def taper_edges(image, width):
"""
taper edges of image (or volume) with cos function
@param image: input image (or volume)
@type image: ndarray
@param width: width of edge
@type width: int
@return: image with smoothened edges, taper_mask
@rtype: array-like
@author: GvdS
"""
dims = list(image.shape) + [0]
val = xp.cos(xp.arange(1, width + 1) * xp.pi / (2. * (width)))
taperX = xp.ones((dims[0]), dtype=xp.float32)
taperY = xp.ones((dims[1]))
taperX[:width] = val[::-1]
taperX[-width:] = val
taperY[:width] = val[::-1]
taperY[-width:] = val
if dims[2] > 1:
taperZ = xp.ones((dims[2]))
taperZ[:width] = val[::-1]
taperZ[-width:] = val
Z, X, Y = xp.meshgrid(taperX, taperY, taperZ)
taper_mask = X * (X < Y) * (X < Z) + Y * (Y <= X) * (Y < Z) + Z * (
Z <= Y) * (Z <= X)
else:
X, Y = xp.meshgrid(taperY, taperX)
taper_mask = X * (X < Y) + Y * (Y <= X)
return image * taper_mask, taper_mask
def maxIndex(volume, num_threads=1024):
nblocks = int(xp.ceil(volume.size / num_threads / 2))
fast_sum = -1000000 * xp.ones((nblocks), dtype=xp.float32)
max_id = xp.zeros((nblocks), dtype=xp.int32)
argmax((
nblocks,
1,
), (num_threads, 1, 1), (volume, fast_sum, max_id, volume.size),
shared_mem=16 * num_threads)
mm = min(max_id[fast_sum.argmax()], volume.size - 1)
indices = xp.unravel_index(mm, volume.shape)
return indices
def initVolume(self, sizeX, sizeY, sizeZ):
"""
initVolume:
@param sizeX:
@param sizeY:
@param sizeZ:
@return:
@author: Thomas Hrabe
"""
from pytom.tompy.tools import create_sphere
if self._radius > 0 or self._smooth > 0:
self._weight = create_sphere((sizeX, sizeY, sizeZ), self._radius,
self._smooth)
else:
self._weight = xp.ones((sizeX, sizeY, sizeZ), dtype=xp.float32)
def exact_filter(tilt_angles, tiltAngle, sX, sY, sliceWidth=1, arr=[]):
"""
exactFilter: Generates the exact weighting function required for weighted backprojection - y-axis is tilt axis
Reference : Optik, Exact filters for general geometry three dimensional reconstuction, vol.73,146,1986.
@param tilt_angles: list of all the tilt angles in one tilt series
@param titlAngle: tilt angle for which the exact weighting function is calculated
@param sizeX: size of weighted image in X
@param sizeY: size of weighted image in Y
@return: filter volume
"""
import numpy as xp
# Calculate the relative angles in radians.
diffAngles = (xp.array(tilt_angles) - tiltAngle) * xp.pi / 180.
