_avgs = avgs[1::2]
odd_avgs = avgs[::2]
for a, w in even_avgs:
if even_a is None:
even_a = a.getVolume()
even_w = w.getVolume()
else:
even_a += a.getVolume()
even_w += w.getVolume()
os.remove(a.getFilename())
os.remove(w.getFilename())
for a, w in odd_avgs:
if odd_a is None:
odd_a = a.getVolume()
odd_w = w.getVolume()
else:
odd_a += a.getVolume()
odd_w += w.getVolume()
os.remove(a.getFilename())
os.remove(w.getFilename())
# determine the resolution
# raise error message in case even_a == None - only one processor used
if even_a == None:
from pytom.basic.exceptions import ParameterError
raise ParameterError(
'cannot split odd / even. Likely you used only one processor - use: mpirun -np 2 (or higher!)?!'
)
if mask and mask.__class__ == str:
from pytom_volume import read, pasteCenter, vol
maskBin = read(mask, 0, 0, 0, 0, 0, 0, 0, 0, 0, binning,
binning, binning)
if even_a.sizeX() != maskBin.sizeX() or even_a.sizeY(
) != maskBin.sizeY() or even_a.sizeZ() != maskBin.sizeZ():
mask = vol(even_a.sizeX(), even_a.sizeY(), even_a.sizeZ())
mask.setAll(0)
pasteCenter(maskBin, mask)
else:
mask = maskBin
fsc = FSC(even_a, odd_a, int(even_a.sizeX() // 2), mask)
band = determineResolution(fsc, 0.5)[1]
aa = even_a + odd_a
ww = even_w + odd_w
fa = fft(aa)
r = complexDiv(fa, ww)
rr = ifft(r)
rr.shiftscale(0.0, 1. / (rr.sizeX() * rr.sizeY() * rr.sizeZ()))
res[class_label] = rr
freqs[class_label] = band
ww2 = reducedToFull(ww)
fftShift(ww2, True)
wedgeSum[class_label] = ww2
print('done')
return res, freqs, wedgeSum
def fromXML(xmlObj):
"""
fromXML: Returns a score object depending on the string constant
@param xmlObj: The DOM object provided
@return: The score object
@author: Thomas Hrabe
"""
type = xmlObj.get('Type')
value = xmlObj.get('Value')
if value == 'NAN':
value = []
if type == 'xcfScore':
score = xcfScore()
elif type == 'nxcfScore':
score = nxcfScore()
elif type == 'FLCFScore':
score = FLCFScore()
# make FLCF default score
elif type == 'undefined':
score = FLCFScore()
elif type == 'SOCScore':
score = SOCScore()
elif type == 'RScore':
score = RScore()
nb = xmlObj.get('NumberBands')
wa = xmlObj.get('WedgeAngle')
nb = nb
wa = wa
if nb.__class__ == str:
nb = int(nb)
if wa.__class__ == str:
wa = int(wa)
score.initAttributes(nb, wa)
elif type == 'FSCScore':
score = FSCScore()
nb = xmlObj.get('NumberBands')
wa = xmlObj.get('WedgeAngle')
nb = nb
wa = wa
if nb.__class__ == str:
nb = int(nb)
if wa.__class__ == str:
wa = int(wa)
score.initAttributes(nb, wa)
elif type == 'FRMScore':
from pytom.frm.FRMAlignment import FRMScore
score = FRMScore()
else:
from pytom.basic.exceptions import ParameterError
raise ParameterError('Type ' + type +
' not available in pytom.alignment.score!')
score.setValue(value)
prElement = xmlObj.xpath('PeakPrior')
if prElement == None:
prElement = xmlObj.xpath('DistanceFunction')
if len(prElement) > 0:
prObject = PeakPrior()
prObject.fromXML(prElement[0])
score._peakPrior = prObject
else:
score._peakPrior = PeakPrior()
removeAutocorrelation = xmlObj.get('RemoveAutocorr')
if removeAutocorrelation == 'True':
removeAutocorrelation = True
else:
removeAutocorrelation = False
score.setRemoveAutocorrelation(flag=removeAutocorrelation)
return score