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 do_volume_mrk03(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_4nnw_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"])
vol = recons3d_4nnw_MPI(myid, data, Tracker["bckgnoise"], 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 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 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)
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)
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 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 main():
import os
import sys
from optparse import OptionParser
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage = progname + """ inputvolume locresvolume maskfile outputfile --radius --falloff --MPI
Locally filer a volume based on local resolution volume (sxlocres.py) within area outlined by the maskfile
"""
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--radius",
type="int",
default=-1,
help=
"if there is no maskfile, sphere with r=radius will be used, by default the radius is nx/2-1"
)
parser.add_option("--falloff",
type="float",
default=0.1,
help="falloff of tanl filter (default 0.1)")
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version")
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 3 or len(args) > 4:
print("See usage " + usage)
sys.exit()
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if options.MPI:
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
sys.argv = mpi_init(len(sys.argv), sys.argv)
number_of_proc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
main_node = 0
if (myid == main_node):
#print sys.argv
vi = get_im(sys.argv[1])
ui = get_im(sys.argv[2])
#print Util.infomask(ui, None, True)
radius = options.radius
nx = vi.get_xsize()
ny = vi.get_ysize()
nz = vi.get_zsize()
dis = [nx, ny, nz]
else:
falloff = 0.0
radius = 0
dis = [0, 0, 0]
vi = None
ui = None
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])
radius = bcast_number_to_all(radius, main_node)
if len(args) == 3:
if (radius == -1): radius = min(nx, ny, nz) // 2 - 1
m = model_circle(radius, nx, ny, nz)
outvol = args[2]
elif len(args) == 4:
if (myid == main_node): m = binarize(get_im(args[2]), 0.5)
else: m = model_blank(nx, ny, nz)
outvol = args[3]
bcast_EMData_to_all(m, myid, main_node)
from filter import filterlocal
filteredvol = filterlocal(ui, vi, m, options.falloff, myid, main_node,
number_of_proc)
if (myid == 0): filteredvol.write_image(outvol)
from mpi import mpi_finalize
mpi_finalize()
else:
vi = get_im(args[0])
ui = get_im(
args[1]
) # resolution volume, values are assumed to be from 0 to 0.5
nn = vi.get_xsize()
falloff = options.falloff
if len(args) == 3:
radius = options.radius
if (radius == -1): radius = nn // 2 - 1
m = model_circle(radius, nn, nn, nn)
outvol = args[2]
elif len(args) == 4:
m = binarize(get_im(args[2]), 0.5)
outvol = args[3]
fftip(vi) # this is the volume to be filtered
# Round all resolution numbers to two digits
for x in range(nn):
for y in range(nn):
for z in range(nn):
ui.set_value_at_fast(x, y, z,
round(ui.get_value_at(x, y, z), 2))
st = Util.infomask(ui, m, True)
filteredvol = model_blank(nn, nn, nn)
cutoff = max(st[2] - 0.01, 0.0)
while (cutoff < st[3]):
cutoff = round(cutoff + 0.01, 2)
pt = Util.infomask(
threshold_outside(ui, cutoff - 0.00501, cutoff + 0.005), m,
True)
if (pt[0] != 0.0):
vovo = fft(filt_tanl(vi, cutoff, falloff))
for x in range(nn):
for y in range(nn):
for z in range(nn):
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))
filteredvol.write_image(outvol)
def main():
import os
import sys
from optparse import OptionParser
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage = (
progname
+ """ inputvolume locresvolume maskfile outputfile --radius --falloff --MPI
Locally filer a volume based on local resolution volume (sxlocres.py) within area outlined by the maskfile
"""
)
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--radius",
type="int",
default=-1,
help="if there is no maskfile, sphere with r=radius will be used, by default the radius is nx/2-1",
)
parser.add_option("--falloff", type="float", default=0.1, help="falloff of tanl filter (default 0.1)")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version")
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 3 or len(args) > 4:
print "See usage " + usage
sys.exit()
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if options.MPI:
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
sys.argv = mpi_init(len(sys.argv), sys.argv)
number_of_proc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
main_node = 0
if myid == main_node:
# print sys.argv
vi = get_im(sys.argv[1])
ui = get_im(sys.argv[2])
# print Util.infomask(ui, None, True)
radius = options.radius
nx = vi.get_xsize()
ny = vi.get_ysize()
nz = vi.get_zsize()
dis = [nx, ny, nz]
else:
falloff = 0.0
radius = 0
dis = [0, 0, 0]
vi = None
ui = None
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])
radius = bcast_number_to_all(radius, main_node)
if len(args) == 3:
if radius == -1:
radius = min(nx, ny, nz) // 2 - 1
m = model_circle(radius, nx, ny, nz)
outvol = args[2]
elif len(args) == 4:
if myid == main_node:
m = binarize(get_im(args[2]), 0.5)
else:
m = model_blank(nx, ny, nz)
outvol = args[3]
bcast_EMData_to_all(m, myid, main_node)
from filter import filterlocal
filteredvol = filterlocal(ui, vi, m, options.falloff, myid, main_node, number_of_proc)
if myid == 0:
filteredvol.write_image(outvol)
from mpi import mpi_finalize
mpi_finalize()
else:
vi = get_im(args[0])
ui = get_im(args[1]) # resolution volume, values are assumed to be from 0 to 0.5
nn = vi.get_xsize()
falloff = options.falloff
if len(args) == 3:
radius = options.radius
if radius == -1:
radius = nn // 2 - 1
m = model_circle(radius, nn, nn, nn)
outvol = args[2]
elif len(args) == 4:
m = binarize(get_im(args[2]), 0.5)
outvol = args[3]
fftip(vi) # this is the volume to be filtered
# Round all resolution numbers to two digits
for x in xrange(nn):
for y in xrange(nn):
for z in xrange(nn):
ui.set_value_at_fast(x, y, z, round(ui.get_value_at(x, y, z), 2))
st = Util.infomask(ui, m, True)
filteredvol = model_blank(nn, nn, nn)
cutoff = max(st[2] - 0.01, 0.0)
while cutoff < st[3]:
cutoff = round(cutoff + 0.01, 2)
pt = Util.infomask(threshold_outside(ui, cutoff - 0.00501, cutoff + 0.005), m, True)
if pt[0] != 0.0:
vovo = fft(filt_tanl(vi, cutoff, falloff))
for x in xrange(nn):
for y in xrange(nn):
for z in xrange(nn):
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))
filteredvol.write_image(outvol)