def gridrot_shift2D(image, ang=0.0, sx=0.0, sy=0.0, scale=1.0):
"""
Rotate and shift an image using gridding in Fourier space.
"""
from EMAN2 import Processor
from fundamentals import fftip, fft
nx = image.get_xsize()
# split shift into integer and fractional parts
isx = int(sx)
fsx = sx - isx
isy = int(sy)
fsy = sy - isy
# prepare
npad = 2
N = nx * npad
K = 6
alpha = 1.75
r = nx / 2
v = K / 2.0 / N
kb = Util.KaiserBessel(alpha, K, r, v, N)
image1 = image.copy(
) # This step is needed, otherwise image will be changed outside the function
# divide out gridding weights
image1.divkbsinh(kb)
# pad and center image, then FFT
image1 = image1.norm_pad(False, npad)
fftip(image1)
# Put the origin of the (real-space) image at the center
image1.center_origin_fft()
# gridding rotation
image1 = image1.fouriergridrot2d(ang, scale, kb)
if (fsx != 0.0 or fsy != 0.0):
params = {
"filter_type": Processor.fourier_filter_types.SHIFT,
"x_shift": float(fsx),
"y_shift": float(fsy),
"z_shift": 0.0
}
image1 = Processor.EMFourierFilter(image1, params)
# put the origin back in the corner
image1.center_origin_fft()
# undo FFT and remove padding (window)
image1 = fft(image1)
image1 = image1.window_center(nx)
Util.cyclicshift(image1, {"dx": isx, "dy": isy, "dz": 0})
return image1
def gridrot_shift2D(image, ang = 0.0, sx = 0.0, sy = 0.0, scale = 1.0):
"""
Rotate and shift an image using gridding on Fourier space.
"""
from EMAN2 import Processor
from fundamentals import fftip, fft
nx = image.get_xsize()
# split shift into integer and fractional parts
isx = int(sx)
fsx = sx - isx
isy = int(sy)
fsy = sy - isy
# prepare
npad = 2
N = nx*npad
K = 6
alpha = 1.75
r = nx/2
v = K/2.0/N
kb = Util.KaiserBessel(alpha, K, r, v, N)
image1 = image.copy() # This step is needed, otherwise image will be changed outside the function
# divide out gridding weights
image1.divkbsinh(kb)
# pad and center image, then FFT
image1 = image1.norm_pad(False, npad)
fftip(image1)
# Put the origin of the (real-space) image at the center
image1.center_origin_fft()
# gridding rotation
image1 = image1.fouriergridrot2d(ang, scale, kb)
if(fsx != 0.0 or fsy != 0.0):
params = {"filter_type" : Processor.fourier_filter_types.SHIFT, "x_shift" : float(fsx), "y_shift" : float(fsy), "z_shift" : 0.0 }
image1 = Processor.EMFourierFilter(image1, params)
# put the origin back in the corner
image1.center_origin_fft()
# undo FFT and remove padding (window)
image1 = fft(image1)
image1 = image1.window_center(nx)
Util.cyclicshift(image1,{"dx":isx,"dy":isy,"dz":0})
return image1
def cml_open_proj(stack, ir, ou, lf, hf, dpsi=1):
from projection import cml_sinogram
from utilities import model_circle, get_params_proj, model_blank, get_im
from fundamentals import fftip
from filter import filt_tanh
# number of projections
if type(stack) == type(""): nprj = EMUtil.get_image_count(stack)
else: nprj = len(stack)
Prj = [] # list of projections
Ori = [
-1
] * 4 * nprj # orientation intial (phi, theta, psi, index) for each projection
for i in xrange(nprj):
image = get_im(stack, i)
# read initial angles if given
try:
Ori[4 * i], Ori[4 * i +
1], Ori[4 * i +
2], s2x, s2y = get_params_proj(image)
except:
pass
if (i == 0):
nx = image.get_xsize()
if (ou < 1): ou = nx // 2 - 1
diameter = int(2 * ou)
mask2D = model_circle(ou, nx, nx)
if ir > 0: mask2D -= model_circle(ir, nx, nx)
# normalize under the mask
[mean_a, sigma, imin, imax] = Util.infomask(image, mask2D, True)
image -= mean_a
Util.mul_scalar(image, 1.0 / sigma)
Util.mul_img(image, mask2D)
# sinogram
sino = cml_sinogram(image, diameter, dpsi)
