def metamove(paramsdict, partids, partstack, outputdir, procid, myid, main_node, nproc):
# Reads from paramsdict["stack"] particles partids set parameters in partstack
# and do refinement as specified in paramsdict
#
# Will create outputdir
# Will write to outputdir output parameters: params-chunk0.txt and params-chunk1.txt
if(myid == main_node):
# Create output directory
log = Logger(BaseLogger_Files())
log.prefix = os.path.join(outputdir)
cmd = "mkdir "+log.prefix
cmdexecute(cmd)
log.prefix += "/"
else: log = None
mpi_barrier(MPI_COMM_WORLD)
ali3d_options.delta = paramsdict["delta"]
ali3d_options.center = paramsdict["center"]
ali3d_options.ts = paramsdict["ts"]
ali3d_options.xr = paramsdict["xr"]
ali3d_options.fl = paramsdict["currentres"]
ali3d_options.aa = paramsdict["aa"]
ali3d_options.maxit = paramsdict["maxit"]
ali3d_options.mask3D = paramsdict["mask3D"]
projdata = getindexdata(paramsdict["stack"], partids, partstack, myid, nproc)
if(paramsdict["delpreviousmax"]):
for i in xrange(len(projdata)):
try: projdata[i].del_attr("previousmax")
except: pass
ali3d_options.ou = paramsdict["radius"] # This is changed in ali3d_base, but the shrank value is needed in vol recons, fixt it!
if(myid == main_node):
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"METAMOVE parameters")
spaces = " "
for q in paramsdict: print(" => ",q+spaces[len(q):],": ",paramsdict[q])
print(" => partids : ",partids)
print(" => partstack : ",partstack)
# Run alignment command
params = ali3d_base(projdata, get_im(paramsdict["refvol"]), \
ali3d_options, paramsdict["shrink"], mpi_comm = MPI_COMM_WORLD, log = log, \
nsoft = paramsdict["nsoft"], saturatecrit = paramsdict["saturatecrit"] )
del log, projdata
# store params
if(myid == main_node):
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: ","ali3d_base_MPI %d"%paramsdict["nsoft"]," number of images:%7d"%len(params))
write_text_row(params, os.path.join(outputdir,"params-chunk%01d.txt"%procid) )
def mergeparfiles(i1,i2,io,p1,p2,po): # 1 - rescued # 2 - good old l1 = map(int, read_text_file( i1 )) l2 = map(int, read_text_file( i2 )) if(l1[0] == 0): write_text_file( l2, io) for ll in xrange(3): p = read_text_row(p2+"%01d.txt"%ll) write_text_row(2, po+"%01d.txt"%ll) else: t = l1 +l2 for i in xrange(len(t)): t[i] = [t[i],i] t.sort() write_text_file( [t[i][0] for i in xrange(len(t))], io) for ll in xrange(3): p = read_text_row(p1+"%01d.txt"%ll) + read_text_row(p2+"%01d.txt"%ll) write_text_row([p[t[i][1]] for i in xrange(len(t))], po+"%01d.txt"%ll) return
def output_volume(freqvol, resolut, apix, outvol, fsc, out_ang_res, nx, ny, nz,
res_overall):
outvol_ang = os.path.splitext(outvol)[0] + "_ang.hdf"
outvol_shifted = os.path.splitext(outvol)[0] + "_shift.hdf"
outvol_shifted_ang = os.path.splitext(outvol_shifted)[0] + "_ang.hdf"
freqvol.write_image(outvol)
if (out_ang_res):
outAngResVol = makeAngRes(freqvol, nx, ny, nz, apix)
outAngResVol.write_image(outvol_ang)
if res_overall != -1.0:
for ifreq in range(len(resolut)):
if resolut[ifreq][0] > res_overall:
break
for jfreq in range(ifreq, len(resolut)):
resolut[jfreq][1] = 0.0
data_freqvol = freqvol.get_3dview()
mask = data_freqvol != 0
percentile_25 = numpy.percentile(data_freqvol[mask], 25)
percentile_75 = numpy.percentile(data_freqvol[mask], 75)
iqr = percentile_75 - percentile_25
mask_low_pass = data_freqvol > percentile_75 + 1.5 * iqr
mask_high_pass = data_freqvol < percentile_25 - 1.5 * iqr
mean_real = 1 / float(
numpy.mean(data_freqvol[mask & mask_low_pass & mask_high_pass]))
overall_res_real = 1 / float(res_overall)
#mean_ang = options.apix / float(EMAN2_cppwrap.Util.infomask(freqvol, m, True)[0])
volume_out_real = makeAngRes(freqvol, nx, ny, nz, 1)
volume_out_real += (overall_res_real - mean_real)
volume_out = makeAngRes(volume_out_real, nx, ny, nz, 1, False)
volume_out.write_image(outvol_shifted)
if out_ang_res:
outAngResVol = makeAngRes(freqvol, nx, ny, nz, apix)
outAngResVol.write_image(outvol_shifted_ang)
if (fsc != None): utilities.write_text_row(resolut, fsc)
def kernel(projections,
stable_subset,
target_threshold,
options,
minimal_subset_size,
number_of_runs,
number_of_winners,
mpi_env,
log,
prefix=""):
from multi_shc import multi_shc, find_common_subset_3
from utilities import wrap_mpi_bcast, write_text_row, write_text_file, wrap_mpi_gatherv, average_angles
from itertools import combinations
import os
if log == None:
from logger import Logger
log = Logger()
stable_subset = wrap_mpi_bcast(stable_subset, 0, mpi_env.main_comm)
if mpi_env.main_rank == 0:
log.add("Start ", number_of_runs, "* 3SHC")
for i in xrange(number_of_runs):
log.add("3SHC --> " + log.prefix + prefix + "_" + str(i))
completed_mshc = 0
params = []
while completed_mshc < number_of_runs:
runs_to_do = min([(number_of_runs - completed_mshc),
mpi_env.subcomms_count])
if mpi_env.subcomm_id < runs_to_do:
out_dir = prefix + "_" + str(completed_mshc + mpi_env.subcomm_id)
if mpi_env.sub_rank == 0:
os.mkdir(log.prefix + out_dir)
out_params, out_vol, out_peaks = multi_shc(projections,
stable_subset,
3,
options,
mpi_env.sub_comm,
log=log.sublog(out_dir +
"/"))
else:
out_params = None
if mpi_env.main_rank in mpi_env.subcomms_roots and mpi_env.subcomm_id < runs_to_do:
params_temp = wrap_mpi_gatherv([out_params], 0, mpi_env.main_comm)
else:
params_temp = wrap_mpi_gatherv([], 0, mpi_env.main_comm)
if mpi_env.main_rank == 0:
params.extend(params_temp)
completed_mshc += runs_to_do
# find common subset
if mpi_env.main_rank == 0:
log.add("Calculate common subset")
best_confs = []
largest_subset = []
largest_subset_error = 999.0
msg = ""
for it in combinations(range(number_of_runs), number_of_winners):
confs = list(it)
input_params = []
for c in confs:
input_params.append(params[c])
subset_thr, subset_size, err_thr, err_size = find_common_subset_3(
input_params,
target_threshold,
minimal_subset_size,
thresholds=True)
msg += str(len(subset_size)) + "(" + str(err_size) + ") "
if len(subset_size) > len(largest_subset) or (
len(subset_size) == len(largest_subset)
and err_size < largest_subset_error):
best_confs = confs
largest_subset = subset_size
largest_subset_error = err_size
log.add(msg)
subset = largest_subset
threshold = largest_subset_error
new_stable_subset = []
for i in subset:
new_stable_subset.append(stable_subset[i])
log.add("Best solutions (winners): ", best_confs)
average_params = []
for i in subset:
temp = [params[j][i] for j in best_confs]
average_params.append(average_angles(temp))
write_text_file(new_stable_subset,
log.prefix + prefix + "_indexes.txt")
write_text_row(average_params, log.prefix + prefix + "_params.txt")
else:
threshold = None
new_stable_subset = None
# broadcast threshold and new stable subset and exit
threshold = wrap_mpi_bcast(threshold, 0, mpi_env.main_comm)
new_stable_subset = wrap_mpi_bcast(new_stable_subset, 0, mpi_env.main_comm)
return threshold, new_stable_subset
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()
def compute_fscs(stack, outputdir, chunkname, newgoodname, fscoutputdir, doit, keepchecking, nproc, myid, main_node):
# Compute reconstructions per group from good particles only to get FSC curves
# We will compute two FSC curves - from not averaged parameters and from averaged parameters
# So, we have to build two sets:
# not averaged (A2+C3) versus (B0+D5)
# averaged (A0+C1) versus (B3+D4)
# This requires pulling good subsets given by goodX*; I am not sure why good, sxconsistency above produced newgood text files.
# Otherwise, I am not sure what newbad will contain.
# Input that should vary:
# "bdb:"+os.path.join(outputdir,"chunk%01d%01d"%(procid,i))
# os.path.join(outputdir,"newgood%01d.txt"%procid)
# Output should be in a separate directory "fscoutputdir"
if(myid == main_node):
if keepchecking:
if(os.path.exists(fscoutputdir)):
doit = 0
print("Directory ",fscoutputdir," exists!")
else:
doit = 1
keepchecking = False
else:
doit = 1
if doit:
cmd = "{} {}".format("mkdir", fscoutputdir)
cmdexecute(cmd)
mpi_barrier(MPI_COMM_WORLD)
# not averaged
doit, keepchecking = checkstep(os.path.join(fscoutputdir,"volfscn0.hdf"), keepchecking, myid, main_node)
if doit:
if(myid == main_node):
# A2+C3
# indices
write_text_file( \
map(int, read_text_file(os.path.join(outputdir,chunkname+"0.txt")))+map(int, read_text_file(os.path.join(outputdir,chunkname+"2.txt"))), \
os.path.join(fscoutputdir,"chunkfn0.txt"))
# params
write_text_row( \
read_text_row(os.path.join(outputdir,newgoodname+"02.txt"))+read_text_row(os.path.join(outputdir,newgoodname+"22.txt")), \
os.path.join(fscoutputdir,"params-chunkfn0.txt"))
mpi_barrier(MPI_COMM_WORLD)
projdata = getindexdata(stack, os.path.join(fscoutputdir,"chunkfn0.txt"), os.path.join(fscoutputdir,"params-chunkfn0.txt"), myid, nproc)
if ali3d_options.CTF: vol = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if(myid == main_node):
vol.write_image(os.path.join(fscoutputdir,"volfscn0.hdf"))
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: 3D reconstruction of", os.path.join(fscoutputdir,"volfscn0.hdf"))
del vol
doit, keepchecking = checkstep(os.path.join(fscoutputdir,"volfscn1.hdf"), keepchecking, myid, main_node)
if doit:
if(myid == main_node):
# B0+D5
# indices
write_text_file( \
map(int, read_text_file(os.path.join(outputdir,chunkname+"1.txt")))+map(int, read_text_file(os.path.join(outputdir,chunkname+"3.txt"))), \
os.path.join(fscoutputdir,"chunkfn1.txt"))
# params
write_text_row( \
read_text_row(os.path.join(outputdir,newgoodname+"10.txt"))+read_text_row(os.path.join(outputdir,newgoodname+"32.txt")), \
os.path.join(fscoutputdir,"params-chunkfn1.txt"))
mpi_barrier(MPI_COMM_WORLD)
projdata = getindexdata(stack, os.path.join(fscoutputdir,"chunkfn1.txt"), os.path.join(fscoutputdir,"params-chunkfn1.txt"), myid, nproc)
if ali3d_options.CTF: vol = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if(myid == main_node):
vol.write_image(os.path.join(fscoutputdir,"volfscn1.hdf"))
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: 3D reconstruction of", os.path.join(fscoutputdir,"volfscn1.hdf"))
del vol
# averaged
doit, keepchecking = checkstep(os.path.join(fscoutputdir,"volfsca0.hdf"), keepchecking, myid, main_node)
if doit:
if(myid == main_node):
# A0+C1
# indices
write_text_file( \
map(int, read_text_file(os.path.join(outputdir,chunkname+"0.txt")))+map(int, read_text_file(os.path.join(outputdir,chunkname+"2.txt"))), \
os.path.join(fscoutputdir,"chunkfa0.txt"))
# params
write_text_row( \
read_text_row(os.path.join(outputdir,newgoodname+"00.txt"))+read_text_row(os.path.join(outputdir,newgoodname+"20.txt")), \
os.path.join(fscoutputdir,"params-chunkfa0.txt"))
mpi_barrier(MPI_COMM_WORLD)
projdata = getindexdata(stack, os.path.join(fscoutputdir,"chunkfa0.txt"), os.path.join(fscoutputdir,"params-chunkfa0.txt"), myid, nproc)
if ali3d_options.CTF: vol = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if(myid == main_node):
vol.write_image(os.path.join(fscoutputdir,"volfsca0.hdf"))
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: 3D reconstruction of", os.path.join(fscoutputdir,"volfsca0.hdf"))
del vol
doit, keepchecking = checkstep(os.path.join(fscoutputdir,"volfsca1.hdf"), keepchecking, myid, main_node)
if doit:
if(myid == main_node):
# B3+D4
write_text_file( \
map(int, read_text_file(os.path.join(outputdir,chunkname+"1.txt")))+map(int, read_text_file(os.path.join(outputdir,chunkname+"3.txt"))), \
os.path.join(fscoutputdir,"chunkfa1.txt"))
# params
write_text_row( \
read_text_row(os.path.join(outputdir,newgoodname+"11.txt"))+read_text_row(os.path.join(outputdir,newgoodname+"31.txt")), \
os.path.join(fscoutputdir,"params-chunkfa1.txt"))
mpi_barrier(MPI_COMM_WORLD)
projdata = getindexdata(stack, os.path.join(fscoutputdir,"chunkfa1.txt"), os.path.join(fscoutputdir,"params-chunkfa1.txt"), myid, nproc)
if ali3d_options.CTF: vol = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if(myid == main_node):
vol.write_image(os.path.join(fscoutputdir,"volfsca1.hdf"))
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: 3D reconstruction of", os.path.join(fscoutputdir,"volfsca1.hdf"))
del vol
# Get updated FSC curves
if(myid == main_node):
if(ali3d_options.mask3D is None): mask = model_circle(radi,nnxo,nnxo,nnxo)
else:
mask = get_im(ali3d_options.mask3D)
if keepchecking:
if(os.path.exists(os.path.join(fscoutputdir,"fscn.txt"))):
doit = 0
else:
doit = 1
keepchecking = False
else: doit = 1
if doit: fsc(get_im(os.path.join(fscoutputdir,"volfscn0.hdf"))*mask,\
get_im(os.path.join(fscoutputdir,"volfscn1.hdf"))*mask,\
1.0,os.path.join(fscoutputdir,"fscn.txt") )
if keepchecking:
if(os.path.exists(os.path.join(fscoutputdir,"fsca.txt"))):
doit = 0
else:
doit = 1
keepchecking = False
else: doit = 1
if doit: fsc(get_im(os.path.join(fscoutputdir,"volfsca0.hdf"))*mask,\
get_im(os.path.join(fscoutputdir,"volfsca1.hdf"))*mask,\
1.0,os.path.join(fscoutputdir,"fsca.txt") )
nfsc = read_text_file(os.path.join(fscoutputdir,"fscn.txt") ,-1)
currentres = 0.5
ns = len(nfsc[1])
for i in xrange(1,ns-1):
if ( (2*nfsc[1][i]/(1.0+nfsc[1][i]) ) < 0.5):
currentres = nfsc[0][i-1]
break
print(" Current resolution ",i,currentres)
else:
currentres = 0.0
currentres = bcast_number_to_all(currentres, source_node = main_node)
if(currentres < 0.0):
if(myid == main_node):
print(" Something wrong with the resolution, cannot continue")
mpi_finalize()
exit()
mpi_barrier(MPI_COMM_WORLD)
return currentres, doit, keepchecking
def main():
from utilities import get_input_from_string
progname = os.path.basename(sys.argv[0])
usage = progname + " stack output_average --radius=particle_radius --xr=xr --yr=yr --ts=ts --thld_err=thld_err --num_ali=num_ali --fl=fl --aa=aa --CTF --verbose --stables"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--radius", type="int", default=-1, help=" particle radius for alignment")
parser.add_option("--xr", type="string" , default="2 1", help="range for translation search in x direction, search is +/xr (default 2,1)")
parser.add_option("--yr", type="string" , default="-1", help="range for translation search in y direction, search is +/yr (default = same as xr)")
parser.add_option("--ts", type="string" , default="1 0.5", help="step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional (default: 1,0.5)")
parser.add_option("--thld_err", type="float", default=0.75, help="threshld of pixel error (default = 0.75)")
parser.add_option("--num_ali", type="int", default=5, help="number of alignments performed for stability (default = 5)")
parser.add_option("--maxit", type="int", default=30, help="number of iterations for each xr (default = 30)")
parser.add_option("--fl", type="float" , default=0.3, help="cut-off frequency of hyperbolic tangent low-pass Fourier filter (default = 0.3)")
parser.add_option("--aa", type="float" , default=0.2, help="fall-off of hyperbolic tangent low-pass Fourier filter (default = 0.2)")
parser.add_option("--CTF", action="store_true", default=False, help="Use CTF correction during the alignment ")
parser.add_option("--verbose", action="store_true", default=False, help="print individual pixel error (default = False)")
parser.add_option("--stables", action="store_true", default=False, help="output the stable particles number in file (default = False)")
parser.add_option("--method", type="string" , default=" ", help="SHC (standard method is default when flag is ommitted)")
(options, args) = parser.parse_args()
if len(args) != 1 and len(args) != 2:
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options"
else:
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
from applications import within_group_refinement, ali2d_ras
from pixel_error import multi_align_stability
from utilities import write_text_file, write_text_row
global_def.BATCH = True
xrng = get_input_from_string(options.xr)
if options.yr == "-1": yrng = xrng
else : yrng = get_input_from_string(options.yr)
step = get_input_from_string(options.ts)
class_data = EMData.read_images(args[0])
nx = class_data[0].get_xsize()
ou = options.radius
num_ali = options.num_ali
if ou == -1: ou = nx/2-2
from utilities import model_circle, get_params2D, set_params2D
mask = model_circle(ou, nx, nx)
if options.CTF :
from filter import filt_ctf
for im in xrange(len(class_data)):
# Flip phases
class_data[im] = filt_ctf(class_data[im], class_data[im].get_attr("ctf"), binary=1)
for im in class_data:
im.set_attr("previousmax", -1.0e10)
try:
t = im.get_attr("xform.align2d") # if they are there, no need to set them!
except:
try:
t = im.get_attr("xform.projection")
d = t.get_params("spider")
set_params2D(im, [0.0, -d["tx"], -d["ty"], 0, 1.0])
except:
set_params2D(im, [0.0, 0.0, 0.0, 0, 1.0])
all_ali_params = []
for ii in xrange(num_ali):
ali_params = []
if options.verbose:
ALPHA = []
SX = []
SY = []
MIRROR = []
if( xrng[0] == 0.0 and yrng[0] == 0.0 ):
avet = ali2d_ras(class_data, randomize = True, ir = 1, ou = ou, rs = 1, step = 1.0, dst = 90.0, \
maxit = options.maxit, check_mirror = True, FH=options.fl, FF=options.aa)
else:
avet = within_group_refinement(class_data, mask, True, 1, ou, 1, xrng, yrng, step, 90.0, \
maxit = options.maxit, FH=options.fl, FF=options.aa, method = options.method)
from utilities import info
#print " avet ",info(avet)
for im in class_data:
alpha, sx, sy, mirror, scale = get_params2D(im)
ali_params.extend([alpha, sx, sy, mirror])
if options.verbose:
ALPHA.append(alpha)
SX.append(sx)
SY.append(sy)
MIRROR.append(mirror)
all_ali_params.append(ali_params)
if options.verbose:
write_text_file([ALPHA, SX, SY, MIRROR], "ali_params_run_%d"%ii)
"""
avet = class_data[0]
from utilities import read_text_file
all_ali_params = []
for ii in xrange(5):
temp = read_text_file( "ali_params_run_%d"%ii,-1)
uuu = []
for k in xrange(len(temp[0])):
uuu.extend([temp[0][k],temp[1][k],temp[2][k],temp[3][k]])
all_ali_params.append(uuu)
"""
stable_set, mir_stab_rate, pix_err = multi_align_stability(all_ali_params, 0.0, 10000.0, options.thld_err, options.verbose, 2*ou+1)
print "%4s %20s %20s %20s %30s %6.2f"%("", "Size of set", "Size of stable set", "Mirror stab rate", "Pixel error prior to pruning the set above threshold of",options.thld_err)
print "Average stat: %10d %20d %20.2f %15.2f"%( len(class_data), len(stable_set), mir_stab_rate, pix_err)
if( len(stable_set) > 0):
if options.stables:
stab_mem = [[0,0.0,0] for j in xrange(len(stable_set))]
for j in xrange(len(stable_set)): stab_mem[j] = [int(stable_set[j][1]), stable_set[j][0], j]
write_text_row(stab_mem, "stable_particles.txt")
stable_set_id = []
particle_pixerr = []
for s in stable_set:
stable_set_id.append(s[1])
particle_pixerr.append(s[0])
from fundamentals import rot_shift2D
avet.to_zero()
l = -1
print "average parameters: angle, x-shift, y-shift, mirror"
for j in stable_set_id:
l += 1
print " %4d %4d %12.2f %12.2f %12.2f %1d"%(l,j, stable_set[l][2][0], stable_set[l][2][1], stable_set[l][2][2], int(stable_set[l][2][3]))
avet += rot_shift2D(class_data[j], stable_set[l][2][0], stable_set[l][2][1], stable_set[l][2][2], stable_set[l][2][3] )
avet /= (l+1)
avet.set_attr('members', stable_set_id)
avet.set_attr('pix_err', pix_err)
avet.set_attr('pixerr', particle_pixerr)
avet.write_image(args[1])
global_def.BATCH = False
def doXfiles(path, source = "chunk", inparams = "params", params = "params", dest = "X"): # will produce X*.txt and paramsX*.txt # Generate six Xfiles from four chunks and export parameters. This is hardwired as it is always done in the same way # AB # indices write_text_file( \ map(int, read_text_file(os.path.join(path,source+"0.txt")))+map(int, read_text_file(os.path.join(path,source+"1.txt"))), \ os.path.join(path,dest+"0.txt")) # params write_text_row( \ read_text_row(os.path.join(path,inparams+"00.txt"))+read_text_row(os.path.join(path,inparams+"10.txt")), \ os.path.join(path,params+dest+"0.txt")) # AC write_text_file( \ map(int, read_text_file(os.path.join(path,source+"0.txt")))+map(int, read_text_file(os.path.join(path,source+"2.txt"))), \ os.path.join(path,dest+"1.txt")) write_text_row( \ read_text_row(os.path.join(path,inparams+"01.txt"))+read_text_row(os.path.join(path,inparams+"20.txt")), \ os.path.join(path,params+dest+"1.txt")) # AD write_text_file( \ map(int, read_text_file(os.path.join(path,source+"0.txt")))+map(int, read_text_file(os.path.join(path,source+"3.txt"))), \ os.path.join(path,dest+"2.txt")) write_text_row( \ read_text_row(os.path.join(path,inparams+"02.txt"))+read_text_row(os.path.join(path,inparams+"30.txt")), \ os.path.join(path,params+dest+"2.txt")) # BC write_text_file( \ map(int, read_text_file(os.path.join(path,source+"1.txt")))+map(int, read_text_file(os.path.join(path,source+"2.txt"))), \ os.path.join(path,dest+"3.txt")) write_text_row( \ read_text_row(os.path.join(path,inparams+"11.txt"))+read_text_row(os.path.join(path,inparams+"21.txt")), \ os.path.join(path,params+dest+"3.txt")) # BD write_text_file( \ map(int, read_text_file(os.path.join(path,source+"1.txt")))+map(int, read_text_file(os.path.join(path,source+"3.txt"))), \ os.path.join(path,dest+"4.txt")) write_text_row( \ read_text_row(os.path.join(path,inparams+"12.txt"))+read_text_row(os.path.join(path,inparams+"31.txt")), \ os.path.join(path,params+dest+"4.txt")) # CD write_text_file( \ map(int, read_text_file(os.path.join(path,source+"2.txt")))+map(int, read_text_file(os.path.join(path,source+"3.txt"))), \ os.path.join(path,dest+"5.txt")) write_text_row( \ read_text_row(os.path.join(path,inparams+"22.txt"))+read_text_row(os.path.join(path,inparams+"32.txt")), \ os.path.join(path,params+dest+"5.txt")) return
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Forms chains of 2D images based on their similarities.
Functionality:
4. Order a 2-D stack of image based on pair-wise similarity (computed as a cross-correlation coefficent).
Options 1-3 require image stack to be aligned. The program will apply orientation parameters if present in headers.
