def main():
import os
import sys
from optparse import OptionParser
from global_def import SPARXVERSION
import global_def
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage2 = progname + """ inputfile outputfile [options]
Functionalities:
1. Helicise input volume and save the result to output volume:
sxhelicon_utils.py input_vol.hdf output_vol.hdf --helicise --dp=27.6 --dphi=166.5 --fract=0.65 --rmax=70 --rmin=1 --apix=1.84 --sym=D1
2. Helicise pdb file and save the result to a new pdb file:
sxhelicon_utils.py input.pdb output.pdb --helicisepdb --dp=27.6 --dphi=166.5 --nrepeats --apix=1.84
3. Generate two lists of image indices used to split segment stack into halves for helical fsc calculation.
sxhelicon_utils.py bdb:big_stack --hfsc='flst' --filament_attr=filament
4. Map of filament distribution in the stack
sxhelicon_utils.py bdb:big_stack --filinfo=info.txt
The output file will contain four columns:
1 2 3 4
first image number last image number number of images in the filament name
5. Predict segments' orientation parameters based on distances between segments and known helical symmetry
sxhelicon_utils.py bdb:big_stack --predict_helical=helical_params.txt --dp=27.6 --dphi=166.5 --apix=1.84
6. Generate disks from filament based reconstructions:
sxheader.py stk.hdf --params=xform.projection --import=params.txt
mpirun -np 2 sxhelicon_utils.py stk.hdf --gendisk='bdb:disk' --ref_nx=100 --ref_ny=100 --ref_nz=200 --apix=1.84 --dp=27.6 --dphi=166.715 --fract=0.67 --rmin=0 --rmax=64 --function="[.,nofunc,helical3c]" --sym="c1" --MPI
7. Stack disks based on helical symmetry parameters
sxhelicon_utils.py disk_to_stack.hdf --stackdisk=stacked_disks.hdf --dphi=166.5 --dp=27.6 --ref_nx=160 --ref_ny=160 --ref_nz=225 --apix=1.84
8. Helical symmetry search:
mpirun -np 3 sxhelicon_utils.py volf0010.hdf outsymsearch --symsearch --dp=27.6 --dphi=166.715 --apix=1.84 --fract=0.65 --rmin=0 --rmax=92.0 --datasym=datasym.txt --dp_step=0.92 --ndp=3 --dphi_step=1.0 --ndphi=10 --MPI
"""
parser = OptionParser(usage2, version=SPARXVERSION)
#parser.add_option("--ir", type="float", default= -1, help="inner radius for rotational correlation > 0 (set to 1) (Angstroms)")
parser.add_option(
"--ou",
type="float",
default=-1,
help=
"outer radius for rotational 2D correlation < int(nx/2)-1 (set to the radius of the particle) (Angstroms)"
)
parser.add_option(
"--rs",
type="int",
default=1,
help="step between rings in rotational correlation >0 (set to 1)")
parser.add_option(
"--xr",
type="string",
default="4 2 1 1 1",
help=
"range for translation search in x direction, search is +/-xr (Angstroms) "
)
parser.add_option(
"--txs",
type="string",
default="1 1 1 0.5 0.25",
help=
"step size of the translation search in x directions, search is -xr, -xr+ts, 0, xr-ts, xr (Angstroms)"
)
parser.add_option("--delta",
type="string",
default="10 6 4 3 2",
help="angular step of reference projections")
parser.add_option("--an",
type="string",
default="-1",
help="angular neighborhood for local searches")
parser.add_option(
"--maxit",
type="int",
default=30,
help=
"maximum number of iterations performed for each angular step (set to 30) "
)
parser.add_option("--CTF",
action="store_true",
default=False,
help="CTF correction")
parser.add_option("--snr",
type="float",
default=1.0,
help="Signal-to-Noise Ratio of the data")
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version")
#parser.add_option("--fourvar", action="store_true", default=False, help="compute Fourier variance")
parser.add_option("--apix",
type="float",
default=-1.0,
help="pixel size in Angstroms")
parser.add_option("--dp",
type="float",
default=-1.0,
help="delta z - translation in Angstroms")
parser.add_option("--dphi",
type="float",
default=-1.0,
help="delta phi - rotation in degrees")
parser.add_option("--rmin",
type="float",
default=0.0,
help="minimal radius for hsearch (Angstroms)")
parser.add_option("--rmax",
type="float",
default=80.0,
help="maximal radius for hsearch (Angstroms)")
parser.add_option("--fract",
type="float",
default=0.7,
help="fraction of the volume used for helical search")
parser.add_option("--sym",
type="string",
default="c1",
help="symmetry of the structure")
parser.add_option("--function",
type="string",
default="helical",
help="name of the reference preparation function")
parser.add_option("--npad",
type="int",
default=2,
help="padding size for 3D reconstruction")
parser.add_option("--debug",
action="store_true",
default=False,
help="debug")
parser.add_option("--volalixshift",
action="store_true",
default=False,
help="Use volalixshift refinement")
parser.add_option(
"--searchxshift",
type="float",
default=0.0,
help=
"search range for x-shift determination: +/- searchxshift (Angstroms)")
parser.add_option(
"--nearby",
type="float",
default=6.0,
help=
"neighborhood within which to search for peaks in 1D ccf for x-shift search (Angstroms)"
)
# filinfo
parser.add_option(
"--filinfo",
type="string",
default="",
help=
"Store in an output text file infomration about distribution of filaments in the stack."