# prepare the cut positions in order to filter (lf: low freq; hf: high freq)
ihf = min(int(2 * hf * diameter), diameter + (diameter + 1) % 2)
ihf = ihf + (ihf + 1) % 2 # index ihf must be odd to take the img part
ilf = max(int(2 * lf * diameter), 0)
ilf = ilf + ilf % 2 # index ilf must be even to fall in the real part
bdf = ihf - ilf + 1
# process lines
nxe = sino.get_xsize()
nye = sino.get_ysize()
prj = model_blank(bdf, 2 * nye)
pp = model_blank(nxe, 2 * nye)
for li in xrange(nye):
# get the line li
line = Util.window(sino, nxe, 1, 1, 0, li - nye // 2, 0)
# u2 (not improve the results)
#line = filt_tanh(line, ou / float(nx), ou / float(nx))
# normalize this line
[mean_l, sigma_l, imin, imax] = Util.infomask(line, None, True)
line = (line - mean_l) / sigma_l
# fft
fftip(line)
# filter (cut part of coef) and create mirror line
Util.cml_prepare_line(prj, line, ilf, ihf, li, nye)
# store the projection
Prj.append(prj)
return Prj, Ori
def do_volume_mrk02(ref_data):
"""
data - projections (scattered between cpus) or the volume. If volume, just do the volume processing
options - the same for all cpus
return - volume the same for all cpus
"""
from EMAN2 import Util
from mpi import mpi_comm_rank, mpi_comm_size, MPI_COMM_WORLD
from filter import filt_table
from reconstruction import recons3d_4nn_MPI, recons3d_4nn_ctf_MPI
from utilities import bcast_EMData_to_all, bcast_number_to_all, model_blank
from fundamentals import rops_table, fftip, fft
import types
# Retrieve the function specific input arguments from ref_data
data = ref_data[0]
Tracker = ref_data[1]
iter = ref_data[2]
mpi_comm = ref_data[3]
# # For DEBUG
# print "Type of data %s" % (type(data))
# print "Type of Tracker %s" % (type(Tracker))
# print "Type of iter %s" % (type(iter))
# print "Type of mpi_comm %s" % (type(mpi_comm))
if(mpi_comm == None): mpi_comm = MPI_COMM_WORLD
myid = mpi_comm_rank(mpi_comm)
nproc = mpi_comm_size(mpi_comm)
try: local_filter = Tracker["local_filter"]
except: local_filter = False
#=========================================================================
# volume reconstruction
if( type(data) == types.ListType ):
if Tracker["constants"]["CTF"]:
vol = recons3d_4nn_ctf_MPI(myid, data, Tracker["constants"]["snr"], \
symmetry=Tracker["constants"]["sym"], npad=Tracker["constants"]["npad"], mpi_comm=mpi_comm, smearstep = Tracker["smearstep"])
else:
vol = recons3d_4nn_MPI (myid, data,\
symmetry=Tracker["constants"]["sym"], npad=Tracker["constants"]["npad"], mpi_comm=mpi_comm)
else:
vol = data
if myid == 0:
from morphology import threshold
from filter import filt_tanl, filt_btwl
from utilities import model_circle, get_im
import types
nx = vol.get_xsize()
if(Tracker["constants"]["mask3D"] == None):
mask3D = model_circle(int(Tracker["constants"]["radius"]*float(nx)/float(Tracker["constants"]["nnxo"])+0.5), nx, nx, nx)
elif(Tracker["constants"]["mask3D"] == "auto"):
from utilities import adaptive_mask
mask3D = adaptive_mask(vol)
else:
if( type(Tracker["constants"]["mask3D"]) == types.StringType ): mask3D = get_im(Tracker["constants"]["mask3D"])
else: mask3D = (Tracker["constants"]["mask3D"]).copy()
nxm = mask3D.get_xsize()
if( nx != nxm):
from fundamentals import rot_shift3D
mask3D = Util.window(rot_shift3D(mask3D,scale=float(nx)/float(nxm)),nx,nx,nx)
nxm = mask3D.get_xsize()
assert(nx == nxm)
stat = Util.infomask(vol, mask3D, False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0/stat[1])
vol = threshold(vol)
Util.mul_img(vol, mask3D)
if( Tracker["PWadjustment"] ):
from utilities import read_text_file, write_text_file
rt = read_text_file( Tracker["PWadjustment"] )
fftip(vol)
ro = rops_table(vol)
