def prg(volume, params):
"""Given a volume, a set of projection angles, and Kaiser-Bessel
window parameters, use gridding to generate projection
"""
Mx = volume.get_xsize()
My = volume.get_ysize()
Mz = volume.get_zsize()
if (Mx == Mz & My == Mz):
volft, kb = prep_vol(volume)
return prgs(volft, kb, params)
else:
volft, kbx, kby, kbz = prep_vol(volume)
return prgs(volft, kbz, params, kbx, kby)
def prj(vol, params, stack=None):
"""
Name
prj - calculate a set of 2-D projection of a 3-D volume using gridding
Input
vol: input volume, all dimensions have to be the same (nx=ny=nz)
params: a list of input parameters given as a list [i][phi, theta, psi, sx, sy], projection in calculated using the three Eulerian angles and then shifted by sx,sy
Output
proj
either: an in-core stack of generated 2-D projections
stack
"""
from sp_utilities import set_params_proj
from sp_projection import prep_vol
volft, kb = prep_vol(vol)
for i in range(len(params)):
proj = prgs(volft, kb, params[i])
set_params_proj(proj, [
params[i][0], params[i][1], params[i][2], -params[i][3],
-params[i][4]
])
proj.set_attr_dict({'ctf_applied': 0})
if (stack):
proj.write_image(stack, i)
else:
if (i == 0): out = []
out.append(proj)
if (stack): return
else: return out
def read_volume(path_vol_1,
path_vol_2,
path_mask=None,
resolution=None,
pixel_size=None):
"""
Reads the 3D density map
:param path_vol_1: Path to the density map
:param path_mask: If provided, the volume is masked.
:return: Volume for density map
"""
print("Read volumes, masking them and prepare them for reprojections")
mask_vol = None
vol2 = None
if path_mask is not None:
mask_vol = sp_utilities.get_im(path_mask)
vol1 = prepare_volume(path_vol_1, mask_vol, resolution, pixel_size)
if path_vol_2:
vol2 = prepare_volume(path_vol_2, mask_vol, resolution, pixel_size)
if mask_vol:
mask_vol = sp_projection.prep_vol(mask_vol, interpolation_method=1)
return vol1, vol2, mask_vol
def prepare_volume(volume_path, mask=None, resolution=None, pixel_size=None):
"""
Prepares the volume for reprojections
:param volume_path: Path to volume file
:param mask: Particle mask
:param resolution: Resolution of the current reconstruction.
:return:
"""
vol = sp_utilities.get_im(volume_path)
if resolution:
vol = vol.process(
"filter.lowpass.gauss",
{
"cutoff_freq": old_div(1.0, resolution),
"apix": pixel_size
},
)
if mask:
vol = vol * mask
vol = sp_projection.prep_vol(vol, interpolation_method=1)
return vol
def generate_helimic(refvol,
outdir,
pixel,
CTF=False,
Cs=2.0,
voltage=200.0,
ampcont=10.0,
nonoise=False,
rand_seed=14567):
from sp_utilities import model_blank, model_gauss, model_gauss_noise, pad, get_im
from random import random
from sp_projection import prgs, prep_vol
from sp_filter import filt_gaussl, filt_ctf
from EMAN2 import EMAN2Ctf
if os.path.exists(outdir):
ERROR(
"Output directory exists, please change the name and restart the program"
)
return
os.mkdir(outdir)
seed(rand_seed)
Util.set_randnum_seed(rand_seed)
angles = []
for i in range(3):
angles.append([0.0 + 60.0 * i, 90.0 - i * 5, 0.0, 0.0, 0.0])
nangle = len(angles)
volfts = get_im(refvol)
nx = volfts.get_xsize()
ny = volfts.get_ysize()
nz = volfts.get_zsize()
volfts, kbx, kby, kbz = prep_vol(volfts)
iprj = 0
width = 500
xstart = 0
ystart = 0
for idef in range(3, 6):
mic = model_blank(2048, 2048)
#defocus = idef*0.2
defocus = idef * 0.6 ##@ming
if CTF:
#ctf = EMAN2Ctf()
#ctf.from_dict( {"defocus":defocus, "cs":Cs, "voltage":voltage, "apix":pixel, "ampcont":ampcont, "bfactor":0.0} )
from sp_utilities import generate_ctf
ctf = generate_ctf(
[defocus, 2, 200, 1.84, 0.0, ampcont, defocus * 0.2, 80]
) ##@ming the range of astigmatism amplitude is between 10 percent and 22 percent. 20 percent is a good choice.