)
# diskali
parser.add_option("--diskali",
action="store_true",
default=False,
help="volume alignment")
parser.add_option(
"--zstep",
type="float",
default=1,
help="Step size for translational search along z (Angstroms)")
# helicise
parser.add_option(
"--helicise",
action="store_true",
default=False,
help="helicise input volume and save results to output volume")
parser.add_option(
"--hfsc",
type="string",
default="",
help=
"Generate two lists of image indices used to split segment stack into halves for helical fsc calculation. The lists will be stored in two text files named using file_prefix with '_even' and '_odd' suffixes, respectively."
)
parser.add_option(
"--filament_attr",
type="string",
default="filament",
help="attribute under which filament identification is stored")
parser.add_option(
"--predict_helical",
type="string",
default="",
help="Generate projection parameters consistent with helical symmetry")
# helicise pdb
parser.add_option(
"--helicisepdb",
action="store_true",
default=False,
help="Helicise pdb file and save the result to a new pdb file")
parser.add_option(
"--nrepeats",
type="int",
default=50,
help=
"Number of time the helical symmetry will be applied to the input file"
)
# input options for generating disks
parser.add_option(
"--gendisk",
type="string",
default="",
help="Name of file under which generated disks will be saved to")
parser.add_option("--ref_nx",
type="int",
default=-1,
help="nx=ny volume size")
parser.add_option(
"--ref_nz",
type="int",
default=-1,
help="nz volume size - computed disks will be nx x ny x rise/apix")
parser.add_option(
"--new_pixel_size",
type="float",
default=-1,
help=
"desired pixel size of the output disks. The default is -1, in which case there is no resampling (unless --match_pixel_rise flag is True)."
)
parser.add_option(
"--maxerror",
type="float",
default=0.1,
help=
"proportional to the maximum amount of error to tolerate between (dp/new_pixel_size) and int(dp/new_pixel_size ), where new_pixel_size is the pixel size calculated when the option --match_pixel_rise flag is True."
)
parser.add_option(
"--match_pixel_rise",
action="store_true",
default=False,
help=
"calculate new pixel size such that the rise is approximately integer number of pixels given the new pixel size. This will be the pixel size of the output disks."
)
# get consistency
parser.add_option(
"--consistency",
type="string",
default="",
help="Name of parameters to get consistency statistics for")
parser.add_option("--phithr",
type="float",
default=2.0,
help="phi threshold for consistency check")
parser.add_option("--ythr",
type="float",
default=2.0,
help="y threshold (in Angstroms) for consistency check")
parser.add_option(
"--segthr",
type="int",
default=3,
help="minimum number of segments/filament for consistency check")
# stack disks
parser.add_option(
"--stackdisk",
type="string",
default="",
help="Name of file under which output volume will be saved to.")
parser.add_option("--ref_ny",
type="int",
default=-1,
help="ny of output volume size. Default is ref_nx")
# symmetry search
parser.add_option("--symsearch",
action="store_true",
default=False,
help="Do helical symmetry search.")