# Closest angle to tiltAngle (but not tiltAngle) sets the maximal frequency of overlap (Crowther's frequency).
# Weights only need to be calculated up to this frequency.
sampling = xp.min(xp.abs(diffAngles)[xp.abs(diffAngles) > 0.001])
crowtherFreq = min(sX // 2,
xp.int32(xp.ceil(sliceWidth / xp.sin(sampling))))
arrCrowther = xp.matrix(
xp.abs(xp.arange(-crowtherFreq, min(sX // 2, crowtherFreq + 1))))
# Calculate weights
wfuncCrowther = 1. / (xp.clip(
1 - xp.array(xp.matrix(xp.abs(xp.sin(diffAngles))).T * arrCrowther)**2,
0, 2)).sum(axis=0)
# Create full with weightFunc
wfunc = xp.ones((sX, sY), dtype=xp.float32)
# row_stack is not implemented in cupy
weightingFunc = xp.column_stack(([
(wfuncCrowther),
] * (sY))).T
wfunc[:, sX // 2 - crowtherFreq:sX // 2 +
min(sX // 2, crowtherFreq + 1)] = weightingFunc
return wfunc
def alignImagesUsingAlignmentResultFile(alignmentResultsFile,
weighting=None,
lowpassFilter=0.9,
binning=1,
circleFilter=False):
import os
from pytom.basic.files import read as readCVol
from pytom_numpy import vol2npy, npy2vol
from pytom.gui.guiFunctions import fmtAR, headerAlignmentResults, datatype, datatypeAR, loadstar
from pytom.reconstruction.reconstructionStructures import Projection, ProjectionList
from pytom.tompy.io import read, write, read_size
from pytom.tompy.tools import taper_edges, create_circle
from pytom.tompy.filter import circle_filter, ramp_filter, exact_filter
import pytom.voltools as vt
from pytom.gpu.initialize import xp, device
print("Create aligned images from alignResults.txt")
alignmentResults = loadstar(alignmentResultsFile, dtype=datatypeAR)
imageList = alignmentResults['FileName']
tilt_angles = alignmentResults['TiltAngle']
imdim = read_size(imageList[0], 'x')
if binning > 1:
imdim = int(float(imdim) / float(binning) + .5)
else:
imdim = imdim
sliceWidth = imdim
if (weighting != None) and (float(weighting) < -0.001):
weightSlice = xp.fft.fftshift(ramp_filter(imdim, imdim))
if circleFilter:
circleFilterRadius = imdim // 2
circleSlice = xp.fft.fftshift(
circle_filter(imdim, imdim, circleFilterRadius))
else:
circleSlice = xp.ones((imdim, imdim))
# design lowpass filter
if lowpassFilter:
if lowpassFilter > 1.:
lowpassFilter = 1.
print("Warning: lowpassFilter > 1 - set to 1 (=Nyquist)")
# weighting filter: arguments: (()dimx, dimy), cutoff radius, sigma
lpf = xp.fft.fftshift(
create_circle((imdim, imdim),
lowpassFilter * (imdim // 2),
sigma=0.4 * lowpassFilter * (imdim // 2)))
projectionList = ProjectionList()
for n, image in enumerate(imageList):
atx = alignmentResults['AlignmentTransX'][n] / binning
aty = alignmentResults['AlignmentTransY'][n] / binning
rot = alignmentResults['InPlaneRotation'][n]
mag = 1 / alignmentResults['Magnification'][n]
projection = Projection(imageList[n],
tiltAngle=tilt_angles[n],
alignmentTransX=atx,
alignmentTransY=aty,
alignmentRotation=rot,
alignmentMagnification=mag)
projectionList.append(projection)
stack = xp.zeros((imdim, imdim, len(imageList)), dtype=xp.float32)
phiStack = xp.zeros((1, 1, len(imageList)), dtype=xp.float32)
thetaStack = xp.zeros((1, 1, len(imageList)), dtype=xp.float32)
offsetStack = xp.zeros((1, 2, len(imageList)), dtype=xp.float32)
for (ii, projection) in enumerate(projectionList):
print(f'Align {projection._filename}')
image = read(str(projection._filename))[::binning, ::binning].squeeze()
if lowpassFilter:
image = xp.abs((xp.fft.ifftn(xp.fft.fftn(image) * lpf)))
tiltAngle = projection._tiltAngle
# normalize to contrast - subtract mean and norm to mean
immean = image.mean()
image = (image - immean) / immean