The ways to use the program:
4.1 Use option initial to specify which image will be used as an initial seed to form the chain.
sxprocess.py input_stack.hdf output_stack.hdf --initial=23 --radius=25
4.2 If options initial is omitted, the program will determine which image best serves as initial seed to form the chain
sxprocess.py input_stack.hdf output_stack.hdf --radius=25
4.3 Use option circular to form a circular chain.
sxprocess.py input_stack.hdf output_stack.hdf --circular--radius=25
4.4 New circular code based on pairwise alignments
sxprocess.py aclf.hdf chain.hdf circle.hdf --align --radius=25 --xr=2 --pairwiseccc=lcc.txt
4.5 Circular ordering based on pairwise alignments
sxprocess.py vols.hdf chain.hdf mask.hdf --dd --radius=25
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--dd", action="store_true", help="Circular ordering without adjustment of orientations", default=False)
parser.add_option("--circular", action="store_true", help="Select circular ordering (first image has to be similar to the last)", default=False)
parser.add_option("--align", action="store_true", help="Compute all pairwise alignments and for the table of their similarities find the best chain", default=False)
parser.add_option("--initial", type="int", default=-1, help="Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)")
parser.add_option("--radius", type="int", default=-1, help="Radius of a circular mask for similarity based ordering")
# import params for 2D alignment
parser.add_option("--ou", type="int", default=-1, help="outer radius for 2D alignment < nx/2-1 (set to the radius of the particle)")
parser.add_option("--xr", type="int", default=0, help="range for translation search in x direction, search is +/xr (0)")
parser.add_option("--yr", type="int", default=0, help="range for translation search in y direction, search is +/yr (0)")
#parser.add_option("--nomirror", action="store_true", default=False, help="Disable checking mirror orientations of images (default False)")
parser.add_option("--pairwiseccc", type="string", default= None, help="Input/output pairwise ccc file")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.dd:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
stack = args[0]
new_stack = args[1]
from utilities import model_circle
from statistics import ccc
from statistics import mono
lend = EMUtil.get_image_count(stack)
lccc = [None]*(lend*(lend-1)/2)
for i in xrange(lend-1):
v1 = get_im( stack, i )
if( i == 0 and nargs == 2):
nx = v1.get_xsize()
ny = v1.get_ysize()
nz = v1.get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny, nz)
else:
mask = get_im(args[2])
for j in xrange(i+1, lend):
lccc[mono(i,j)] = [ccc(v1, get_im( stack, j ), mask), 0]
order = tsp(lccc)
if(len(order) != lend):
print " problem with data length"
from sys import exit
exit()
print "Total sum of cccs :",TotalDistance(order, lccc)
print "ordering :",order
for i in xrange(lend): get_im(stack, order[i]).write_image( new_stack, i )
elif options.align:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
from utilities import get_params2D, model_circle
from fundamentals import rot_shift2D
from statistics import ccc
from time import time
from alignment import align2d, align2d_scf
from multi_shc import mult_transform
stack = args[0]
new_stack = args[1]
d = EMData.read_images(stack)
"""
# will align anyway
try:
ttt = d[0].get_attr('xform.params2d')
for i in xrange(len(d)):
alpha, sx, sy, mirror, scale = get_params2D(d[i])
d[i] = rot_shift2D(d[i], alpha, sx, sy, mirror)
except:
pass
"""
nx = d[0].get_xsize()
ny = d[0].get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny)
if(options.xr < 0): xrng = 0
else: xrng = options.xr
if(options.yr < 0): yrng = xrng
else: yrng = options.yr
initial = max(options.initial, 0)
from statistics import mono
lend = len(d)
lccc = [None]*(lend*(lend-1)/2)
from utilities import read_text_row
if options.pairwiseccc == None or not os.path.exists(options.pairwiseccc) :
st = time()
for i in xrange(lend-1):
for j in xrange(i+1, lend):
# j>i meaning mono entry (i,j) or (j,i) indicates T i->j (from smaller index to larger)
#alpha, sx, sy, mir, peak = align2d(d[i],d[j], xrng, yrng, step=options.ts, first_ring=options.ir, last_ring=radius, mode = "F")
alpha, sx, sy, mir, peak = align2d_scf(d[i],d[j], xrng, yrng, ou=radius)
lccc[mono(i,j)] = [ccc(d[j], rot_shift2D(d[i], alpha, sx, sy, mir, 1.0), mask), alpha, sx, sy, mir]
#print " %4d %10.1f"%(i,time()-st)
if(not os.path.exists(options.pairwiseccc)):
from utilities import write_text_row
write_text_row([[initial,0,0,0,0]]+lccc,options.pairwiseccc)
elif(os.path.exists(options.pairwiseccc)):
lccc = read_text_row(options.pairwiseccc)
initial = int(lccc[0][0] + 0.1)
del lccc[0]
for i in xrange(len(lccc)):
T = Transform({"type":"2D","alpha":lccc[i][1],"tx":lccc[i][2],"ty":lccc[i][3],"mirror":int(lccc[i][4]+0.1)})
lccc[i] = [lccc[i][0],T]
tdummy = Transform({"type":"2D"})
maxsum = -1.023
for m in xrange(0,lend):#initial, initial+1):
indc = range( lend )
lsnake = [[m, tdummy, 0.0]]
del indc[m]
lsum = 0.0
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = lccc[mono(indc[i], lsnake[-1][0])][0]
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
# Here we need transformation from the current to the previous,
# meaning indc[i] -> lsnake[-1][0]
T = lccc[mono(indc[i], lsnake[-1][0])][1]
# If direction is from larger to smaller index, the transformation has to be inverted
if( indc[i] > lsnake[-1][0] ): T = T.inverse()
lsnake.append([qi,T, maxcit])
lsum += maxcit
del indc[indc.index(qi)]
T = lccc[mono(indc[-1], lsnake[-1][0])][1]
if( indc[-1] > lsnake[-1][0]): T = T.inverse()
lsnake.append([indc[-1], T, lccc[mono(indc[-1], lsnake[-1][0])][0]])
print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(lend)]
print " Initial image selected : ",init,maxsum," ",TotalDistance([snake[m][0] for m in xrange(lend)], lccc)
#for q in snake: print q
from copy import deepcopy
trans=deepcopy([snake[i][1] for i in xrange(len(snake))])
print [snake[i][0] for i in xrange(len(snake))]
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Forms chains of 2D images based on their similarities.
Functionality:
4. Order a 2-D stack of image based on pair-wise similarity (computed as a cross-correlation coefficent).
Options 1-3 require image stack to be aligned. The program will apply orientation parameters if present in headers.
The ways to use the program:
4.1 Use option initial to specify which image will be used as an initial seed to form the chain.
sxprocess.py input_stack.hdf output_stack.hdf --initial=23 --radius=25
4.2 If options initial is omitted, the program will determine which image best serves as initial seed to form the chain
sxprocess.py input_stack.hdf output_stack.hdf --radius=25
4.3 Use option circular to form a circular chain.
sxprocess.py input_stack.hdf output_stack.hdf --circular--radius=25
4.4 New circular code based on pairwise alignments
sxprocess.py aclf.hdf chain.hdf circle.hdf --align --radius=25 --xr=2 --pairwiseccc=lcc.txt
4.5 Circular ordering based on pairwise alignments
sxprocess.py vols.hdf chain.hdf mask.hdf --dd --radius=25
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--dd", action="store_true", help="Circular ordering without adjustment of orientations", default=False)
parser.add_option("--circular", action="store_true", help="Select circular ordering (first image has to be similar to the last)", default=False)
parser.add_option("--align", action="store_true", help="Compute all pairwise alignments and for the table of their similarities find the best chain", default=False)
parser.add_option("--initial", type="int", default=-1, help="Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)")
parser.add_option("--radius", type="int", default=-1, help="Radius of a circular mask for similarity based ordering")
# import params for 2D alignment
parser.add_option("--ou", type="int", default=-1, help="outer radius for 2D alignment < nx/2-1 (set to the radius of the particle)")
parser.add_option("--xr", type="int", default=0, help="range for translation search in x direction, search is +/xr (0)")
parser.add_option("--yr", type="int", default=0, help="range for translation search in y direction, search is +/yr (0)")
#parser.add_option("--nomirror", action="store_true", default=False, help="Disable checking mirror orientations of images (default False)")
parser.add_option("--pairwiseccc", type="string", default= None, help="Input/output pairwise ccc file")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.dd:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
stack = args[0]
new_stack = args[1]
from utilities import model_circle
from statistics import ccc
from statistics import mono
lend = EMUtil.get_image_count(stack)
lccc = [None]*(lend*(lend-1)/2)
for i in xrange(lend-1):
v1 = get_im( stack, i )
if( i == 0 and nargs == 2):
nx = v1.get_xsize()
ny = v1.get_ysize()
nz = v1.get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny, nz)
else:
mask = get_im(args[2])
for j in xrange(i+1, lend):
lccc[mono(i,j)] = [ccc(v1, get_im( stack, j ), mask), 0]
order = tsp(lccc)
if(len(order) != lend):
print " problem with data length"
from sys import exit
exit()
print "Total sum of cccs :",TotalDistance(order, lccc)
print "ordering :",order
for i in xrange(lend): get_im(stack, order[i]).write_image( new_stack, i )
elif options.align:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
from utilities import get_params2D, model_circle
from fundamentals import rot_shift2D
from statistics import ccc
from time import time
from alignment import align2d, align2d_scf
from multi_shc import mult_transform
stack = args[0]
new_stack = args[1]
d = EMData.read_images(stack)
"""
# will align anyway
try:
ttt = d[0].get_attr('xform.params2d')
for i in xrange(len(d)):
alpha, sx, sy, mirror, scale = get_params2D(d[i])
d[i] = rot_shift2D(d[i], alpha, sx, sy, mirror)
except:
pass
"""
nx = d[0].get_xsize()
ny = d[0].get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny)
if(options.xr < 0): xrng = 0
else: xrng = options.xr
if(options.yr < 0): yrng = xrng
else: yrng = options.yr
initial = max(options.initial, 0)
from statistics import mono
lend = len(d)
lccc = [None]*(lend*(lend-1)/2)
from utilities import read_text_row
if options.pairwiseccc == None or not os.path.exists(options.pairwiseccc) :
st = time()
for i in xrange(lend-1):
for j in xrange(i+1, lend):
# j>i meaning mono entry (i,j) or (j,i) indicates T i->j (from smaller index to larger)
#alpha, sx, sy, mir, peak = align2d(d[i],d[j], xrng, yrng, step=options.ts, first_ring=options.ir, last_ring=radius, mode = "F")
alpha, sx, sy, mir, peak = align2d_scf(d[i],d[j], xrng, yrng, ou=radius)
lccc[mono(i,j)] = [ccc(d[j], rot_shift2D(d[i], alpha, sx, sy, mir, 1.0), mask), alpha, sx, sy, mir]
#print " %4d %10.1f"%(i,time()-st)
if(not os.path.exists(options.pairwiseccc)):
from utilities import write_text_row
write_text_row([[initial,0,0,0,0]]+lccc,options.pairwiseccc)
elif(os.path.exists(options.pairwiseccc)):
lccc = read_text_row(options.pairwiseccc)
initial = int(lccc[0][0] + 0.1)
del lccc[0]
for i in xrange(len(lccc)):
T = Transform({"type":"2D","alpha":lccc[i][1],"tx":lccc[i][2],"ty":lccc[i][3],"mirror":int(lccc[i][4]+0.1)})
lccc[i] = [lccc[i][0],T]
tdummy = Transform({"type":"2D"})
maxsum = -1.023
for m in xrange(0,lend):#initial, initial+1):
indc = range( lend )
lsnake = [[m, tdummy, 0.0]]
del indc[m]
lsum = 0.0
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = lccc[mono(indc[i], lsnake[-1][0])][0]
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
# Here we need transformation from the current to the previous,
# meaning indc[i] -> lsnake[-1][0]
T = lccc[mono(indc[i], lsnake[-1][0])][1]
# If direction is from larger to smaller index, the transformation has to be inverted
if( indc[i] > lsnake[-1][0] ): T = T.inverse()
lsnake.append([qi,T, maxcit])
lsum += maxcit
del indc[indc.index(qi)]
T = lccc[mono(indc[-1], lsnake[-1][0])][1]
if( indc[-1] > lsnake[-1][0]): T = T.inverse()
lsnake.append([indc[-1], T, lccc[mono(indc[-1], lsnake[-1][0])][0]])
print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(lend)]
print " Initial image selected : ",init,maxsum," ",TotalDistance([snake[m][0] for m in xrange(lend)], lccc)
#for q in snake: print q
from copy import deepcopy
trans=deepcopy([snake[i][1] for i in xrange(len(snake))])
print [snake[i][0] for i in xrange(len(snake))]
"""
for m in xrange(lend):
prms = trans[m].get_params("2D")
print " %3d %7.1f %7.1f %7.1f %2d %6.2f"%(snake[m][0], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"], snake[m][2])
"""
for k in xrange(lend-2,0,-1):
T = snake[k][1]
for i in xrange(k+1, lend):
trans[i] = T*trans[i]
# To add - apply all transformations and do the overall centering.
for m in xrange(lend):
prms = trans[m].get_params("2D")
#print " %3d %7.1f %7.1f %7.1f %2d %6.2f"%(snake[m][0], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"], snake[m][2])
#rot_shift2D(d[snake[m][0]], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"]).write_image(new_stack, m)
rot_shift2D(d[snake[m][0]], prms["alpha"], 0.0,0.0, prms["mirror"]).write_image(new_stack, m)
order = tsp(lccc)
if(len(order) != lend):
print " problem with data length"
from sys import exit
exit()
print TotalDistance(order, lccc)
print order
ibeg = order.index(init)
order = [order[(i+ibeg)%lend] for i in xrange(lend)]
print TotalDistance(order, lccc)
print order
snake = [tdummy]
for i in xrange(1,lend):
# Here we need transformation from the current to the previous,
# meaning order[i] -> order[i-1]]
T = lccc[mono(order[i], order[i-1])][1]
# If direction is from larger to smaller index, the transformation has to be inverted
if( order[i] > order[i-1] ): T = T.inverse()
snake.append(T)
assert(len(snake) == lend)
from copy import deepcopy
trans = deepcopy(snake)
for k in xrange(lend-2,0,-1):
T = snake[k]
for i in xrange(k+1, lend):
trans[i] = T*trans[i]
# Try to smooth the angles - complicated, I am afraid one would have to use angles forward and backwards
# and find their average??
# In addition, one would have to recenter them
"""
trms = []
for m in xrange(lend):
prms = trans[m].get_params("2D")
trms.append([prms["alpha"], prms["mirror"]])
for i in xrange(3):
for m in xrange(lend):
mb = (m-1)%lend
me = (m+1)%lend
# angles order mb,m,me
# calculate predicted angles mb->m
"""
for m in xrange(lend):
prms = trans[m].get_params("2D")
#rot_shift2D(d[order[m]], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"]).write_image("metro.hdf", m)
rot_shift2D(d[order[m]], prms["alpha"], 0.0,0.0, prms["mirror"]).write_image(args[2], m)
"""
# This was an effort to get number of loops, inconclusive, to say the least
from numpy import outer, zeros, float32, sqrt
lend = len(d)
cor = zeros(lend,float32)
cor = outer(cor, cor)
for i in xrange(lend): cor[i][i] = 1.0
for i in xrange(lend-1):
for j in xrange(i+1, lend):
cor[i,j] = lccc[mono(i,j)][0]
cor[j,i] = cor[i,j]
lmbd, eigvec = pca(cor)
from utilities import write_text_file
nvec=20
print [lmbd[j] for j in xrange(nvec)]
print " G"
mm = [-1]*lend
for i in xrange(lend): # row
mi = -1.0e23
for j in xrange(nvec):
qt = eigvec[j][i]
if(abs(qt)>mi):
mi = abs(qt)
mm[i] = j
for j in xrange(nvec):
qt = eigvec[j][i]
print round(qt,3), # eigenvector
print mm[i]
print
for j in xrange(nvec):
qt = []
for i in xrange(lend):
if(mm[i] == j): qt.append(i)
if(len(qt)>0): write_text_file(qt,"loop%02d.txt"%j)
"""
"""
print [lmbd[j] for j in xrange(nvec)]
print " B"
mm = [-1]*lend
for i in xrange(lend): # row
mi = -1.0e23
for j in xrange(nvec):
qt = eigvec[j][i]/sqrt(lmbd[j])
if(abs(qt)>mi):
mi = abs(qt)
mm[i] = j
for j in xrange(nvec):
qt = eigvec[j][i]/sqrt(lmbd[j])
print round(qt,3), # eigenvector
print mm[i]
print
"""
"""
lend=3
cor = zeros(lend,float32)
cor = outer(cor, cor)
cor[0][0] =136.77
cor[0][1] = 79.15
cor[0][2] = 37.13
cor[1][0] = 79.15
cor[2][0] = 37.13
cor[1][1] = 50.04
cor[1][2] = 21.65
cor[2][1] = 21.65
cor[2][2] = 13.26
lmbd, eigvec = pca(cor)
print lmbd
print eigvec
for i in xrange(lend): # row
for j in xrange(lend): print eigvec[j][i], # eigenvector
print
print " B"
for i in xrange(lend): # row
for j in xrange(lend): print eigvec[j][i]/sqrt(lmbd[j]), # eigenvector
print
print " G"
for i in xrange(lend): # row
for j in xrange(lend): print eigvec[j][i]*sqrt(lmbd[j]), # eigenvector
print
"""
else:
nargs = len(args)
if nargs != 2:
print "must provide name of input and output file!"
return
from utilities import get_params2D, model_circle
from fundamentals import rot_shift2D
from statistics import ccc
from time import time
from alignment import align2d
from multi_shc import mult_transform
stack = args[0]
new_stack = args[1]
d = EMData.read_images(stack)
try:
ttt = d[0].get_attr('xform.params2d')
for i in xrange(len(d)):
alpha, sx, sy, mirror, scale = get_params2D(d[i])
d[i] = rot_shift2D(d[i], alpha, sx, sy, mirror)
except:
pass
nx = d[0].get_xsize()
ny = d[0].get_ysize()
if options.radius < 1 : radius = nx//2-2
else: radius = options.radius
mask = model_circle(radius, nx, ny)
init = options.initial
if init > -1 :
print " initial image: %d" % init
temp = d[init].copy()
temp.write_image(new_stack, 0)
del d[init]
k = 1
lsum = 0.0
while len(d) > 1:
maxcit = -111.
for i in xrange(len(d)):
cuc = ccc(d[i], temp, mask)
if cuc > maxcit:
maxcit = cuc
qi = i
# print k, maxcit
lsum += maxcit
temp = d[qi].copy()
del d[qi]
temp.write_image(new_stack, k)
k += 1
print lsum
d[0].write_image(new_stack, k)
else:
if options.circular :
print "Using options.circular"
# figure the "best circular" starting image
maxsum = -1.023
for m in xrange(len(d)):
indc = range(len(d) )
lsnake = [-1]*(len(d)+1)
lsnake[0] = m
lsnake[-1] = m
del indc[m]
temp = d[m].copy()
lsum = 0.0
direction = +1
k = 1
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = ccc(d[indc[i]], temp, mask)
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
lsnake[k] = qi
lsum += maxcit
del indc[indc.index(qi)]
direction = -direction
for i in xrange( 1,len(d) ):
if( direction > 0 ):
if(lsnake[i] == -1):
temp = d[lsnake[i-1]].copy()
#print " forw ",lsnake[i-1]
k = i
break
else:
if(lsnake[len(d) - i] == -1):
temp = d[lsnake[len(d) - i +1]].copy()
#print " back ",lsnake[len(d) - i +1]
k = len(d) - i
break
lsnake[lsnake.index(-1)] = indc[-1]
#print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(len(d))]
print " Initial image selected : ",init,maxsum
print lsnake
for m in xrange(len(d)): d[snake[m]].write_image(new_stack, m)
else:
# figure the "best" starting image
maxsum = -1.023
for m in xrange(len(d)):
indc = range(len(d) )
lsnake = [m]
del indc[m]
temp = d[m].copy()
lsum = 0.0
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = ccc(d[indc[i]], temp, mask)
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
lsnake.append(qi)
lsum += maxcit
temp = d[qi].copy()
del indc[indc.index(qi)]
lsnake.append(indc[-1])
#print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(len(d))]
print " Initial image selected : ",init,maxsum
print lsnake
for m in xrange(len(d)): d[snake[m]].write_image(new_stack, m)
def main():
from optparse import OptionParser
from global_def import SPARXVERSION
from EMAN2 import EMData
from logger import Logger, BaseLogger_Files
import sys, os, time
global Tracker, Blockdata
from global_def import ERROR
progname = os.path.basename(sys.argv[0])
usage = progname + " --output_dir=output_dir --isac_dir=output_dir_of_isac "
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--adjust_to_analytic_model",
action="store_true",
default=False,
help="adjust power spectrum of 2-D averages to an analytic model ")
parser.add_option(
"--adjust_to_given_pw2",
action="store_true",
default=False,
help="adjust power spectrum to 2-D averages to given 1D power spectrum"
)
parser.add_option("--B_enhance",
action="store_true",
default=False,
help="using B-factor to enhance 2-D averages")
parser.add_option("--no_adjustment",
action="store_true",
default=False,
help="No power spectrum adjustment")
options_list = []
adjust_to_analytic_model = False
for q in sys.argv[1:]:
if (q[:26] == "--adjust_to_analytic_model"):
adjust_to_analytic_model = True
options_list.append(q)
break
adjust_to_given_pw2 = False
for q in sys.argv[1:]:
if (q[:21] == "--adjust_to_given_pw2"):
adjust_to_given_pw2 = True
options_list.append(q)
break
B_enhance = False
for q in sys.argv[1:]:
if (q[:11] == "--B_enhance"):
B_enhance = True
options_list.append(q)
break
no_adjustment = False
for q in sys.argv[1:]:
if (q[:15] == "--no_adjustment"):
no_adjustment = True
options_list.append(q)
break
if len(options_list) == 0:
if (Blockdata["myid"] == Blockdata["main_node"]):
print(
"specify one of the following options to start: 1. adjust_to_analytic_model; 2. adjust_to_given_pw2; 3. B_enhance; 4. no_adjustment"
)
if len(options_list) > 1:
ERROR(
"The specified options are exclusive. Use only one of them to start",
"sxcompute_isac_avg.py", 1, Blockdata["myid"])
# options in common
parser.add_option(
"--isac_dir",
type="string",
default='',
help="ISAC run output directory, input directory for this command")
parser.add_option(
"--output_dir",
type="string",
default='',
help="output directory where computed averages are saved")
parser.add_option("--pixel_size",
type="float",
default=-1.0,
help="pixel_size of raw images")
parser.add_option(
"--fl",
type="float",
default=-1.0,
help=
"low pass filter, =-1, not applied; =1, using FH1 (initial resolution), =2 using FH2 (resolution after local alignment), or user provided value"
)
parser.add_option("--stack",
type="string",
default="",
help="data stack used in ISAC")
parser.add_option("--radius", type="int", default=-1, help="radius")
parser.add_option("--xr",
type="float",
default=-1.0,
help="local alignment search range")
parser.add_option("--ts",
type="float",
default=1.0,
help="local alignment search step")
parser.add_option("--fh",
type="float",
default=-1.,
help="local alignment high frequencies limit")
parser.add_option("--maxit",
type="int",
default=5,
help="local alignment iterations")
parser.add_option("--navg",
type="int",
default=-1,
help="number of aveages")
parser.add_option("--skip_local_alignment",
action="store_true",
default=False,
help="skip local alignment")
parser.add_option(
"--noctf",
action="store_true",
default=False,
help=
"no ctf correction, useful for negative stained data. always ctf for cryo data"
)
if B_enhance:
parser.add_option(
"--B_start",
type="float",
default=10.0,
help=
"start frequency (1./Angstrom) of power spectrum for B_factor estimation"
)
parser.add_option(
"--Bfactor",
type="float",
default=-1.0,
help=
"User defined bactors (e.g. 45.0[A^2]). By default, the program automatically estimates B-factor. "
)
if adjust_to_given_pw2:
parser.add_option("--modelpw",
type="string",
default='',
help="1-D reference power spectrum")
checking_flag = 0
if (Blockdata["myid"] == Blockdata["main_node"]):
if not os.path.exists(options.modelpw): checking_flag = 1
checking_flag = bcast_number_to_all(checking_flag,
Blockdata["main_node"],
MPI_COMM_WORLD)
if checking_flag == 1:
ERROR("User provided power spectrum does not exist",
"sxcompute_isac_avg.py", 1, Blockdata["myid"])
(options, args) = parser.parse_args(sys.argv[1:])
Tracker = {}
Constants = {}
Constants["isac_dir"] = options.isac_dir
Constants["masterdir"] = options.output_dir
Constants["pixel_size"] = options.pixel_size
Constants["orgstack"] = options.stack
Constants["radius"] = options.radius
Constants["xrange"] = options.xr
Constants["xstep"] = options.ts
Constants["FH"] = options.fh
Constants["maxit"] = options.maxit
Constants["navg"] = options.navg
Constants["low_pass_filter"] = options.fl
if B_enhance:
Constants["B_start"] = options.B_start
Constants["Bfactor"] = options.Bfactor
if adjust_to_given_pw2: Constants["modelpw"] = options.modelpw
Tracker["constants"] = Constants
# -------------------------------------------------------------
#
# Create and initialize Tracker dictionary with input options # State Variables
#<<<---------------------->>>imported functions<<<---------------------------------------------
from utilities import get_im, bcast_number_to_all, write_text_file, read_text_file, wrap_mpi_bcast, write_text_row
from utilities import cmdexecute
from filter import filt_tanl
from time import sleep
from logger import Logger, BaseLogger_Files
import user_functions
import string
from string import split, atoi, atof
import json
#x_range = max(Tracker["constants"]["xrange"], int(1./Tracker["ini_shrink"])+1)
#y_range = x_range
####-----------------------------------------------------------
# Create Master directory
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
if Tracker["constants"]["masterdir"] == Tracker["constants"]["isac_dir"]:
masterdir = os.path.join(Tracker["constants"]["isac_dir"], "sharpen")
else:
masterdir = Tracker["constants"]["masterdir"]
if (Blockdata["myid"] == Blockdata["main_node"]):
msg = "Postprocessing ISAC 2D averages starts"
print(line, "Postprocessing ISAC 2D averages starts")
if not masterdir:
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir = "sharpen_" + Tracker["constants"]["isac_dir"]
os.mkdir(masterdir)
else:
if os.path.exists(masterdir):
print("%s already exists" % masterdir)
else:
os.mkdir(masterdir)
li = len(masterdir)
else:
li = 0
li = mpi_bcast(li, 1, MPI_INT, Blockdata["main_node"], MPI_COMM_WORLD)[0]
masterdir = mpi_bcast(masterdir, li, MPI_CHAR, Blockdata["main_node"],
MPI_COMM_WORLD)
masterdir = string.join(masterdir, "")
Tracker["constants"]["masterdir"] = masterdir
log_main = Logger(BaseLogger_Files())
log_main.prefix = Tracker["constants"]["masterdir"] + "/"
while not os.path.exists(Tracker["constants"]["masterdir"]):
print("Node ", Blockdata["myid"], " waiting...",
Tracker["constants"]["masterdir"])
sleep(1)
mpi_barrier(MPI_COMM_WORLD)
if (Blockdata["myid"] == Blockdata["main_node"]):
init_dict = {}
print(Tracker["constants"]["isac_dir"])
Tracker["directory"] = os.path.join(Tracker["constants"]["isac_dir"],
"2dalignment")
core = read_text_row(
os.path.join(Tracker["directory"], "initial2Dparams.txt"))
for im in xrange(len(core)):
init_dict[im] = core[im]
del core
else:
init_dict = 0
init_dict = wrap_mpi_bcast(init_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
###
if (Blockdata["myid"] == Blockdata["main_node"]):
#Tracker["constants"]["orgstack"] = "bdb:"+ os.path.join(Tracker["constants"]["isac_dir"],"../","sparx_stack")
image = get_im(Tracker["constants"]["orgstack"], 0)
Tracker["constants"]["nnxo"] = image.get_xsize()
try:
ctf_params = image.get_attr("ctf")
if Tracker["constants"]["pixel_size"] == -1.:
Tracker["constants"]["pixel_size"] = ctf_params.apix
except:
print("pixel size value is not given.")
