def average_sub_pl(self, pl, name_prefix, weight_average):
"""For worker node, do two things, averaging & obtaining the even/odd partitions to save some time.
@param pl: particle list
@type ps: L{pytom.basic.structures.ParticleList}
@param name_prefix: name prefix output densities
@type name_prefix: C{str}
@param weight_average: weighted average
@type weight_average: C{str}
"""
from pytom.basic.structures import ParticleList
even = ParticleList('.')
odd = ParticleList('.')
for i in range(len(pl)):
if i % 2 == 0:
even.append(pl[i])
else:
odd.append(pl[i])
even.average(name_prefix + 'even.em',
progressBar=False,
createInfoVolumes=False,
_mpiParallel=False,
weighting=weight_average)
odd.average(name_prefix + 'odd.em',
progressBar=False,
createInfoVolumes=False,
_mpiParallel=False,
weighting=weight_average)
def average_sub_pl(self, pl, name_prefix, weight_average):
"""For worker node, do two things, averaging & obtaining the even/odd partitions to save some time.
"""
from pytom.basic.structures import ParticleList
even = ParticleList('.')
odd = ParticleList('.')
for i in xrange(len(pl)):
if i % 2 == 0:
even.append(pl[i])
else:
odd.append(pl[i])
even.average(name_prefix + 'even.em',
progressBar=False,
createInfoVolumes=False,
_mpiParallel=False,
weighting=weight_average)
odd.average(name_prefix + 'odd.em',
progressBar=False,
createInfoVolumes=False,
_mpiParallel=False,
weighting=weight_average)
from pytom_volume import read
from sh.frm import frm_align_vol
from pytom.tools.maths import rotation_distance, euclidianDistance
from pytom.tools.timing import Timing
from pytom.basic.structures import ParticleList
from pytom.basic.structures import Shift, Rotation
pl = ParticleList('.')
pl.fromXMLFile('/fs/home/ychen/4Chen/first100.xml')
r = read('/fs/home/ychen/4Chen/avg_first100.em')
for pp in pl:
v = read(pp.getFilename())
pos, ang = frm_align_vol(v, [-60.0, 60.0], r, [8, 32], 10, mask=30)
pp.setShift(
Shift([
pos[0] - v.sizeX() / 2, pos[1] - v.sizeY() / 2,
pos[2] - v.sizeZ() / 2
]))
pp.setRotation(Rotation(ang))
pl.average('average.em', True)
def growingAverageNew(particleList=None,angleObject=None,maskFile=None,scoreObject=None,startClassNumber=0,destinationDirectory='.',preprocessing = None,binning=1,verbose=False):
"""
"""
from pytom.alignment.alignmentFunctions import bestAlignment
from pytom.basic.structures import Reference,Particle,Rotation,ParticleList
from pytom.alignment.preprocessing import Preprocessing
if not preprocessing:
preprocessing = Preprocessing()
numberOfClasses = len(particleList.splitByClass())
if verbose:
print('Processing ' + str(numberOfClasses) + ' classes.')
print('Generating start average')
startAverageList = particleList.particlesFromClass(float(startClassNumber))
startAverageList.average(destinationDirectory + '/GA_it0.em',progressBar=verbose)
currentReference = Reference(destinationDirectory + '/GA_it0.em')
growingAverageParticleList = ParticleList(particleList.getDirectory())
for p in startAverageList:
p.setRotation(Rotation(0,0,0))
growingAverageParticleList.append(p)
for i in range(2,numberOfClasses):
currentParticleList = particleList.particlesFromClass(float(i))
if verbose:
print('Generating ' + str(i) + '. class average')
currentParticleList.average(destinationDirectory + '/CA_it'+str(i)+'.em',progressBar=verbose)
currentParticle = Particle(destinationDirectory + '/CA_it'+str(i)+'.em',wedgeInfo=currentParticleList[0].getWedgeInfo())
if verbose:
print('Running alignment iteration ' + str(i))
print(currentParticle)
print(currentReference)
currentPeak = bestAlignment(currentParticle.getVolume(),currentReference.getVolume(),currentReference.getWeighting(),currentParticle.getWedgeInfo(),angleObject,scoreObject,maskFile,preprocessing=preprocessing,binning=binning)
if verbose:
print('Parameters determined:')
print(currentPeak)
for p in currentParticleList:
p.setRotation(currentPeak.getRotation())
p.setShift(currentPeak.getShift())
growingAverageParticleList.append(p)
if verbose:
print('Generating growing average ' + str(i))
growingAverageParticleList.average(destinationDirectory + '/GA_it'+ str(i) +'.em',progressBar=verbose)
currentReference = Reference(destinationDirectory + '/GA_it'+ str(i) +'.em')
angleObject.reset()