# smoothen borders to prevent high contrast oscillations
image = taper_edges(image, imdim // 30)[0]
# transform projection according to tilt alignment
transX = projection._alignmentTransX / binning
transY = projection._alignmentTransY / binning
rot = float(projection._alignmentRotation)
mag = float(projection._alignmentMagnification)
inputImage = xp.expand_dims(image, 2).copy()
outputImage = xp.zeros_like(inputImage, dtype=xp.float32)
vt.transform(inputImage.astype(xp.float32),
rotation=[0, 0, rot],
rotation_order='rxyz',
output=outputImage,
device=device,
translation=[transX, transY, 0],
scale=[mag, mag, 1],
interpolation='filt_bspline')
image = outputImage.squeeze()
# smoothen once more to avoid edges
image = taper_edges(image, imdim // 30)[0]
# analytical weighting
if (weighting != None) and (weighting < 0):
# image = (ifft(complexRealMult(fft(image), w_func)) / (image.sizeX() * image.sizeY() * image.sizeZ()))
image = xp.fft.ifftn(
xp.fft.fftn(image) * weightSlice * circleSlice)
elif (weighting != None) and (weighting > 0):
weightSlice = xp.fft.fftshift(
exact_filter(tilt_angles, tiltAngle, imdim, imdim, sliceWidth))
image = xp.fft.ifftn(
xp.fft.fftn(image) * weightSlice * circleSlice)
thetaStack[0, 0, ii] = int(round(projection.getTiltAngle()))
offsetStack[0, :, ii] = xp.array([
int(round(projection.getOffsetX())),
int(round(projection.getOffsetY()))
])
stack[:, :, ii] = image
arrays = []
for fname, arr in (('stack.mrc', stack), ('offsetStack.mrc', offsetStack),
('thetaStack.mrc', thetaStack), ('phiStack.mrc',
phiStack)):
if 'gpu' in device:
arr = arr.get()
import numpy as np
res = npy2vol(np.array(arr, dtype='float32', order='F'), 3)
arrays.append(res)
#
# write('stack.mrc', stack)
# stack = readCVol('stack.mrc')
# write('offsetstack.mrc', offsetStack)
# offsetStack = readCVol('offsetstack.mrc')
# write('thetastack.mrc', thetaStack)
# thetaStack = readCVol('thetastack.mrc')
# write('phistack.mrc', phiStack)
# phiStack = readCVol('phistack.mrc')
#
# os.remove('stack.mrc')
# os.remove('offsetstack.mrc')
# os.remove('thetastack.mrc')
# os.remove('psistack.mrc')
return arrays
def alignImageUsingAlignmentResultFile(alignmentResultsFile,
indexImage,
weighting=None,
lowpassFilter=0.9,
binning=1,
circleFilter=False):
import pytom_freqweight
from pytom_numpy import vol2npy
from pytom.gui.guiFunctions import fmtAR, headerAlignmentResults, datatype, datatypeAR, loadstar
from pytom.reconstruction.reconstructionStructures import Projection, ProjectionList
from pytom.tompy.io import read, write, read_size
from pytom.tompy.tools import taper_edges, create_circle
from pytom.tompy.filter import circle_filter, ramp_filter, exact_filter, ellipse_filter
import pytom.voltools as vt
from pytom.gpu.initialize import xp, device
# print("Create aligned images from alignResults.txt")
alignmentResults = loadstar(alignmentResultsFile, dtype=datatypeAR)
imageList = alignmentResults['FileName']
tilt_angles = alignmentResults['TiltAngle']
imdimX = read_size(imageList[0], 'x')
imdimY = read_size(imageList[0], 'y')
if binning > 1:
imdimX = int(float(imdimX) / float(binning) + .5)
imdimY = int(float(imdimY) / float(binning) + .5)
sliceWidth = imdimX
if (weighting != None) and (float(weighting) < -0.001):
weightSlice = xp.fft.fftshift(ramp_filter(imdimY, imdimX))
if circleFilter:
circleFilterRadiusX = imdimX // 2
circleFilterRadiusY = imdimY // 2
circleSlice = xp.fft.fftshift(
ellipse_filter(imdimX, imdimY, circleFilterRadiusX,
circleFilterRadiusY))
else:
circleSlice = xp.ones((imdimX, imdimY))
# design lowpass filter
if lowpassFilter:
if lowpassFilter > 1.:
lowpassFilter = 1.
