def test_FRM(self):
import swig_frm
from sh_alignment.frm import frm_align
from pytom_volume import vol, rotate, shift
from pytom.basic.structures import Rotation, Shift
from pytom.tools.maths import rotation_distance
v = vol(32,32,32)
v.setAll(0)
vMod = vol(32,32,32)
vRot = vol(32,32,32)
v.setV(1,10,10,10)
v.setV(1,20,20,20)
v.setV(1,15,15,15)
v.setV(1,7,21,7)
rotation = Rotation(10,20,30)
shiftO = Shift(1,-3,5)
rotate(v,vRot,rotation.getPhi(),rotation.getPsi(),rotation.getTheta())
shift(vRot,vMod,shiftO.getX(),shiftO.getY(),shiftO.getZ())
pos, ang, score = frm_align(vMod, None, v, None, [4, 64], 10)
rotdist = rotation_distance(ang1=rotation, ang2=ang)
diffx = shiftO[0] - (pos[0] - 16)
diffy = shiftO[1] - (pos[1] - 16)
diffz = shiftO[2] - (pos[2] - 16)
self.assertTrue( rotdist < 5., msg='Rotations are different')
self.assertTrue( diffx < .5, msg='x-difference > .5')
self.assertTrue( diffy < .5, msg='y-difference > .5')
self.assertTrue( diffz < .5, msg='z-difference > .5')
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,
particle='',
reference=-1.0,
score=-1.0,
shift=-1.0,
rotation=-1.0,
angleObject=-1):
from pytom.basic.structures import Particle, Reference, Shift, Rotation
from numpy import long
if particle.__class__ == str:
self._particle = Particle(particle)
elif particle.__class__ == Particle:
self._particle = particle
else:
self._particle = Particle()
if reference.__class__ == str:
self._reference = Reference(reference)
elif reference.__class__ == Reference:
self._reference = reference
else:
self._reference = Reference()
if shift.__class__ == list:
self._shift = Shift(shift)
elif shift.__class__ == float:
self._shift = Shift()
else:
self._shift = shift
if rotation.__class__ == list:
self._rotation = Rotation(rotation)
elif rotation.__class__ == Rotation:
self._rotation = rotation
else:
self._rotation = Rotation()
if score.__class__ == float:
from pytom.score.score import xcfScore
self._score = xcfScore()
else:
self._score = score
if angleObject.__class__ == float or isinstance(
angleObject, (int, long)):
from pytom.angles.angleList import AngleList
self._angleObject = AngleList()
else:
self._angleObject = angleObject
def getShift(self):
from pytom.basic.structures import Shift
if self._shift.__class__ == list:
return Shift(self._shift)
else:
return self._shift
def frm_proxy(p, ref, freq, offset, binning, mask):
from pytom_volume import read, pasteCenter, vol
from pytom.basic.transformations import resize
from pytom.basic.structures import Shift, Rotation
from sh_alignment.frm import frm_align
import time
v = p.getVolume(binning)
if mask.__class__ == str:
maskBin = read(mask, 0, 0, 0, 0, 0, 0, 0, 0, 0, binning, binning,
binning)
if v.sizeX() != maskBin.sizeX() or v.sizeY() != maskBin.sizeY(
) or v.sizeZ() != maskBin.sizeZ():
mask = vol(v.sizeX(), v.sizeY(), v.sizeZ())
mask.setAll(0)
pasteCenter(maskBin, mask)
else:
mask = maskBin
pos, angle, score = frm_align(v, p.getWedge(), ref.getVolume(), None,
[4, 64], freq, offset, mask)
return (Shift([
pos[0] - v.sizeX() // 2, pos[1] - v.sizeY() // 2,
pos[2] - v.sizeZ() // 2
]), Rotation(angle), score, p.getFilename())
def general_transform2d(v, rot=None, shift=None, scale=None, order=[0, 1, 2], crop=True):
"""Perform general transformation of 2D data using 3rd order spline interpolation.
@param v: volume in 2d (it's got to be an image)
@type v: L{pytom_volume.vol}
@param rot: rotate
@type rot: float
@param shift: shift
@type shift: L{pytom.basic.structures.Shift} or list [x,y]
@param scale: uniform scale
@type scale: float
@param order: the order in which the three operations are performed (smaller means first) \
e.g.: [2,1,0]: rotation: 2, scale: 1, translation:0 => translation 1st
@type order: list
@param crop: crop the resulting volume to have the same size as original volume (default: True)
@type crop: boolean
@return: pytom_volume
"""
from pytom.basic.structures import Shift
from pytom_volume import vol
if not isinstance(v,vol):
if isinstance(v,tuple) and isinstance(v[0],vol):
v = v[0]
else:
raise TypeError('general_transform2d: v must be of type pytom_volume.vol! Got ' + str(v.__class__) + ' instead!')
if v.sizeZ() != 1:
raise RuntimeError('general_transform2d: v must be 2D!')
if rot is None:
rot = [0., 0., 0.]
elif rot.__class__ != int and rot.__class__ != float:
raise RuntimeError("Please provide only 1 angle because you are dealing with 2D data!")
else:
rot = [rot, 0., 0.]
if shift.__class__ == list and len(shift) == 2:
shift = Shift(shift[0], shift[1], 0.)
if shift.__class__ == list and len(shift) == 3:
shift = Shift(shift[0], shift[1], 0.) # you cannot shift 2D image along z axis, can you?