i = idef - 4
for k in range(1):
psi = 90 + 10 * i
proj = prgs(
volfts, kbz,
[angles[idef - 3][0], angles[idef - 3][1], psi, 0.0, 0.0], kbx,
kby)
proj = Util.window(proj, 320, nz)
mic += pad(proj, 2048, 2048, 1, 0.0, 750 * i, 20 * i, 0)
if not nonoise: mic += model_gauss_noise(30.0, 2048, 2048)
if CTF:
#apply CTF
mic = filt_ctf(mic, ctf)
if not nonoise:
mic += filt_gaussl(model_gauss_noise(17.5, 2048, 2048), 0.3)
mic.write_image("%s/mic%1d.hdf" % (outdir, idef - 3), 0)
def mode_meridien(reconfile,
classavgstack,
classdocs,
partangles,
selectdoc,
maxshift,
outerrad,
outanglesdoc,
outaligndoc,
interpolation_method=1,
outliers=None,
goodclassparttemplate=None,
alignopt='apsh',
ringstep=1,
log=None,
verbose=False):
# Resample reference
recondata = EMAN2.EMData(reconfile)
idim = recondata['nx']
reconprep = prep_vol(recondata,
npad=2,
interpolation_method=interpolation_method)
# Initialize output angles
outangleslist = []
outalignlist = []
# Read class lists
classdoclist = glob.glob(classdocs)
partangleslist = read_text_row(partangles)
# Loop through class lists
for classdoc in classdoclist: # [classdoclist[32]]: #
# Strip out three-digit filenumber
classexample = os.path.splitext(classdoc)
classnum = int(classexample[0][-3:])
# Initial average
[avg_phi_init, avg_theta_init] = average_angles(partangleslist,
classdoc,
selectdoc=selectdoc)
# Look for outliers
if outliers:
[avg_phi_final, avg_theta_final] = average_angles(
partangleslist,
classdoc,
selectdoc=selectdoc,
init_angles=[avg_phi_init, avg_theta_init],
threshold=outliers,
goodpartdoc=goodclassparttemplate.format(classnum),
log=log,
verbose=verbose)
else:
[avg_phi_final, avg_theta_final] = [avg_phi_init, avg_theta_init]
# Compute re-projection
refprjreal = prgl(reconprep, [avg_phi_final, avg_theta_final, 0, 0, 0],
interpolation_method=1,
return_real=True)
# Align to class average
classavg = get_im(classavgstack, classnum)
# Alignment using self-correlation function
if alignopt == 'scf':
ang_align2d, sxs, sys, mirrorflag, peak = align2d_scf(classavg,
refprjreal,
maxshift,
maxshift,
ou=outerrad)
# Weird results
elif alignopt == 'align2d':
# Set search range
currshift = 0
txrng = tyrng = search_range(idim, outerrad, currshift, maxshift)
# Perform alignment
ang_align2d, sxs, sys, mirrorflag, peak = align2d(
classavg, refprjreal, txrng, tyrng, last_ring=outerrad)
# Direct3 (angles seemed to be quantized)
elif alignopt == 'direct3':
[[ang_align2d, sxs, sys, mirrorflag,
peak]] = align2d_direct3([classavg],
refprjreal,
maxshift,
maxshift,
ou=outerrad)
# APSH-like alignment (default)
else:
[[ang_align2d, sxs, sys, mirrorflag,
scale]] = apsh(refprjreal,
classavg,
outerradius=outerrad,
maxshift=maxshift,
ringstep=ringstep)
outalignlist.append([ang_align2d, sxs, sys, mirrorflag, 1])
msg = "Particle list %s: ang_align2d=%s sx=%s sy=%s mirror=%s\n" % (
classdoc, ang_align2d, sxs, sys, mirrorflag)
print_log_msg(msg, log, verbose)
# Check for mirroring
if mirrorflag == 1:
tempeulers = list(
compose_transform3(avg_phi_final, avg_theta_final, 0, 0, 0, 0,
1, 0, 180, 0, 0, 0, 0, 1))
combinedparams = list(
compose_transform3(tempeulers[0], tempeulers[1], tempeulers[2],
tempeulers[3], tempeulers[4], 0, 1, 0, 0,
-ang_align2d, 0, 0, 0, 1))
else:
combinedparams = list(
compose_transform3(avg_phi_final, avg_theta_final, 0, 0, 0, 0,
1, 0, 0, -ang_align2d, 0, 0, 0, 1))
# compose_transform3: returns phi,theta,psi, tx,ty,tz, scale
outangleslist.append(combinedparams)
# End class-loop
write_text_row(outangleslist, outanglesdoc)
write_text_row(outalignlist, outaligndoc)
print_log_msg(
'Wrote alignment parameters to %s and %s\n' %
(outanglesdoc, outaligndoc), log, verbose)
del recondata # Clean up
def compare_projs(reconfile,
classavgstack,
inputanglesdoc,
outdir,
interpolation_method=1,
log=None,
verbose=False):
"""
Make comparison stack between class averages (even-numbered (starts from 0)) and re-projections (odd-numbered).