# Here unless I am mistaken it is enough to take the beginning of the reference pw.
for i in xrange(1,len(ro)): ro[i] = (rt[i]/ro[i])**Tracker["upscale"]
#write_text_file(rops_table(filt_table( vol, ro),1),"foo.txt")
if Tracker["constants"]["sausage"]:
ny = vol.get_ysize()
y = float(ny)
from math import exp
for i in xrange(len(ro)): ro[i] *= \
(1.0+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.10)/0.025)**2)+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.215)/0.025)**2))
if local_filter:
# skip low-pass filtration
vol = fft( filt_table( vol, ro) )
else:
if( type(Tracker["lowpass"]) == types.ListType ):
vol = fft( filt_table( filt_table(vol, Tracker["lowpass"]), ro) )
else:
vol = fft( filt_table( filt_tanl(vol, Tracker["lowpass"], Tracker["falloff"]), ro) )
del ro
else:
if Tracker["constants"]["sausage"]:
ny = vol.get_ysize()
y = float(ny)
ro = [0.0]*(ny//2+2)
from math import exp
for i in xrange(len(ro)): ro[i] = \
(1.0+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.10)/0.025)**2)+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.215)/0.025)**2))
fftip(vol)
filt_table(vol, ro)
del ro
if not local_filter:
if( type(Tracker["lowpass"]) == types.ListType ):
vol = filt_table(vol, Tracker["lowpass"])
else:
vol = filt_tanl(vol, Tracker["lowpass"], Tracker["falloff"])
if Tracker["constants"]["sausage"]: vol = fft(vol)
if local_filter:
from morphology import binarize
if(myid == 0): nx = mask3D.get_xsize()
else: nx = 0
nx = bcast_number_to_all(nx, source_node = 0)
# only main processor needs the two input volumes
if(myid == 0):
mask = binarize(mask3D, 0.5)
locres = get_im(Tracker["local_filter"])
lx = locres.get_xsize()
if(lx != nx):
if(lx < nx):
from fundamentals import fdecimate, rot_shift3D
mask = Util.window(rot_shift3D(mask,scale=float(lx)/float(nx)),lx,lx,lx)
vol = fdecimate(vol, lx,lx,lx)
else: ERROR("local filter cannot be larger than input volume","user function",1)
stat = Util.infomask(vol, mask, False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0/stat[1])
else:
lx = 0
locres = model_blank(1,1,1)
vol = model_blank(1,1,1)
lx = bcast_number_to_all(lx, source_node = 0)
if( myid != 0 ): mask = model_blank(lx,lx,lx)
bcast_EMData_to_all(mask, myid, 0, comm=mpi_comm)
from filter import filterlocal
vol = filterlocal( locres, vol, mask, Tracker["falloff"], myid, 0, nproc)
if myid == 0:
if(lx < nx):
from fundamentals import fpol
vol = fpol(vol, nx,nx,nx)
vol = threshold(vol)
vol = filt_btwl(vol, 0.38, 0.5)# This will have to be corrected.
Util.mul_img(vol, mask3D)
del mask3D
# vol.write_image('toto%03d.hdf'%iter)
else:
vol = model_blank(nx,nx,nx)
else:
if myid == 0:
#from utilities import write_text_file
#write_text_file(rops_table(vol,1),"goo.txt")
stat = Util.infomask(vol, mask3D, False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0/stat[1])
vol = threshold(vol)
vol = filt_btwl(vol, 0.38, 0.5)# This will have to be corrected.