if crop:
vv= general_transform_crop(v, rot=rot, shift=shift, scale=[scale, scale, 1], order=order)
else:
vv = general_transform(v, rot, shift, [scale, scale, 1], order)
return vv
def writeCroppedParticles(particleListName, output, center, cubesize):
"""
@param particleListName: name of particle list
@type particleListName: str
@param output: Name of output particles
@type output: str
@param center: center of output particles in template orientation
@type center: list
@param cubesize: Size of output particles in pixel
@type cubesize: int
"""
from pytom.basic.structures import ParticleList, Particle, Shift
from pytom_volume import transformSpline as transform
from pytom_volume import subvolume, vol
pl = ParticleList()
pl.fromXMLFile(filename=particleListName)
#copy particle list for list of cropped particles
pl_new = pl.copy()
pvol = pl[0].getVolume()
sizeX = pvol.sizeX()
sizeY = pvol.sizeY()
sizeZ = pvol.sizeZ()
pvol_ali = vol(sizeX, sizeY, sizeZ)
subV = vol(cubesize, cubesize, cubesize)
sub_startX = center[0]-cubesize/2
sub_startY = center[1]-cubesize/2
sub_startZ = center[2]-cubesize/2
if (sub_startX < 0) or (sub_startY < 0) or (sub_startZ < 0):
raise ValueError('cubesize too large :(')
for (ipart, part) in enumerate(pl):
pvol_ali.setAll(0)
subV.setAll(0)
pvol = part.getVolume()
rot = part.getRotation()
rotinvert = rot.invert()
shiftV = part.getShift()
transform(pvol, pvol_ali, rotinvert[0], rotinvert[1], rotinvert[2],
sizeX/2, sizeY/2, sizeZ/2, -shiftV[0], -shiftV[1], -shiftV[2], 0, 0, 0)
# box out subvolume
subV = subvolume(pvol_ali, sub_startX, sub_startY, sub_startZ, cubesize, cubesize, cubesize)
transform(subV, subV, rot[0], rot[1], rot[2], cubesize/2, cubesize/2, cubesize/2, 0, 0, 0, 0, 0, 0)
fname = part.getFilename()
idx = fname.split('_')[-1].split('.')[0]
nfname = output+'_'+idx+'.em'
print("write file " + nfname)
subV.write(nfname)
pl_new[ipart].setFilename(newFilename=nfname)
pl_new[ipart].setShift(shift=Shift(0,0,0))
return pl_new
def run(self, verbose=False):
from sh_alignment.frm import frm_align
from pytom.basic.structures import Shift, Rotation
from pytom.tools.ProgressBar import FixedProgBar
while True:
# get the job
try:
job = self.get_job()
except:
if verbose:
print(self.node_name + ': end')
break # get some non-job message, break it
if verbose:
prog = FixedProgBar(0,
len(job.particleList) - 1,
self.node_name + ':')
i = 0
ref = job.reference[0].getVolume()
# run the job
for p in job.particleList:
if verbose:
prog.update(i)
i += 1
v = p.getVolume()
pos, angle, score = frm_align(v, p.getWedge(), ref, None,
job.bw_range, job.freq,
job.peak_offset,
job.mask.getVolume())
p.setShift(
Shift([
pos[0] - v.sizeX() / 2, pos[1] - v.sizeY() / 2,
pos[2] - v.sizeZ() / 2
]))
p.setRotation(Rotation(angle))
p.setScore(FRMScore(score))
# average the particle list
name_prefix = os.path.join(
self.destination, self.node_name + '_' + str(job.max_iter))
self.average_sub_pl(job.particleList, name_prefix, job.weighting)
# send back the result
self.send_result(
FRMResult(name_prefix, job.particleList, self.mpi_id))
pytom_mpi.finalise()
def FRMAlignmentWrapper(particle,wedgeParticle, reference, wedgeReference,bandwidth, highestFrequency, mask = None , peakPrior = None):
"""
FRMAlignmentWrapper: Wrapper for frm_align to handle PyTom objects.
@param particle: The particle
@type particle: L{pytom.basic.structures.Particle}
@param wedgeParticle: Wedge object of particle
@type wedgeParticle: L{pytom.basic.structures.Wedge}
@param reference: Reference used for alignment
@type reference: L{pytom.basic.structures.Reference}
@param wedgeReference: Information about reference wedge
@type wedgeReference: L{pytom.basic.structures.Wedge}
@param bandwidth: The bandwidth of the spherical harmonics - lowestBand used, highestBand used
@type bandwidth: [lowestBand,highestBand]
@param highestFrequency: Highest frequency for lowpass filter in fourierspace
@type highestFrequency: int
@param mask: Mask that is applied to the particle
@type mask: L{pytom.basic.structures.Mask}
@param peakPrior: Maximum distance of peak from origin
@type peakPrior: L{pytom.score.score.PeakPrior} or an integer
@return: Returns a list of [L{pytom.basic.structures.Shift}, L{pytom.basic.structures.Rotation}, scoreValue]
"""
from pytom.basic.structures import Particle,Reference,Mask,Wedge,Shift,Rotation
from pytom.score.score import PeakPrior
from sh_alignment.frm import frm_align
if particle.__class__ == Particle:
particle = particle.getVolume()
if reference.__class__ == Reference:
reference = reference.getVolume()
if mask.__class__ == Mask:
mask = mask.getVolume()
else:
mask = None
if bandwidth.__class__ == list and len(bandwidth) != 2:
raise RuntimeError('Bandwidth parameter must be a list of two integers!')