Tracker["ini_shrink"] = float(
get_im(os.path.join(Tracker["directory"], "aqfinal.hdf"),
0).get_xsize()) / Tracker["constants"]["nnxo"]
else:
Tracker["ini_shrink"] = 0
Tracker = wrap_mpi_bcast(Tracker,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
#print(Tracker["constants"]["pixel_size"], "pixel_size")
x_range = max(Tracker["constants"]["xrange"],
int(1. / Tracker["ini_shrink"]) + 1)
y_range = x_range
if (Blockdata["myid"] == Blockdata["main_node"]):
parameters = read_text_row(
os.path.join(Tracker["constants"]["isac_dir"],
"all_parameters.txt"))
else:
parameters = 0
parameters = wrap_mpi_bcast(parameters,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
params_dict = {}
list_dict = {}
#parepare params_dict
if Tracker["constants"]["navg"] < 0:
navg = EMUtil.get_image_count(
os.path.join(Tracker["constants"]["isac_dir"],
"class_averages.hdf"))
else:
navg = min(
Tracker["constants"]["navg"],
EMUtil.get_image_count(
os.path.join(Tracker["constants"]["isac_dir"],
"class_averages.hdf")))
global_dict = {}
ptl_list = []
memlist = []
if (Blockdata["myid"] == Blockdata["main_node"]):
for iavg in xrange(navg):
params_of_this_average = []
image = get_im(
os.path.join(Tracker["constants"]["isac_dir"],
"class_averages.hdf"), iavg)
members = image.get_attr("members")
memlist.append(members)
for im in xrange(len(members)):
abs_id = members[im]
global_dict[abs_id] = [iavg, im]
P = combine_params2( init_dict[abs_id][0], init_dict[abs_id][1], init_dict[abs_id][2], init_dict[abs_id][3], \
parameters[abs_id][0], parameters[abs_id][1]/Tracker["ini_shrink"], parameters[abs_id][2]/Tracker["ini_shrink"], parameters[abs_id][3])
if parameters[abs_id][3] == -1: print("wrong one")
params_of_this_average.append([P[0], P[1], P[2], P[3], 1.0])
ptl_list.append(abs_id)
params_dict[iavg] = params_of_this_average
list_dict[iavg] = members
write_text_row(
params_of_this_average,
os.path.join(Tracker["constants"]["masterdir"],
"params_avg_%03d.txt" % iavg))
ptl_list.sort()
init_params = [None for im in xrange(len(ptl_list))]
for im in xrange(len(ptl_list)):
init_params[im] = [ptl_list[im]] + params_dict[global_dict[
ptl_list[im]][0]][global_dict[ptl_list[im]][1]]
write_text_row(
init_params,
os.path.join(Tracker["constants"]["masterdir"],
"init_isac_params.txt"))
else:
params_dict = 0
list_dict = 0
memlist = 0
params_dict = wrap_mpi_bcast(params_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
list_dict = wrap_mpi_bcast(list_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
memlist = wrap_mpi_bcast(memlist,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
# Now computing!
del init_dict
tag_sharpen_avg = 1000
## always apply low pass filter to B_enhanced images to suppress noise in high frequencies
enforced_to_H1 = False
if options.B_enhance:
if Tracker["constants"]["low_pass_filter"] == -1:
print("User does not provide low pass filter")
enforced_to_H1 = True
if navg < Blockdata["nproc"]: # Each CPU do one average
FH_list = [None for im in xrange(navg)]
for iavg in xrange(navg):
if Blockdata["myid"] == iavg:
mlist = [None for i in xrange(len(list_dict[iavg]))]
for im in xrange(len(mlist)):
mlist[im] = get_im(Tracker["constants"]["orgstack"],
list_dict[iavg][im])
set_params2D(mlist[im],
params_dict[iavg][im],
xform="xform.align2d")
if options.noctf:
new_avg, frc, plist = compute_average_noctf(
mlist, Tracker["constants"]["radius"])
else:
new_avg, frc, plist = compute_average_ctf(
mlist, Tracker["constants"]["radius"])
FH1 = get_optimistic_res(frc)
#write_text_file(frc, os.path.join(Tracker["constants"]["masterdir"], "fsc%03d_before_ali.txt"%iavg))
if not options.skip_local_alignment:
new_average1 = within_group_refinement([mlist[kik] for kik in xrange(0,len(mlist),2)], maskfile= None, randomize= False, ir=1.0, \
ou=Tracker["constants"]["radius"], rs=1.0, xrng=[x_range], yrng=[y_range], step=[Tracker["constants"]["xstep"]], \
dst=0.0, maxit=Tracker["constants"]["maxit"], FH = max(Tracker["constants"]["FH"], FH1), FF=0.1)
new_average2 = within_group_refinement([mlist[kik] for kik in xrange(1,len(mlist),2)], maskfile= None, randomize= False, ir=1.0, \
ou=Tracker["constants"]["radius"], rs=1.0, xrng=[x_range], yrng=[y_range], step=[Tracker["constants"]["xstep"]], \
dst=0.0, maxit=Tracker["constants"]["maxit"], FH = max(Tracker["constants"]["FH"], FH1), FF=0.1)
if options.noctf:
new_avg, frc, plist = compute_average_noctf(
mlist, Tracker["constants"]["radius"])
else:
new_avg, frc, plist = compute_average_ctf(
mlist, Tracker["constants"]["radius"])
FH2 = get_optimistic_res(frc)
#write_text_file(frc, os.path.join(Tracker["constants"]["masterdir"], "fsc%03d.txt"%iavg))
#if Tracker["constants"]["nopwadj"]: # pw adjustment, 1. analytic model 2. PDB model 3. B-facttor enhancement
else:
FH2 = 0.0
FH_list[iavg] = [FH1, FH2]
if options.B_enhance:
new_avg, gb = apply_enhancement(
new_avg, Tracker["constants"]["B_start"],
Tracker["constants"]["pixel_size"],
Tracker["constants"]["Bfactor"])
print("Process avg %d %f %f %f" %
(iavg, gb, FH1, FH2))
elif options.adjust_to_given_pw2:
roo = read_text_file(Tracker["constants"]["modelpw"], -1)
roo = roo[0] # always put pw in the first column
new_avg = adjust_pw_to_model(
new_avg, Tracker["constants"]["pixel_size"], roo)
elif options.adjust_to_analytic_model:
new_avg = adjust_pw_to_model(
new_avg, Tracker["constants"]["pixel_size"], None)
elif options.no_adjustment:
pass
print("Process avg %d %f %f" % (iavg, FH1, FH2))
if Tracker["constants"]["low_pass_filter"] != -1.:
if Tracker["constants"]["low_pass_filter"] == 1.:
low_pass_filter = FH1
elif Tracker["constants"]["low_pass_filter"] == 2.:
low_pass_filter = FH2
if options.skip_local_alignment: low_pass_filter = FH1
else:
low_pass_filter = Tracker["constants"][
"low_pass_filter"]
if low_pass_filter >= 0.45: low_pass_filter = 0.45
new_avg = filt_tanl(new_avg, low_pass_filter, 0.1)
new_avg.set_attr("members", list_dict[iavg])
new_avg.set_attr("n_objects", len(list_dict[iavg]))
mpi_barrier(MPI_COMM_WORLD)
for im in xrange(navg): # avg
if im == Blockdata[
"myid"] and Blockdata["myid"] != Blockdata["main_node"]:
send_EMData(new_avg, Blockdata["main_node"], tag_sharpen_avg)
elif Blockdata["myid"] == Blockdata["main_node"]:
if im != Blockdata["main_node"]:
new_avg_other_cpu = recv_EMData(im, tag_sharpen_avg)
new_avg_other_cpu.set_attr("members", memlist[im])
new_avg_other_cpu.write_image(
os.path.join(Tracker["constants"]["masterdir"],
"class_averages.hdf"), im)
else:
new_avg.write_image(
os.path.join(Tracker["constants"]["masterdir"],
"class_averages.hdf"), im)
if not options.skip_local_alignment:
if im == Blockdata["myid"]:
write_text_row(
plist,
os.path.join(Tracker["constants"]["masterdir"],
"ali2d_local_params_avg_%03d.txt" % im))
if Blockdata["myid"] == im and Blockdata["myid"] != Blockdata[
"main_node"]:
wrap_mpi_send(plist_dict[im], Blockdata["main_node"],
MPI_COMM_WORLD)
elif im != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(im, MPI_COMM_WORLD)
plist_dict[im] = dummy
if im == Blockdata["myid"] and im != Blockdata["main_node"]:
wrap_mpi_send(FH_list[im], Blockdata["main_node"],
MPI_COMM_WORLD)
elif im != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(im, MPI_COMM_WORLD)
FH_list[im] = dummy
else:
if im == Blockdata["myid"] and im != Blockdata["main_node"]:
wrap_mpi_send(FH_list, Blockdata["main_node"],
MPI_COMM_WORLD)
elif im != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(im, MPI_COMM_WORLD)
FH_list[im] = dummy[im]
mpi_barrier(MPI_COMM_WORLD)
else:
FH_list = [[0, 0.0, 0.0] for im in xrange(navg)]
image_start, image_end = MPI_start_end(navg, Blockdata["nproc"],
Blockdata["myid"])
if Blockdata["myid"] == Blockdata["main_node"]:
cpu_dict = {}
for iproc in xrange(Blockdata["nproc"]):
local_image_start, local_image_end = MPI_start_end(
navg, Blockdata["nproc"], iproc)
for im in xrange(local_image_start, local_image_end):
cpu_dict[im] = iproc
else:
cpu_dict = 0
cpu_dict = wrap_mpi_bcast(cpu_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
slist = [None for im in xrange(navg)]
ini_list = [None for im in xrange(navg)]
avg1_list = [None for im in xrange(navg)]
avg2_list = [None for im in xrange(navg)]
plist_dict = {}
data_list = [None for im in xrange(navg)]
if Blockdata["myid"] == Blockdata["main_node"]: print("read data")
for iavg in xrange(image_start, image_end):
mlist = [None for i in xrange(len(list_dict[iavg]))]
for im in xrange(len(mlist)):
mlist[im] = get_im(Tracker["constants"]["orgstack"],
list_dict[iavg][im])
set_params2D(mlist[im],
params_dict[iavg][im],
xform="xform.align2d")
data_list[iavg] = mlist
print("read data done %d" % Blockdata["myid"])
#if Blockdata["myid"] == Blockdata["main_node"]: print("start to compute averages")
for iavg in xrange(image_start, image_end):
mlist = data_list[iavg]
if options.noctf:
new_avg, frc, plist = compute_average_noctf(
mlist, Tracker["constants"]["radius"])
else:
new_avg, frc, plist = compute_average_ctf(
mlist, Tracker["constants"]["radius"])
FH1 = get_optimistic_res(frc)
#write_text_file(frc, os.path.join(Tracker["constants"]["masterdir"], "fsc%03d_before_ali.txt"%iavg))
if not options.skip_local_alignment:
new_average1 = within_group_refinement([mlist[kik] for kik in xrange(0,len(mlist),2)], maskfile= None, randomize= False, ir=1.0, \
ou=Tracker["constants"]["radius"], rs=1.0, xrng=[x_range], yrng=[y_range], step=[Tracker["constants"]["xstep"]], \
dst=0.0, maxit=Tracker["constants"]["maxit"], FH=max(Tracker["constants"]["FH"], FH1), FF=0.1)
new_average2 = within_group_refinement([mlist[kik] for kik in xrange(1,len(mlist),2)], maskfile= None, randomize= False, ir=1.0, \
ou= Tracker["constants"]["radius"], rs=1.0, xrng=[ x_range], yrng=[y_range], step=[Tracker["constants"]["xstep"]], \
dst=0.0, maxit=Tracker["constants"]["maxit"], FH = max(Tracker["constants"]["FH"], FH1), FF=0.1)
if options.noctf:
new_avg, frc, plist = compute_average_noctf(
mlist, Tracker["constants"]["radius"])
else:
new_avg, frc, plist = compute_average_ctf(
mlist, Tracker["constants"]["radius"])
plist_dict[iavg] = plist
FH2 = get_optimistic_res(frc)
else:
FH2 = 0.0
#write_text_file(frc, os.path.join(Tracker["constants"]["masterdir"], "fsc%03d.txt"%iavg))
FH_list[iavg] = [iavg, FH1, FH2]
if options.B_enhance:
new_avg, gb = apply_enhancement(
new_avg, Tracker["constants"]["B_start"],
Tracker["constants"]["pixel_size"],
Tracker["constants"]["Bfactor"])
print("Process avg %d %f %f %f" % (iavg, gb, FH1, FH2))
elif options.adjust_to_given_pw2:
roo = read_text_file(Tracker["constants"]["modelpw"], -1)
roo = roo[0] # always on the first column
new_avg = adjust_pw_to_model(
new_avg, Tracker["constants"]["pixel_size"], roo)
print("Process avg %d %f %f" % (iavg, FH1, FH2))
elif adjust_to_analytic_model:
new_avg = adjust_pw_to_model(
new_avg, Tracker["constants"]["pixel_size"], None)
print("Process avg %d %f %f" % (iavg, FH1, FH2))
elif options.no_adjustment:
pass
if Tracker["constants"]["low_pass_filter"] != -1.:
new_avg = filt_tanl(new_avg,
Tracker["constants"]["low_pass_filter"],
0.1)
if Tracker["constants"]["low_pass_filter"] != -1.:
if Tracker["constants"]["low_pass_filter"] == 1.:
low_pass_filter = FH1
elif Tracker["constants"]["low_pass_filter"] == 2.:
low_pass_filter = FH2
if options.skip_local_alignment: low_pass_filter = FH1
else:
low_pass_filter = Tracker["constants"]["low_pass_filter"]
if low_pass_filter >= 0.45: low_pass_filter = 0.45
new_avg = filt_tanl(new_avg, low_pass_filter, 0.1)
else:
if enforced_to_H1: new_avg = filt_tanl(new_avg, FH1, 0.1)
if options.B_enhance: new_avg = fft(new_avg)
new_avg.set_attr("members", list_dict[iavg])
new_avg.set_attr("n_objects", len(list_dict[iavg]))
slist[iavg] = new_avg
## send to main node to write
mpi_barrier(MPI_COMM_WORLD)
for im in xrange(navg):
# avg
if cpu_dict[im] == Blockdata[
"myid"] and Blockdata["myid"] != Blockdata["main_node"]:
send_EMData(slist[im], Blockdata["main_node"], tag_sharpen_avg)
elif cpu_dict[im] == Blockdata["myid"] and Blockdata[
"myid"] == Blockdata["main_node"]:
slist[im].set_attr("members", memlist[im])
slist[im].write_image(
os.path.join(Tracker["constants"]["masterdir"],
"class_averages.hdf"), im)
elif cpu_dict[im] != Blockdata["myid"] and Blockdata[
"myid"] == Blockdata["main_node"]:
new_avg_other_cpu = recv_EMData(cpu_dict[im], tag_sharpen_avg)
new_avg_other_cpu.set_attr("members", memlist[im])
new_avg_other_cpu.write_image(
os.path.join(Tracker["constants"]["masterdir"],
"class_averages.hdf"), im)
if not options.skip_local_alignment:
if cpu_dict[im] == Blockdata["myid"]:
write_text_row(
plist_dict[im],
os.path.join(Tracker["constants"]["masterdir"],
"ali2d_local_params_avg_%03d.txt" % im))
if cpu_dict[im] == Blockdata[
"myid"] and cpu_dict[im] != Blockdata["main_node"]:
wrap_mpi_send(plist_dict[im], Blockdata["main_node"],
MPI_COMM_WORLD)
wrap_mpi_send(FH_list, Blockdata["main_node"],
MPI_COMM_WORLD)
elif cpu_dict[im] != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(cpu_dict[im], MPI_COMM_WORLD)
plist_dict[im] = dummy
dummy = wrap_mpi_recv(cpu_dict[im], MPI_COMM_WORLD)
FH_list[im] = dummy[im]
else:
if cpu_dict[im] == Blockdata[
"myid"] and cpu_dict[im] != Blockdata["main_node"]:
wrap_mpi_send(FH_list, Blockdata["main_node"],
MPI_COMM_WORLD)
elif cpu_dict[im] != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(cpu_dict[im], MPI_COMM_WORLD)
FH_list[im] = dummy[im]
mpi_barrier(MPI_COMM_WORLD)
mpi_barrier(MPI_COMM_WORLD)
if not options.skip_local_alignment:
if Blockdata["myid"] == Blockdata["main_node"]:
ali3d_local_params = [None for im in xrange(len(ptl_list))]
for im in xrange(len(ptl_list)):
ali3d_local_params[im] = [ptl_list[im]] + plist_dict[
global_dict[ptl_list[im]][0]][global_dict[ptl_list[im]][1]]
write_text_row(
ali3d_local_params,
os.path.join(Tracker["constants"]["masterdir"],
"ali2d_local_params.txt"))
write_text_row(
FH_list,
os.path.join(Tracker["constants"]["masterdir"], "FH_list.txt"))
else:
if Blockdata["myid"] == Blockdata["main_node"]:
write_text_row(
FH_list,
os.path.join(Tracker["constants"]["masterdir"], "FH_list.txt"))
mpi_barrier(MPI_COMM_WORLD)
target_xr = 3
target_yr = 3
if (Blockdata["myid"] == 0):
cmd = "{} {} {} {} {} {} {} {} {} {}".format("sxchains.py", os.path.join(Tracker["constants"]["masterdir"],"class_averages.hdf"),\
os.path.join(Tracker["constants"]["masterdir"],"junk.hdf"),os.path.join(Tracker["constants"]["masterdir"],"ordered_class_averages.hdf"),\
"--circular","--radius=%d"%Tracker["constants"]["radius"] , "--xr=%d"%(target_xr+1),"--yr=%d"%(target_yr+1),"--align", ">/dev/null")
junk = cmdexecute(cmd)
cmd = "{} {}".format(
"rm -rf",
os.path.join(Tracker["constants"]["masterdir"], "junk.hdf"))
junk = cmdexecute(cmd)
from mpi import mpi_finalize
mpi_finalize()
exit()
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Generic 2-D image processing programs.
Functionality:
1. Phase flip a stack of images and write output to new file:
sxprocess.py input_stack.hdf output_stack.hdf --phase_flip
2. Resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.
The window size will change accordingly.
sxprocess input.hdf output.hdf --changesize --ratio=0.5
3. Compute average power spectrum of a stack of 2D images with optional padding (option wn) with zeroes.
sxprocess.py input_stack.hdf powerspectrum.hdf --pw [--wn=1024]
4. Generate a stack of projections bdb:data and micrographs with prefix mic (i.e., mic0.hdf, mic1.hdf etc) from structure input_structure.hdf, with CTF applied to both projections and micrographs:
sxprocess.py input_structure.hdf data mic --generate_projections format="bdb":apix=5.2:CTF=True:boxsize=64
5. Retrieve original image numbers in the selected ISAC group (here group 12 from generation 3):
sxprocess.py bdb:test3 class_averages_generation_3.hdf list3_12.txt --isacgroup=12 --params=originalid
6. Retrieve original image numbers of images listed in ISAC output stack of averages:
sxprocess.py select1.hdf ohk.txt
7. Adjust rotationally averaged power spectrum of an image to that of a reference image or a reference 1D power spectrum stored in an ASCII file.
Optionally use a tangent low-pass filter. Also works for a stack of images, in which case the output is also a stack.
sxprocess.py vol.hdf ref.hdf avol.hdf < 0.25 0.2> --adjpw
sxprocess.py vol.hdf pw.txt avol.hdf < 0.25 0.2> --adjpw
8. Generate a 1D rotationally averaged power spectrum of an image.
sxprocess.py vol.hdf --rotwp=rotpw.txt
# Output will contain three columns:
(1) rotationally averaged power spectrum
(2) logarithm of the rotationally averaged power spectrum
(3) integer line number (from zero to approximately to half the image size)
9. Apply 3D transformation (rotation and/or shift) to a set of orientation parameters associated with projection data.
sxprocess.py --transfromparams=phi,theta,psi,tx,ty,tz input.txt output.txt
The output file is then imported and 3D transformed volume computed:
sxheader.py bdb:p --params=xform.projection --import=output.txt
mpirun -np 2 sxrecons3d_n.py bdb:p tvol.hdf --MPI
The reconstructed volume is in the position of the volume computed using the input.txt parameters and then
transformed with rot_shift3D(vol, phi,theta,psi,tx,ty,tz)
10. Import ctf parameters from the output of sxcter into windowed particle headers.
There are three possible input files formats: (1) all particles are in one stack, (2 aor 3) particles are in stacks, each stack corresponds to a single micrograph.
In each case the particles should contain a name of the micrograph of origin stores using attribute name 'ptcl_source_image'.
Normally this is done by e2boxer.py during windowing.
Particles whose defocus or astigmatism error exceed set thresholds will be skipped, otherwise, virtual stacks with the original way preceded by G will be created.
sxprocess.py --input=bdb:data --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
# Output will be a vritual stack bdb:Gdata
sxprocess.py --input="bdb:directory/stacks*" --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
To concatenate output files:
cd directory
e2bdb.py . --makevstack=bdb:allparticles --filt=G
IMPORTANT: Please do not move (or remove!) any input/intermediate EMAN2DB files as the information is linked between them.