Arguments:
reconfile : Input volume from which to generate re-projections
classavgstack ; Input image stack
inputanglesdoc : Input Euler angles doc
outdir ; Output directory
interpolation_method : Interpolation method: nearest neighbor (nn, 0), trilinear (1, default), gridding (-1)
log : Logger object
verbose : (boolean) Whether to write additional information to screen
Returns:
compstack : Stack of comparisons between input image stack (even-numbered (starts from 0)) and input volume (odd-numbered)
"""
recondata = EMAN2.EMData(reconfile)
nx = recondata.get_xsize()
# Resample reference
reconprep = prep_vol(recondata,
npad=2,
interpolation_method=interpolation_method)
ccclist = []
# Here you need actual radius to compute proper ccc's, but if you do, you have to deal with translations, PAP
mask = model_circle(nx // 2 - 2, nx, nx)
mask.write_image(os.path.join(outdir, 'maskalign.hdf'))
compstack = os.path.join(outdir, 'comp-proj-reproj.hdf')
# Number of images may have changed
nimg1 = EMAN2.EMUtil.get_image_count(classavgstack)
angleslist = read_text_row(inputanglesdoc)
for imgnum in range(nimg1):
# Get class average
classimg = get_im(classavgstack, imgnum)
# Compute re-projection
prjimg = prgl(reconprep,
angleslist[imgnum],
interpolation_method=1,
return_real=False)
# Calculate 1D power spectra
rops_dst = rops_table(classimg * mask)
rops_src = rops_table(prjimg)
# Set power spectrum of reprojection to the data.
# Since data has an envelope, it would make more sense to set data to reconstruction,
# but to do it one would have to know the actual resolution of the data.
# you can check sxprocess.py --adjpw to see how this is done properly PAP
table = [0.0] * len(rops_dst) # initialize table
for j in range(len(rops_dst)):
table[j] = sqrt(rops_dst[j] / rops_src[j])
prjimg = fft(filt_table(
prjimg,
table)) # match FFT amplitudes of re-projection and class average
cccoeff = ccc(prjimg, classimg, mask)
#print imgnum, cccoeff
classimg.set_attr_dict({'cross-corr': cccoeff})
prjimg.set_attr_dict({'cross-corr': cccoeff})
montagestack = []
montagestack.append(prjimg)
montagestack.append(classimg)
comparison_pair = montage2(montagestack, ncol=2, marginwidth=1)
comparison_pair.write_image(compstack, imgnum)
ccclist.append(cccoeff)
del angleslist
meanccc = sum(ccclist) / nimg1
print_log_msg("Average CCC is %s\n" % meanccc, log, verbose)
nimg2 = EMAN2.EMUtil.get_image_count(compstack)
for imgnum in range(nimg2): # xrange will be deprecated in Python3
prjimg = get_im(compstack, imgnum)
meanccc1 = prjimg.get_attr_default('mean-cross-corr', -1.0)
prjimg.set_attr_dict({'mean-cross-corr': meanccc})
write_header(compstack, prjimg, imgnum)
return compstack