if peakPrior and peakPrior.__class__ == PeakPrior:
peakPrior = int(peakPrior.getRadius())
if not peakPrior or peakPrior < 0.0001:
peakPrior = None
pos, angle, score = frm_align(particle, wedgeParticle.getWedgeObject(), reference*mask, wedgeReference.getWedgeObject(), bandwidth, int(highestFrequency), peakPrior)
return [Shift([pos[0]-particle.sizeX()/2, pos[1]-particle.sizeY()/2, pos[2]-particle.sizeZ()/2]), Rotation(angle), score]
def vector2transRot(self, rot_trans):
"""
convert 6-dimensional vector to rotation and translation
@param rot_trans: rotation and translation vector (6-dim: z1,z2,x \
angles, x,y,z, translations)
@type rot_trans: L{list}
@return: rotation of vol2, translation of vol2
@rtype: L{pytom.basic.Rotation}, L{pytom.basic.Shift}
@author: FF
"""
from pytom.basic.structures import Rotation, Shift
rot = Rotation()
trans = Shift()
for ii in range(0, 3):
rot[ii] = self.rot_trans[ii]
for ii in range(3, 6):
trans[ii - 3] = self.rot_trans[ii]
return rot, trans
def run(self, verbose=False):
from pytom.gui.additional.frm import frm_align
from sh_alignment.constrained_frm import frm_constrained_align, AngularConstraint
from pytom.basic.structures import Shift, Rotation
from pytom.tools.ProgressBar import FixedProgBar
while True:
# get the job
try:
job = self.get_job()
except:
if verbose:
print self.node_name + ': end'
break # get some non-job message, break it
if verbose:
prog = FixedProgBar(0,
len(job.particleList) - 1,
self.node_name + ':')
i = 0
ref = job.reference.getVolume()
# run the job
for p in job.particleList:
if verbose:
prog.update(i)
i += 1
v = p.getVolume()
if job.constraint:
constraint = job.constraint
if job.constraint.type == AngularConstraint.ADP_ANGLE: # set the constraint around certain angle
rot = p.getRotation()
constraint.setAngle(rot.getPhi(), rot.getPsi(),
rot.getTheta())
pos, angle, score = frm_constrained_align(
v, p.getWedge(), ref, None, job.bw_range, job.freq,
job.peak_offset, job.mask.getVolume(), constraint)
else:
pos, angle, score = frm_align(v, p.getWedge(), ref, None,
job.bw_range, job.freq,
job.peak_offset,
job.mask.getVolume())
p.setShift(
Shift([
pos[0] - v.sizeX() / 2, pos[1] - v.sizeY() / 2,
pos[2] - v.sizeZ() / 2
]))
p.setRotation(Rotation(angle))
p.setScore(FRMScore(score))
# average the particle list
name_prefix = self.node_name + '_' + str(job.max_iter)
self.average_sub_pl(job.particleList, name_prefix, job.weighting)
# send back the result
self.send_result(
FRMResult(name_prefix, job.particleList, self.mpi_id))
pytom_mpi.finalise()
def alignTwoVolumes(particle,reference,angleObject,mask,score,preprocessing,progressBar=False):
"""
alignTwoVolumes: align two volumes with respect to each other
@param particle: volume to be aligned
@param reference: reference volume (not translated and rotated)
@param angleObject: angular sampling
@param mask: mask volume
@param score: score type
@param preprocessing: preprocessing parameters
@param progressBar: show progress bar
@type progressBar: bool
"""
from pytom.alignment.structures import GrowingAverageInterimResult
from pytom.basic.structures import Rotation,Shift
partVolume = particle.getVolume()
refVolume = reference.getVolume()
refWeight = reference.getWeighting()
peak = bestAlignment(partVolume,refVolume,refWeight,particle.getWedge(),
angleObject,score,mask,preprocessing)
score.setValue(peak.getScoreValue())
return GrowingAverageInterimResult(particle,reference,Rotation(peak.getRotation()),Shift(peak.getShift()),score)
def bestAlignment(particle, reference, referenceWeighting, wedgeInfo, rotations,
scoreObject=0, mask=None, preprocessing=None, progressBar=False, binning=1,
bestPeak=None, verbose=False):
"""
bestAlignment: Determines best alignment of particle relative to the reference
@param particle: A particle
@type particle: L{pytom_volume.vol}
@param reference: A reference
@type reference: L{pytom_volume.vol}
@param referenceWeighting: Fourier weighting of the reference (sum of wedges for instance)
@type referenceWeighting: L{pytom.basic.structures.vol}
@param wedgeInfo: What does the wedge look alike?
@type wedgeInfo: L{pytom.basic.structures.Wedge}
@param rotations: All rotations to be scanned
@type rotations: L{pytom.angles.AngleObject}
@param scoreObject:
@type scoreObject: L{pytom.score.score.Score}
@param mask: real-space mask for correlation function
@type mask: L{pytom.basic.structures.Particle}
@param preprocessing: Class storing preprocessing of particle and reference such as bandpass
@type preprocessing: L{pytom.alignment.preprocessing.Preprocessing}
@param progressBar: Display progress bar of alignment. False by default.
@param binning: binning factor - e.g. binning=2 reduces size by FACTOR of 2
@type binning: int or float
@param bestPeak: Initialise best peak with old values.
@param verbose: Print out infos. Writes CC volume to disk!!! Default is False
@return: Returns the best rotation for particle and the corresponding scoring result.