11. Scale 3D shifts. The shifts in the input five columns text file with 3D orientation parameters will be DIVIDED by the scale factor
sxprocess.py orientationparams.txt scaledparams.txt scale=0.5
12. Generate adaptive mask from a given 3-D volume.
"""
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--order",
action="store_true",
help=
"Two arguments are required: name of input stack and desired name of output stack. The output stack is the input stack sorted by similarity in terms of cross-correlation coefficent.",
default=False)
parser.add_option("--order_lookup",
action="store_true",
help="Test/Debug.",
default=False)
parser.add_option("--order_metropolis",
action="store_true",
help="Test/Debug.",
default=False)
parser.add_option("--order_pca",
action="store_true",
help="Test/Debug.",
default=False)
parser.add_option(
"--initial",
type="int",
default=-1,
help=
"Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)"
)
parser.add_option(
"--circular",
action="store_true",
help=
"Select circular ordering (fisr image has to be similar to the last",
default=False)
parser.add_option(
"--radius",
type="int",
default=-1,
help="Radius of a circular mask for similarity based ordering")
parser.add_option(
"--changesize",
action="store_true",
help=
"resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.",
default=False)
parser.add_option(
"--ratio",
type="float",
default=1.0,
help=
"The ratio of new to old image size (if <1 the pixel size will increase and image size decrease, if>1, the other way round"
)
parser.add_option(
"--pw",
action="store_true",
help=
"compute average power spectrum of a stack of 2-D images with optional padding (option wn) with zeroes",
default=False)
parser.add_option(
"--wn",
type="int",
default=-1,
help=
"Size of window to use (should be larger/equal than particle box size, default padding to max(nx,ny))"
)
parser.add_option("--phase_flip",
action="store_true",
help="Phase flip the input stack",
default=False)
parser.add_option(
"--makedb",
metavar="param1=value1:param2=value2",
type="string",
action="append",
help=
"One argument is required: name of key with which the database will be created. Fill in database with parameters specified as follows: --makedb param1=value1:param2=value2, e.g. 'gauss_width'=1.0:'pixel_input'=5.2:'pixel_output'=5.2:'thr_low'=1.0"
)
parser.add_option(
"--generate_projections",
metavar="param1=value1:param2=value2",
type="string",
action="append",
help=
"Three arguments are required: name of input structure from which to generate projections, desired name of output projection stack, and desired prefix for micrographs (e.g. if prefix is 'mic', then micrographs mic0.hdf, mic1.hdf etc will be generated). Optional arguments specifying format, apix, box size and whether to add CTF effects can be entered as follows after --generate_projections: format='bdb':apix=5.2:CTF=True:boxsize=100, or format='hdf', etc., where format is bdb or hdf, apix (pixel size) is a float, CTF is True or False, and boxsize denotes the dimension of the box (assumed to be a square). If an optional parameter is not specified, it will default as follows: format='bdb', apix=2.5, CTF=False, boxsize=64."
)
parser.add_option(
"--isacgroup",
type="int",
help=
"Retrieve original image numbers in the selected ISAC group. See ISAC documentation for details.",
default=-1)
parser.add_option(
"--isacselect",
action="store_true",
help=
"Retrieve original image numbers of images listed in ISAC output stack of averages. See ISAC documentation for details.",
default=False)
parser.add_option(
"--params",
type="string",
default=None,
help="Name of header of parameter, which one depends on specific option"
)
parser.add_option(
"--adjpw",
action="store_true",
help="Adjust rotationally averaged power spectrum of an image",
default=False)
parser.add_option(
"--rotpw",
type="string",
default=None,
help=
"Name of the text file to contain rotationally averaged power spectrum of the input image."
)
parser.add_option(
"--transformparams",
type="string",
default=None,
help=
"Transform 3D projection orientation parameters using six 3D parameters (phi, theta,psi,sx,sy,sz). Input: --transformparams=45.,66.,12.,-2,3,-5.5 desired six transformation of the reconstructed structure. Output: file with modified orientation parameters."
)
# import ctf estimates done using cter
parser.add_option("--input",
type="string",
default=None,
help="Input particles.")
parser.add_option(
"--importctf",
type="string",
default=None,
help="Name of the file containing CTF parameters produced by sxcter.")
parser.add_option(
"--defocuserror",
type="float",
default=1000000.0,
help=
"Exclude micrographs whose relative defocus error as estimated by sxcter is larger than defocuserror percent. The error is computed as (std dev defocus)/defocus*100%"
)
parser.add_option(
"--astigmatismerror",
type="float",
default=360.0,
help=
"Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sxcter is larger than astigmatismerror degrees."
)
# import ctf estimates done using cter
parser.add_option(
"--scale",
type="float",
default=-1.0,
help=
"Divide shifts in the input 3D orientation parameters text file by the scale factor."
)
# generate adaptive mask from an given 3-Db volue
parser.add_option("--adaptive_mask",
action="store_true",
help="create adavptive 3-D mask from a given volume",
default=False)
parser.add_option(
"--nsigma",
type="float",
default=1.,
help=
"number of times of sigma of the input volume to obtain the the large density cluster"
)
parser.add_option(
"--ndilation",
type="int",
default=3,
help=
"number of times of dilation applied to the largest cluster of density"
)
parser.add_option(
"--kernel_size",
type="int",
default=11,
help="convolution kernel for smoothing the edge of the mask")
parser.add_option(
"--gauss_standard_dev",
type="int",
default=9,
help="stanadard deviation value to generate Gaussian edge")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.phase_flip:
nargs = len(args)
if nargs != 2:
print "must provide name of input and output file!"
return
from EMAN2 import Processor
instack = args[0]
outstack = args[1]
nima = EMUtil.get_image_count(instack)
from filter import filt_ctf
for i in xrange(nima):
img = EMData()
img.read_image(instack, i)
try:
ctf = img.get_attr('ctf')
except:
print "no ctf information in input stack! Exiting..."
return
dopad = True
sign = 1
binary = 1 # phase flip
assert img.get_ysize() > 1
dict = ctf.to_dict()
dz = dict["defocus"]
cs = dict["cs"]
voltage = dict["voltage"]
pixel_size = dict["apix"]
b_factor = dict["bfactor"]
ampcont = dict["ampcont"]
dza = dict["dfdiff"]
azz = dict["dfang"]
if dopad and not img.is_complex(): ip = 1
else: ip = 0
params = {
"filter_type": Processor.fourier_filter_types.CTF_,
"defocus": dz,
"Cs": cs,
"voltage": voltage,
"Pixel_size": pixel_size,
"B_factor": b_factor,
"amp_contrast": ampcont,
"dopad": ip,
"binary": binary,
"sign": sign,
"dza": dza,
"azz": azz
}
tmp = Processor.EMFourierFilter(img, params)
tmp.set_attr_dict({"ctf": ctf})
tmp.write_image(outstack, i)
elif options.changesize:
nargs = len(args)
if nargs != 2:
ERROR("must provide name of input and output file!", "change size",
1)
return
from utilities import get_im
instack = args[0]
outstack = args[1]
sub_rate = float(options.ratio)
nima = EMUtil.get_image_count(instack)
from fundamentals import resample
for i in xrange(nima):
resample(get_im(instack, i), sub_rate).write_image(outstack, i)
elif options.isacgroup > -1:
nargs = len(args)
if nargs != 3:
ERROR("Three files needed on input!", "isacgroup", 1)
return
from utilities import get_im
instack = args[0]
m = get_im(args[1], int(options.isacgroup)).get_attr("members")
l = []
for k in m:
l.append(int(get_im(args[0], k).get_attr(options.params)))
from utilities import write_text_file
write_text_file(l, args[2])
elif options.isacselect:
nargs = len(args)
if nargs != 2:
ERROR("Two files needed on input!", "isacgroup", 1)
return
from utilities import get_im
nima = EMUtil.get_image_count(args[0])
m = []
for k in xrange(nima):
m += get_im(args[0], k).get_attr("members")
m.sort()
from utilities import write_text_file
write_text_file(m, args[1])
elif options.pw:
nargs = len(args)
if nargs < 2:
ERROR("must provide name of input and output file!", "pw", 1)
return
from utilities import get_im
d = get_im(args[0])
nx = d.get_xsize()
ny = d.get_ysize()
if nargs == 3: mask = get_im(args[2])
wn = int(options.wn)
if wn == -1:
wn = max(nx, ny)
else:
if ((wn < nx) or (wn < ny)):
ERROR("window size cannot be smaller than the image size",
"pw", 1)
n = EMUtil.get_image_count(args[0])
from utilities import model_blank, model_circle, pad
from EMAN2 import periodogram
p = model_blank(wn, wn)
for i in xrange(n):
d = get_im(args[0], i)
if nargs == 3:
d *= mask
st = Util.infomask(d, None, True)
d -= st[0]
p += periodogram(pad(d, wn, wn, 1, 0.))
p /= n
p.write_image(args[1])
elif options.adjpw:
if len(args) < 3:
ERROR(
"filt_by_rops input target output fl aa (the last two are optional parameters of a low-pass filter)",
"adjpw", 1)
return
img_stack = args[0]
from math import sqrt
from fundamentals import rops_table, fft
from utilities import read_text_file, get_im
from filter import filt_tanl, filt_table
if (args[1][-3:] == 'txt'):
rops_dst = read_text_file(args[1])
else:
rops_dst = rops_table(get_im(args[1]))
out_stack = args[2]
if (len(args) > 4):
fl = float(args[3])
aa = float(args[4])
else:
fl = -1.0
aa = 0.0
nimage = EMUtil.get_image_count(img_stack)
for i in xrange(nimage):
img = fft(get_im(img_stack, i))
rops_src = rops_table(img)
assert len(rops_dst) == len(rops_src)
table = [0.0] * len(rops_dst)
for j in xrange(len(rops_dst)):
table[j] = sqrt(rops_dst[j] / rops_src[j])
if (fl > 0.0):
img = filt_tanl(img, fl, aa)
img = fft(filt_table(img, table))
img.write_image(out_stack, i)
elif options.rotpw != None:
if len(args) != 1:
ERROR("Only one input permitted", "rotpw", 1)
return
from utilities import write_text_file, get_im
from fundamentals import rops_table
from math import log10
t = rops_table(get_im(args[0]))
x = range(len(t))
r = [0.0] * len(x)
for i in x:
r[i] = log10(t[i])
write_text_file([t, r, x], options.rotpw)
elif options.transformparams != None:
if len(args) != 2:
ERROR(
"Please provide names of input and output files with orientation parameters",
"transformparams", 1)
return
from utilities import read_text_row, write_text_row
transf = [0.0] * 6
spl = options.transformparams.split(',')
for i in xrange(len(spl)):
transf[i] = float(spl[i])
write_text_row(rotate_shift_params(read_text_row(args[0]), transf),
args[1])
elif options.makedb != None:
nargs = len(args)
if nargs != 1:
print "must provide exactly one argument denoting database key under which the input params will be stored"
return
dbkey = args[0]
print "database key under which params will be stored: ", dbkey
gbdb = js_open_dict("e2boxercache/gauss_box_DB.json")
parmstr = 'dummy:' + options.makedb[0]
(processorname, param_dict) = parsemodopt(parmstr)
dbdict = {}
for pkey in param_dict:
if (pkey == 'invert_contrast') or (pkey == 'use_variance'):
if param_dict[pkey] == 'True':
dbdict[pkey] = True
else:
dbdict[pkey] = False
else:
dbdict[pkey] = param_dict[pkey]
gbdb[dbkey] = dbdict
elif options.generate_projections:
nargs = len(args)
if nargs != 3:
ERROR("Must provide name of input structure(s) from which to generate projections, name of output projection stack, and prefix for output micrographs."\
"sxprocess - generate projections",1)
return
inpstr = args[0]
outstk = args[1]
micpref = args[2]
parmstr = 'dummy:' + options.generate_projections[0]
(processorname, param_dict) = parsemodopt(parmstr)
parm_CTF = False
parm_format = 'bdb'
parm_apix = 2.5
if 'CTF' in param_dict:
if param_dict['CTF'] == 'True':
parm_CTF = True
if 'format' in param_dict:
parm_format = param_dict['format']
if 'apix' in param_dict:
parm_apix = float(param_dict['apix'])
boxsize = 64
if 'boxsize' in param_dict:
boxsize = int(param_dict['boxsize'])
print "pixel size: ", parm_apix, " format: ", parm_format, " add CTF: ", parm_CTF, " box size: ", boxsize
scale_mult = 2500
sigma_add = 1.5
sigma_proj = 30.0
sigma2_proj = 17.5
sigma_gauss = 0.3
sigma_mic = 30.0
sigma2_mic = 17.5
sigma_gauss_mic = 0.3
if 'scale_mult' in param_dict:
scale_mult = float(param_dict['scale_mult'])
if 'sigma_add' in param_dict:
sigma_add = float(param_dict['sigma_add'])
if 'sigma_proj' in param_dict:
sigma_proj = float(param_dict['sigma_proj'])
if 'sigma2_proj' in param_dict:
sigma2_proj = float(param_dict['sigma2_proj'])
if 'sigma_gauss' in param_dict:
sigma_gauss = float(param_dict['sigma_gauss'])
if 'sigma_mic' in param_dict:
sigma_mic = float(param_dict['sigma_mic'])
if 'sigma2_mic' in param_dict:
sigma2_mic = float(param_dict['sigma2_mic'])
if 'sigma_gauss_mic' in param_dict:
sigma_gauss_mic = float(param_dict['sigma_gauss_mic'])
from filter import filt_gaussl, filt_ctf
from utilities import drop_spider_doc, even_angles, model_gauss, delete_bdb, model_blank, pad, model_gauss_noise, set_params2D, set_params_proj
from projection import prep_vol, prgs
seed(14567)
delta = 29
angles = even_angles(delta, 0.0, 89.9, 0.0, 359.9, "S")
nangle = len(angles)
modelvol = []
nvlms = EMUtil.get_image_count(inpstr)
from utilities import get_im
for k in xrange(nvlms):
modelvol.append(get_im(inpstr, k))
nx = modelvol[0].get_xsize()
if nx != boxsize:
ERROR("Requested box dimension does not match dimension of the input model.", \
"sxprocess - generate projections",1)
nvol = 10
volfts = [[] for k in xrange(nvlms)]
for k in xrange(nvlms):
for i in xrange(nvol):
sigma = sigma_add + random() # 1.5-2.5
addon = model_gauss(sigma, boxsize, boxsize, boxsize, sigma,
sigma, 38, 38, 40)
scale = scale_mult * (0.5 + random())
vf, kb = prep_vol(modelvol[k] + scale * addon)
volfts[k].append(vf)
del vf, modelvol
if parm_format == "bdb":
stack_data = "bdb:" + outstk
delete_bdb(stack_data)
else:
stack_data = outstk + ".hdf"
Cs = 2.0
pixel = parm_apix
voltage = 120.0
ampcont = 10.0
ibd = 4096 / 2 - boxsize
iprj = 0
width = 240
xstart = 8 + boxsize / 2
ystart = 8 + boxsize / 2
rowlen = 17
from random import randint
params = []
for idef in xrange(3, 8):
irow = 0
icol = 0
mic = model_blank(4096, 4096)
defocus = idef * 0.5 #0.2
if parm_CTF:
astampl = defocus * 0.15
astangl = 50.0
ctf = generate_ctf([
defocus, Cs, voltage, pixel, ampcont, 0.0, astampl, astangl
])
for i in xrange(nangle):
for k in xrange(12):
dphi = 8.0 * (random() - 0.5)
dtht = 8.0 * (random() - 0.5)
psi = 360.0 * random()
phi = angles[i][0] + dphi
tht = angles[i][1] + dtht
s2x = 4.0 * (random() - 0.5)
s2y = 4.0 * (random() - 0.5)
params.append([phi, tht, psi, s2x, s2y])
ivol = iprj % nvol
#imgsrc = randint(0,nvlms-1)
imgsrc = iprj % nvlms
proj = prgs(volfts[imgsrc][ivol], kb,
[phi, tht, psi, -s2x, -s2y])
x = xstart + irow * width
y = ystart + icol * width
mic += pad(proj, 4096, 4096, 1, 0.0, x - 2048, y - 2048, 0)
proj = proj + model_gauss_noise(sigma_proj, nx, nx)
if parm_CTF:
proj = filt_ctf(proj, ctf)
proj.set_attr_dict({"ctf": ctf, "ctf_applied": 0})
proj = proj + filt_gaussl(
model_gauss_noise(sigma2_proj, nx, nx), sigma_gauss)
proj.set_attr("origimgsrc", imgsrc)
proj.set_attr("test_id", iprj)
# flags describing the status of the image (1 = true, 0 = false)
set_params2D(proj, [0.0, 0.0, 0.0, 0, 1.0])
set_params_proj(proj, [phi, tht, psi, s2x, s2y])
proj.write_image(stack_data, iprj)
icol += 1
if icol == rowlen:
icol = 0
irow += 1
iprj += 1
mic += model_gauss_noise(sigma_mic, 4096, 4096)
if parm_CTF:
#apply CTF
mic = filt_ctf(mic, ctf)
mic += filt_gaussl(model_gauss_noise(sigma2_mic, 4096, 4096),
sigma_gauss_mic)
mic.write_image(micpref + "%1d.hdf" % (idef - 3), 0)
drop_spider_doc("params.txt", params)
elif options.importctf != None:
print ' IMPORTCTF '
from utilities import read_text_row, write_text_row
from random import randint
import subprocess
grpfile = 'groupid%04d' % randint(1000, 9999)
ctfpfile = 'ctfpfile%04d' % randint(1000, 9999)
cterr = [options.defocuserror / 100.0, options.astigmatismerror]
ctfs = read_text_row(options.importctf)
for kk in xrange(len(ctfs)):
root, name = os.path.split(ctfs[kk][-1])
ctfs[kk][-1] = name[:-4]
if (options.input[:4] != 'bdb:'):
ERROR('Sorry, only bdb files implemented', 'importctf', 1)
d = options.input[4:]
#try: str = d.index('*')
#except: str = -1
from string import split
import glob
uu = os.path.split(d)
uu = os.path.join(uu[0], 'EMAN2DB', uu[1] + '.bdb')
flist = glob.glob(uu)
for i in xrange(len(flist)):
root, name = os.path.split(flist[i])
root = root[:-7]
name = name[:-4]
fil = 'bdb:' + os.path.join(root, name)
sourcemic = EMUtil.get_all_attributes(fil, 'ptcl_source_image')
nn = len(sourcemic)
gctfp = []
groupid = []
for kk in xrange(nn):
junk, name2 = os.path.split(sourcemic[kk])
name2 = name2[:-4]
ctfp = [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
for ll in xrange(len(ctfs)):
if (name2 == ctfs[ll][-1]):
# found correct
if (ctfs[ll][8] / ctfs[ll][0] <= cterr[0]):
# acceptable defocus error
ctfp = ctfs[ll][:8]
if (ctfs[ll][10] > cterr[1]):
# error of astigmatism exceed the threshold, set astigmatism to zero.
ctfp[6] = 0.0
ctfp[7] = 0.0
gctfp.append(ctfp)
groupid.append(kk)
break
if (len(groupid) > 0):
write_text_row(groupid, grpfile)
write_text_row(gctfp, ctfpfile)
cmd = "{} {} {} {}".format(
'e2bdb.py', fil, '--makevstack=bdb:' + root + 'G' + name,
'--list=' + grpfile)
#print cmd
subprocess.call(cmd, shell=True)
cmd = "{} {} {} {}".format('sxheader.py',
'bdb:' + root + 'G' + name,
'--params=ctf',
'--import=' + ctfpfile)
#print cmd
subprocess.call(cmd, shell=True)
else:
print ' >>> Group ', name, ' skipped.'
cmd = "{} {} {}".format("rm -f", grpfile, ctfpfile)
subprocess.call(cmd, shell=True)
elif options.scale > 0.0:
from utilities import read_text_row, write_text_row
scale = options.scale
nargs = len(args)
if nargs != 2:
print "Please provide names of input and output file!"
return
p = read_text_row(args[0])
for i in xrange(len(p)):
p[i][3] /= scale
p[i][4] /= scale
write_text_row(p, args[1])
elif options.adaptive_mask:
from utilities import get_im
from morphology import adaptive_mask
nsigma = options.nsigma
ndilation = options.ndilation
kernel_size = options.kernel_size
gauss_standard_dev = options.gauss_standard_dev
nargs = len(args)
if nargs > 2:
print "Too many inputs are given, try again!"
return
else:
inputvol = get_im(args[0])
input_path, input_file_name = os.path.split(args[0])
input_file_name_root, ext = os.path.splitext(input_file_name)
if nargs == 2: mask_file_name = args[1]
else:
mask_file_name = "adaptive_mask_for" + input_file_name_root + ".hdf" # Only hdf file is output.
mask3d = adaptive_mask(inputvol, nsigma, ndilation, kernel_size,
gauss_standard_dev)
mask3d.write_image(mask_file_name)
else:
ERROR("Please provide option name", "sxprocess.py", 1)
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Generic 2-D image processing programs.
Functionality:
1. Phase flip a stack of images and write output to new file:
sxprocess.py input_stack.hdf output_stack.hdf --phase_flip
2. Resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.
The window size will change accordingly.
sxprocess input.hdf output.hdf --changesize --ratio=0.5
3. Compute average power spectrum of a stack of 2D images with optional padding (option wn) with zeroes or a 3-D volume.
sxprocess.py input_stack.hdf powerspectrum.hdf --pw [--wn=1024]
4. Generate a stack of projections bdb:data and micrographs with prefix mic (i.e., mic0.hdf, mic1.hdf etc) from structure input_structure.hdf, with CTF applied to both projections and micrographs:
sxprocess.py input_structure.hdf data mic --generate_projections format="bdb":apix=5.2:CTF=True:boxsize=64
5. Retrieve original image numbers in the selected ISAC group (here group 12 from generation 3):
sxprocess.py bdb:test3 class_averages_generation_3.hdf list3_12.txt --isacgroup=12 --params=originalid
6. Retrieve original image numbers of images listed in ISAC output stack of averages:
sxprocess.py select1.hdf ohk.txt
7. Adjust rotationally averaged power spectrum of an image to that of a reference image or a reference 1D power spectrum stored in an ASCII file.
Optionally use a tangent low-pass filter. Also works for a stack of images, in which case the output is also a stack.
sxprocess.py vol.hdf ref.hdf avol.hdf < 0.25 0.2> --adjpw
sxprocess.py vol.hdf pw.txt avol.hdf < 0.25 0.2> --adjpw
8. Generate a 1D rotationally averaged power spectrum of an image.
sxprocess.py vol.hdf --rotwp=rotpw.txt
# Output will contain three columns:
(1) rotationally averaged power spectrum
(2) logarithm of the rotationally averaged power spectrum
(3) integer line number (from zero to approximately to half the image size)
9. Apply 3D transformation (rotation and/or shift) to a set of orientation parameters associated with projection data.
sxprocess.py --transfromparams=phi,theta,psi,tx,ty,tz input.txt output.txt
The output file is then imported and 3D transformed volume computed:
sxheader.py bdb:p --params=xform.projection --import=output.txt
mpirun -np 2 sxrecons3d_n.py bdb:p tvol.hdf --MPI
The reconstructed volume is in the position of the volume computed using the input.txt parameters and then
transformed with rot_shift3D(vol, phi,theta,psi,tx,ty,tz)
10. Import ctf parameters from the output of sxcter into windowed particle headers.
There are three possible input files formats: (1) all particles are in one stack, (2 aor 3) particles are in stacks, each stack corresponds to a single micrograph.
In each case the particles should contain a name of the micrograph of origin stores using attribute name 'ptcl_source_image'.
Normally this is done by e2boxer.py during windowing.
Particles whose defocus or astigmatism error exceed set thresholds will be skipped, otherwise, virtual stacks with the original way preceded by G will be created.
sxprocess.py --input=bdb:data --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
# Output will be a vritual stack bdb:Gdata
sxprocess.py --input="bdb:directory/stacks*" --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
To concatenate output files:
cd directory
e2bdb.py . --makevstack=bdb:allparticles --filt=G
IMPORTANT: Please do not move (or remove!) any input/intermediate EMAN2DB files as the information is linked between them.
11. Scale 3D shifts. The shifts in the input five columns text file with 3D orientation parameters will be DIVIDED by the scale factor
sxprocess.py orientationparams.txt scaledparams.txt scale=0.5
12. Generate 3D mask from a given 3-D volume automatically or using threshold provided by user.
13. Postprocess 3-D or 2-D images:
for 3-D volumes: calculate FSC with provided mask; weight summed volume with FSC; estimate B-factor from FSC weighted summed two volumes; apply negative B-factor to the weighted volume.
for 2-D images: calculate B-factor and apply negative B-factor to 2-D images.
