def bandCF(volume, reference, band=[0, 100]):
"""
bandCF:
@param volume: The volume
@param reference: The reference
@param band: [a,b] - specify the lower and upper end of band. [0,1] if not set.
@return: First parameter - The correlation of the two volumes in the specified ring.
Second parameter - The bandpass filter used.
@rtype: List - [L{pytom_volume.vol},L{pytom_freqweight.weight}]
@author: Thomas Hrabe
@todo: does not work yet -> test is disabled
"""
if gpu:
import cupy as xp
else:
import numpy as xp
import pytom_volume
from math import sqrt
from pytom.basic import fourier
from pytom.basic.filter import bandpassFilter
from pytom.basic.correlation import nXcf
vf = bandpassFilter(volume, band[0], band[1], fourierOnly=True)
rf = bandpassFilter(reference, band[0], band[1], vf[1], fourierOnly=True)
v = pytom_volume.reducedToFull(vf[0])
r = pytom_volume.reducedToFull(rf[0])
absV = pytom_volume.abs(v)
absR = pytom_volume.abs(r)
pytom_volume.power(absV, 2)
pytom_volume.power(absR, 2)
sumV = abs(pytom_volume.sum(absV))
sumR = abs(pytom_volume.sum(absR))
if sumV == 0:
sumV = 1
if sumR == 0:
sumR = 1
pytom_volume.conjugate(rf[0])
fresult = vf[0] * rf[0]
#transform back to real space
result = fourier.ifft(fresult)
fourier.iftshift(result)
result.shiftscale(0, 1 / float(sqrt(sumV * sumR)))
return [result, vf[1]]
def bandpass(self, lowfreq, hifreq, smooth=0., bpf=None):
"""
bandpass filter image
@param lowfreq: lowest frequency of filter (=hi-pass)
@type lowfreq: L{float}
@param hifreq: highest frequency of filter (=low-pass)
@type hifreq: L{float}
@param smooth: smoothing
@type smooth: L{float}
@param bpf: bandpass filter object
@return: bandpass filter object
@rtype: L{pytom.basic.structures.BandPassFilter}
"""
from pytom.basic.filter import bandpassFilter
res = bandpassFilter(volume=self.data,
lowestFrequency=lowfreq,
highestFrequency=hifreq,
bpf=None,
smooth=smooth,
fourierOnly=False)
self.data = res[0]
bpf = res[1]
return bpf
def bandpass_in_nyquist(self, lowfreq, hifreq, smooth=0., bpf=None):
"""
bandpass filter image with frequencies specified in Nyquist
@param lowfreq: lowest frequency of filter in Nyquist (=hi-pass)
@param hifreq: highest frequency of filter in Nyquist (=low-pass)
@param smooth: smoothing in Nyquist
@param bpf: bandpass filter object
@return: bandpass filter object
@rtype: L{pytom.basic.structures.BandPassFilter}
"""
from pytom.basic.filter import bandpassFilter
res = bandpassFilter(volume=self.data,
lowestFrequency=lowfreq * self.dims[0] / 2.,
highestFrequency=hifreq * self.dims[0] / 2.,
bpf=None,
smooth=smooth * self.dims[0] / 2.,
fourierOnly=False)
self.data = res[0]
bpf = res[1]
return bpf
def calculateCorrelationVector(particle,
particleList,
mask,
particleIndex,
applyWedge=True,
binningFactor=0,
lowestFrequency=0,
highestFrequency=1):
"""
calculateCorrelationVector:
@param particle: the current particle
@param particleList: all the other particles
@param mask: corellation under a mask
@param applyWedge: Apply constrained correlation? True by default. Set to false for rotation classification for instance.