@author: Thomas Hrabe
"""
from pytom.basic.correlation import subPixelPeak, subPixelPeakParabolic
from pytom.alignment.structures import Peak
from pytom_volume import peak, vol, vol_comp
from pytom.basic.filter import filter,rotateWeighting
from pytom.basic.structures import Rotation, Shift, Particle, Mask
from pytom.angles.angle import AngleObject
from pytom.alignment.preprocessing import Preprocessing
from pytom.basic.transformations import resize, resizeFourier
binningType = 'Fourier' # or 'Fourier'
assert isinstance(rotations, AngleObject), "bestAlignment: rotations must be " \
"AngleObject!"
currentRotation = rotations.nextRotation()
if currentRotation == [None,None,None]:
raise Exception('bestAlignment: No rotations are sampled! Something is wrong with input rotations')
assert particle.__class__ == vol, "particle not of type vol"
assert reference.__class__ == vol, "reference not of type vol"
assert (referenceWeighting.__class__ == vol or referenceWeighting.__class__ == str), \
"referenceWeighting not volume or str"
if mask:
assert mask.__class__ == Mask, "Mask not of type Mask"
m = mask.getVolume()
if scoreObject == 0 or not scoreObject:
from pytom.score.score import xcfScore
scoreObject = xcfScore()
# fix binning
if binning == 0:
binning = 1
if binning != 1:
particleUnbinned = vol(particle.sizeX(), particle.sizeY(), particle.sizeZ())
particleUnbinned.copyVolume(particle)
particle = resize(volume=particle, factor=1./binning, interpolation=binningType)
if type(particle) == tuple:
particle = particle[0]
referenceUnbinned = vol(reference.sizeX(), reference.sizeY(), reference.sizeZ())
referenceUnbinned.copyVolume(reference)
reference = resize(volume=reference, factor=1./binning, interpolation=binningType)
if type(reference) == tuple:
reference = reference[0]
if mask:
m = resize(volume=m, factor=1./binning, interpolation='Spline')
if not referenceWeighting.__class__ == str:
referenceWeightingUnbinned = vol_comp(referenceWeighting.sizeX(), referenceWeighting.sizeY(),
referenceWeighting.sizeZ())
referenceWeightingUnbinned.copyVolume(referenceWeighting)
if binning != 1:
referenceWeighting = resizeFourier(fvol=referenceWeighting, factor=1./binning)
centerX, centerY, centerZ = int(particle.sizeX()/2), int(particle.sizeY()/2), int(particle.sizeZ()/2)
# create buffer volume for transformed particle
particleCopy = vol(particle.sizeX(),particle.sizeY(),particle.sizeZ())
particle = wedgeInfo.apply(particle) #apply wedge to itself
if preprocessing is None:
preprocessing = Preprocessing()
preprocessing.setTaper( taper=particle.sizeX()/10.)
particle = preprocessing.apply(volume=particle, bypassFlag=True) # filter particle to some resolution
particleCopy.copyVolume(particle)
# compute standard veviation volume really only if needed
if mask and (scoreObject._type=='FLCFScore'):
from pytom_volume import sum
from pytom.basic.correlation import meanUnderMask, stdUnderMask
p = sum(m)
meanV = meanUnderMask(particle, m, p)
stdV = stdUnderMask(particle, m, p, meanV)
else:
meanV = None
stdV = None
while currentRotation != [None,None,None]:
if mask:
m = mask.getVolume(currentRotation)
if binning != 1:
m = resize(volume=m, factor=1./binning, interpolation='Spline')
#update stdV if mask is not a sphere
# compute standard deviation volume really only if needed
if not mask.isSphere() and (scoreObject._type=='FLCFScore'):
meanV = meanUnderMask(particle, m, p)
stdV = stdUnderMask(particle, m, p, meanV)
else:
m = None
simulatedVol = _rotateWedgeReference(reference, currentRotation, wedgeInfo, m, [centerX, centerY, centerZ])
simulatedVol = preprocessing.apply(volume=simulatedVol, bypassFlag=True)
#weight particle
if not referenceWeighting.__class__ == str:
from pytom_freqweight import weight
weightingRotated = rotateWeighting(weighting=referenceWeighting, z1=currentRotation[0],
z2=currentRotation[1], x=currentRotation[2], isReducedComplex=True,
returnReducedComplex=True, binarize=False)
particleCopy.copyVolume(particle)
r = list(filter(particleCopy, weight(weightingRotated)))
particleCopy = r[0]
scoringResult = scoreObject.score(particleCopy, simulatedVol, m, stdV)
pk = peak(scoringResult)
#with subPixelPeak
[peakValue,peakPosition] = subPixelPeak(scoreVolume=scoringResult, coordinates=pk,
interpolation='Quadratic', verbose=False)
#[peakValue,peakPosition] = subPixelPeakParabolic(scoreVolume=scoringResult, coordinates=pk, verbose=False)
# determine shift relative to center
shiftX = (peakPosition[0] - centerX) * binning
shiftY = (peakPosition[1] - centerY) * binning
shiftZ = (peakPosition[2] - centerZ) * binning
#NANs would fail this test.