Util.mul_img(vol, mask3D)
del mask3D
# vol.write_image('toto%03d.hdf'%iter)
# broadcast volume
bcast_EMData_to_all(vol, myid, 0, comm=mpi_comm)
#=========================================================================
return vol
def dovolume( ref_data ):
from utilities import print_msg, read_text_row
from filter import fit_tanh, filt_tanl
from fundamentals import fshift
from morphology import threshold
# Prepare the reference in 3D alignment, this function corresponds to what do_volume does.
# Input: list ref_data
# 0 - mask
# 1 - center flag
# 2 - raw average
# 3 - fsc result
# Output: filtered, centered, and masked reference image
# apply filtration (FSC) to reference image:
global ref_ali2d_counter
ref_ali2d_counter += 1
fl = ref_data[2].cmp("dot",ref_data[2], {"negative":0, "mask":ref_data[0]} )
print_msg("do_volume user function Step = %5d GOAL = %10.3e\n"%(ref_ali2d_counter,fl))
stat = Util.infomask(ref_data[2], ref_data[0], False)
vol = ref_data[2] - stat[0]
Util.mul_scalar(vol, 1.0/stat[1])
vol = threshold(vol)
#Util.mul_img(vol, ref_data[0])
try:
aa = read_text_row("flaa.txt")[0]
fl = aa[0]
aa=aa[1]
except:
fl = 0.4
aa = 0.2
msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n"%(fl, aa)
print_msg(msg)
from utilities import read_text_file
from fundamentals import rops_table, fftip, fft
from filter import filt_table, filt_btwl
fftip(vol)
try:
rt = read_text_file( "pwreference.txt" )
ro = rops_table(vol)
# Here unless I am mistaken it is enough to take the beginning of the reference pw.
for i in xrange(1,len(ro)): ro[i] = (rt[i]/ro[i])**0.5
vol = fft( filt_table( filt_tanl(vol, fl, aa), ro) )
msg = "Power spectrum adjusted\n"
print_msg(msg)
except:
vol = fft( filt_tanl(vol, fl, aa) )
stat = Util.infomask(vol, ref_data[0], False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0/stat[1])
vol = threshold(vol)
vol = filt_btwl(vol, 0.38, 0.5)
Util.mul_img(vol, ref_data[0])
if ref_data[1] == 1:
cs = volf.phase_cog()
msg = "Center x = %10.3f Center y = %10.3f Center z = %10.3f\n"%(cs[0], cs[1], cs[2])
print_msg(msg)
volf = fshift(volf, -cs[0], -cs[1], -cs[2])
else: cs = [0.0]*3
return vol, cs
def cml_open_proj(stack, ir, ou, lf, hf, dpsi = 1):
from projection import cml_sinogram
from utilities import model_circle, get_params_proj, model_blank, get_im
from fundamentals import fftip
from filter import filt_tanh
# number of projections
if type(stack) == type(""): nprj = EMUtil.get_image_count(stack)
else: nprj = len(stack)
Prj = [] # list of projections
Ori = [-1] * 4 * nprj # orientation intial (phi, theta, psi, index) for each projection
for i in xrange(nprj):
image = get_im(stack, i)
# read initial angles if given
try: Ori[4*i], Ori[4*i+1], Ori[4*i+2], s2x, s2y = get_params_proj(image)
except: pass
if(i == 0):
nx = image.get_xsize()
if(ou < 1): ou = nx // 2 - 1
diameter = int(2 * ou)
mask2D = model_circle(ou, nx, nx)
if ir > 0: mask2D -= model_circle(ir, nx, nx)
# normalize under the mask
[mean_a, sigma, imin, imax] = Util.infomask(image, mask2D, True)
image -= mean_a
Util.mul_scalar(image, 1.0/sigma)
Util.mul_img(image, mask2D)
# sinogram
sino = cml_sinogram(image, diameter, dpsi)
# prepare the cut positions in order to filter (lf: low freq; hf: high freq)
ihf = min(int(2 * hf * diameter), diameter + (diameter + 1) % 2)
ihf = ihf + (ihf + 1) % 2 # index ihf must be odd to take the img part
ilf = max(int(2 * lf * diameter), 0)