parser.add_option(
"--ndp",
type="int",
default=12,
help=
"In symmetrization search, number of delta z steps equals to 2*ndp+1")
parser.add_option(
"--ndphi",
type="int",
default=12,
help=
"In symmetrization search, number of dphi steps equals to 2*ndphi+1")
parser.add_option(
"--dp_step",
type="float",
default=0.1,
help="delta z step for symmetrization [Angstroms] (default 0.1)")
parser.add_option(
"--dphi_step",
type="float",
default=0.1,
help="dphi step for symmetrization [degrees] (default 0.1)")
parser.add_option("--datasym",
type="string",
default="datasym.txt",
help="symdoc")
parser.add_option(
"--symdoc",
type="string",
default="",
help="text file containing helical symmetry parameters dp and dphi")
# filament statistics in the stack
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 1 or len(args) > 5:
print("Various helical reconstruction related functionalities: " +
usage2)
print("Please run '" + progname + " -h' for detailed options")
else:
if len(options.hfsc) > 0:
if len(args) != 1:
print("Incorrect number of parameters")
sys.exit()
from applications import imgstat_hfsc
imgstat_hfsc(args[0], options.hfsc, options.filament_attr)
sys.exit()
elif len(options.filinfo) > 0:
if len(args) != 1:
print("Incorrect number of parameters")
sys.exit()
from EMAN2 import EMUtil
filams = EMUtil.get_all_attributes(args[0], "filament")
ibeg = 0
filcur = filams[0]
n = len(filams)
inf = []
i = 1
while (i <= n):
if (i < n): fis = filams[i]
else: fis = ""
if (fis != filcur):
iend = i - 1
inf.append([ibeg, iend, iend - ibeg + 1, filcur])
ibeg = i
filcur = fis
i += 1
from utilities import write_text_row
write_text_row(inf, options.filinfo)
sys.exit()
if len(options.stackdisk) > 0:
if len(args) != 1:
print("Incorrect number of parameters")
sys.exit()
dpp = (float(options.dp) / options.apix)
rise = int(dpp)
if (abs(float(rise) - dpp) > 1.0e-3):
print(" dpp has to be integer multiplicity of the pixel size")
sys.exit()
from utilities import get_im
v = get_im(args[0])
from applications import stack_disks
ref_ny = options.ref_ny
if ref_ny < 0:
ref_ny = options.ref_nx
sv = stack_disks(v, options.ref_nx, ref_ny, options.ref_nz,
options.dphi, rise)
sv.write_image(options.stackdisk)
sys.exit()
if len(options.consistency) > 0:
if len(args) != 1:
print("Incorrect number of parameters")
sys.exit()
from development import consistency_params
consistency_params(args[0],
options.consistency,
options.dphi,
options.dp,
options.apix,
phithr=options.phithr,
ythr=options.ythr,
THR=options.segthr)
sys.exit()
rminp = int((float(options.rmin) / options.apix) + 0.5)
rmaxp = int((float(options.rmax) / options.apix) + 0.5)
from utilities import get_input_from_string, get_im
xr = get_input_from_string(options.xr)
txs = get_input_from_string(options.txs)
irp = 1
if options.ou < 0: oup = -1
else: oup = int((options.ou / options.apix) + 0.5)
xrp = ''
txsp = ''
for i in xrange(len(xr)):
xrp += " " + str(float(xr[i]) / options.apix)
for i in xrange(len(txs)):
txsp += " " + str(float(txs[i]) / options.apix)
searchxshiftp = int((options.searchxshift / options.apix) + 0.5)
nearbyp = int((options.nearby / options.apix) + 0.5)
zstepp = int((options.zstep / options.apix) + 0.5)
if options.MPI:
from mpi import mpi_init, mpi_finalize
sys.argv = mpi_init(len(sys.argv), sys.argv)
if len(options.predict_helical) > 0:
if len(args) != 1:
print("Incorrect number of parameters")
sys.exit()
if options.dp < 0:
print(
"Helical symmetry paramter rise --dp should not be negative"
)
sys.exit()
from applications import predict_helical_params
predict_helical_params(args[0], options.dp, options.dphi,
options.apix, options.predict_helical)
sys.exit()
if options.helicise:
if len(args) != 2:
print("Incorrect number of parameters")
sys.exit()
if options.dp < 0:
print(
"Helical symmetry paramter rise --dp should not be negative"
)
sys.exit()
from utilities import get_im, sym_vol
vol = get_im(args[0])
vol = sym_vol(vol, options.sym)