assert peakValue == peakValue, "peakValue seems to be NaN"
newPeak = Peak(peakValue, Rotation(currentRotation), Shift(shiftX, shiftY, shiftZ))
if verbose:
print('Rotation: z1=%3.1f, z2=%3.1f, x=%3.1f; Dx=%2.2f, Dy=%2.2f, Dz=%2.2f, CC=%2.3f' % \
(currentRotation[0], currentRotation[1], currentRotation[2], shiftX, shiftY, shiftZ, peakValue))
if bestPeak is None:
bestPeak = newPeak
if verbose:
scoringResult.write('BestScore.em')
if bestPeak < newPeak:
bestPeak = newPeak
if verbose:
scoringResult.write('BestScore.em')
currentRotation = rotations.nextRotation()
# repeat ccf for binned sampling to get translation accurately
if binning != 1:
m = mask.getVolume(bestPeak.getRotation())
centerX, centerY, centerZ = int(particleUnbinned.sizeX()/2), int(particleUnbinned.sizeY()/2), \
int(particleUnbinned.sizeZ()/2)
simulatedVol = _rotateWedgeReference(referenceUnbinned, bestPeak.getRotation(), wedgeInfo, m,
[centerX, centerY, centerZ])
simulatedVol = preprocessing.apply(volume=simulatedVol, bypassFlag=True)
if mask and scoreObject._type=='FLCFScore':
p = sum(m)
meanV = meanUnderMask(volume=particleUnbinned, mask=m, p=p)
stdV = stdUnderMask(volume=particleUnbinned, mask=m, p=p, meanV=meanV)
scoreObject._peakPrior.reset_weight()
scoringResult = scoreObject.score(particle=particleUnbinned, reference=simulatedVol, mask=m, stdV=stdV)
pk = peak(scoringResult)
[peakValue,peakPosition] = subPixelPeak(scoreVolume=scoringResult, coordinates=pk, interpolation='Quadratic',
verbose=False)
shiftX = (peakPosition[0] - centerX)
shiftY = (peakPosition[1] - centerY)
shiftZ = (peakPosition[2] - centerZ)
bestPeak = Peak(peakValue, bestPeak.getRotation(), Shift(shiftX, shiftY, shiftZ))
if verbose:
print('BestAlignment: z1=%3.1f, z2=%3.1f, x=%3.1f; Dx=%2.2f, Dy=%2.2f, Dz=%2.2f, CC=%2.3f' % \
(bestPeak.getRotation()[0], bestPeak.getRotation()[1], bestPeak.getRotation()[2],
bestPeak.getShift()[0], bestPeak.getShift()[1], bestPeak.getShift()[2], bestPeak.getScoreValue()))
rotations.reset()
scoreObject._peakPrior.reset_weight()
return bestPeak
def run(self, verbose=False):
from sh_alignment.frm import frm_align
from sh_alignment.constrained_frm import frm_constrained_align, AngularConstraint
from pytom.basic.structures import Shift, Rotation
from pytom.tools.ProgressBar import FixedProgBar
from pytom.basic.transformations import resize, resizeFourier
binningType = 'Fourier'
while True:
# get the job
try:
job = self.get_job()
except:
if verbose:
print(self.node_name + ': end')
break # get some non-job message, break it
if verbose:
prog = FixedProgBar(0,
len(job.particleList) - 1,
self.node_name + ':')
i = 0
ref = job.reference.getVolume()
if job.binning > 1:
ref = resize(volume=ref,
factor=1. / job.binning,
interpolation=binningType)
if type(ref) == tuple:
ref = ref[0]
# re-set max frequency in case it exceeds Nyquist - a bit brute force
job.freq = min(job.freq, ref.sizeX() // 2 - 1)
# run the job
for p in job.particleList:
if verbose:
prog.update(i)
i += 1
v = p.getVolume()
if job.binning > 1:
v = resize(volume=v,
factor=1. / job.binning,
interpolation=binningType)
if type(v) == tuple:
v = v[0]
mask = job.mask.getVolume()
if job.binning > 1:
mask = resize(volume=mask,
factor=1. / job.binning,
interpolation='Spline')
if type(mask) == tuple:
mask = mask[0]
if job.constraint:
constraint = job.constraint
if job.constraint.type == AngularConstraint.ADP_ANGLE: # set the constraint around certain angle
rot = p.getRotation()
constraint.setAngle(rot.getPhi(), rot.getPsi(),
rot.getTheta())
#pos, angle, score = frm_constrained_align(v, p.getWedge(), ref, None, job.bw_range, job.freq, job.peak_offset, job.mask.getVolume(), constraint)
if job.binning > 1:
pos, angle, score = frm_constrained_align(
v, p.getWedge(), ref, None, job.bw_range, job.freq,
job.peak_offset / job.binning, mask, constraint)
else:
pos, angle, score = frm_constrained_align(
v, p.getWedge(), ref, None, job.bw_range, job.freq,
job.peak_offset, mask, constraint)
else:
#pos, angle, score = frm_align(v, p.getWedge(), ref, None, job.bw_range, job.freq, job.peak_offset, job.mask.getVolume())
#if job.binning >1:
# print(job.peak_offset)
# print(type(job.peak_offset))
# print(job.peak_offset/job.binning)
# print(type(job.binning))
# pos, angle, score = frm_align(v, p.getWedge(), ref, None, job.bw_range, job.freq,
# job.peak_offset/job.binning, mask)
#else:
pos, angle, score = frm_align(v, p.getWedge(), ref, None,
job.bw_range, job.freq,
job.peak_offset, mask)
if job.binning > 1:
pos[0] = job.binning * (pos[0] - v.sizeX() / 2)
pos[1] = job.binning * (pos[1] - v.sizeY() / 2)
pos[2] = job.binning * (pos[2] - v.sizeZ() / 2)
p.setShift(Shift([pos[0], pos[1], pos[2]]))
else:
p.setShift(
Shift([
pos[0] - v.sizeX() / 2, pos[1] - v.sizeY() / 2,
pos[2] - v.sizeZ() / 2
]))
p.setRotation(Rotation(angle))
p.setScore(FRMScore(score))
# average the particle list
name_prefix = os.path.join(
job.destination, self.node_name + '_' + str(job.max_iter))
self.average_sub_pl(job.particleList, name_prefix, job.weighting)
# send back the result
self.send_result(
FRMResult(name_prefix, job.particleList, self.mpi_id))
pytom_mpi.finalise()
def run(self, verbose=False):
from sh_alignment.frm import frm_align
from pytom.basic.structures import Shift, Rotation
from pytom.tools.ProgressBar import FixedProgBar
from pytom.basic.fourier import convolute
from pytom_volume import read, power
while True:
# get the job
try:
job = self.get_job()
except:
if verbose:
print(self.node_name + ': end')
break # get some non-job message, break it
if verbose:
prog = FixedProgBar(0,
len(job.particleList) - 1,
self.node_name + ':')
i = 0
ref = []
ref.append(job.reference[0].getVolume())
ref.append(job.reference[1].getVolume())
# convolute with the approximation of the CTF
if job.sum_ctf_sqr:
ctf = read(job.sum_ctf_sqr)
power(ctf,
0.5) # the number of CTFs should not matter, should it?