ilf = ilf + ilf % 2 # index ilf must be even to fall in the real part
bdf = ihf - ilf + 1
# process lines
nxe = sino.get_xsize()
nye = sino.get_ysize()
prj = model_blank(bdf, 2*nye)
pp = model_blank(nxe, 2*nye)
for li in xrange(nye):
# get the line li
line = Util.window(sino, nxe, 1, 1, 0, li-nye//2, 0)
# u2 (not improve the results)
#line = filt_tanh(line, ou / float(nx), ou / float(nx))
# normalize this line
[mean_l, sigma_l, imin, imax] = Util.infomask(line, None, True)
line = (line - mean_l) / sigma_l
# fft
fftip(line)
# filter (cut part of coef) and create mirror line
Util.cml_prepare_line(prj, line, ilf, ihf, li, nye)
# store the projection
Prj.append(prj)
return Prj, Ori
def do_volume_mrk02(ref_data):
"""
data - projections (scattered between cpus) or the volume. If volume, just do the volume processing
options - the same for all cpus
return - volume the same for all cpus
"""
from EMAN2 import Util
from mpi import mpi_comm_rank, mpi_comm_size, MPI_COMM_WORLD
from filter import filt_table
from reconstruction import recons3d_4nn_MPI, recons3d_4nn_ctf_MPI
from utilities import bcast_EMData_to_all, bcast_number_to_all, model_blank
from fundamentals import rops_table, fftip, fft
import types
# Retrieve the function specific input arguments from ref_data
data = ref_data[0]
Tracker = ref_data[1]
iter = ref_data[2]
mpi_comm = ref_data[3]
# # For DEBUG
# print "Type of data %s" % (type(data))
# print "Type of Tracker %s" % (type(Tracker))
# print "Type of iter %s" % (type(iter))
# print "Type of mpi_comm %s" % (type(mpi_comm))
if (mpi_comm == None): mpi_comm = MPI_COMM_WORLD
myid = mpi_comm_rank(mpi_comm)
nproc = mpi_comm_size(mpi_comm)
try:
local_filter = Tracker["local_filter"]
except:
local_filter = False
#=========================================================================
# volume reconstruction
if (type(data) == types.ListType):
if Tracker["constants"]["CTF"]:
vol = recons3d_4nn_ctf_MPI(myid, data, Tracker["constants"]["snr"], \
symmetry=Tracker["constants"]["sym"], npad=Tracker["constants"]["npad"], mpi_comm=mpi_comm, smearstep = Tracker["smearstep"])
else:
vol = recons3d_4nn_MPI (myid, data,\
symmetry=Tracker["constants"]["sym"], npad=Tracker["constants"]["npad"], mpi_comm=mpi_comm)
else:
vol = data
if myid == 0:
from morphology import threshold
from filter import filt_tanl, filt_btwl
from utilities import model_circle, get_im
import types
nx = vol.get_xsize()
if (Tracker["constants"]["mask3D"] == None):
mask3D = model_circle(
int(Tracker["constants"]["radius"] * float(nx) /
float(Tracker["constants"]["nnxo"]) + 0.5), nx, nx, nx)
elif (Tracker["constants"]["mask3D"] == "auto"):
from utilities import adaptive_mask
mask3D = adaptive_mask(vol)
else:
if (type(Tracker["constants"]["mask3D"]) == types.StringType):
mask3D = get_im(Tracker["constants"]["mask3D"])
else:
mask3D = (Tracker["constants"]["mask3D"]).copy()
nxm = mask3D.get_xsize()
if (nx != nxm):
from fundamentals import rot_shift3D
mask3D = Util.window(
rot_shift3D(mask3D, scale=float(nx) / float(nxm)), nx, nx,
nx)
nxm = mask3D.get_xsize()
assert (nx == nxm)
stat = Util.infomask(vol, mask3D, False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0 / stat[1])
vol = threshold(vol)
Util.mul_img(vol, mask3D)
if (Tracker["PWadjustment"]):
from utilities import read_text_file, write_text_file
rt = read_text_file(Tracker["PWadjustment"])
fftip(vol)
ro = rops_table(vol)