14. Winow stack file -reduce size of images without changing the pixel size.
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--order", action="store_true", help="Two arguments are required: name of input stack and desired name of output stack. The output stack is the input stack sorted by similarity in terms of cross-correlation coefficent.", default=False)
parser.add_option("--order_lookup", action="store_true", help="Test/Debug.", default=False)
parser.add_option("--order_metropolis", action="store_true", help="Test/Debug.", default=False)
parser.add_option("--order_pca", action="store_true", help="Test/Debug.", default=False)
parser.add_option("--initial", type="int", default=-1, help="Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)")
parser.add_option("--circular", action="store_true", help="Select circular ordering (fisr image has to be similar to the last", default=False)
parser.add_option("--radius", type="int", default=-1, help="Radius of a circular mask for similarity based ordering")
parser.add_option("--changesize", action="store_true", help="resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.", default=False)
parser.add_option("--ratio", type="float", default=1.0, help="The ratio of new to old image size (if <1 the pixel size will increase and image size decrease, if>1, the other way round")
parser.add_option("--pw", action="store_true", help="compute average power spectrum of a stack of 2-D images with optional padding (option wn) with zeroes", default=False)
parser.add_option("--wn", type="int", default=-1, help="Size of window to use (should be larger/equal than particle box size, default padding to max(nx,ny))")
parser.add_option("--phase_flip", action="store_true", help="Phase flip the input stack", default=False)
parser.add_option("--makedb", metavar="param1=value1:param2=value2", type="string",
action="append", help="One argument is required: name of key with which the database will be created. Fill in database with parameters specified as follows: --makedb param1=value1:param2=value2, e.g. 'gauss_width'=1.0:'pixel_input'=5.2:'pixel_output'=5.2:'thr_low'=1.0")
parser.add_option("--generate_projections", metavar="param1=value1:param2=value2", type="string",
action="append", help="Three arguments are required: name of input structure from which to generate projections, desired name of output projection stack, and desired prefix for micrographs (e.g. if prefix is 'mic', then micrographs mic0.hdf, mic1.hdf etc will be generated). Optional arguments specifying format, apix, box size and whether to add CTF effects can be entered as follows after --generate_projections: format='bdb':apix=5.2:CTF=True:boxsize=100, or format='hdf', etc., where format is bdb or hdf, apix (pixel size) is a float, CTF is True or False, and boxsize denotes the dimension of the box (assumed to be a square). If an optional parameter is not specified, it will default as follows: format='bdb', apix=2.5, CTF=False, boxsize=64.")
parser.add_option("--isacgroup", type="int", help="Retrieve original image numbers in the selected ISAC group. See ISAC documentation for details.", default=-1)
parser.add_option("--isacselect", action="store_true", help="Retrieve original image numbers of images listed in ISAC output stack of averages. See ISAC documentation for details.", default=False)
parser.add_option("--params", type="string", default=None, help="Name of header of parameter, which one depends on specific option")
parser.add_option("--adjpw", action="store_true", help="Adjust rotationally averaged power spectrum of an image", default=False)
parser.add_option("--rotpw", type="string", default=None, help="Name of the text file to contain rotationally averaged power spectrum of the input image.")
parser.add_option("--transformparams", type="string", default=None, help="Transform 3D projection orientation parameters using six 3D parameters (phi, theta,psi,sx,sy,sz). Input: --transformparams=45.,66.,12.,-2,3,-5.5 desired six transformation of the reconstructed structure. Output: file with modified orientation parameters.")
# import ctf estimates done using cter
parser.add_option("--input", type="string", default= None, help="Input particles.")
parser.add_option("--importctf", type="string", default= None, help="Name of the file containing CTF parameters produced by sxcter.")
parser.add_option("--defocuserror", type="float", default=1000000.0, help="Exclude micrographs whose relative defocus error as estimated by sxcter is larger than defocuserror percent. The error is computed as (std dev defocus)/defocus*100%")
parser.add_option("--astigmatismerror", type="float", default=360.0, help="Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sxcter is larger than astigmatismerror degrees.")
# import ctf estimates done using cter
parser.add_option("--scale", type="float", default=-1.0, help="Divide shifts in the input 3D orientation parameters text file by the scale factor.")
# generate adaptive mask from an given 3-D volume
parser.add_option("--adaptive_mask", action="store_true", help="create adavptive 3-D mask from a given volume", default=False)
parser.add_option("--nsigma", type="float", default= 1., help="number of times of sigma of the input volume to obtain the the large density cluster")
parser.add_option("--ndilation", type="int", default= 3, help="number of times of dilation applied to the largest cluster of density")
parser.add_option("--kernel_size", type="int", default= 11, help="convolution kernel for smoothing the edge of the mask")
parser.add_option("--gauss_standard_dev", type="int", default= 9, help="stanadard deviation value to generate Gaussian edge")
parser.add_option("--threshold", type="float", default= 9999., help="threshold provided by user to binarize input volume")
parser.add_option("--ne", type="int", default= 0, help="number of times to erode the binarized input image")
parser.add_option("--nd", type="int", default= 0, help="number of times to dilate the binarized input image")
parser.add_option("--postprocess", action="store_true", help="postprocess unfiltered odd, even 3-D volumes",default=False)
parser.add_option("--fsc_weighted", action="store_true", help="postprocess unfiltered odd, even 3-D volumes")
parser.add_option("--low_pass_filter", action="store_true", default=False, help="postprocess unfiltered odd, even 3-D volumes")
parser.add_option("--ff", type="float", default=.25, help="low pass filter stop band frequency in absolute unit")
parser.add_option("--aa", type="float", default=.1, help="low pass filter falloff" )
parser.add_option("--mask", type="string", help="input mask file", default=None)
parser.add_option("--output", type="string", help="output file name", default="postprocessed.hdf")
parser.add_option("--pixel_size", type="float", help="pixel size of the data", default=1.0)
parser.add_option("--B_start", type="float", help="starting frequency in Angstrom for B-factor estimation", default=10.)
parser.add_option("--FSC_cutoff", type="float", help="stop frequency in Angstrom for B-factor estimation", default=0.143)
parser.add_option("--2d", action="store_true", help="postprocess isac 2-D averaged images",default=False)
parser.add_option("--window_stack", action="store_true", help="window stack images using a smaller window size", default=False)
parser.add_option("--box", type="int", default= 0, help="the new window size ")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.phase_flip:
nargs = len(args)
if nargs != 2:
print "must provide name of input and output file!"
return
from EMAN2 import Processor
instack = args[0]
outstack = args[1]
nima = EMUtil.get_image_count(instack)
from filter import filt_ctf
for i in xrange(nima):
img = EMData()
img.read_image(instack, i)
try:
ctf = img.get_attr('ctf')
except:
print "no ctf information in input stack! Exiting..."
return
dopad = True
sign = 1
binary = 1 # phase flip
assert img.get_ysize() > 1
dict = ctf.to_dict()
dz = dict["defocus"]
cs = dict["cs"]
voltage = dict["voltage"]
pixel_size = dict["apix"]
b_factor = dict["bfactor"]
ampcont = dict["ampcont"]
dza = dict["dfdiff"]
azz = dict["dfang"]
if dopad and not img.is_complex(): ip = 1
else: ip = 0
params = {"filter_type": Processor.fourier_filter_types.CTF_,
"defocus" : dz,
"Cs": cs,
"voltage": voltage,
"Pixel_size": pixel_size,
"B_factor": b_factor,
"amp_contrast": ampcont,
"dopad": ip,
"binary": binary,
"sign": sign,
"dza": dza,
"azz":azz}
tmp = Processor.EMFourierFilter(img, params)
tmp.set_attr_dict({"ctf": ctf})
tmp.write_image(outstack, i)
elif options.changesize:
nargs = len(args)
if nargs != 2:
ERROR("must provide name of input and output file!", "change size", 1)
return
from utilities import get_im
instack = args[0]
outstack = args[1]
sub_rate = float(options.ratio)
nima = EMUtil.get_image_count(instack)
from fundamentals import resample
for i in xrange(nima):
resample(get_im(instack, i), sub_rate).write_image(outstack, i)
elif options.isacgroup>-1:
nargs = len(args)
if nargs != 3:
ERROR("Three files needed on input!", "isacgroup", 1)
return
from utilities import get_im
instack = args[0]
m=get_im(args[1],int(options.isacgroup)).get_attr("members")
l = []
for k in m:
l.append(int(get_im(args[0],k).get_attr(options.params)))
from utilities import write_text_file
write_text_file(l, args[2])
elif options.isacselect:
nargs = len(args)
if nargs != 2:
ERROR("Two files needed on input!", "isacgroup", 1)
return
from utilities import get_im
nima = EMUtil.get_image_count(args[0])
m = []
for k in xrange(nima):
m += get_im(args[0],k).get_attr("members")
m.sort()
from utilities import write_text_file
write_text_file(m, args[1])
elif options.pw:
nargs = len(args)
if nargs < 2:
ERROR("must provide name of input and output file!", "pw", 1)
return
from utilities import get_im, write_text_file
from fundamentals import rops_table
d = get_im(args[0])
ndim = d.get_ndim()
if ndim ==3:
pw = rops_table(d)
write_text_file(pw, args[1])
else:
nx = d.get_xsize()
ny = d.get_ysize()
if nargs ==3: mask = get_im(args[2])
wn = int(options.wn)
if wn == -1:
wn = max(nx, ny)
else:
if( (wn<nx) or (wn<ny) ): ERROR("window size cannot be smaller than the image size","pw",1)
n = EMUtil.get_image_count(args[0])
from utilities import model_blank, model_circle, pad
from EMAN2 import periodogram
p = model_blank(wn,wn)
for i in xrange(n):
d = get_im(args[0], i)
if nargs==3:
d *=mask
st = Util.infomask(d, None, True)
d -= st[0]
p += periodogram(pad(d, wn, wn, 1, 0.))
p /= n
p.write_image(args[1])
elif options.adjpw:
if len(args) < 3:
ERROR("filt_by_rops input target output fl aa (the last two are optional parameters of a low-pass filter)","adjpw",1)
return
img_stack = args[0]
from math import sqrt
from fundamentals import rops_table, fft
from utilities import read_text_file, get_im
from filter import filt_tanl, filt_table
if( args[1][-3:] == 'txt'):
rops_dst = read_text_file( args[1] )
else:
rops_dst = rops_table(get_im( args[1] ))
out_stack = args[2]
if(len(args) >4):
fl = float(args[3])
aa = float(args[4])
else:
fl = -1.0
aa = 0.0
nimage = EMUtil.get_image_count( img_stack )
for i in xrange(nimage):
img = fft(get_im(img_stack, i) )
rops_src = rops_table(img)
assert len(rops_dst) == len(rops_src)
table = [0.0]*len(rops_dst)
for j in xrange( len(rops_dst) ):
table[j] = sqrt( rops_dst[j]/rops_src[j] )
if( fl > 0.0):
img = filt_tanl(img, fl, aa)
img = fft(filt_table(img, table))
img.write_image(out_stack, i)
elif options.rotpw != None:
if len(args) != 1:
ERROR("Only one input permitted","rotpw",1)
return
from utilities import write_text_file, get_im
from fundamentals import rops_table
from math import log10
t = rops_table(get_im(args[0]))
x = range(len(t))
r = [0.0]*len(x)
for i in x: r[i] = log10(t[i])
write_text_file([t,r,x],options.rotpw)
elif options.transformparams != None:
if len(args) != 2:
ERROR("Please provide names of input and output files with orientation parameters","transformparams",1)
return
from utilities import read_text_row, write_text_row
transf = [0.0]*6
spl=options.transformparams.split(',')
for i in xrange(len(spl)): transf[i] = float(spl[i])
write_text_row( rotate_shift_params(read_text_row(args[0]), transf) , args[1])
elif options.makedb != None:
nargs = len(args)
if nargs != 1:
print "must provide exactly one argument denoting database key under which the input params will be stored"
return
dbkey = args[0]
print "database key under which params will be stored: ", dbkey
gbdb = js_open_dict("e2boxercache/gauss_box_DB.json")
parmstr = 'dummy:'+options.makedb[0]
(processorname, param_dict) = parsemodopt(parmstr)
dbdict = {}
for pkey in param_dict:
if (pkey == 'invert_contrast') or (pkey == 'use_variance'):
if param_dict[pkey] == 'True':
dbdict[pkey] = True
else:
dbdict[pkey] = False
else:
dbdict[pkey] = param_dict[pkey]
gbdb[dbkey] = dbdict
elif options.generate_projections:
nargs = len(args)
if nargs != 3:
ERROR("Must provide name of input structure(s) from which to generate projections, name of output projection stack, and prefix for output micrographs."\
"sxprocess - generate projections",1)
return
inpstr = args[0]
outstk = args[1]
micpref = args[2]
parmstr = 'dummy:'+options.generate_projections[0]
(processorname, param_dict) = parsemodopt(parmstr)
parm_CTF = False
parm_format = 'bdb'
parm_apix = 2.5
if 'CTF' in param_dict:
if param_dict['CTF'] == 'True':
parm_CTF = True
if 'format' in param_dict:
parm_format = param_dict['format']
if 'apix' in param_dict:
parm_apix = float(param_dict['apix'])
boxsize = 64
if 'boxsize' in param_dict:
boxsize = int(param_dict['boxsize'])
print "pixel size: ", parm_apix, " format: ", parm_format, " add CTF: ", parm_CTF, " box size: ", boxsize
scale_mult = 2500
sigma_add = 1.5
sigma_proj = 30.0
sigma2_proj = 17.5
sigma_gauss = 0.3
sigma_mic = 30.0
sigma2_mic = 17.5
sigma_gauss_mic = 0.3
if 'scale_mult' in param_dict:
scale_mult = float(param_dict['scale_mult'])
if 'sigma_add' in param_dict:
sigma_add = float(param_dict['sigma_add'])
if 'sigma_proj' in param_dict:
sigma_proj = float(param_dict['sigma_proj'])
if 'sigma2_proj' in param_dict:
sigma2_proj = float(param_dict['sigma2_proj'])
if 'sigma_gauss' in param_dict:
sigma_gauss = float(param_dict['sigma_gauss'])
if 'sigma_mic' in param_dict:
sigma_mic = float(param_dict['sigma_mic'])
if 'sigma2_mic' in param_dict:
sigma2_mic = float(param_dict['sigma2_mic'])
if 'sigma_gauss_mic' in param_dict:
sigma_gauss_mic = float(param_dict['sigma_gauss_mic'])
from filter import filt_gaussl, filt_ctf
from utilities import drop_spider_doc, even_angles, model_gauss, delete_bdb, model_blank,pad,model_gauss_noise,set_params2D, set_params_proj
from projection import prep_vol,prgs
seed(14567)
delta = 29
angles = even_angles(delta, 0.0, 89.9, 0.0, 359.9, "S")
nangle = len(angles)
modelvol = []
nvlms = EMUtil.get_image_count(inpstr)
from utilities import get_im
for k in xrange(nvlms): modelvol.append(get_im(inpstr,k))
nx = modelvol[0].get_xsize()
if nx != boxsize:
ERROR("Requested box dimension does not match dimension of the input model.", \
"sxprocess - generate projections",1)
nvol = 10
volfts = [[] for k in xrange(nvlms)]
for k in xrange(nvlms):
for i in xrange(nvol):
sigma = sigma_add + random() # 1.5-2.5
addon = model_gauss(sigma, boxsize, boxsize, boxsize, sigma, sigma, 38, 38, 40 )
scale = scale_mult * (0.5+random())
vf, kb = prep_vol(modelvol[k] + scale*addon)
volfts[k].append(vf)
del vf, modelvol
if parm_format == "bdb":
stack_data = "bdb:"+outstk
delete_bdb(stack_data)
else:
stack_data = outstk + ".hdf"
Cs = 2.0
pixel = parm_apix
voltage = 120.0
ampcont = 10.0
ibd = 4096/2-boxsize
iprj = 0
width = 240
xstart = 8 + boxsize/2
ystart = 8 + boxsize/2
rowlen = 17
from random import randint
params = []
for idef in xrange(3, 8):
irow = 0
icol = 0
mic = model_blank(4096, 4096)
defocus = idef * 0.5#0.2
if parm_CTF:
astampl=defocus*0.15
astangl=50.0
ctf = generate_ctf([defocus, Cs, voltage, pixel, ampcont, 0.0, astampl, astangl])
for i in xrange(nangle):
for k in xrange(12):
dphi = 8.0*(random()-0.5)
dtht = 8.0*(random()-0.5)
psi = 360.0*random()
phi = angles[i][0]+dphi
tht = angles[i][1]+dtht
s2x = 4.0*(random()-0.5)
s2y = 4.0*(random()-0.5)
params.append([phi, tht, psi, s2x, s2y])
ivol = iprj % nvol
#imgsrc = randint(0,nvlms-1)
imgsrc = iprj % nvlms
proj = prgs(volfts[imgsrc][ivol], kb, [phi, tht, psi, -s2x, -s2y])
x = xstart + irow * width
y = ystart + icol * width
mic += pad(proj, 4096, 4096, 1, 0.0, x-2048, y-2048, 0)
proj = proj + model_gauss_noise( sigma_proj, nx, nx )
if parm_CTF:
proj = filt_ctf(proj, ctf)
proj.set_attr_dict({"ctf":ctf, "ctf_applied":0})
proj = proj + filt_gaussl(model_gauss_noise(sigma2_proj, nx, nx), sigma_gauss)
proj.set_attr("origimgsrc",imgsrc)
proj.set_attr("test_id", iprj)
# flags describing the status of the image (1 = true, 0 = false)
set_params2D(proj, [0.0, 0.0, 0.0, 0, 1.0])
set_params_proj(proj, [phi, tht, psi, s2x, s2y])
proj.write_image(stack_data, iprj)
icol += 1
if icol == rowlen:
icol = 0
irow += 1
iprj += 1
mic += model_gauss_noise(sigma_mic,4096,4096)
if parm_CTF:
#apply CTF
mic = filt_ctf(mic, ctf)
mic += filt_gaussl(model_gauss_noise(sigma2_mic, 4096, 4096), sigma_gauss_mic)
mic.write_image(micpref + "%1d.hdf" % (idef-3), 0)
drop_spider_doc("params.txt", params)
elif options.importctf != None:
print ' IMPORTCTF '
from utilities import read_text_row,write_text_row
from random import randint
import subprocess
grpfile = 'groupid%04d'%randint(1000,9999)
ctfpfile = 'ctfpfile%04d'%randint(1000,9999)
cterr = [options.defocuserror/100.0, options.astigmatismerror]
ctfs = read_text_row(options.importctf)
for kk in xrange(len(ctfs)):
root,name = os.path.split(ctfs[kk][-1])
ctfs[kk][-1] = name[:-4]
if(options.input[:4] != 'bdb:'):
ERROR('Sorry, only bdb files implemented','importctf',1)
d = options.input[4:]
#try: str = d.index('*')
#except: str = -1
from string import split
import glob
uu = os.path.split(d)
uu = os.path.join(uu[0],'EMAN2DB',uu[1]+'.bdb')
flist = glob.glob(uu)
for i in xrange(len(flist)):
root,name = os.path.split(flist[i])
root = root[:-7]
name = name[:-4]
fil = 'bdb:'+os.path.join(root,name)
sourcemic = EMUtil.get_all_attributes(fil,'ptcl_source_image')
nn = len(sourcemic)
gctfp = []
groupid = []
for kk in xrange(nn):
junk,name2 = os.path.split(sourcemic[kk])
name2 = name2[:-4]
ctfp = [-1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]
for ll in xrange(len(ctfs)):
if(name2 == ctfs[ll][-1]):
# found correct
if(ctfs[ll][8]/ctfs[ll][0] <= cterr[0]):
# acceptable defocus error
ctfp = ctfs[ll][:8]
if(ctfs[ll][10] > cterr[1] ):
# error of astigmatism exceed the threshold, set astigmatism to zero.
ctfp[6] = 0.0
ctfp[7] = 0.0
gctfp.append(ctfp)
groupid.append(kk)
break
if(len(groupid) > 0):
write_text_row(groupid, grpfile)
write_text_row(gctfp, ctfpfile)
cmd = "{} {} {} {}".format('e2bdb.py',fil,'--makevstack=bdb:'+root+'G'+name,'--list='+grpfile)
#print cmd
subprocess.call(cmd, shell=True)
cmd = "{} {} {} {}".format('sxheader.py','bdb:'+root+'G'+name,'--params=ctf','--import='+ctfpfile)
#print cmd
subprocess.call(cmd, shell=True)
else:
print ' >>> Group ',name,' skipped.'
cmd = "{} {} {}".format("rm -f",grpfile,ctfpfile)
subprocess.call(cmd, shell=True)
elif options.scale > 0.0:
from utilities import read_text_row,write_text_row
scale = options.scale
nargs = len(args)
if nargs != 2:
print "Please provide names of input and output file!"
return
p = read_text_row(args[0])
for i in xrange(len(p)):
p[i][3] /= scale
p[i][4] /= scale
write_text_row(p, args[1])
elif options.adaptive_mask:
from utilities import get_im
from morphology import adaptive_mask, binarize, erosion, dilation
nsigma = options.nsigma
ndilation = options.ndilation
kernel_size = options.kernel_size
gauss_standard_dev = options.gauss_standard_dev
nargs = len(args)
if nargs ==0:
print " Create 3D mask from a given volume, either automatically or from the user provided threshold."
elif nargs > 2:
print "Too many inputs are given, try again!"
return
else:
inputvol = get_im(args[0])
input_path, input_file_name = os.path.split(args[0])
input_file_name_root,ext=os.path.splitext(input_file_name)
if nargs == 2: mask_file_name = args[1]
else: mask_file_name = "adaptive_mask_for_"+input_file_name_root+".hdf" # Only hdf file is output.
if options.threshold !=9999.:
mask3d = binarize(inputvol, options.threshold)
for i in xrange(options.ne): mask3d = erosion(mask3d)
for i in xrange(options.nd): mask3d = dilation(mask3d)
else:
mask3d = adaptive_mask(inputvol, nsigma, ndilation, kernel_size, gauss_standard_dev)
mask3d.write_image(mask_file_name)
elif options.postprocess:
from utilities import get_im
from fundamentals import rot_avg_table
from morphology import compute_bfactor,power
from statistics import fsc
from filter import filt_table, filt_gaussinv
from EMAN2 import periodogram
e1 = get_im(args[0],0)
if e1.get_zsize()==1:
nimage = EMUtil.get_image_count(args[0])
if options.mask !=None: m = get_im(options.mask)
else: m = None
for i in xrange(nimage):
e1 = get_im(args[0],i)
if m: e1 *=m
guinerline = rot_avg_table(power(periodogram(e1),.5))
freq_max = 1/(2.*pixel_size)
freq_min = 1./options.B_start
b,junk=compute_bfactor(guinerline, freq_min, freq_max, pixel_size)
tmp = b/pixel_size**2
sigma_of_inverse=sqrt(2./tmp)
e1 = filt_gaussinv(e1,sigma_of_inverse)
if options.low_pass_filter:
from filter import filt_tanl
e1 =filt_tanl(e1,options.ff, options.aa)
e1.write_image(options.output)
else:
nargs = len(args)
e1 = get_im(args[0])
if nargs >1: e2 = get_im(args[1])
if options.mask !=None: m = get_im(options.mask)
else: m =None
pixel_size = options.pixel_size
from math import sqrt
if m !=None:
e1 *=m
if nargs >1 :e2 *=m
if options.fsc_weighted:
frc = fsc(e1,e2,1)
## FSC is done on masked two images
#### FSC weighting sqrt((2.*fsc)/(1+fsc));
fil = len(frc[1])*[None]
for i in xrange(len(fil)):
if frc[1][i]>=options.FSC_cutoff: tmp = frc[1][i]
else: tmp = 0.0
fil[i] = sqrt(2.*tmp/(1.+tmp))
if nargs>1: e1 +=e2
if options.fsc_weighted: e1=filt_table(e1,fil)
guinerline = rot_avg_table(power(periodogram(e1),.5))
freq_max = 1/(2.*pixel_size)
freq_min = 1./options.B_start
b,junk = compute_bfactor(guinerline, freq_min, freq_max, pixel_size)
tmp = b/pixel_size**2
sigma_of_inverse=sqrt(2./tmp)
e1 = filt_gaussinv(e1,sigma_of_inverse)
if options.low_pass_filter:
from filter import filt_tanl
e1 =filt_tanl(e1,options.ff, options.aa)
e1.write_image(options.output)
elif options.window_stack:
nargs = len(args)
if nargs ==0:
print " Reduce image size of a stack"
return
else:
output_stack_name = None
inputstack = args[0]
if nargs ==2:output_stack_name = args[1]
input_path,input_file_name=os.path.split(inputstack)
input_file_name_root,ext=os.path.splitext(input_file_name)
if input_file_name_root[0:3]=="bdb":stack_is_bdb= True
else: stack_is_bdb= False
if output_stack_name is None:
if stack_is_bdb: output_stack_name ="bdb:reduced_"+input_file_name_root[4:]
else:output_stack_name = "reduced_"+input_file_name_root+".hdf" # Only hdf file is output.
nimage = EMUtil.get_image_count(inputstack)
from fundamentals import window2d
for i in xrange(nimage):
image = EMData()
image.read_image(inputstack,i)
w = window2d(image,options.box,options.box)
w.write_image(output_stack_name,i)
else: ERROR("Please provide option name","sxprocess.py",1)
def main():
from utilities import write_text_row, drop_image, model_gauss_noise, get_im, set_params_proj, wrap_mpi_bcast, model_circle
import user_functions
from applications import MPI_start_end
from optparse import OptionParser
from global_def import SPARXVERSION
from EMAN2 import EMData
from multi_shc import multi_shc, do_volume
from logger import Logger, BaseLogger_Files
import sys
import os
import time
import socket
progname = os.path.basename(sys.argv[0])
usage = progname + " stack [output_directory] initial_volume --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translational_search_step --delta=angular_step --an=angular_neighborhood --center=center_type --fl --aa --ref_a=S --sym=c1"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--ir", type= "int", default= 1, help="inner radius for rotational correlation > 0 (set to 1)")
parser.add_option("--ou", type= "int", default= -1, help="outer radius for rotational correlation < int(nx/2)-1 (set to the radius of the particle)")
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= "-1", help="range for translation search in x direction, search is +/xr (default 0)")
parser.add_option("--yr", type="string", default= "-1", help="range for translation search in y direction, search is +/yr (default = same as xr)")
parser.add_option("--ts", type="string", default= "1", help="step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional")
parser.add_option("--delta", type="string", default= "-1", help="angular step of reference projections during initialization step (default automatically selected based on radius of the structure.)")