ref0 = ref[0]
ref1 = ref[1]
ref0 = convolute(ref0, ctf, True)
ref1 = convolute(ref1, ctf, True)
ref = [ref0, ref1]
if job.bfactor and job.bfactor != 'None':
# restore_kernel = create_bfactor_restore_vol(ref.sizeX(), job.sampleInformation.getPixelSize(), job.bfactor)
from pytom_volume import vol, read
bfactor_kernel = read(job.bfactor)
unit = vol(bfactor_kernel)
unit.setAll(1)
restore_kernel = unit / bfactor_kernel
# run the job
for p in job.particleList:
if verbose:
prog.update(i)
i += 1
v = p.getVolume()
# if weights is None: # create the weights according to the bfactor
# if job.bfactor == 0:
# weights = [1 for k in xrange(job.freq)]
# else:
# restore_fnc = create_bfactor_restore_fnc(ref.sizeX(), job.sampleInformation.getPixelSize(), job.bfactor)
# # cut out the corresponding part and square it to get the weights!
# weights = restore_fnc[1:job.freq+1]**2
if job.bfactor and job.bfactor != 'None':
v = convolute(v, restore_kernel,
True) # if bfactor is set, restore it
pos, angle, score = frm_align(v, p.getWedge(),
ref[int(p.getClass())], None,
job.bw_range, job.freq,
job.peak_offset,
job.mask.getVolume())
p.setShift(
Shift([
pos[0] - v.sizeX() / 2, pos[1] - v.sizeY() / 2,
pos[2] - v.sizeZ() / 2
]))
p.setRotation(Rotation(angle))
p.setScore(FRMScore(score))
# average the particle list
name_prefix = self.node_name + '_' + str(job.max_iter)
pair = ParticleListPair('', job.ctf_conv_pl, None, None)
pair.set_phase_flip_pl(job.particleList)
self.average_sub_pl(
pair.get_ctf_conv_pl(),
name_prefix) # operate on the CTF convoluted projection!
# send back the result
self.send_result(
FRMResult(name_prefix, job.particleList, self.mpi_id))
pytom_mpi.finalise()
def create_RandomParticleList(reffile,
pl_filename='pl.xml',
pdir='./testparticles',
nparticles=10):
"""
@param reffile: reference file
@type reffile: C{str}
@param nparticles: number of particles (default: 10)
@type nparticles: C{int}
@param pl_filename: particle list filename
@type pl_filename: C{str}
@param pdir: particle directory
@type pdir: C{str}
@return: particleList
@rtype: L{pytom.basic.ParticleList}
"""
from pytom.basic.structures import Particle, ParticleList, Rotation, Shift, Wedge
from pytom_volume import vol, rotate, shift, read
from pytom.basic.transformations import general_transform_crop
from pytom.basic.functions import initSphere
from pytom.simulation.whiteNoise import add as addNoise
import random
from os import mkdir
from pytom.score.score import FLCFScore as score
try:
mkdir(pdir)
except FileExistsError:
print('directory ' + pdir + ' existed already - using this one')
random.seed(0)
a = 0
wedge = Wedge(wedgeAngles=[30.0, 30.0], cutoffRadius=50.0)
pl = ParticleList(directory='./')
ref1 = read(reffile)
ref2 = initSphere(sizeX=ref1.sizeX(),
sizeY=ref1.sizeY(),
sizeZ=ref1.sizeZ(),
radius=45)
#ref2.write('testData/mask_45.em')
parts = {0: ref1, 1: ref2}
for ii in range(0, nparticles):
if not ii % 2:
ref = read(reffile)
else:
ref = initSphere(sizeX=ref1.sizeX(),
sizeY=ref1.sizeY(),
sizeZ=ref1.sizeZ(),
radius=30,
smooth=30 / 10)
rot = Rotation(random.uniform(0, 360), random.uniform(0, 360),
random.uniform(0, 180))
shift = Shift(x=a * random.uniform(-5, 5),
y=a * random.uniform(-5, 5),
z=a * random.uniform(-5, 5))
rotvol = general_transform_crop(v=ref,
rot=rot,
shift=shift,
scale=None,
order=[0, 1, 2])
# add some noise
noisy = addNoise(volume=rotvol, SNR=1)
fname = pdir + '/particle_' + str(ii) + '.em'
#noisy.write( fname)
p = Particle(filename=fname,
rotation=rot,
shift=shift,
wedge=wedge,
className=0,
pickPosition=None,
score=score,
sourceInfo=None)
p.setScoreValue(0.0)
wg = p.getWedge().getWedgeObject()
wg.apply(noisy, Rotation(0, 0, 0)).write(fname)
pl.append(particle=p)
pl.setFileName(filename=pl_filename)
pl.toXMLFile(filename=pl_filename)
return pl
def create_RandomParticleList(reffile,
pl_filename='pl.xml',
pdir='./testparticles',
nparticles=10):
"""
@param reffile: reference file
@type reffile: C{str}
@param nparticles: number of particles (default: 10)
@type nparticles: C{int}
@param pl_filename: particle list filename
@type pl_filename: C{str}
@param pdir: particle directory
@type pdir: C{str}
@return: particleList
@rtype: L{pytom.basic.ParticleList}
"""
from pytom.basic.structures import Particle, ParticleList, Rotation, Shift
from pytom_volume import vol, rotate, shift, read
from pytom.basic.transformations import general_transform_crop
from pytom.simulation.whiteNoise import add as addNoise
import random
from os import mkdir
from pytom.score.score import FLCFScore as score
try:
mkdir(pdir)
except FileExistsError:
print('directory ' + pdir + ' existed already - using this one')
random.seed(0)
pl = ParticleList(directory='./')
ref = read(reffile)
for ii in range(0, nparticles):
rot = Rotation(random.uniform(0, 360), random.uniform(0, 360),
random.uniform(0, 180))
shift = Shift(x=random.uniform(-5, 5),
y=random.uniform(-5, 5),
z=random.uniform(-5, 5))
rotvol = general_transform_crop(v=ref,
rot=rot,
shift=shift,
scale=None,
order=[0, 1, 2])
# add some noise
noisy = addNoise(volume=rotvol, SNR=1)
fname = pdir + '/particle_' + str(ii) + '.em'
noisy.write(fname)
p = Particle(filename=fname,
rotation=rot,
shift=shift,
wedge=None,
className=0,
pickPosition=None,
score=score,
sourceInfo=None)
p.setScoreValue(0.0)
pl.append(particle=p)
pl.setFileName(filename=pl_filename)
pl.toXMLFile(filename=pl_filename)
return pl
def general_transform(v, rot=None, shift=None, scale=None, order=[0, 1, 2]):
"""Perform general transformation using 3rd order spline interpolation.