@param binningFactor: Binning of data when read. Default is 0 (larger values according to libtomc notation)
@param lowestFrequency: Lowest frequency for bandpass
@param highestFrequency: Highest frequency for bandpass
"""
from pytom.basic.structures import Particle, ParticleList, Mask
from pytom.cluster.correlationMatrixStructures import CorrelationVector
from pytom_volume import vol, rotate, shift
from pytom.basic.filter import bandpassFilter, filter
assert particle.__class__ == Particle
assert particleList.__class__ == ParticleList
assert mask.__class__ == Mask or mask.__class__ == str
from pytom.score.score import FLCFScore
from pytom.tools.memory import read as readBuffer
from pytom_volume import read
if mask.__class__ == str:
mask = read(mask, 0, 0, 0, 0, 0, 0, 0, 0, 0, int(binningFactor),
int(binningFactor), int(binningFactor))
else:
mask = read(mask.getFilename(), 0, 0, 0, 0, 0, 0, 0, 0, 0,
int(binningFactor), int(binningFactor), int(binningFactor))
#sc = nxcfScore()
sc = FLCFScore()
correlationVector = CorrelationVector(particle, particleList,
particleIndex)
particleRotation = particle.getRotation()
particleShift = particle.getShift()
particleShifted = None
otherParticleShifted = None
particleRotated = None
otherParticleRotated = None
bandpassFilterObject = None
for particleIndex in range(len(particleList)):
otherParticle = particleList[particleIndex]
#read from disk
particleVolume = read(particle.getFilename(), 0, 0, 0, 0, 0, 0, 0, 0,
0, int(binningFactor), int(binningFactor),
int(binningFactor))
#otherParticleVolume = read(otherParticle.getFilename(),binningX=binningFactor,binningY=binningFactor,binningZ=binningFactor)
otherParticleVolume = read(otherParticle.getFilename(), 0, 0, 0, 0, 0,
0, 0, 0, 0, int(binningFactor),
int(binningFactor), int(binningFactor))
#initialise memory for buffer volumes
if not particleRotated:
particleRotated = vol(particleVolume.sizeX(),
particleVolume.sizeY(),
particleVolume.sizeZ())
otherParticleRotated = vol(particleVolume.sizeX(),
particleVolume.sizeY(),
particleVolume.sizeZ())
particleShifted = vol(particleVolume.sizeX(),
particleVolume.sizeY(),
particleVolume.sizeZ())
otherParticleShifted = vol(particleVolume.sizeX(),
particleVolume.sizeY(),
particleVolume.sizeZ())
#get settings
rotationOtherParticle = otherParticle.getRotation()
otherParticleShift = otherParticle.getShift()
#apply shift determined
if particleShift.getX() != 0 or particleShift.getY(
) != 0 or particleShift.getZ() != 0:
shift(particleVolume, particleShifted, -particleShift[0],
-particleShift[1], -particleShift[2])
else:
particleShifted = particleVolume
if otherParticleShift.getX() != 0 or otherParticleShift.getY(
) != 0 or otherParticleShift.getZ() != 0:
shift(otherParticleVolume, otherParticleShifted,
-otherParticleShift[0], -otherParticleShift[1],
-otherParticleShift[2])
else:
otherParticleShifted = otherParticleVolume
#apply rotation determined
if particleRotation.getZ1() != 0 or particleRotation.getX(
) != 0 or particleRotation.getZ2() != 0:
rotate(otherParticleShifted, otherParticleRotated,
-particleRotation.getZ2(), -particleRotation.getZ1(),
-particleRotation.getX())
otherParticleRotated = otherParticleRotated * mask
else:
otherParticleRotated = otherParticleVolume
if rotationOtherParticle.getZ1() != 0 or rotationOtherParticle.getX(
) != 0 or rotationOtherParticle.getZ2() != 0:
rotate(particleShifted, particleRotated,
-rotationOtherParticle.getZ2(),
-rotationOtherParticle.getZ1(),
-rotationOtherParticle.getX())
particleRotated = particleRotated * mask
else:
particleRotated = particleVolume
applyWedge = particleRotation.getZ1() != 0 or particleRotation.getX(
) != 0 or particleRotation.getZ2() != 0
applyWedge = applyWedge or rotationOtherParticle.getZ1(
) != 0 or rotationOtherParticle.getX(
) != 0 or rotationOtherParticle.getZ2() != 0
#apply cross wedge
if applyWedge:
particleWedge = particle.getWedge()
otherParticleWedge = otherParticle.getWedge()
particleWedge.setRotation(particleRotation)
otherParticleWedge.setRotation(rotationOtherParticle)
particleVolume = otherParticleWedge.apply(particleRotated)
otherParticleVolume = particleWedge.apply(otherParticleRotated)
#apply bandpass
if 0 <= lowestFrequency < 1 and 0 < highestFrequency <= 1:
if not bandpassFilterObject:
bandpassString = str(lowestFrequency) + ':' + str(
highestFrequency) + ';'
r = bandpassFilter(particleVolume, bandpassString)
particleVolume = r[0]
bandpassFilterObject = r[1]
#print 'calculateCorrelationVector : Init bandpass'
else:
r = list(filter(particleVolume, bandpassFilterObject))
particleVolume = r[0]
#print 'calculateCorrelationVector : existing bandpass'
r = list(filter(otherParticleVolume, bandpassFilterObject))
otherParticleVolume = r[0]
#particleVolume.write('p.em')
#otherParticleVolume.write('op.em')
#assert False
#apply scoring here
value = sc.scoringCoefficient(otherParticleVolume, particleVolume,
mask)
if value != value:
print(
'Error during calculation of correlationMatrix! Check files written to disk (error_part.em,error_otherPart.em). ABORTING!'