#parser.add_option("--an", type="string", default= "-1", help="angular neighborhood for local searches (phi and theta)")
parser.add_option("--center", type="float", default= -1, help="-1: average shift method; 0: no centering; 1: center of gravity (default=-1)")
parser.add_option("--maxit", type="int", default= 400, help="maximum number of iterations performed for the GA part (set to 400) ")
parser.add_option("--outlier_percentile",type="float", default= 95, help="percentile above which outliers are removed every iteration")
parser.add_option("--iteration_start",type="int", default= 0, help="starting iteration for rviper, 0 means go to the most recent one (default).")
parser.add_option("--CTF", action="store_true", default=False, help="Use CTF (Default no CTF correction)")
parser.add_option("--snr", type="float", default= 1.0, help="Signal-to-Noise Ratio of the data (default 1.0)")
parser.add_option("--ref_a", type="string", default= "S", help="method for generating the quasi-uniformly distributed projection directions (default S)")
parser.add_option("--sym", type="string", default= "c1", help="symmetry of the refined structure")
parser.add_option("--npad", type="int", default= 2, help="padding size for 3D reconstruction (default=2)")
parser.add_option("--startangles", action="store_true", default=False, help="Use orientation parameters in the input file header to jumpstart the procedure")
#options introduced for the do_volume function
parser.add_option("--fl", type="float", default=0.12, help="cut-off frequency of hyperbolic tangent low-pass Fourier filte (default 0.12)")
parser.add_option("--aa", type="float", default=0.1, help="fall-off of hyperbolic tangent low-pass Fourier filter (default 0.1)")
parser.add_option("--pwreference", type="string", default="", help="text file with a reference power spectrum (default no power spectrum adjustment)")
parser.add_option("--mask3D", type="string", default=None, help="3D mask file (default a sphere WHAT RADIUS??)")
(options, args) = parser.parse_args(sys.argv[1:])
#print( " args ",args)
if( len(args) == 3):
volinit = args[2]
masterdir = args[1]
elif(len(args) == 2):
volinit = args[1]
masterdir = ""
else:
print( "usage: " + usage)
print( "Please run '" + progname + " -h' for detailed options")
return 1
orgstack = args[0]
#print( orgstack,masterdir,volinit )
# INPUT PARAMETERS
radi = options.ou
global_def.BATCH = True
ali3d_options.ir = options.ir
ali3d_options.rs = options.rs
ali3d_options.ou = options.ou
ali3d_options.xr = options.xr
ali3d_options.yr = options.yr
ali3d_options.ts = options.ts
ali3d_options.an = "-1"
ali3d_options.sym = options.sym
ali3d_options.delta = options.delta
ali3d_options.npad = options.npad
ali3d_options.center = options.center
ali3d_options.CTF = options.CTF
ali3d_options.ref_a = options.ref_a
ali3d_options.snr = options.snr
ali3d_options.mask3D = options.mask3D
ali3d_options.pwreference = options.pwreference
ali3d_options.fl = 0.4
ali3d_options.aa = 0.1
if( ali3d_options.xr == "-1" ): ali3d_options.xr = "2"
"""
print( options)
print( 'ali3d_options', ali3d_options.ir ,\
ali3d_options.rs ,\
ali3d_options.ou ,\
ali3d_options.xr ,\
ali3d_options.yr ,\
ali3d_options.ts ,\
ali3d_options.an ,\
ali3d_options.sym ,\
ali3d_options.delta ,\
ali3d_options.npad ,\
ali3d_options.center ,\
ali3d_options.CTF ,\
ali3d_options.ref_a ,\
ali3d_options.snr ,\
ali3d_options.mask3D ,\
ali3d_options.fl ,\
ali3d_options.aa \
)
#exit()
"""
mpi_init(0, [])
nproc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
main_node = 0
#mpi_finalize()
#exit()
nxinit = -1 #int(280*0.3*2)
nsoft = 0
mempernode = 4.0e9
# PARAMETERS OF THE PROCEDURE
# threshold error
thresherr = 0
fq = 0.11 # low-freq limit to which fuse ref volumes. Should it be estimated somehow?
# Get the pixel size, if none set to 1.0, and the original image size
if(myid == main_node):
a = get_im(orgstack)
nnxo = a.get_xsize()
if ali3d_options.CTF:
i = a.get_attr('ctf')
pixel_size = i.apix
else:
pixel_size = 1.0
del a
else:
nnxo = 0
pixel_size = 1.0
pixel_size = bcast_number_to_all(pixel_size, source_node = main_node)
nnxo = bcast_number_to_all(nnxo, source_node = main_node)
if(radi < 1): radi = nnxo//2-2
elif((2*radi+2)>nnxo): ERROR("HERE","particle radius set too large!",1)
ali3d_options.ou = radi
if(nxinit < 0): nxinit = min(32, nnxo)
nxshrink = nxinit
minshrink = 32.0/float(nnxo)
shrink = max(float(nxshrink)/float(nnxo),minshrink)
# MASTER DIRECTORY
if(myid == main_node):
print( " masterdir ",masterdir)
if( masterdir == ""):
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir = "master"+timestring
li = len(masterdir)
cmd = "{} {}".format("mkdir", masterdir)
cmdexecute(cmd)
keepchecking = 0
else:
li = 0
keepchecking = 1
else:
li = 0
keepchecking = 1
li = mpi_bcast(li,1,MPI_INT,main_node,MPI_COMM_WORLD)[0]
if( li > 0 ):
masterdir = mpi_bcast(masterdir,li,MPI_CHAR,main_node,MPI_COMM_WORLD)
masterdir = string.join(masterdir,"")
# create a vstack from input stack to the local stack in masterdir
# Stack name set to default
stack = "bdb:"+masterdir+"/rdata"
# Initialization of stacks
if(myid == main_node):
if keepchecking:
if(os.path.exists(os.path.join(masterdir,"EMAN2DB/rdata.bdb"))): doit = False
else: doit = True
else: doit = True
if doit:
if(orgstack[:4] == "bdb:"): cmd = "{} {} {}".format("e2bdb.py", orgstack,"--makevstack="+stack)
else: cmd = "{} {} {}".format("sxcpy.py", orgstack, stack)
cmdexecute(cmd)
cmd = "{} {}".format("sxheader.py --consecutive --params=originalid", stack)
cmdexecute(cmd)
keepchecking = False
total_stack = EMUtil.get_image_count(stack)
junk = get_im(stack)
nnxo = junk.get_xsize()
del junk
else:
total_stack = 0
nnxo = 0
total_stack = bcast_number_to_all(total_stack, source_node = main_node)
nnxo = bcast_number_to_all(nnxo, source_node = main_node)
# INITIALIZATION
# Run exhaustive projection matching to get initial orientation parameters
# Estimate initial resolution
initdir = os.path.join(masterdir,"main000")
# make sure the initial volume is not set to zero outside of a mask, as if it is it will crach the program
if( myid == main_node and (not options.startangles)):
viv = get_im(volinit)
if(options.mask3D == None): mask33d = model_circle(radi,nnxo,nnxo,nnxo)
else: mask33d = (options.mask3D).copy()
st = Util.infomask(viv, mask33d, False)
if( st[0] == 0.0 ):
viv += (model_blank(nnxo,nnxo,nnxo,1.0) - mask33d)*model_gauss_noise(st[1]/1000.0,nnxo,nnxo,nnxo)
viv.write_image(volinit)
del mask33d, viv
doit, keepchecking = checkstep(initdir, keepchecking, myid, main_node)
if doit:
partids = os.path.join(masterdir, "ids.txt")
partstack = os.path.join(masterdir, "paramszero.txt")
xr = min(8,(nnxo - (2*radi+1))//2)
if(xr > 3): ts = "2"
else: ts = "1"
delta = int(options.delta)
if(delta <= 0.0):
delta = "%f"%round(degrees(atan(1.0/float(radi))), 2)
paramsdict = { "stack":stack,"delta":"2.0", "ts":ts, "xr":"%f"%xr, "an":"-1", "center":options.center, "maxit":1, \
"currentres":0.4, "aa":0.1, "radius":radi, "nsoft":0, "delpreviousmax":True, "shrink":1.0, "saturatecrit":1.0, \
"refvol":volinit, "mask3D":options.mask3D}
if(options.startangles):
if( myid == main_node ):
cmd = "mkdir "+initdir
cmdexecute(cmd)
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"INITIALIZATION")
cmd = "{} {}".format("sxheader.py --params=xform.projection --export="+os.path.join(initdir,"params-chunk0.txt"), stack)
cmdexecute(cmd)
print(line,"Executed successfully: ","Imported initial parameters from the input stack")
else:
if( myid == main_node ):
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"INITIALIZATION")
write_text_file(range(total_stack), partids)
write_text_row([[0.0,0.0,0.0,0.0,0.0] for i in xrange(total_stack) ], partstack)
metamove(paramsdict, partids, partstack, initdir, 0, myid, main_node, nproc)
if(myid == main_node):
print(line,"Executed successfully: ","initialization ali3d_base_MPI %d"%nsoft)
# store params
partids = [None]*2
for procid in xrange(2): partids[procid] = os.path.join(initdir,"chunk%01d.txt"%procid)
partstack = [None]*2
for procid in xrange(2): partstack[procid] = os.path.join(initdir,"params-chunk%01d.txt"%procid)
from random import shuffle
if(myid == main_node):
# split randomly
params = read_text_row(os.path.join(initdir,"params-chunk0.txt"))
assert(len(params) == total_stack)
ll = range(total_stack)
shuffle(ll)
l1 = ll[:total_stack//2]
l2 = ll[total_stack//2:]
del ll
l1.sort()
l2.sort()
write_text_file(l1,partids[0])
write_text_file(l2,partids[1])
write_text_row([params[i] for i in l1], partstack[0])
write_text_row([params[i] for i in l2], partstack[1])
del params, l1, l2
mpi_barrier(MPI_COMM_WORLD)
# Now parallel
vol = [None]*2
for procid in xrange(2):
projdata = getindexdata(stack, partids[procid], partstack[procid], myid, nproc)
if ali3d_options.CTF: vol[procid] = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol[procid] = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if( myid == main_node):
vol[procid].write_image(os.path.join(initdir,"vol%01d.hdf"%procid) )
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print( line,"Generated inivol #%01d "%procid)
if(myid == main_node):
currentres = get_resolution(vol, radi, nnxo, initdir)
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print( line,"Initial resolution %6.4f"%currentres)
write_text_file([currentres],os.path.join(initdir,"current_resolution.txt"))
else: currentres = 0.0
currentres = bcast_number_to_all(currentres, source_node = main_node)
else:
if(myid == main_node): currentres = read_text_file(os.path.join(initdir,"current_resolution.txt"))[0]
else: currentres = 0.0
currentres = bcast_number_to_all(currentres, source_node = main_node)
# set for the first iteration
nxshrink = min(max(32, int((currentres+paramsdict["aa"]/2.)*2*nnxo + 0.5)), nnxo)
shrink = float(nxshrink)/nnxo
tracker = {"previous-resolution":currentres, "movedup":False,"eliminated-outliers":False,\
"previous-nx":nxshrink, "previous-shrink":shrink, "extension":0, "bestsolution":0}
previousoutputdir = initdir
# MAIN ITERATION
mainiteration = 0
keepgoing = 1
while(keepgoing):
mainiteration += 1
# prepare output directory
mainoutputdir = os.path.join(masterdir,"main%03d"%mainiteration)
if(myid == main_node):
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"MAIN ITERATION #",mainiteration, shrink, nxshrink)
if keepchecking:
if(os.path.exists(mainoutputdir)):
doit = 0
print("Directory ",mainoutputdir," exists!")
else:
doit = 1
keepchecking = False
else:
doit = 1
if doit:
cmd = "{} {}".format("mkdir", mainoutputdir)
cmdexecute(cmd)
# prepare names of input file names, they are in main directory,
# log subdirectories contain outputs from specific refinements
partids = [None]*2
for procid in xrange(2): partids[procid] = os.path.join(previousoutputdir,"chunk%01d.txt"%procid)
partstack = [None]*2
for procid in xrange(2): partstack[procid] = os.path.join(previousoutputdir,"params-chunk%01d.txt"%procid)
mpi_barrier(MPI_COMM_WORLD)
#mpi_finalize()
#exit()
#print("RACING A ",myid)
outvol = [os.path.join(previousoutputdir,"vol%01d.hdf"%procid) for procid in xrange(2)]
for procid in xrange(2):
doit, keepchecking = checkstep(outvol[procid], keepchecking, myid, main_node)
if doit:
from multi_shc import do_volume
projdata = getindexdata(stack, partids[procid], partstack[procid], myid, nproc)
if ali3d_options.CTF: vol = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if( myid == main_node):
vol.write_image(outvol[procid])
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print( line,"Generated inivol #%01d "%procid)
del vol
if(myid == main_node):
if keepchecking:
procid = 1
if(os.path.join(mainoutputdir,"fusevol%01d.hdf"%procid)):
doit = 0
else:
doit = 1
keepchecking = False
else:
doit = 1
if doit:
vol = [get_im(outvol[procid]) for procid in xrange(2) ]
fq = 0.11 # which part to fuse
fuselowf(vol, fq)
for procid in xrange(2): vol[procid].write_image(os.path.join(mainoutputdir,"fusevol%01d.hdf"%procid) )
del vol
else: doit = 0
mpi_barrier(MPI_COMM_WORLD)
doit = bcast_number_to_all(doit, source_node = main_node)
# Refine two groups at a current resolution
lastring = int(shrink*radi + 0.5)
if(lastring < 2):
print( line,"ERROR!! lastring too small ", radi, shrink, lastring)
break
# REFINEMENT
# Part "a" SHC
for procid in xrange(2):
coutdir = os.path.join(mainoutputdir,"loga%01d"%procid)
doit, keepchecking = checkstep(coutdir , keepchecking, myid, main_node)
paramsdict = { "stack":stack,"delta":"%f"%round(degrees(atan(1.0/lastring)), 2) , "ts":"1", "xr":"2", "an":"-1", "center":options.center, "maxit":1500, \
"currentres":currentres, "aa":0.1, "radius":radi, "nsoft":1, "saturatecrit":0.75, "delpreviousmax":True, "shrink":shrink, \
"refvol":os.path.join(mainoutputdir,"fusevol%01d.hdf"%procid),"mask3D":options.mask3D }
if doit:
metamove(paramsdict, partids[procid], partstack[procid], coutdir, procid, myid, main_node, nproc)
partstack = [None]*2
for procid in xrange(2): partstack[procid] = os.path.join(mainoutputdir, "loga%01d"%procid, "params-chunk%01d.txt"%procid)
for procid in xrange(2):
outvol = os.path.join(mainoutputdir,"loga%01d"%procid,"shcvol%01d.hdf"%procid)
doit, keepchecking = checkstep(outvol, keepchecking, myid, main_node)
if doit:
from multi_shc import do_volume
projdata = getindexdata(stack, partids[procid], partstack[procid], myid, nproc)
if ali3d_options.CTF: vol = recons3d_4nn_ctf_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
else: vol = recons3d_4nn_MPI(myid, projdata, symmetry=ali3d_options.sym, npad = 2)
del projdata
if( myid == main_node):
vol.write_image(outvol)
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print( line,"Generated shcvol #%01d "%procid)
del vol
if(myid == main_node):
if keepchecking:
procid = 1
if(os.path.join(mainoutputdir,"loga%01d"%procid,"fusevol%01d.hdf"%procid) ):
doit = 0
else:
doit = 1
keepchecking = False
else:
doit = 1
if doit:
vol = []
for procid in xrange(2): vol.append(get_im(os.path.join(mainoutputdir,"loga%01d"%procid,"shcvol%01d.hdf"%procid) ))
fq = 0.11 # which part to fuse
fuselowf(vol, fq)
for procid in xrange(2): vol[procid].write_image( os.path.join(mainoutputdir,"loga%01d"%procid,"fusevol%01d.hdf"%procid) )
del vol
else: doit = 0
mpi_barrier(MPI_COMM_WORLD)
doit = bcast_number_to_all(doit, source_node = main_node)
# Part "b" deterministic
partstack = [None]*2
for procid in xrange(2): partstack[procid] = os.path.join(mainoutputdir,"loga%01d"%procid,"params-chunk%01d.txt"%procid)
for procid in xrange(2):
coutdir = os.path.join(mainoutputdir,"logb%01d"%procid)
doit, keepchecking = checkstep(coutdir, keepchecking, myid, main_node)
# Run exhaustive to finish up matching
paramsdict = { "stack":stack,"delta":"%f"%round(degrees(atan(1.0/lastring)), 2) , "ts":"1", "xr":"2", "an":"-1", "center":options.center, "maxit":10, \
"currentres":currentres, "aa":0.1, "radius":radi, "nsoft":0, "saturatecrit":0.95, "delpreviousmax":True, "shrink":shrink, \
"refvol":os.path.join(mainoutputdir,"loga%01d"%procid,"fusevol%01d.hdf"%procid), "mask3D":options.mask3D }
if doit:
metamove(paramsdict, partids[procid], partstack[procid], coutdir, procid, myid, main_node, nproc)
partstack = [None]*2
for procid in xrange(2): partstack[procid] = os.path.join(mainoutputdir,"logb%01d"%procid,"params-chunk%01d.txt"%procid)
# Compute current resolution, store result in main directory
doit, keepchecking = checkstep(os.path.join(mainoutputdir,"current_resolution.txt"), keepchecking, myid, main_node)
newres = 0.0
if doit:
newres = compute_resolution(stack, mainoutputdir, partids, partstack, radi, nnxo, ali3d_options.CTF, myid, main_node, nproc)
else:
if(myid == main_node): newres = read_text_file( os.path.join(mainoutputdir,"current_resolution.txt") )[0]
newres = bcast_number_to_all(newres, source_node = main_node)
# Here I have code to generate presentable results. IDs and params have to be merged and stored and an overall volume computed.
doit, keepchecking = checkstep(os.path.join(mainoutputdir,"volf.hdf"), keepchecking, myid, main_node)
if doit:
if( myid == main_node ):
pinids = map(int, read_text_file(partids[0]) ) + map(int, read_text_file(partids[1]) )
params = read_text_row(partstack[0]) + read_text_row(partstack[1])
assert(len(pinids) == len(params))
for i in xrange(len(pinids)):
pinids[i] = [ pinids[i], params[i] ]
del params
pinids.sort()
write_text_file([pinids[i][0] for i in xrange(len(pinids))], os.path.join(mainoutputdir,"indexes.txt"))
write_text_row( [pinids[i][1] for i in xrange(len(pinids))], os.path.join(mainoutputdir,"params.txt"))
mpi_barrier(MPI_COMM_WORLD)
ali3d_options.fl = newres
ali3d_options.ou = radi
projdata = getindexdata(stack, os.path.join(mainoutputdir,"indexes.txt"), os.path.join(mainoutputdir,"params.txt"), myid, nproc)
volf = do_volume(projdata, ali3d_options, mainiteration, mpi_comm = MPI_COMM_WORLD)
if(myid == main_node): volf.write_image(os.path.join(mainoutputdir,"volf.hdf"))
mpi_barrier(MPI_COMM_WORLD)
#print("RACING X ",myid)
if(newres == currentres):
for procid in xrange(2):
coutdir = os.path.join(mainoutputdir,"logc%01d"%procid)
doit, keepchecking = checkstep(coutdir, keepchecking, myid, main_node)
if doit:
# Do cross-check of the results
paramsdict = { "stack":stack,"delta":"%f"%round(degrees(atan(1.0/lastring)), 2) , "ts":"1", "xr":"2", "an":"-1", "center":options.center, "maxit":1, \
"currentres":newres, "aa":0.1, "radius":radi, "nsoft":0, "saturatecrit":0.95, "delpreviousmax":True, "shrink":shrink, \
"refvol":os.path.join(mainoutputdir,"vol%01d.hdf"%(1-procid)), "mask3D":options.mask3D }
# The cross-check uses parameters from step "b" to make sure shifts are correct.
# As the check is exhaustive, angles are ignored
metamove(paramsdict, partids[procid], partstack[procid], coutdir, procid, myid, main_node, nproc)
# identify bad apples
doit, keepchecking = checkstep(os.path.join(mainoutputdir,"badapples.txt"), keepchecking, myid, main_node)
if doit:
if(myid == main_node):
from utilities import get_symt
from pixel_error import max_3D_pixel_error
ts = get_symt(ali3d_options.sym)
badapples = []
deltaerror = 2.0
total_images_now = 0
for procid in xrange(2):
bad = []
ids = map(int,read_text_file( partids[procid] ))
total_images_now += len(ids)
oldp = read_text_row(partstack[procid])
newp = read_text_row(os.path.join(mainoutputdir,"logc%01d"%procid,"params-chunk%01d.txt"%procid))
for i in xrange(len(ids)):
t1 = Transform({"type":"spider","phi":oldp[i][0],"theta":oldp[i][1],"psi":oldp[i][2]})
t1.set_trans(Vec2f(-oldp[i][3]*shrink, -oldp[i][4]*shrink))
t2 = Transform({"type":"spider","phi":newp[i][0],"theta":newp[i][1],"psi":newp[i][2]})
t2.set_trans(Vec2f(-newp[i][3]*shrink, -newp[i][4]*shrink))
if(len(ts) > 1):
# only do it if it is not c1
pixel_error = +1.0e23
for kts in ts:
ut = t2*kts
# we do not care which position minimizes the error
pixel_error = min(max_3D_pixel_error(t1, ut, lastring), pixel_error)
else:
pixel_error = max_3D_pixel_error(t1, t2, lastring)
if(pixel_error > deltaerror):
bad.append(i)
if(len(bad)>0):
badapples += [ids[bad[i]] for i in xrange(len(bad))]
for i in xrange(len(bad)-1,-1,-1):
del oldp[bad[i]],ids[bad[i]]
if(len(ids) == 0):
ERROR("sxpetite","program diverged, all images have large angular errors, most likely the initial model is badly off",1)
else:
# This generate new parameters, hopefully to be used as starting ones in the new iteration
write_text_file(ids,os.path.join(mainoutputdir,"chunk%01d.txt"%procid))
write_text_row(oldp,os.path.join(mainoutputdir,"params-chunk%01d.txt"%procid))
if(len(badapples)>0):
badapples.sort()
write_text_file(badapples,os.path.join(mainoutputdir,"badapples.txt"))
eli = 100*float(len(badapples))/float(total_images_now)
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Elimination of outliers: %5.1f percent"%eli )
else: eli = 0.0
del badapples, oldp,ids,bad,newp,ts
else: eli =0.0
eli = bcast_number_to_all(eli, source_node = main_node)
# This part under MPI
if(eli > 0.0):
# Compute current resolution
depres = compute_resolution(stack, mainoutputdir, \
[os.path.join(mainoutputdir,"chunk%01d.txt"%procid) for procid in xrange(2)], \
[os.path.join(mainoutputdir,"params-chunk%01d.txt"%procid) for procid in xrange(2)], \
radi, nnxo, ali3d_options.CTF, myid, main_node, nproc)
depres = bcast_number_to_all(depres, source_node = main_node)
if(depres < newres):
# elimination of outliers decreased resolution, ignore the effort
eliminated_outliers = False
else:
eliminated_outliers = True
newres = depres
"""
# It does not seem to be needed, as data is there, we just point to the directory
for procid in xrange(2):
# set pointers to current parameters in main, which are for the reduced set stored above
partids[procid] = os.path.join(mainoutputdir,"chunk%01d.txt"%procid
partstack[procid] = os.path.join(mainoutputdir,"params-chunk%01d.txt"%procid)
"""
else:
eliminated_outliers = False
else:
eliminated_outliers = False
if(myid == main_node and not eliminated_outliers):
for procid in xrange(2):
# This is standard path, copy parameters to be used to the main
cmd = "{} {} {}".format("cp -p ", partids[procid] , os.path.join(mainoutputdir,"chunk%01d.txt"%procid))
cmdexecute(cmd)
cmd = "{} {} {}".format("cp -p ", partstack[procid], os.path.join(mainoutputdir,"params-chunk%01d.txt"%procid))
cmdexecute(cmd)
keepgoing = 0
if( newres > currentres or (eliminated_outliers and not tracker["eliminated-outliers"])):
if(myid == main_node): print(" Resolution improved, full steam ahead!")