# Here unless I am mistaken it is enough to take the beginning of the reference pw.
for i in xrange(1, len(ro)):
ro[i] = (rt[i] / ro[i])**Tracker["upscale"]
#write_text_file(rops_table(filt_table( vol, ro),1),"foo.txt")
if Tracker["constants"]["sausage"]:
ny = vol.get_ysize()
y = float(ny)
from math import exp
for i in xrange(len(ro)): ro[i] *= \
(1.0+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.10)/0.025)**2)+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.215)/0.025)**2))
if local_filter:
# skip low-pass filtration
vol = fft(filt_table(vol, ro))
else:
if (type(Tracker["lowpass"]) == types.ListType):
vol = fft(
filt_table(filt_table(vol, Tracker["lowpass"]), ro))
else:
vol = fft(
filt_table(
filt_tanl(vol, Tracker["lowpass"],
Tracker["falloff"]), ro))
del ro
else:
if Tracker["constants"]["sausage"]:
ny = vol.get_ysize()
y = float(ny)
ro = [0.0] * (ny // 2 + 2)
from math import exp
for i in xrange(len(ro)): ro[i] = \
(1.0+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.10)/0.025)**2)+1.0*exp(-(((i/y/Tracker["constants"]["pixel_size"])-0.215)/0.025)**2))
fftip(vol)
filt_table(vol, ro)
del ro
if not local_filter:
if (type(Tracker["lowpass"]) == types.ListType):
vol = filt_table(vol, Tracker["lowpass"])
else:
vol = filt_tanl(vol, Tracker["lowpass"],
Tracker["falloff"])
if Tracker["constants"]["sausage"]: vol = fft(vol)
if local_filter:
from morphology import binarize
if (myid == 0): nx = mask3D.get_xsize()
else: nx = 0
nx = bcast_number_to_all(nx, source_node=0)
# only main processor needs the two input volumes
if (myid == 0):
mask = binarize(mask3D, 0.5)
locres = get_im(Tracker["local_filter"])
lx = locres.get_xsize()
if (lx != nx):
if (lx < nx):
from fundamentals import fdecimate, rot_shift3D
mask = Util.window(
rot_shift3D(mask, scale=float(lx) / float(nx)), lx, lx,
lx)
vol = fdecimate(vol, lx, lx, lx)
else:
ERROR("local filter cannot be larger than input volume",
"user function", 1)
stat = Util.infomask(vol, mask, False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0 / stat[1])
else:
lx = 0
locres = model_blank(1, 1, 1)
vol = model_blank(1, 1, 1)
lx = bcast_number_to_all(lx, source_node=0)
if (myid != 0): mask = model_blank(lx, lx, lx)
bcast_EMData_to_all(mask, myid, 0, comm=mpi_comm)
from filter import filterlocal
vol = filterlocal(locres, vol, mask, Tracker["falloff"], myid, 0,
nproc)
if myid == 0:
if (lx < nx):
from fundamentals import fpol
vol = fpol(vol, nx, nx, nx)
vol = threshold(vol)
vol = filt_btwl(vol, 0.38, 0.5) # This will have to be corrected.
Util.mul_img(vol, mask3D)
del mask3D
# vol.write_image('toto%03d.hdf'%iter)
else:
vol = model_blank(nx, nx, nx)
else:
if myid == 0:
#from utilities import write_text_file
#write_text_file(rops_table(vol,1),"goo.txt")
stat = Util.infomask(vol, mask3D, False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0 / stat[1])
vol = threshold(vol)
vol = filt_btwl(vol, 0.38, 0.5) # This will have to be corrected.
Util.mul_img(vol, mask3D)
del mask3D
# vol.write_image('toto%03d.hdf'%iter)
# broadcast volume
bcast_EMData_to_all(vol, myid, 0, comm=mpi_comm)
#=========================================================================
return vol
def dovolume(ref_data):