hvol = vol.helicise(options.apix, options.dp, options.dphi,
options.fract, rmaxp, rminp)
hvol = sym_vol(hvol, options.sym)
hvol.write_image(args[1])
sys.exit()
if options.helicisepdb:
if len(args) != 2:
print("Incorrect number of parameters")
sys.exit()
if options.dp < 0:
print(
"Helical symmetry paramter rise --dp should not be negative"
)
sys.exit()
from math import cos, sin, radians
from copy import deepcopy
import numpy
from numpy import zeros, dot, float32
dp = options.dp
dphi = options.dphi
nperiod = options.nrepeats
infile = open(args[0], "r")
pall = infile.readlines()
infile.close()
p = []
pos = []
lkl = -1
for i in xrange(len(pall)):
if ((pall[i])[:4] == 'ATOM'):
if (lkl == -1): lkl = i
p.append(pall[i])
pos.append(i)
n = len(p)
X = zeros((3, len(p)), dtype=float32)
X_new = zeros((3, len(p)), dtype=float32)
for i in xrange(len(p)):
element = deepcopy(p[i])
X[0, i] = float(element[30:38])
X[1, i] = float(element[38:46])
X[2, i] = float(element[46:54])
pnew = []
for j in xrange(-nperiod, nperiod + 1):
for i in xrange(n):
pnew.append(deepcopy(p[i]))
dphi = radians(dphi)
m = zeros((3, 3), dtype=float32)
t = zeros((3, 1), dtype=float32)
m[2][2] = 1.0
t[0, 0] = 0.0
t[1, 0] = 0.0
for j in xrange(-nperiod, nperiod + 1):
if j != 0:
rd = j * dphi
m[0][0] = cos(rd)
m[0][1] = sin(rd)
m[1][0] = -m[0][1]
m[1][1] = m[0][0]
t[2, 0] = j * dp
X_new = dot(m, X) + t
for i in xrange(n):
pnew[j * n +
i] = pnew[j * n + i][:30] + "%8.3f" % (float(
X_new[0, i])) + "%8.3f" % (float(
X_new[1, i])) + "%8.3f" % (float(
X_new[2, i])) + pnew[j * n + i][54:]
outfile = open(args[1], "w")
outfile.writelines(pall[0:lkl])
outfile.writelines(pnew)
outfile.writelines("END\n")
outfile.close()
sys.exit()
if options.volalixshift:
if options.maxit > 1:
print(
"Inner iteration for x-shift determinatin is restricted to 1"
)
sys.exit()
if len(args) < 4: mask = None
else: mask = args[3]
from applications import volalixshift_MPI
global_def.BATCH = True
volalixshift_MPI(args[0], args[1], args[2], searchxshiftp,
options.apix, options.dp, options.dphi,
options.fract, rmaxp, rminp, mask, options.maxit,
options.CTF, options.snr, options.sym,
options.function, options.npad, options.debug,
nearbyp)
global_def.BATCH = False
if options.diskali:
#if options.maxit > 1:
# print "Inner iteration for disk alignment is restricted to 1"
# sys.exit()
if len(args) < 4: mask = None
else: mask = args[3]
global_def.BATCH = True
if (options.sym[:1] == "d" or options.sym[:1] == "D"):
from development import diskaliD_MPI
diskaliD_MPI(args[0], args[1], args[2], mask, options.dp,
options.dphi, options.apix, options.function,
zstepp, options.fract, rmaxp, rminp, options.CTF,
options.maxit, options.sym)
else:
from applications import diskali_MPI
diskali_MPI(args[0], args[1], args[2], mask, options.dp,
options.dphi, options.apix, options.function,
zstepp, options.fract, rmaxp, rminp, options.CTF,
options.maxit, options.sym)
global_def.BATCH = False
if options.symsearch:
if len(options.symdoc) < 1:
if options.dp < 0 or options.dphi < 0:
print(
"Enter helical symmetry parameters either using --symdoc or --dp and --dphi"
)
sys.exit()
if options.dp < 0 or options.dphi < 0:
# read helical symmetry parameters from symdoc
from utilities import read_text_row
hparams = read_text_row(options.symdoc)
dp = hparams[0][0]
dphi = hparams[0][1]
else:
dp = options.dp
dphi = options.dphi
from applications import symsearch_MPI
if len(args) < 3:
mask = None
else:
mask = args[2]
global_def.BATCH = True
symsearch_MPI(args[0], args[1], mask, dp, options.ndp,
options.dp_step, dphi, options.ndphi,
options.dphi_step, rminp, rmaxp, options.fract,
options.sym, options.function, options.datasym,
options.apix, options.debug)
global_def.BATCH = False
elif len(options.gendisk) > 0:
from applications import gendisks_MPI
global_def.BATCH = True
if len(args) == 1: mask3d = None
else: mask3d = args[1]
if options.dp < 0:
print(
"Helical symmetry paramter rise --dp must be explictly set!"