if( newres > currentres ): tracker["movedup"] = True
else: tracker["movedup"] = False
shrink = max(min(2*newres + paramsdict["aa"], 1.0),minshrink)
tracker["extension"] = 4
nxshrink = min(int(nnxo*shrink + 0.5) + tracker["extension"],nnxo)
tracker["previous-resolution"] = newres
currentres = newres
tracker["bestsolution"] = mainiteration
bestoutputdir = mainoutputdir
tracker["eliminated-outliers"] = eliminated_outliers
keepgoing = 1
elif(newres < currentres):
if(not tracker["movedup"] and tracker["extension"] < 2 and mainiteration > 1):
keepgoing = 0
if(myid == main_node): print(" Cannot improve resolution, the best result is in the directory main%03d"%tracker["bestsolution"])
else:
if(not tracker["movedup"] and tracker["extension"] > 1 and mainiteration > 1):
if(myid == main_node): print(" Resolution decreased. Will decrease target resolution and will fall back on the best so far: main%03d"%tracker["bestsolution"])
bestoutputdir = os.path.join(masterdir,"main%03d"%tracker["bestsolution"])
elif( tracker["movedup"] and tracker["extension"] > 1 and mainiteration > 1):
if(myid == main_node): print(" Resolution decreased. Will decrease target resolution and will try starting from previous stage: main%03d"%(mainiteration - 1))
bestoutputdir = os.path.join(masterdir,"main%03d"%(mainiteration-1))
elif( mainiteration == 1):
if(myid == main_node): print(" Resolution decreased in the first iteration. It is expected, not to worry")
bestoutputdir = mainoutputdir
tracker["extension"] += 1
else: # missing something here?
if(myid == main_node): print(" Should not be here, ERROR 175!")
break
mpi_finalize()
exit()
if( bestoutputdir != mainoutputdir ):
# This is the key, we just reset the main to previous, so it will be eventually used as a starting in the next iteration
mainoutputdir = bestoutputdir
"""
# Set data from the main previous best to the current.
for procid in xrange(2):
partids[procid] = os.path.join(bestoutputdir,"chunk%01d.txt"%procid)
partstack[procid] = os.path.join(bestoutputdir,"params-chunk%01d.txt"%procid)
"""
if(myid == main_node):
currentres = read_text_file( os.path.join(bestoutputdir,"current_resolution.txt") )[0]
currentres = bcast_number_to_all(currentres, source_node = main_node)
shrink = max(min(2*currentres + paramsdict["aa"], 1.0), minshrink)
tracker["extension"] -= 1
nxshrink = min(int(nnxo*shrink + 0.5) + tracker["extension"],nnxo)
tracker["previous-resolution"] = newres
tracker["eliminated-outliers"] = eliminated_outliers
tracker["movedup"] = False
keepgoing = 1
elif(newres == currentres):
if( tracker["extension"] > 0 ):
if(myid == main_node): print("The resolution did not improve. This is look ahead move. Let's try to relax slightly and hope for the best")
tracker["extension"] -= 1
tracker["movedup"] = False
shrink = max(min(2*currentres + paramsdict["aa"], 1.0), minshrink)
nxshrink = min(int(nnxo*shrink + 0.5) + tracker["extension"],nnxo)
if( tracker["previous-nx"] == nnxo ):
keepgoing = 0
else:
tracker["previous-resolution"] = newres
currentres = newres
tracker["eliminated-outliers"] = eliminated_outliers
tracker["movedup"] = False
keepgoing = 1
else:
if(myid == main_node): print("The resolution did not improve.")
keepgoing = 0
if( keepgoing == 1 ):
if(myid == main_node):
print(" New shrink and image dimension :",shrink,nxshrink)
"""
# It does not look like it is necessary, we just have to point to the directory as the files should be there.
# Will continue, so update the params files
for procid in xrange(2):
# partids ads partstack contain parameters to be used as starting in the next iteration
if(not os.path.exists(os.path.join(mainoutputdir,"chunk%01d.txt"%procid))):
cmd = "{} {} {}".format("cp -p ", partids[procid] , os.path.join(mainoutputdir,"chunk%01d.txt"%procid))
cmdexecute(cmd)
if(not os.path.exists(os.path.join(mainoutputdir,"params-chunk%01d.txt"%procid))):
cmd = "{} {} {}".format("cp -p ", partstack[procid], os.path.join(mainoutputdir,"params-chunk%01d.txt"%procid))
cmdexecute(cmd)
"""
previousoutputdir = mainoutputdir
tracker["previous-shrink"] = shrink
tracker["previous-nx"] = nxshrink
else:
if(myid == main_node):
print(" Terminating, the best solution is in the directory main%03d"%tracker["bestsolution"])
mpi_barrier(MPI_COMM_WORLD)
mpi_finalize()
def main():
from optparse import OptionParser
from global_def import SPARXVERSION
from EMAN2 import EMData
from logger import Logger, BaseLogger_Files
import sys, os, time
global Tracker, Blockdata
from global_def import ERROR
progname = os.path.basename(sys.argv[0])
usage = progname + " --output_dir=output_dir --isac_dir=output_dir_of_isac "
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--pw_adjustment", type ="string", default ='analytical_model', \
help="adjust power spectrum of 2-D averages to an analytic model. Other opions: no_adjustment; bfactor; a text file of 1D rotationally averaged PW")
#### Four options for --pw_adjustment:
# 1> analytical_model(default);
# 2> no_adjustment;
# 3> bfactor;
# 4> adjust_to_given_pw2(user has to provide a text file that contains 1D rotationally averaged PW)
# options in common
parser.add_option(
"--isac_dir",
type="string",
default='',
help="ISAC run output directory, input directory for this command")
parser.add_option(
"--output_dir",
type="string",
default='',
help="output directory where computed averages are saved")
parser.add_option(
"--pixel_size",
type="float",
default=-1.0,
help=
"pixel_size of raw images. one can put 1.0 in case of negative stain data"
)
parser.add_option(
"--fl",
type="float",
default=-1.0,
help=
"low pass filter, = -1.0, not applied; =0.0, using FH1 (initial resolution), = 1.0 using FH2 (resolution after local alignment), or user provided value in absolute freqency [0.0:0.5]"
)
parser.add_option("--stack",
type="string",
default="",
help="data stack used in ISAC")
parser.add_option("--radius", type="int", default=-1, help="radius")
parser.add_option("--xr",
type="float",
default=-1.0,
help="local alignment search range")
#parser.add_option("--ts", type ="float", default =1.0, help= "local alignment search step")
parser.add_option("--fh",
type="float",
default=-1.0,
help="local alignment high frequencies limit")
#parser.add_option("--maxit", type ="int", default =5, help= "local alignment iterations")
parser.add_option("--navg",
type="int",
default=1000000,
help="number of aveages")
parser.add_option("--local_alignment",
action="store_true",
default=False,
help="do local alignment")
parser.add_option(
"--noctf",
action="store_true",
default=False,
help=
"no ctf correction, useful for negative stained data. always ctf for cryo data"
)
parser.add_option(
"--B_start",
type="float",
default=45.0,
help=
"start frequency (Angstrom) of power spectrum for B_factor estimation")
parser.add_option(
"--Bfactor",
type="float",
default=-1.0,
help=
"User defined bactors (e.g. 25.0[A^2]). By default, the program automatically estimates B-factor. "
)
(options, args) = parser.parse_args(sys.argv[1:])
adjust_to_analytic_model = False
adjust_to_given_pw2 = False
B_enhance = False
no_adjustment = False
if options.pw_adjustment == 'analytical_model':
adjust_to_analytic_model = True
elif options.pw_adjustment == 'no_adjustment':
no_adjustment = True
elif options.pw_adjustment == 'bfactor':
B_enhance = True
else:
adjust_to_given_pw2 = True
from utilities import get_im, bcast_number_to_all, write_text_file, read_text_file, wrap_mpi_bcast, write_text_row
from utilities import cmdexecute
from filter import filt_tanl
from logger import Logger, BaseLogger_Files
import user_functions
import string
from string import split, atoi, atof
import json
mpi_init(0, [])
nproc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
Blockdata = {}
# MPI stuff
Blockdata["nproc"] = nproc
Blockdata["myid"] = myid
Blockdata["main_node"] = 0
Blockdata["shared_comm"] = mpi_comm_split_type(MPI_COMM_WORLD,
MPI_COMM_TYPE_SHARED, 0,
MPI_INFO_NULL)
Blockdata["myid_on_node"] = mpi_comm_rank(Blockdata["shared_comm"])
Blockdata["no_of_processes_per_group"] = mpi_comm_size(
Blockdata["shared_comm"])
masters_from_groups_vs_everything_else_comm = mpi_comm_split(
MPI_COMM_WORLD, Blockdata["main_node"] == Blockdata["myid_on_node"],
Blockdata["myid_on_node"])
Blockdata["color"], Blockdata["no_of_groups"], balanced_processor_load_on_nodes = get_colors_and_subsets(Blockdata["main_node"], MPI_COMM_WORLD, Blockdata["myid"], \
Blockdata["shared_comm"], Blockdata["myid_on_node"], masters_from_groups_vs_everything_else_comm)
# We need two nodes for processing of volumes
Blockdata["node_volume"] = [
Blockdata["no_of_groups"] - 3, Blockdata["no_of_groups"] - 2,
Blockdata["no_of_groups"] - 1
] # For 3D stuff take three last nodes
# We need two CPUs for processing of volumes, they are taken to be main CPUs on each volume
# We have to send the two myids to all nodes so we can identify main nodes on two selected groups.
Blockdata["nodes"] = [Blockdata["node_volume"][0]*Blockdata["no_of_processes_per_group"],Blockdata["node_volume"][1]*Blockdata["no_of_processes_per_group"], \
Blockdata["node_volume"][2]*Blockdata["no_of_processes_per_group"]]
# End of Blockdata: sorting requires at least three nodes, and the used number of nodes be integer times of three
global_def.BATCH = True
global_def.MPI = True
if adjust_to_given_pw2:
checking_flag = 0
if (Blockdata["myid"] == Blockdata["main_node"]):
if not os.path.exists(options.pw_adjustment): checking_flag = 1
checking_flag = bcast_number_to_all(checking_flag,
Blockdata["main_node"],
MPI_COMM_WORLD)
if checking_flag == 1:
ERROR("User provided power spectrum does not exist",
"sxcompute_isac_avg.py", 1, Blockdata["myid"])
Tracker = {}
Constants = {}
Constants["isac_dir"] = options.isac_dir
Constants["masterdir"] = options.output_dir
Constants["pixel_size"] = options.pixel_size
Constants["orgstack"] = options.stack
Constants["radius"] = options.radius
Constants["xrange"] = options.xr
Constants["FH"] = options.fh
Constants["low_pass_filter"] = options.fl
#Constants["maxit"] = options.maxit
Constants["navg"] = options.navg
Constants["B_start"] = options.B_start
Constants["Bfactor"] = options.Bfactor
if adjust_to_given_pw2: Constants["modelpw"] = options.pw_adjustment
Tracker["constants"] = Constants
# -------------------------------------------------------------
#
# Create and initialize Tracker dictionary with input options # State Variables
#<<<---------------------->>>imported functions<<<---------------------------------------------
#x_range = max(Tracker["constants"]["xrange"], int(1./Tracker["ini_shrink"])+1)
#y_range = x_range
####-----------------------------------------------------------
# Create Master directory and associated subdirectories
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
if Tracker["constants"]["masterdir"] == Tracker["constants"]["isac_dir"]:
masterdir = os.path.join(Tracker["constants"]["isac_dir"], "sharpen")
else:
masterdir = Tracker["constants"]["masterdir"]
if (Blockdata["myid"] == Blockdata["main_node"]):
msg = "Postprocessing ISAC 2D averages starts"
print(line, "Postprocessing ISAC 2D averages starts")
if not masterdir:
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir = "sharpen_" + Tracker["constants"]["isac_dir"]
os.mkdir(masterdir)
else:
if os.path.exists(masterdir):
print("%s already exists" % masterdir)
else:
os.mkdir(masterdir)
subdir_path = os.path.join(masterdir, "ali2d_local_params_avg")
if not os.path.exists(subdir_path): os.mkdir(subdir_path)
subdir_path = os.path.join(masterdir, "params_avg")
if not os.path.exists(subdir_path): os.mkdir(subdir_path)
li = len(masterdir)
else:
li = 0
li = mpi_bcast(li, 1, MPI_INT, Blockdata["main_node"], MPI_COMM_WORLD)[0]
masterdir = mpi_bcast(masterdir, li, MPI_CHAR, Blockdata["main_node"],
MPI_COMM_WORLD)
masterdir = string.join(masterdir, "")
Tracker["constants"]["masterdir"] = masterdir
log_main = Logger(BaseLogger_Files())
log_main.prefix = Tracker["constants"]["masterdir"] + "/"
while not os.path.exists(Tracker["constants"]["masterdir"]):
print("Node ", Blockdata["myid"], " waiting...",
Tracker["constants"]["masterdir"])
sleep(1)
mpi_barrier(MPI_COMM_WORLD)
if (Blockdata["myid"] == Blockdata["main_node"]):
init_dict = {}
print(Tracker["constants"]["isac_dir"])
Tracker["directory"] = os.path.join(Tracker["constants"]["isac_dir"],
"2dalignment")
core = read_text_row(
os.path.join(Tracker["directory"], "initial2Dparams.txt"))
for im in range(len(core)):
init_dict[im] = core[im]
del core
else:
init_dict = 0
init_dict = wrap_mpi_bcast(init_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
###
do_ctf = True
if options.noctf: do_ctf = False
if (Blockdata["myid"] == Blockdata["main_node"]):
if do_ctf: print("CTF correction is on")
else: print("CTF correction is off")
if options.local_alignment: print("local refinement is on")
else: print("local refinement is off")
if B_enhance: print("Bfactor is to be applied on averages")
elif adjust_to_given_pw2:
print("PW of averages is adjusted to a given 1D PW curve")
elif adjust_to_analytic_model:
print("PW of averages is adjusted to analytical model")
else:
print("PW of averages is not adjusted")
#Tracker["constants"]["orgstack"] = "bdb:"+ os.path.join(Tracker["constants"]["isac_dir"],"../","sparx_stack")
image = get_im(Tracker["constants"]["orgstack"], 0)
Tracker["constants"]["nnxo"] = image.get_xsize()
if Tracker["constants"]["pixel_size"] == -1.0:
print(
"Pixel size value is not provided by user. extracting it from ctf header entry of the original stack."
)
try:
ctf_params = image.get_attr("ctf")
Tracker["constants"]["pixel_size"] = ctf_params.apix
except:
ERROR(
"Pixel size could not be extracted from the original stack.",
"sxcompute_isac_avg.py", 1,
Blockdata["myid"]) # action=1 - fatal error, exit
## Now fill in low-pass filter
isac_shrink_path = os.path.join(Tracker["constants"]["isac_dir"],
"README_shrink_ratio.txt")
if not os.path.exists(isac_shrink_path):
ERROR(
"%s does not exist in the specified ISAC run output directory"
% (isac_shrink_path), "sxcompute_isac_avg.py", 1,
Blockdata["myid"]) # action=1 - fatal error, exit
isac_shrink_file = open(isac_shrink_path, "r")
isac_shrink_lines = isac_shrink_file.readlines()
isac_shrink_ratio = float(
isac_shrink_lines[5]
) # 6th line: shrink ratio (= [target particle radius]/[particle radius]) used in the ISAC run
isac_radius = float(
isac_shrink_lines[6]
) # 7th line: particle radius at original pixel size used in the ISAC run
isac_shrink_file.close()
print("Extracted parameter values")
print("ISAC shrink ratio : {0}".format(isac_shrink_ratio))
print("ISAC particle radius : {0}".format(isac_radius))
Tracker["ini_shrink"] = isac_shrink_ratio
else:
Tracker["ini_shrink"] = 0.0
Tracker = wrap_mpi_bcast(Tracker,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
#print(Tracker["constants"]["pixel_size"], "pixel_size")
x_range = max(Tracker["constants"]["xrange"],
int(1. / Tracker["ini_shrink"] + 0.99999))
a_range = y_range = x_range
if (Blockdata["myid"] == Blockdata["main_node"]):
parameters = read_text_row(
os.path.join(Tracker["constants"]["isac_dir"],
"all_parameters.txt"))
else:
parameters = 0
parameters = wrap_mpi_bcast(parameters,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
params_dict = {}
list_dict = {}
#parepare params_dict
#navg = min(Tracker["constants"]["navg"]*Blockdata["nproc"], EMUtil.get_image_count(os.path.join(Tracker["constants"]["isac_dir"], "class_averages.hdf")))
navg = min(
Tracker["constants"]["navg"],
EMUtil.get_image_count(
os.path.join(Tracker["constants"]["isac_dir"],
"class_averages.hdf")))
global_dict = {}
ptl_list = []
memlist = []
if (Blockdata["myid"] == Blockdata["main_node"]):
print("Number of averages computed in this run is %d" % navg)
for iavg in range(navg):
params_of_this_average = []
image = get_im(
os.path.join(Tracker["constants"]["isac_dir"],
"class_averages.hdf"), iavg)
members = sorted(image.get_attr("members"))
memlist.append(members)
for im in range(len(members)):
abs_id = members[im]
global_dict[abs_id] = [iavg, im]
P = combine_params2( init_dict[abs_id][0], init_dict[abs_id][1], init_dict[abs_id][2], init_dict[abs_id][3], \
parameters[abs_id][0], parameters[abs_id][1]/Tracker["ini_shrink"], parameters[abs_id][2]/Tracker["ini_shrink"], parameters[abs_id][3])
if parameters[abs_id][3] == -1:
print(
"WARNING: Image #{0} is an unaccounted particle with invalid 2D alignment parameters and should not be the member of any classes. Please check the consitency of input dataset."
.format(abs_id)
) # How to check what is wrong about mirror = -1 (Toshio 2018/01/11)
params_of_this_average.append([P[0], P[1], P[2], P[3], 1.0])
ptl_list.append(abs_id)
params_dict[iavg] = params_of_this_average
list_dict[iavg] = members
write_text_row(
params_of_this_average,
os.path.join(Tracker["constants"]["masterdir"], "params_avg",
"params_avg_%03d.txt" % iavg))
ptl_list.sort()
init_params = [None for im in range(len(ptl_list))]
for im in range(len(ptl_list)):
init_params[im] = [ptl_list[im]] + params_dict[global_dict[
ptl_list[im]][0]][global_dict[ptl_list[im]][1]]
write_text_row(
init_params,
os.path.join(Tracker["constants"]["masterdir"],
"init_isac_params.txt"))
else:
params_dict = 0
list_dict = 0
memlist = 0
params_dict = wrap_mpi_bcast(params_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
list_dict = wrap_mpi_bcast(list_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
memlist = wrap_mpi_bcast(memlist,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