@param v: volume
@type v: L{pytom_volume.vol}
@param rot: rotate
@type rot: pytom.basic.structures.Rotate or list
@param shift: shift
@type shift: pytom.basic.structures.Shift or list
@param scale: scale / magnification along each dimension
@type scale: list
@param order: the order in which the three operations are performed (smaller means first)
@type order: list
@return: pytom_volume
"""
from pytom.basic.structures import Rotation, Shift
from pytom_volume import vol
if not isinstance(v,vol):
raise TypeError('general_transform: v must be of type pytom_volume.vol! Got ' + str(v.__class__) + ' instead!')
if rot is None:
rot = Rotation(0.,0.,0.)
if rot.__class__ == list and len(rot) == 3:
rot = Rotation(rot[0], rot[1], rot[2])
if shift is None:
shift = Shift(0.,0.,0.)
if shift.__class__ == list and len(shift) == 3:
shift = Shift(shift[0], shift[1], shift[2])
if scale is None:
scale = [1.0, 1.0, 1.0]
if scale.__class__ == list and len(scale) == 3:
#check
if int(v.sizeX()*scale[0]) < 1 or int(v.sizeY()*scale[1]) < 1 or int(v.sizeZ()*scale[2]) < 1:
raise Exception("Scale not possible! Please check all the dimension after scaling is bigger than 1!")
else:
raise Exception("Scale parameter invalid! Should be a list of 3 values!")
from pytom_volume import vol, general_transform
from pytom.tools.maths import Matrix
# invert matrix
rotM = rot.toMatrix(True)
shiftM = shift.toMatrix()
scaleM = Matrix(4,4)
scaleM[0,0] = scale[0]
scaleM[1,1] = scale[1]
scaleM[2,2] = scale[2]
scaleM[3,3] = 1
# multiply them according to the order
all_mtx = [None, None, None]
try:
if order[2] > order[0]: # rotation first
rotCenter1 = Shift(-int(v.sizeX()/2), -int(v.sizeY()/2), -int(v.sizeZ()/2)).toMatrix()
rotCenter2 = Shift(int(v.sizeX()/2), int(v.sizeY()/2), int(v.sizeZ()/2)).toMatrix()
else: # scale first, so the center is different
rotCenter1 = Shift(-int(v.sizeX()*scale)/2, -int(v.sizeY()*scale)/2, -int(v.sizeZ()*scale)/2).toMatrix()
rotCenter2 = Shift(int(v.sizeX()*scale)/2, int(v.sizeY()*scale)/2, int(v.sizeZ()*scale)/2).toMatrix()
all_mtx[order[0]] = rotCenter2 * (rotM * rotCenter1) # for the rotation center!
all_mtx[order[1]] = shiftM
all_mtx[order[2]] = scaleM
except:
raise Exception("The given order is wrong! Should be a list of 0,1,2!")
mtx = all_mtx[2] * (all_mtx[1] * all_mtx[0])
res = vol(int(v.sizeX()*scale[0]), int(v.sizeY()*scale[1]), int(v.sizeZ()*scale[2]))
general_transform(v, res, mtx._matrix)
return res
def __init__(self,
vol1,
vol2,
score,
mask=None,
iniRot=None,
iniTrans=None,
opti='fmin_powell',
interpolation='linear',
verbose=False):
"""
alignment of a particle against a reference
@param vol1: (constant) volume
@type vol1: L{pytom_volume.vol}
@param vol2: volume that is matched to reference
@type vol2: L{pytom_volume.vol}
@param score: score for alignment - e.g., pytom.basic.correlation.nxcc
@type score: L{pytom.basic.correlation}
@param mask: mask correlation is constrained on
@type mask: L{pytom_volume.vol}
@param iniRot: initial rotation of vol2
@type iniRot: L{pytom.basic.Rotation}
@param iniTrans: initial translation of vol2
@type iniTrans: L{pytom.basic.Shift}
@param opti: optimizer ('fmin_powell', 'fmin', 'fmin_cg', 'fmin_slsqp', 'fmin_bfgs')
@param interpolation: interpolation type - 'linear' (default) or 'spline'
@type interpolation: str
@type opti: L{str}
@author: FF
"""
from pytom.basic.normalise import normaliseUnderMask, mean0std1
from pytom.tools.macros import volumesSameSize
from pytom_volume import vol
from pytom.basic.structures import Rotation, Shift
assert isinstance(interpolation,
str), "interpolation must be of type str"
self.verbose = verbose
if not volumesSameSize(vol1, vol2):
raise RuntimeError('Vol1 and vol2 must have same size!')