)
sys.exit()
gendisks_MPI(args[0], mask3d, options.ref_nx, options.apix,
options.dp, options.dphi, options.fract, rmaxp, rminp,
options.CTF, options.function, options.sym,
options.gendisk, options.maxerror,
options.new_pixel_size, options.match_pixel_rise)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()
def main():
import os
import sys
from optparse import OptionParser
from global_def import SPARXVERSION
import global_def
arglist = []
for arg in sys.argv:
arglist.append( arg )
progname = os.path.basename(arglist[0])
usage2 = progname + """ inputfile outputfile [options]
Functionalities:
1. Helicise input volume and save the result to output volume:
sxhelicon_utils.py input_vol.hdf output_vol.hdf --helicise --dp=27.6 --dphi=166.5 --fract=0.65 --rmax=70 --rmin=1 --apix=1.84 --sym=D1
2. Helicise pdb file and save the result to a new pdb file:
sxhelicon_utils.py input.pdb output.pdb --helicisepdb --dp=27.6 --dphi=166.5 --nrepeats --apix=1.84
3. Generate two lists of image indices used to split segment stack into halves for helical fsc calculation.
sxhelicon_utils.py bdb:big_stack --hfsc='flst' --filament_attr=filament
4. Map of filament distribution in the stack
sxhelicon_utils.py bdb:big_stack --filinfo=info.txt
The output file will contain four columns:
1 2 3 4
first image number last image number number of images in the filament name
5. Predict segments' orientation parameters based on distances between segments and known helical symmetry
sxhelicon_utils.py bdb:big_stack --predict_helical=helical_params.txt --dp=27.6 --dphi=166.5 --apix=1.84
6. Generate disks from filament based reconstructions:
sxheader.py stk.hdf --params=xform.projection --import=params.txt
# horatio active_refactoring Jy51i1EwmLD4tWZ9_00000_1
# sxheader.py stk.hdf --params=active --one
mpirun -np 2 sxhelicon_utils.py stk.hdf --gendisk='bdb:disk' --ref_nx=100 --ref_ny=100 --ref_nz=200 --apix=1.84 --dp=27.6 --dphi=166.715 --fract=0.67 --rmin=0 --rmax=64 --function="[.,nofunc,helical3c]" --sym="c1" --MPI
7. Stack disks based on helical symmetry parameters
sxhelicon_utils.py disk_to_stack.hdf --stackdisk=stacked_disks.hdf --dphi=166.5 --dp=27.6 --ref_nx=160 --ref_ny=160 --ref_nz=225 --apix=1.84
8. Helical symmetry search:
mpirun -np 3 sxhelicon_utils.py volf0010.hdf outsymsearch --symsearch --dp=27.6 --dphi=166.715 --apix=1.84 --fract=0.65 --rmin=0 --rmax=92.0 --datasym=datasym.txt --dp_step=0.92 --ndp=3 --dphi_step=1.0 --ndphi=10 --MPI
"""
parser = OptionParser(usage2,version=SPARXVERSION)
#parser.add_option("--ir", type="float", default= -1, help="inner radius for rotational correlation > 0 (set to 1) (Angstroms)")
parser.add_option("--ou", type="float", default= -1, help="outer radius for rotational 2D correlation < int(nx/2)-1 (set to the radius of the particle) (Angstroms)")
parser.add_option("--rs", type="int", default= 1, help="step between rings in rotational correlation >0 (set to 1)" )
parser.add_option("--xr", type="string", default= "4 2 1 1 1", help="range for translation search in x direction, search is +/-xr (Angstroms) ")
parser.add_option("--txs", type="string", default= "1 1 1 0.5 0.25", help="step size of the translation search in x directions, search is -xr, -xr+ts, 0, xr-ts, xr (Angstroms)")
parser.add_option("--delta", type="string", default= "10 6 4 3 2", help="angular step of reference projections")
parser.add_option("--an", type="string", default= "-1", help="angular neighborhood for local searches")
parser.add_option("--maxit", type="int", default= 30, help="maximum number of iterations performed for each angular step (set to 30) ")
parser.add_option("--CTF", action="store_true", default=False, help="CTF correction")
parser.add_option("--snr", type="float", default= 1.0, help="Signal-to-Noise Ratio of the data")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version")
#parser.add_option("--fourvar", action="store_true", default=False, help="compute Fourier variance")
parser.add_option("--apix", type="float", default= -1.0, help="pixel size in Angstroms")
parser.add_option("--dp", type="float", default= -1.0, help="delta z - translation in Angstroms")
parser.add_option("--dphi", type="float", default= -1.0, help="delta phi - rotation in degrees")