)
print(particle.getFilename(), otherParticle.getFilename())
particleVolume.write('error_part.em')
otherParticleVolume.write('error_otherPart.em')
assert False
correlationVector.append(value)
return correlationVector
def apply(self, volume, bypassFlag=False, downscale=1, particle=None):
"""
apply: Performs preprocessing of volume and reference
@param volume: volume to be pre-processed
@type volume: L{pytom_volume.vol}
@param bypassFlag: Set if only bandpassFilter needed. False otherwise and all routines will be processed.
@param downscale: not used anymore
@param particle: particle Volume to be subtracted from input volume
@type particle: L{pytom_volume.vol}
@return: Returns modified volume
@author: Thomas Hrabe
"""
from pytom_volume import vol
if self._bandpassOn:
from pytom.basic.filter import bandpassFilter
# if frequencies specified in Nyquist, 0.5 being highest
# fixed wrong adjustment of frequencies upon binning - FF
if self._highestFrequency < 1:
highestFrequency = self._highestFrequency * volume.sizeX()
lowestFrequency = self._lowestFrequency * volume.sizeX()
else:
highestFrequency = self._highestFrequency
lowestFrequency = self._lowestFrequency
v = bandpassFilter(volume=volume,
lowestFrequency=lowestFrequency,
highestFrequency=highestFrequency,
bpf=0,
smooth=self._bandpassSmooth)
volume = v[0]
if self._prerotateOn and (not bypassFlag):
from pytom_volume import rotate
rot = vol(volume.sizeX(), volume.sizeY(), volume.sizeZ())
rotation = self.prerotate
rotate(volume, rot, rotation[0], rotation[1], rotation[2])
volume = rot
if self._weightingOn and (not bypassFlag):
from pytom_volume import read
from pytom_freqweight import weight
from pytom.basic.fourier import fft, ifft
wedgeSum = read(self._weightingFile)
fVolume = fft(volume)
weighting = weight(wedgeSum)
weighting.apply(fVolume)
volume = ifft(fVolume)
if self._substractParticle and particle.__class__ == vol:
volume -= particle
if self._taper > 0:
from pytom.tools.macros import volumesSameSize
if self._taperMask is None or not volumesSameSize(
volume, self._taperMask):
from pytom.basic.functions import taper_edges
volume, self._taperMask = taper_edges(volume, self._taper)
else:
volume = volume * self._taperMask
return volume
def bandCC(volume,reference,band,verbose = False):
"""
bandCC: Determines the normalised correlation coefficient within a band
@param volume: The volume
@type volume: L{pytom_volume.vol}
@param reference: The reference
@type reference: L{pytom_volume.vol}
@param band: [a,b] - specify the lower and upper end of band.
@return: First parameter - The correlation of the two volumes in the specified band.
Second parameter - The bandpass filter used.
@rtype: List - [float,L{pytom_freqweight.weight}]
@author: Thomas Hrabe
"""
import pytom_volume
from pytom.basic.filter import bandpassFilter
from pytom.basic.correlation import xcf
from math import sqrt
if verbose:
print('lowest freq : ', band[0],' highest freq' , band[1])
vf = bandpassFilter(volume,band[0],band[1],fourierOnly=True)
rf = bandpassFilter(reference,band[0],band[1],vf[1],fourierOnly=True)
ccVolume = pytom_volume.vol_comp(rf[0].sizeX(),rf[0].sizeY(),rf[0].sizeZ())
ccVolume.copyVolume(rf[0])
pytom_volume.conj_mult(ccVolume,vf[0])
cc = pytom_volume.sum(ccVolume)
cc = cc.real
v = vf[0]
r = rf[0]
absV = pytom_volume.abs(v)
absR = pytom_volume.abs(r)
pytom_volume.power(absV,2)
pytom_volume.power(absR,2)
sumV = pytom_volume.sum(absV)
sumR = pytom_volume.sum(absR)
sumV = abs(sumV)
sumR = abs(sumR)
if sumV == 0:
sumV =1
if sumR == 0:
sumR =1
cc = cc / (sqrt(sumV*sumR))
#numerical errors will be punished with nan
if abs(cc) > 1.1 :
cc = float('nan')
return [cc,vf[1]];
if help is True:
print(helper)
sys.exit()
if not filename or not target:
print(helper)
sys.exit()
v = read(filename)
if lowestFrequency:
lowestFrequency = int(lowestFrequency)
else:
lowestFrequency = 0
if highestFrequency:
highestFrequency = int(highestFrequency)
else:
highestFrequency = v.sizeX() / 2
if smooth:
smooth = int(smooth)
else:
smooth = 0
r = bandpassFilter(
v,
str(lowestFrequency) + ':' + str(highestFrequency) + ';', None, smooth)
r[0].write(target)