# normalize constant volume
if mask:
(v, p) = normaliseUnderMask(vol1, mask)
else:
v = mean0std1(vol1, True)
self.vol1 = v
self.vol2 = vol2
self.rotvol2 = vol(self.vol1.sizeX(), self.vol2.sizeY(),
self.vol2.sizeZ())
self.mask = mask
if not iniRot:
iniRot = Rotation()
if not iniTrans:
iniTrans = Shift()
self.rot_trans = self.transRot2vector(rot=iniRot, trans=iniTrans)
self.score = score
self.val = -100000.
self.centX = int(self.vol1.sizeX() // 2)
self.centY = int(self.vol1.sizeY() // 2)
self.centZ = int(self.vol1.sizeZ() // 2)
self.binning = 1
self.interpolation = interpolation
# set optimizer
self.opti = opti
if opti == 'fmin':
self.optimizer = scipy.optimize.fmin
elif opti == 'fmin_slsqp':
self.optimizer = scipy.optimize.fmin_slsqp
elif opti == 'fmin_cg':
self.optimizer = scipy.optimize.fmin_cg
elif opti == 'fmin_bfgs':
self.optimizer = scipy.optimize.fmin_bfgs
elif opti == 'fmin_powell':
self.optimizer = scipy.optimize.fmin_powell
else:
raise TypeError('opti must be of type str')
def _startGrowingAverageLoop(self):
"""
_startGrowingAverageLoop: Loops over all particles in self.particleList and computes growing average
"""
from pytom.alignment.structures import GrowingAverageInterimResult
from pytom.basic.structures import Rotation,Shift
from pytom.alignment.alignmentFunctions import alignTwoVolumes
numberParticles = len(self._particleList)
self._resultList = []
result = GrowingAverageInterimResult(self._particleList[self._startParticleNumber],self._reference,Rotation(0,0,0),Shift(0,0,0),self._score)
#init result list with first element
self._resultList.append(result)
self._createNewAverage(self._startParticleNumber)
for particleIterator in range(numberParticles):
if particleIterator == self._startParticleNumber:
continue
print('Running particle no ' + str(particleIterator))
particle = self._particleList[particleIterator]
#determine alignment of current reference with particle
result = alignTwoVolumes(particle,self._reference,self._angleObject,self._maskFile,self._score,self._preprocessing)
self._angleObject.reset()
self._resultList.append(result)
self._createNewAverage(particleIterator)
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)
class MaximisationResult(PyTomClass):
"""
MaximisationResult : Stores results of one maximisation process
"""
def __init__(self,
particle='',
reference=-1.0,
score=-1.0,
shift=-1.0,
rotation=-1.0,
angleObject=-1):
from pytom.basic.structures import Particle, Reference, Shift, Rotation
from numpy import long
if particle.__class__ == str:
self._particle = Particle(particle)
elif particle.__class__ == Particle:
self._particle = particle
else:
self._particle = Particle()
if reference.__class__ == str:
self._reference = Reference(reference)
elif reference.__class__ == Reference:
self._reference = reference
else:
self._reference = Reference()
if shift.__class__ == list:
self._shift = Shift(shift)
elif shift.__class__ == float:
self._shift = Shift()
else:
self._shift = shift
if rotation.__class__ == list:
self._rotation = Rotation(rotation)
elif rotation.__class__ == Rotation:
self._rotation = rotation
else:
self._rotation = Rotation()
if score.__class__ == float:
from pytom.score.score import xcfScore
self._score = xcfScore()
else:
self._score = score
if angleObject.__class__ == float or isinstance(
angleObject, (int, long)):
from pytom.angles.angleList import AngleList
self._angleObject = AngleList()
else:
self._angleObject = angleObject
def toParticle(self):
"""
toParticle: Converts this object to a Particle object.
@return:
@rtype: L{pytom.basic.structures.Particle}
"""
from pytom.basic.structures import Particle
particle = self._particle
particle.setRotation(self._rotation)
particle.setShift(self._shift)
particle.setScore(self._score)
return particle
def getParticle(self):
return self._particle
def getShift(self):
from pytom.basic.structures import Shift
if self._shift.__class__ == list:
return Shift(self._shift)
else:
return self._shift
def setShift(self, shift):
from pytom.basic.structures import Shift
assert shift.__class__ == Shift
self._shift = shift
def getAngleObject(self):
return self._angleObject
def getRotation(self):
from pytom.basic.structures import Rotation
if self._rotation.__class__ == list:
return Rotation(self._rotation[0], self._rotation[1],
self._rotation[2])
else:
return self._rotation.copy()
def getScore(self):
"""
getScore: Returns score object
"""
return self._score
def setRotation(self, rotation):
"""
setRotation:
@param rotation:
"""
from pytom.basic.structures import Rotation
if rotation.__class__ == list:
rotation = Rotation(rotation)
self._rotation = rotation
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 toXML(self):
"""
toXML : Compiles a XML from result object
@author: Thomas Hrabe
"""
from lxml import etree
resultElement = etree.Element("Result")
resultElement.append(self._particle.toXML())
if self._reference.hasGeneratedByInfo():
from pytom.basic.structures import Reference
newRef = Reference(self._reference.getReferenceFilename())
resultElement.append(newRef.toXML())
else:
resultElement.append(self._reference.toXML())
resultElement.append(self._shift.toXML())
resultElement.append(self._rotation.toXML())
resultElement.append(self._score.toXML())
resultElement.append(self._angleObject.toXML())
return resultElement
def copy(self):
return MaximisationResult(self._particle, self._reference, self._score,
self._shift, self._rotation,
self._angleObject)