parser.add_option("--rmin", type="float", default= 0.0, help="minimal radius for hsearch (Angstroms)")
parser.add_option("--rmax", type="float", default= 80.0, help="maximal radius for hsearch (Angstroms)")
parser.add_option("--fract", type="float", default= 0.7, help="fraction of the volume used for helical search")
parser.add_option("--sym", type="string", default= "c1", help="symmetry of the structure")
parser.add_option("--function", type="string", default="helical", help="name of the reference preparation function")
parser.add_option("--npad", type="int", default= 2, help="padding size for 3D reconstruction")
parser.add_option("--debug", action="store_true", default=False, help="debug")
parser.add_option("--volalixshift", action="store_true", default=False, help="Use volalixshift refinement")
parser.add_option("--searchxshift", type="float", default= 0.0, help="search range for x-shift determination: +/- searchxshift (Angstroms)")
parser.add_option("--nearby", type="float", default= 6.0, help="neighborhood within which to search for peaks in 1D ccf for x-shift search (Angstroms)")
# filinfo
parser.add_option( "--filinfo", type="string", default="", help="Store in an output text file infomration about distribution of filaments in the stack." )
# diskali
parser.add_option("--diskali", action="store_true", default=False, help="volume alignment")
parser.add_option("--zstep", type="float", default= 1, help="Step size for translational search along z (Angstroms)")
# helicise
parser.add_option("--helicise", action="store_true", default=False, help="helicise input volume and save results to output volume")
parser.add_option("--hfsc", type="string", default="", help="Generate two lists of image indices used to split segment stack into halves for helical fsc calculation. The lists will be stored in two text files named using file_prefix with '_even' and '_odd' suffixes, respectively." )
parser.add_option("--filament_attr", type="string", default="filament", help="attribute under which filament identification is stored" )
parser.add_option("--predict_helical", type="string", default="", help="Generate projection parameters consistent with helical symmetry")
# helicise pdb
parser.add_option("--helicisepdb", action="store_true", default=False, help="Helicise pdb file and save the result to a new pdb file")
parser.add_option("--nrepeats", type="int", default= 50, help="Number of time the helical symmetry will be applied to the input file")
# input options for generating disks
parser.add_option("--gendisk", type="string", default="", help="Name of file under which generated disks will be saved to")
parser.add_option("--ref_nx", type="int", default= -1, help="nx=ny volume size" )
parser.add_option("--ref_nz", type="int", default= -1, help="nz volume size - computed disks will be nx x ny x rise/apix" )
parser.add_option("--new_pixel_size", type="float", default= -1, help="desired pixel size of the output disks. The default is -1, in which case there is no resampling (unless --match_pixel_rise flag is True).")
parser.add_option("--maxerror", type="float", default= 0.1, help="proportional to the maximum amount of error to tolerate between (dp/new_pixel_size) and int(dp/new_pixel_size ), where new_pixel_size is the pixel size calculated when the option --match_pixel_rise flag is True.")
parser.add_option("--match_pixel_rise", action="store_true", default=False, help="calculate new pixel size such that the rise is approximately integer number of pixels given the new pixel size. This will be the pixel size of the output disks.")
# get consistency
parser.add_option("--consistency", type="string", default="", help="Name of parameters to get consistency statistics for")
parser.add_option("--phithr", type="float", default= 2.0, help="phi threshold for consistency check")
parser.add_option("--ythr", type="float", default= 2.0, help="y threshold (in Angstroms) for consistency check")
parser.add_option("--segthr", type="int", default= 3, help="minimum number of segments/filament for consistency check")
# stack disks
parser.add_option("--stackdisk", type="string", default="", help="Name of file under which output volume will be saved to.")