from utilities import print_msg, read_text_row
from filter import fit_tanh, filt_tanl
from fundamentals import fshift
from morphology import threshold
# Prepare the reference in 3D alignment, this function corresponds to what do_volume does.
# Input: list ref_data
# 0 - mask
# 1 - center flag
# 2 - raw average
# 3 - fsc result
# Output: filtered, centered, and masked reference image
# apply filtration (FSC) to reference image:
global ref_ali2d_counter
ref_ali2d_counter += 1
fl = ref_data[2].cmp("dot", ref_data[2], {
"negative": 0,
"mask": ref_data[0]
})
print_msg("do_volume user function Step = %5d GOAL = %10.3e\n" %
(ref_ali2d_counter, fl))
stat = Util.infomask(ref_data[2], ref_data[0], False)
vol = ref_data[2] - stat[0]
Util.mul_scalar(vol, 1.0 / stat[1])
vol = threshold(vol)
#Util.mul_img(vol, ref_data[0])
try:
aa = read_text_row("flaa.txt")[0]
fl = aa[0]
aa = aa[1]
except:
fl = 0.4
aa = 0.2
msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n" % (
fl, aa)
print_msg(msg)
from utilities import read_text_file
from fundamentals import rops_table, fftip, fft
from filter import filt_table, filt_btwl
fftip(vol)
try:
rt = read_text_file("pwreference.txt")
ro = rops_table(vol)
# Here unless I am mistaken it is enough to take the beginning of the reference pw.
for i in xrange(1, len(ro)):
ro[i] = (rt[i] / ro[i])**0.5
vol = fft(filt_table(filt_tanl(vol, fl, aa), ro))
msg = "Power spectrum adjusted\n"
print_msg(msg)
except:
vol = fft(filt_tanl(vol, fl, aa))
stat = Util.infomask(vol, ref_data[0], False)
vol -= stat[0]
Util.mul_scalar(vol, 1.0 / stat[1])
vol = threshold(vol)
vol = filt_btwl(vol, 0.38, 0.5)
Util.mul_img(vol, ref_data[0])
if ref_data[1] == 1:
cs = volf.phase_cog()
msg = "Center x = %10.3f Center y = %10.3f Center z = %10.3f\n" % (
cs[0], cs[1], cs[2])
print_msg(msg)
volf = fshift(volf, -cs[0], -cs[1], -cs[2])
else:
cs = [0.0] * 3
return vol, cs
def filterlocal(ui, vi, m, falloff, myid, main_node, number_of_proc): from mpi import mpi_init, mpi_comm_size, mpi_comm_rank, MPI_COMM_WORLD from mpi import mpi_reduce, mpi_bcast, mpi_barrier, mpi_gatherv, mpi_send, mpi_recv from mpi import MPI_SUM, MPI_FLOAT, MPI_INT from utilities import bcast_number_to_all, bcast_list_to_all, model_blank, bcast_EMData_to_all, reduce_EMData_to_root from morphology import threshold_outside from filter import filt_tanl from fundamentals import fft, fftip if(myid == main_node): nx = vi.get_xsize() ny = vi.get_ysize() nz = vi.get_zsize() # Round all resolution numbers to two digits for x in xrange(nx): for y in xrange(ny): for z in xrange(nz): ui.set_value_at_fast( x,y,z, round(ui.get_value_at(x,y,z), 2) ) dis = [nx,ny,nz] else: falloff = 0.0 radius = 0 dis = [0,0,0] falloff = bcast_number_to_all(falloff, main_node) dis = bcast_list_to_all(dis, myid, source_node = main_node) if(myid != main_node): nx = int(dis[0]) ny = int(dis[1]) nz = int(dis[2]) vi = model_blank(nx,ny,nz) ui = model_blank(nx,ny,nz) bcast_EMData_to_all(vi, myid, main_node) bcast_EMData_to_all(ui, myid, main_node) fftip(vi) # volume to be filtered st = Util.infomask(ui, m, True) filteredvol = model_blank(nx,ny,nz) cutoff = max(st[2] - 0.01,0.0) while(cutoff < st[3] ): cutoff = round(cutoff + 0.01, 2) #if(myid == main_node): print cutoff,st pt = Util.infomask( threshold_outside(ui, cutoff - 0.00501, cutoff + 0.005), m, True) # Ideally, one would want to check only slices in question... if(pt[0] != 0.0): #print cutoff,pt[0] vovo = fft( filt_tanl(vi, cutoff, falloff) ) for z in xrange(myid, nz, number_of_proc): for x in xrange(nx): for y in xrange(ny): if(m.get_value_at(x,y,z) > 0.5): if(round(ui.get_value_at(x,y,z),2) == cutoff): filteredvol.set_value_at_fast(x,y,z,vovo.get_value_at(x,y,z)) mpi_barrier(MPI_COMM_WORLD) reduce_EMData_to_root(filteredvol, myid, main_node, MPI_COMM_WORLD) return filteredvol