print("Warning: lowpassFilter > 1 - set to 1 (=Nyquist)")
# weighting filter: arguments: (()dimx, dimy), cutoff radius, sigma
# lpf = xp.fft.fftshift(create_circle((imdimX,imdimY),lowpassFilter*(imdim//2), sigma=0.4*lowpassFilter*(imdim//2)))
projectionList = ProjectionList()
for n, image in enumerate(imageList):
atx = alignmentResults['AlignmentTransX'][n]
aty = alignmentResults['AlignmentTransY'][n]
rot = alignmentResults['InPlaneRotation'][n]
mag = 1 / (alignmentResults['Magnification'][n])
projection = Projection(imageList[n],
tiltAngle=tilt_angles[n],
alignmentTransX=atx,
alignmentTransY=aty,
alignmentRotation=rot,
alignmentMagnification=mag)
projectionList.append(projection)
imdim = min(imdimY, imdimX)
for (ii, projection) in enumerate(projectionList):
if not ii == indexImage:
continue
from pytom.tompy.transform import resize
# print(f'read {projection._filename}')
image = read(str(projection._filename)).squeeze()
if binning > 1:
image = resize(image, 1 / binning)
#write(f'test/image_{ii}.mrc', image, tilt_angle=tilt_angles[ii])
tiltAngle = projection._tiltAngle
# 1 -- normalize to contrast - subtract mean and norm to mean
immean = image.mean()
image = (image - immean) / immean
# 2 -- smoothen borders to prevent high contrast oscillations
image = taper_edges(image, imdim // 30)[0]
# 3 -- square if needed
if 0 and imdimY != imdimX:
newImage = xp.zeros((imdim, imdim, 1), dtype=xp.float32)
pasteCenter(image, newImage)
image = newImage
# 4 -- transform projection according to tilt alignment
transX = projection._alignmentTransX / binning
transY = projection._alignmentTransY / binning
rot = float(projection._alignmentRotation)
mag = float(projection._alignmentMagnification)
inputImage = xp.expand_dims(image, 2).copy()
outputImage = xp.zeros_like(inputImage, dtype=xp.float32)
vt.transform(
inputImage.astype(xp.float32),
rotation=[0, 0, rot],
rotation_order='rxyz',
output=outputImage,
center=[inputImage.shape[0] // 2, inputImage.shape[1] // 2, 0],
device=device,
translation=[transX, transY, 0],
scale=[mag, mag, 1],
interpolation='filt_bspline')
del image
image = outputImage.squeeze()
# 5 -- Optional Low Pass Filter
if lowpassFilter:
from pytom.tompy.filter import bandpass_circle
image = bandpass_circle(
image,
high=lowpassFilter * (min(imdimX, imdimY) // 2),
sigma=0.4 * lowpassFilter * (min(imdimX, imdimY) // 2))
# image = xp.abs((xp.fft.ifftn(xp.fft.fftn(image) * lpf)))
# 6 -- smoothen once more to avoid edges
image = taper_edges(image, imdim // 30)[0]
# 7 -- analytical weighting
if (weighting != None) and (weighting < 0):
# image = (ifft(complexRealMult(fft(image), w_func)) / (image.sizeX() * image.sizeY() * image.sizeZ()))
image = xp.fft.ifftn(
xp.fft.fftn(image) * weightSlice.T * circleSlice).real
elif (weighting != None) and (weighting > 0):
weightSlice = xp.fft.fftshift(
exact_filter(tilt_angles, tiltAngle, imdim, imdim, sliceWidth))
image = xp.fft.ifftn(
xp.fft.fftn(image) * weightSlice * circleSlice).real
del inputImage, outputImage, circleSlice
write(f'inputImage_{ii}.mrc', image)
return image.astype(xp.float32)