parser.add_option("--ref_ny", type="int", default=-1, help="ny of output volume size. Default is ref_nx" )
# symmetry search
parser.add_option("--symsearch", action="store_true", default=False, help="Do helical symmetry search." )
parser.add_option("--ndp", type="int", default= 12, help="In symmetrization search, number of delta z steps equals to 2*ndp+1")
parser.add_option("--ndphi", type="int", default= 12, help="In symmetrization search, number of dphi steps equals to 2*ndphi+1")
parser.add_option("--dp_step", type="float", default= 0.1, help="delta z step for symmetrization [Angstroms] (default 0.1)")
parser.add_option("--dphi_step", type="float", default= 0.1, help="dphi step for symmetrization [degrees] (default 0.1)")
parser.add_option("--datasym", type="string", default="datasym.txt", help="symdoc")
parser.add_option("--symdoc", type="string", default="", help="text file containing helical symmetry parameters dp and dphi")
# filament statistics in the stack
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 1 or len(args) > 5:
print "Various helical reconstruction related functionalities: " + usage2
print "Please run '" + progname + " -h' for detailed options"
else:
if len(options.hfsc) > 0:
if len(args) != 1:
print "Incorrect number of parameters"
sys.exit()
from applications import imgstat_hfsc
imgstat_hfsc( args[0], options.hfsc, options.filament_attr)
sys.exit()
elif len(options.filinfo) > 0:
if len(args) != 1:
print "Incorrect number of parameters"
sys.exit()
from EMAN2 import EMUtil
filams = EMUtil.get_all_attributes(args[0], "filament")
ibeg = 0
filcur = filams[0]
n = len(filams)
inf = []
i = 1
while( i <= n):
if(i < n): fis = filams[i]
else: fis = ""
if( fis != filcur ):
iend = i-1
inf.append([ibeg,iend,iend-ibeg+1,filcur])
ibeg = i
filcur = fis
i += 1
from utilities import write_text_row
write_text_row(inf, options.filinfo)
sys.exit()
if len(options.stackdisk) > 0:
if len(args) != 1:
print "Incorrect number of parameters"
sys.exit()
dpp = (float(options.dp)/options.apix)
rise = int(dpp)
if(abs(float(rise) - dpp)>1.0e-3):
print " dpp has to be integer multiplicity of the pixel size"
sys.exit()
from utilities import get_im
v = get_im(args[0])
from applications import stack_disks
ref_ny = options.ref_ny
if ref_ny < 0:
ref_ny = options.ref_nx
sv = stack_disks(v, options.ref_nx, ref_ny, options.ref_nz, options.dphi, rise)
sv.write_image(options.stackdisk)
sys.exit()
if len(options.consistency) > 0:
if len(args) != 1:
print "Incorrect number of parameters"
sys.exit()
from development import consistency_params
consistency_params(args[0], options.consistency, options.dphi, options.dp, options.apix,phithr=options.phithr, ythr=options.ythr, THR=options.segthr)
sys.exit()
rminp = int((float(options.rmin)/options.apix) + 0.5)
rmaxp = int((float(options.rmax)/options.apix) + 0.5)
from utilities import get_input_from_string, get_im
xr = get_input_from_string(options.xr)
txs = get_input_from_string(options.txs)
irp = 1
if options.ou < 0: oup = -1
else: oup = int( (options.ou/options.apix) + 0.5)
xrp = ''
txsp = ''
for i in xrange(len(xr)):
xrp += " "+str(float(xr[i])/options.apix)
for i in xrange(len(txs)):
txsp += " "+str(float(txs[i])/options.apix)
searchxshiftp = int( (options.searchxshift/options.apix) + 0.5)
nearbyp = int( (options.nearby/options.apix) + 0.5)
zstepp = int( (options.zstep/options.apix) + 0.5)
if options.MPI:
from mpi import mpi_init, mpi_finalize
sys.argv = mpi_init(len(sys.argv), sys.argv)
if len(options.predict_helical) > 0:
if len(args) != 1:
print "Incorrect number of parameters"
sys.exit()
if options.dp < 0:
print "Helical symmetry paramter rise --dp should not be negative"
sys.exit()
from applications import predict_helical_params
predict_helical_params(args[0], options.dp, options.dphi, options.apix, options.predict_helical)
sys.exit()
if options.helicise:
if len(args) != 2:
print "Incorrect number of parameters"
sys.exit()
if options.dp < 0:
print "Helical symmetry paramter rise --dp should not be negative"
sys.exit()
from utilities import get_im, sym_vol
vol = get_im(args[0])
vol = sym_vol(vol, options.sym)
hvol = vol.helicise(options.apix, options.dp, options.dphi, options.fract, rmaxp, rminp)
hvol = sym_vol(hvol, options.sym)
hvol.write_image(args[1])
sys.exit()
if options.helicisepdb:
if len(args) != 2:
print "Incorrect number of parameters"
sys.exit()
if options.dp < 0:
print "Helical symmetry paramter rise --dp should not be negative"
sys.exit()
from math import cos, sin, radians
from copy import deepcopy
import numpy
from numpy import zeros,dot,float32
dp = options.dp
dphi = options.dphi
nperiod = options.nrepeats
infile =open(args[0],"r")
pall = infile.readlines()
infile.close()
p = []
pos = []
lkl = -1
for i in xrange( len(pall) ):
if( (pall[i])[:4] == 'ATOM'):
if( lkl == -1 ): lkl = i
p.append( pall[i] )
pos.append(i)
n = len(p)
X = zeros( (3,len(p) ), dtype=float32 )
X_new = zeros( (3,len(p) ), dtype=float32 )
for i in xrange( len(p) ):
element = deepcopy( p[i] )
X[0,i]=float(element[30:38])
X[1,i]=float(element[38:46])
X[2,i]=float(element[46:54])
pnew = []
for j in xrange(-nperiod, nperiod+1):
for i in xrange( n ):
pnew.append( deepcopy(p[i]) )
dphi = radians(dphi)
m = zeros( (3,3 ), dtype=float32 )
t = zeros( (3,1 ), dtype=float32 )
m[2][2] = 1.0
t[0,0] = 0.0
t[1,0] = 0.0
for j in xrange(-nperiod, nperiod+1):
if j != 0:
rd = j*dphi
m[0][0] = cos(rd)
m[0][1] = sin(rd)
m[1][0] = -m[0][1]
m[1][1] = m[0][0]
t[2,0] = j*dp
X_new = dot(m, X) + t
for i in xrange( n ):
pnew[j*n+i] = pnew[j*n+i][:30] + "%8.3f"%( float(X_new[0,i]) )+"%8.3f"%( float(X_new[1,i]) )+"%8.3f"%( float(X_new[2,i]) ) + pnew[j*n+i][54:]
outfile=open(args[1],"w")
outfile.writelines(pall[0:lkl])
outfile.writelines(pnew)
outfile.writelines("END\n")
outfile.close()
sys.exit()
if options.volalixshift:
if options.maxit > 1:
print "Inner iteration for x-shift determinatin is restricted to 1"
sys.exit()
if len(args) < 4: mask = None
else: mask = args[3]
from applications import volalixshift_MPI
global_def.BATCH = True
volalixshift_MPI(args[0], args[1], args[2], searchxshiftp, options.apix, options.dp, options.dphi, options.fract, rmaxp, rminp, mask, options.maxit, options.CTF, options.snr, options.sym, options.function, options.npad, options.debug, nearbyp)
global_def.BATCH = False
if options.diskali:
#if options.maxit > 1:
# print "Inner iteration for disk alignment is restricted to 1"
# sys.exit()
if len(args) < 4: mask = None
else: mask = args[3]
global_def.BATCH = True
if(options.sym[:1] == "d" or options.sym[:1] == "D" ):
from development import diskaliD_MPI
diskaliD_MPI(args[0], args[1], args[2], mask, options.dp, options.dphi, options.apix, options.function, zstepp, options.fract, rmaxp, rminp, options.CTF, options.maxit, options.sym)
else:
from applications import diskali_MPI
diskali_MPI(args[0], args[1], args[2], mask, options.dp, options.dphi, options.apix, options.function, zstepp, options.fract, rmaxp, rminp, options.CTF, options.maxit, options.sym)
global_def.BATCH = False
if options.symsearch:
if len(options.symdoc) < 1:
if options.dp < 0 or options.dphi < 0:
print "Enter helical symmetry parameters either using --symdoc or --dp and --dphi"
sys.exit()
if options.dp < 0 or options.dphi < 0:
# read helical symmetry parameters from symdoc
from utilities import read_text_row
hparams=read_text_row(options.symdoc)
dp = hparams[0][0]
dphi = hparams[0][1]
else:
dp = options.dp
dphi = options.dphi
from applications import symsearch_MPI
if len(args) < 3:
mask = None
else:
mask= args[2]
global_def.BATCH = True
symsearch_MPI(args[0], args[1], mask, dp, options.ndp, options.dp_step, dphi, options.ndphi, options.dphi_step, rminp, rmaxp, options.fract, options.sym, options.function, options.datasym, options.apix, options.debug)
global_def.BATCH = False
elif len(options.gendisk)> 0:
from applications import gendisks_MPI
global_def.BATCH = True
if len(args) == 1: mask3d = None
else: mask3d = args[1]
if options.dp < 0:
print "Helical symmetry paramter rise --dp must be explictly set!"
sys.exit()
gendisks_MPI(args[0], mask3d, options.ref_nx, options.apix, options.dp, options.dphi, options.fract, rmaxp, rminp, options.CTF, options.function, options.sym, options.gendisk, options.maxerror, options.new_pixel_size, options.match_pixel_rise)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()