# Now computing!
del init_dict
tag_sharpen_avg = 1000
## always apply low pass filter to B_enhanced images to suppress noise in high frequencies
enforced_to_H1 = False
if B_enhance:
if Tracker["constants"]["low_pass_filter"] == -1.0:
enforced_to_H1 = True
if navg < Blockdata["nproc"]: # Each CPU do one average
ERROR("number of nproc is larger than number of averages",
"sxcompute_isac_avg.py", 1, Blockdata["myid"])
else:
FH_list = [[0, 0.0, 0.0] for im in range(navg)]
image_start, image_end = MPI_start_end(navg, Blockdata["nproc"],
Blockdata["myid"])
if Blockdata["myid"] == Blockdata["main_node"]:
cpu_dict = {}
for iproc in range(Blockdata["nproc"]):
local_image_start, local_image_end = MPI_start_end(
navg, Blockdata["nproc"], iproc)
for im in range(local_image_start, local_image_end):
cpu_dict[im] = iproc
else:
cpu_dict = 0
cpu_dict = wrap_mpi_bcast(cpu_dict,
Blockdata["main_node"],
communicator=MPI_COMM_WORLD)
slist = [None for im in range(navg)]
ini_list = [None for im in range(navg)]
avg1_list = [None for im in range(navg)]
avg2_list = [None for im in range(navg)]
plist_dict = {}
data_list = [None for im in range(navg)]
if Blockdata["myid"] == Blockdata["main_node"]:
if B_enhance:
print(
"Avg ID B-factor FH1(Res before ali) FH2(Res after ali)"
)
else:
print("Avg ID FH1(Res before ali) FH2(Res after ali)")
for iavg in range(image_start, image_end):
mlist = EMData.read_images(Tracker["constants"]["orgstack"],
list_dict[iavg])
for im in range(len(mlist)):
#mlist[im]= get_im(Tracker["constants"]["orgstack"], list_dict[iavg][im])
set_params2D(mlist[im],
params_dict[iavg][im],
xform="xform.align2d")
if options.local_alignment:
"""
new_average1 = within_group_refinement([mlist[kik] for kik in range(0,len(mlist),2)], maskfile= None, randomize= False, ir=1.0, \
ou=Tracker["constants"]["radius"], rs=1.0, xrng=[x_range], yrng=[y_range], step=[Tracker["constants"]["xstep"]], \
dst=0.0, maxit=Tracker["constants"]["maxit"], FH=max(Tracker["constants"]["FH"], FH1), FF=0.02, method="")
new_average2 = within_group_refinement([mlist[kik] for kik in range(1,len(mlist),2)], maskfile= None, randomize= False, ir=1.0, \
ou= Tracker["constants"]["radius"], rs=1.0, xrng=[ x_range], yrng=[y_range], step=[Tracker["constants"]["xstep"]], \
dst=0.0, maxit=Tracker["constants"]["maxit"], FH = max(Tracker["constants"]["FH"], FH1), FF=0.02, method="")
new_avg, frc, plist = compute_average(mlist, Tracker["constants"]["radius"], do_ctf)
"""
new_avg, plist, FH2 = refinement_2d_local(
mlist,
Tracker["constants"]["radius"],
a_range,
x_range,
y_range,
CTF=do_ctf,
SNR=1.0e10)
plist_dict[iavg] = plist
FH1 = -1.0
else:
new_avg, frc, plist = compute_average(
mlist, Tracker["constants"]["radius"], do_ctf)
FH1 = get_optimistic_res(frc)
FH2 = -1.0
#write_text_file(frc, os.path.join(Tracker["constants"]["masterdir"], "fsc%03d.txt"%iavg))
FH_list[iavg] = [iavg, FH1, FH2]
if B_enhance:
new_avg, gb = apply_enhancement(
new_avg, Tracker["constants"]["B_start"],
Tracker["constants"]["pixel_size"],
Tracker["constants"]["Bfactor"])
print(" %6d %6.3f %4.3f %4.3f" % (iavg, gb, FH1, FH2))
elif adjust_to_given_pw2:
roo = read_text_file(Tracker["constants"]["modelpw"], -1)
roo = roo[0] # always on the first column
new_avg = adjust_pw_to_model(
new_avg, Tracker["constants"]["pixel_size"], roo)
print(" %6d %4.3f %4.3f " % (iavg, FH1, FH2))
elif adjust_to_analytic_model:
new_avg = adjust_pw_to_model(
new_avg, Tracker["constants"]["pixel_size"], None)
print(" %6d %4.3f %4.3f " % (iavg, FH1, FH2))
elif no_adjustment:
pass
if Tracker["constants"]["low_pass_filter"] != -1.0:
if Tracker["constants"]["low_pass_filter"] == 0.0:
low_pass_filter = FH1
elif Tracker["constants"]["low_pass_filter"] == 1.0:
low_pass_filter = FH2
if not options.local_alignment: low_pass_filter = FH1
else:
low_pass_filter = Tracker["constants"]["low_pass_filter"]
if low_pass_filter >= 0.45: low_pass_filter = 0.45
new_avg = filt_tanl(new_avg, low_pass_filter, 0.02)
else: # No low pass filter but if enforced
if enforced_to_H1: new_avg = filt_tanl(new_avg, FH1, 0.02)
if B_enhance: new_avg = fft(new_avg)
new_avg.set_attr("members", list_dict[iavg])
new_avg.set_attr("n_objects", len(list_dict[iavg]))
slist[iavg] = new_avg
print(
strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>",
"Refined average %7d" % iavg)
## send to main node to write
mpi_barrier(MPI_COMM_WORLD)
for im in range(navg):
# avg
if cpu_dict[im] == Blockdata[
"myid"] and Blockdata["myid"] != Blockdata["main_node"]:
send_EMData(slist[im], Blockdata["main_node"], tag_sharpen_avg)
elif cpu_dict[im] == Blockdata["myid"] and Blockdata[
"myid"] == Blockdata["main_node"]:
slist[im].set_attr("members", memlist[im])
slist[im].set_attr("n_objects", len(memlist[im]))
slist[im].write_image(
os.path.join(Tracker["constants"]["masterdir"],
"class_averages.hdf"), im)
elif cpu_dict[im] != Blockdata["myid"] and Blockdata[
"myid"] == Blockdata["main_node"]:
new_avg_other_cpu = recv_EMData(cpu_dict[im], tag_sharpen_avg)
new_avg_other_cpu.set_attr("members", memlist[im])
new_avg_other_cpu.set_attr("n_objects", len(memlist[im]))
new_avg_other_cpu.write_image(
os.path.join(Tracker["constants"]["masterdir"],
"class_averages.hdf"), im)
if options.local_alignment:
if cpu_dict[im] == Blockdata["myid"]:
write_text_row(
plist_dict[im],
os.path.join(Tracker["constants"]["masterdir"],
"ali2d_local_params_avg",
"ali2d_local_params_avg_%03d.txt" % im))
if cpu_dict[im] == Blockdata[
"myid"] and cpu_dict[im] != Blockdata["main_node"]:
wrap_mpi_send(plist_dict[im], Blockdata["main_node"],
MPI_COMM_WORLD)
wrap_mpi_send(FH_list, Blockdata["main_node"],
MPI_COMM_WORLD)
elif cpu_dict[im] != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(cpu_dict[im], MPI_COMM_WORLD)
plist_dict[im] = dummy
dummy = wrap_mpi_recv(cpu_dict[im], MPI_COMM_WORLD)
FH_list[im] = dummy[im]
else:
if cpu_dict[im] == Blockdata[
"myid"] and cpu_dict[im] != Blockdata["main_node"]:
wrap_mpi_send(FH_list, Blockdata["main_node"],
MPI_COMM_WORLD)
elif cpu_dict[im] != Blockdata["main_node"] and Blockdata[
"myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(cpu_dict[im], MPI_COMM_WORLD)
FH_list[im] = dummy[im]
mpi_barrier(MPI_COMM_WORLD)
mpi_barrier(MPI_COMM_WORLD)
if options.local_alignment:
if Blockdata["myid"] == Blockdata["main_node"]:
ali3d_local_params = [None for im in range(len(ptl_list))]
for im in range(len(ptl_list)):
ali3d_local_params[im] = [ptl_list[im]] + plist_dict[
global_dict[ptl_list[im]][0]][global_dict[ptl_list[im]][1]]
write_text_row(
ali3d_local_params,
os.path.join(Tracker["constants"]["masterdir"],
"ali2d_local_params.txt"))
write_text_row(
FH_list,
os.path.join(Tracker["constants"]["masterdir"], "FH_list.txt"))
else:
if Blockdata["myid"] == Blockdata["main_node"]:
write_text_row(
FH_list,
os.path.join(Tracker["constants"]["masterdir"], "FH_list.txt"))
mpi_barrier(MPI_COMM_WORLD)
target_xr = 3
target_yr = 3
if (Blockdata["myid"] == 0):
cmd = "{} {} {} {} {} {} {} {} {} {}".format("sxchains.py", os.path.join(Tracker["constants"]["masterdir"],"class_averages.hdf"),\
os.path.join(Tracker["constants"]["masterdir"],"junk.hdf"),os.path.join(Tracker["constants"]["masterdir"],"ordered_class_averages.hdf"),\
"--circular","--radius=%d"%Tracker["constants"]["radius"] , "--xr=%d"%(target_xr+1),"--yr=%d"%(target_yr+1),"--align", ">/dev/null")
junk = cmdexecute(cmd)
cmd = "{} {}".format(
"rm -rf",
os.path.join(Tracker["constants"]["masterdir"], "junk.hdf"))
junk = cmdexecute(cmd)
from mpi import mpi_finalize
mpi_finalize()
exit()
def main():
from utilities import write_text_row, drop_image, model_gauss_noise, get_im, set_params_proj, wrap_mpi_bcast, model_circle
import user_functions
from applications import MPI_start_end
from optparse import OptionParser
from global_def import SPARXVERSION
from EMAN2 import EMData
from multi_shc import multi_shc, do_volume
from logger import Logger, BaseLogger_Files
import sys
import os
import time
import socket
progname = os.path.basename(sys.argv[0])
usage = progname + " stack [output_directory] initial_volume --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translational_search_step --delta=angular_step --an=angular_neighborhood --CTF --fl --aa --ref_a=S --sym=c1"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--ir", type= "int", default= 1, help="inner radius for rotational correlation > 0 (set to 1)")
parser.add_option("--ou", type= "int", default= -1, help="outer radius for rotational correlation < int(nx/2)-1 (set to the radius of the particle)")
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= "-1", help="range for translation search in x direction, search is +/xr (default 0)")
parser.add_option("--yr", type="string", default= "-1", help="range for translation search in y direction, search is +/yr (default = same as xr)")
parser.add_option("--ts", type="string", default= "1", help="step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional")
parser.add_option("--delta", type="string", default= "-1", help="angular step of reference projections during initialization step (default automatically selected based on radius of the structure.)")
parser.add_option("--an", type="string", default= "-1", help="angular neighborhood for local searches (phi and theta) (Default exhaustive searches)")
parser.add_option("--CTF", action="store_true", default=False, help="Use CTF (Default no CTF correction)")
parser.add_option("--shrink", type="float", default= 1.0, help="Reduce data size by shrink factor (default 1.0)")
parser.add_option("--snr", type="float", default= 1.0, help="Signal-to-Noise Ratio of the data (default 1.0)")
parser.add_option("--ref_a", type="string", default= "S", help="method for generating the quasi-uniformly distributed projection directions (default S)")
parser.add_option("--sym", type="string", default= "c1", help="symmetry of the refined structure")
parser.add_option("--npad", type="int", default= 2, help="padding size for 3D reconstruction (default=2)")
#options introduced for the do_volume function
parser.add_option("--fl", type="float", default=0.12, help="cut-off frequency of hyperbolic tangent low-pass Fourier filte (default 0.12)")
parser.add_option("--aa", type="float", default=0.1, help="fall-off of hyperbolic tangent low-pass Fourier filter (default 0.1)")
parser.add_option("--pwreference", type="string", default="", help="text file with a reference power spectrum (default no power spectrum adjustment)")
parser.add_option("--mask3D", type="string", default=None, help="3D mask file (default a sphere WHAT RADIUS??)")
(options, args) = parser.parse_args(sys.argv[1:])
#print( " args ",args)
if( len(args) == 3):
volinit = args[2]
masterdir = args[1]
elif(len(args) == 2):
volinit = args[1]
masterdir = ""
else:
print( "usage: " + usage)
print( "Please run '" + progname + " -h' for detailed options")
return 1
stack = args[0]
# INPUT PARAMETERS
radi = options.ou
global_def.BATCH = True
ali3d_options.ir = options.ir
ali3d_options.rs = options.rs
ali3d_options.ou = options.ou
ali3d_options.xr = options.xr
ali3d_options.yr = options.yr
ali3d_options.ts = options.ts
ali3d_options.an = "-1"
ali3d_options.sym = options.sym
ali3d_options.delta = options.delta
ali3d_options.npad = options.npad
ali3d_options.CTF = options.CTF
ali3d_options.ref_a = options.ref_a
ali3d_options.snr = options.snr
ali3d_options.mask3D = options.mask3D
ali3d_options.pwreference = "" # It will have to be turned on after exhaustive done by setting to options.pwreference
ali3d_options.fl = 0.4
ali3d_options.initfl = 0.4
ali3d_options.aa = 0.1
mpi_init(0, [])
nproc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
main_node = 0
# Get the pixel size, if none set to 1.0, and the original image size
if(myid == main_node):
total_stack = EMUtil.get_image_count(stack)
a = get_im(stack)
nxinit = a.get_xsize()
if ali3d_options.CTF:
i = a.get_attr('ctf')
pixel_size = i.apix
fq = pixel_size/fq
else:
pixel_size = 1.0
# No pixel size, fusing computed as 5 Fourier pixels
fq = 5.0/nxinit
del a
else:
total_stack = 0
nxinit = 0
pixel_size = 1.0
total_stack = bcast_number_to_all(total_stack, source_node = main_node)
pixel_size = bcast_number_to_all(pixel_size, source_node = main_node)
nxinit = bcast_number_to_all(nxinit, source_node = main_node)
if(radi < 1): radi = nxinit//2-2
elif((2*radi+2)>nxinit): ERROR("Particle radius set too large!","sxcenter_projections",1,myid)
ali3d_options.ou = radi
shrink = options.shrink
nxshrink = int(nxinit*shrink+0.5)
angular_neighborhood = "-1"
# MASTER DIRECTORY
if(myid == main_node):
print( " masterdir ",masterdir)
if( masterdir == ""):
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir = "master"+timestring
li = len(masterdir)
cmd = "{} {}".format("mkdir", masterdir)
junk = cmdexecute(cmd)
else:
li = 0
li = mpi_bcast(li,1,MPI_INT,main_node,MPI_COMM_WORLD)[0]
if( li > 0 ):
masterdir = mpi_bcast(masterdir,li,MPI_CHAR,main_node,MPI_COMM_WORLD)
masterdir = string.join(masterdir,"")
nnxo = nxinit
# INITIALIZATION
initdir = masterdir
# This is initial setting, has to be initialized here, we do not want it to run too long.
# INITIALIZATION THAT FOLLOWS WILL HAVE TO BE CHANGED SO THE USER CAN PROVIDE INITIAL GUESS OF RESOLUTION
# If we new the initial resolution, it could be done more densely
if(options.xr == "-1"): xr = "%d"%((nnxo - (2*radi-1))//2)
else: xr = options.xr
if(options.yr == "-1"): yr = xr
else: yr = options.yr
delta = float(options.delta)
if(delta <= 0.0): delta = "%f"%round(degrees(atan(1.0/float(radi))), 2)
else: delta = "%f"%delta
paramsdict = { "stack":stack,"delta":delta, "ts":"1.0", "xr":xr, "an":angular_neighborhood, \
"center":"0", "maxit":1, "local":False,\
"lowpass":options.fl, "initialfl":0.4, "falloff":options.aa, "radius":radi, \
"nsoft":0, "delpreviousmax":True, "shrink":options.shrink, "saturatecrit":1.0, "pixercutoff":2.0,\
"refvol":volinit, "mask3D":options.mask3D}
partids = os.path.join(masterdir, "ids.txt")
partstack = os.path.join(masterdir, "paramszero.txt")
if( myid == main_node ):
write_text_file(range(total_stack), partids)
write_text_row([[0.0,0.0,0.0,0.0,0.0] for i in xrange(total_stack) ], partstack)
run3Dalignment(paramsdict, partids, partstack, initdir, 0, myid, main_node, nproc)
mpi_barrier(MPI_COMM_WORLD)
mpi_finalize()
def run3Dalignment(paramsdict, partids, partstack, outputdir, procid, myid, main_node, nproc):
# Reads from paramsdict["stack"] particles partids set parameters in partstack
# and do refinement as specified in paramsdict
#
# Will create outputdir
# Will write to outputdir output parameters: params-chunk0.txt and params-chunk1.txt
if(myid == main_node):
# Create output directory
log = Logger(BaseLogger_Files())
log.prefix = os.path.join(outputdir)
#cmd = "mkdir "+log.prefix
#junk = cmdexecute(cmd)
log.prefix += "/"
else: log = None
mpi_barrier(MPI_COMM_WORLD)
ali3d_options.delta = paramsdict["delta"]
ali3d_options.ts = paramsdict["ts"]
ali3d_options.xr = paramsdict["xr"]
# low pass filter is applied to shrank data, so it has to be adjusted
ali3d_options.fl = paramsdict["lowpass"]/paramsdict["shrink"]
ali3d_options.initfl = paramsdict["initialfl"]/paramsdict["shrink"]
ali3d_options.aa = paramsdict["falloff"]
ali3d_options.maxit = paramsdict["maxit"]
ali3d_options.mask3D = paramsdict["mask3D"]
ali3d_options.an = paramsdict["an"]
ali3d_options.ou = paramsdict["radius"] # This is changed in ali3d_base, but the shrank value is needed in vol recons, fixt it!
shrinkage = paramsdict["shrink"]
projdata = getindexdata(paramsdict["stack"], partids, partstack, myid, nproc)
onx = projdata[0].get_xsize()
last_ring = ali3d_options.ou
if last_ring < 0: last_ring = int(onx/2) - 2
mask2D = model_circle(last_ring,onx,onx) - model_circle(ali3d_options.ir,onx,onx)
if(shrinkage < 1.0):
# get the new size
masks2D = resample(mask2D, shrinkage)
nx = masks2D.get_xsize()
masks2D = model_circle(int(last_ring*shrinkage+0.5),nx,nx) - model_circle(max(int(ali3d_options.ir*shrinkage+0.5),1),nx,nx)
nima = len(projdata)
oldshifts = [0.0,0.0]*nima
for im in xrange(nima):
#data[im].set_attr('ID', list_of_particles[im])
ctf_applied = projdata[im].get_attr_default('ctf_applied', 0)
phi,theta,psi,sx,sy = get_params_proj(projdata[im])
projdata[im] = fshift(projdata[im], sx, sy)
set_params_proj(projdata[im],[phi,theta,psi,0.0,0.0])
# For local SHC set anchor
#if(nsoft == 1 and an[0] > -1):
# set_params_proj(data[im],[phi,tetha,psi,0.0,0.0], "xform.anchor")
oldshifts[im] = [sx,sy]
if ali3d_options.CTF :
ctf_params = projdata[im].get_attr("ctf")
if ctf_applied == 0:
st = Util.infomask(projdata[im], mask2D, False)
projdata[im] -= st[0]
projdata[im] = filt_ctf(projdata[im], ctf_params)
projdata[im].set_attr('ctf_applied', 1)
if(shrinkage < 1.0):
#phi,theta,psi,sx,sy = get_params_proj(projdata[im])
projdata[im] = resample(projdata[im], shrinkage)
st = Util.infomask(projdata[im], None, True)
projdata[im] -= st[0]
st = Util.infomask(projdata[im], masks2D, True)
projdata[im] /= st[1]
#sx *= shrinkage
#sy *= shrinkage
#set_params_proj(projdata[im], [phi,theta,psi,sx,sy])
if ali3d_options.CTF :
ctf_params.apix /= shrinkage
projdata[im].set_attr('ctf', ctf_params)
else:
st = Util.infomask(projdata[im], None, True)
projdata[im] -= st[0]
st = Util.infomask(projdata[im], mask2D, True)
projdata[im] /= st[1]
del mask2D
if(shrinkage < 1.0): del masks2D
"""
if(paramsdict["delpreviousmax"]):
for i in xrange(len(projdata)):
try: projdata[i].del_attr("previousmax")
except: pass
"""
if(myid == main_node):
print_dict(paramsdict,"3D alignment parameters")
print(" => actual lowpass : "******" => actual init lowpass : "******" => PW adjustment : ",ali3d_options.pwreference)
print(" => partids : ",partids)
print(" => partstack : ",partstack)
if(ali3d_options.fl > 0.46): ERROR("Low pass filter in 3D alignment > 0.46 on the scale of shrank data","sxcenter_projections",1,myid)
# Run alignment command, it returns params per CPU
params = center_projections_3D(projdata, paramsdict["refvol"], \
ali3d_options, onx, shrinkage, \
mpi_comm = MPI_COMM_WORLD, myid = myid, main_node = main_node, log = log )
del log, projdata
params = wrap_mpi_gatherv(params, main_node, MPI_COMM_WORLD)
# store params
if(myid == main_node):
for im in xrange(nima):
params[im][0] = params[im][0]/shrinkage +oldshifts[im][0]
params[im][1] = params[im][1]/shrinkage +oldshifts[im][1]
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: ","3D alignment"," number of images:%7d"%len(params))
write_text_row(params, os.path.join(outputdir,"params.txt") )
def main():
from utilities import write_text_row, drop_image, model_gauss_noise, get_im, set_params_proj, wrap_mpi_bcast, model_circle
import user_functions
from applications import MPI_start_end
from optparse import OptionParser
from global_def import SPARXVERSION
from EMAN2 import EMData
from multi_shc import multi_shc, do_volume
from logger import Logger, BaseLogger_Files
import sys
import os
import time
import socket
progname = os.path.basename(sys.argv[0])
usage = progname + " stack [output_directory] initial_volume --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translational_search_step --delta=angular_step --an=angular_neighborhood --CTF --fl --aa --ref_a=S --sym=c1"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--ir", type= "int", default= 1, help="inner radius for rotational correlation > 0 (set to 1)")
parser.add_option("--ou", type= "int", default= -1, help="outer radius for rotational correlation < int(nx/2)-1 (set to the radius of the particle)")
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= "-1", help="range for translation search in x direction, search is +/xr (default 0)")
parser.add_option("--yr", type="string", default= "-1", help="range for translation search in y direction, search is +/yr (default = same as xr)")
parser.add_option("--ts", type="string", default= "1", help="step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional")
parser.add_option("--delta", type="string", default= "-1", help="angular step of reference projections during initialization step (default automatically selected based on radius of the structure.)")
parser.add_option("--an", type="string", default= "-1", help="angular neighborhood for local searches (phi and theta) (Default exhaustive searches)")
parser.add_option("--CTF", action="store_true", default=False, help="Use CTF (Default no CTF correction)")
parser.add_option("--shrink", type="float", default= 1.0, help="Reduce data size by shrink factor (default 1.0)")
parser.add_option("--snr", type="float", default= 1.0, help="Signal-to-Noise Ratio of the data (default 1.0)")
parser.add_option("--ref_a", type="string", default= "S", help="method for generating the quasi-uniformly distributed projection directions (default S)")
parser.add_option("--sym", type="string", default= "c1", help="symmetry of the refined structure")
parser.add_option("--npad", type="int", default= 2, help="padding size for 3D reconstruction (default=2)")
#options introduced for the do_volume function
parser.add_option("--fl", type="float", default=0.12, help="cut-off frequency of hyperbolic tangent low-pass Fourier filte (default 0.12)")
parser.add_option("--aa", type="float", default=0.1, help="fall-off of hyperbolic tangent low-pass Fourier filter (default 0.1)")
parser.add_option("--pwreference", type="string", default="", help="text file with a reference power spectrum (default no power spectrum adjustment)")
parser.add_option("--mask3D", type="string", default=None, help="3D mask file (default a sphere WHAT RADIUS??)")
(options, args) = parser.parse_args(sys.argv[1:])
#print( " args ",args)
if( len(args) == 3):
volinit = args[2]
masterdir = args[1]
elif(len(args) == 2):
volinit = args[1]
masterdir = ""
else:
print( "usage: " + usage)
print( "Please run '" + progname + " -h' for detailed options")
return 1
stack = args[0]
# INPUT PARAMETERS
radi = options.ou
global_def.BATCH = True
ali3d_options.ir = options.ir
ali3d_options.rs = options.rs
ali3d_options.ou = options.ou
ali3d_options.xr = options.xr
ali3d_options.yr = options.yr
ali3d_options.ts = options.ts
ali3d_options.an = "-1"
ali3d_options.sym = options.sym
ali3d_options.delta = options.delta
ali3d_options.npad = options.npad
ali3d_options.CTF = options.CTF
ali3d_options.ref_a = options.ref_a
ali3d_options.snr = options.snr
ali3d_options.mask3D = options.mask3D
ali3d_options.pwreference = "" # It will have to be turned on after exhaustive done by setting to options.pwreference
ali3d_options.fl = 0.4
ali3d_options.initfl = 0.4
ali3d_options.aa = 0.1
mpi_init(0, [])
nproc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
main_node = 0
# Get the pixel size, if none set to 1.0, and the original image size
if(myid == main_node):
total_stack = EMUtil.get_image_count(stack)
a = get_im(stack)
nxinit = a.get_xsize()
if ali3d_options.CTF:
i = a.get_attr('ctf')
pixel_size = i.apix
fq = pixel_size/fq
else:
pixel_size = 1.0
# No pixel size, fusing computed as 5 Fourier pixels
fq = 5.0/nxinit
del a
else:
total_stack = 0
nxinit = 0
pixel_size = 1.0
total_stack = bcast_number_to_all(total_stack, source_node = main_node)
pixel_size = bcast_number_to_all(pixel_size, source_node = main_node)
nxinit = bcast_number_to_all(nxinit, source_node = main_node)
if(radi < 1): radi = nxinit//2-2
elif((2*radi+2)>nxinit): ERROR("Particle radius set too large!","sxcenter_projections",1,myid)
ali3d_options.ou = radi
shrink = options.shrink
nxshrink = int(nxinit*shrink+0.5)
angular_neighborhood = "-1"
# MASTER DIRECTORY
if(myid == main_node):
print( " masterdir ",masterdir)
if( masterdir == ""):
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir = "master"+timestring
li = len(masterdir)
cmd = "{} {}".format("mkdir", masterdir)
cmdexecute(cmd)
else:
li = 0
li = mpi_bcast(li,1,MPI_INT,main_node,MPI_COMM_WORLD)[0]
if( li > 0 ):
masterdir = mpi_bcast(masterdir,li,MPI_CHAR,main_node,MPI_COMM_WORLD)
masterdir = string.join(masterdir,"")
nnxo = nxinit
# INITIALIZATION
initdir = masterdir
# This is initial setting, has to be initialized here, we do not want it to run too long.
# INITIALIZATION THAT FOLLOWS WILL HAVE TO BE CHANGED SO THE USER CAN PROVIDE INITIAL GUESS OF RESOLUTION
# If we new the initial resolution, it could be done more densely
if(options.xr == "-1"): xr = "%d"%((nnxo - (2*radi-1))//2)
else: xr = options.xr
if(options.yr == "-1"): yr = xr
else: yr = options.yr
delta = float(options.delta)
if(delta <= 0.0): delta = "%f"%round(degrees(atan(1.0/float(radi))), 2)
else: delta = "%f"%delta
paramsdict = { "stack":stack,"delta":delta, "ts":"1.0", "xr":xr, "an":angular_neighborhood, \
"center":"0", "maxit":1, "local":False,\
"lowpass":options.fl, "initialfl":0.4, "falloff":options.aa, "radius":radi, \
"nsoft":0, "delpreviousmax":True, "shrink":options.shrink, "saturatecrit":1.0, "pixercutoff":2.0,\
"refvol":volinit, "mask3D":options.mask3D}
partids = os.path.join(masterdir, "ids.txt")
partstack = os.path.join(masterdir, "paramszero.txt")
if( myid == main_node ):
write_text_file(range(total_stack), partids)
write_text_row([[0.0,0.0,0.0,0.0,0.0] for i in xrange(total_stack) ], partstack)
run3Dalignment(paramsdict, partids, partstack, initdir, 0, myid, main_node, nproc)
mpi_barrier(MPI_COMM_WORLD)
mpi_finalize()
def run3Dalignment(paramsdict, partids, partstack, outputdir, procid, myid, main_node, nproc):
# Reads from paramsdict["stack"] particles partids set parameters in partstack
# and do refinement as specified in paramsdict
#
# Will create outputdir
# Will write to outputdir output parameters: params-chunk0.txt and params-chunk1.txt
if(myid == main_node):
# Create output directory
log = Logger(BaseLogger_Files())
log.prefix = os.path.join(outputdir)
#cmd = "mkdir "+log.prefix
#cmdexecute(cmd)
log.prefix += "/"
else: log = None
mpi_barrier(MPI_COMM_WORLD)
ali3d_options.delta = paramsdict["delta"]
ali3d_options.ts = paramsdict["ts"]
ali3d_options.xr = paramsdict["xr"]
# low pass filter is applied to shrank data, so it has to be adjusted
ali3d_options.fl = paramsdict["lowpass"]/paramsdict["shrink"]
ali3d_options.initfl = paramsdict["initialfl"]/paramsdict["shrink"]
ali3d_options.aa = paramsdict["falloff"]
ali3d_options.maxit = paramsdict["maxit"]
ali3d_options.mask3D = paramsdict["mask3D"]
ali3d_options.an = paramsdict["an"]
ali3d_options.ou = paramsdict["radius"] # This is changed in ali3d_base, but the shrank value is needed in vol recons, fixt it!
shrinkage = paramsdict["shrink"]
projdata = getindexdata(paramsdict["stack"], partids, partstack, myid, nproc)
onx = projdata[0].get_xsize()
last_ring = ali3d_options.ou
if last_ring < 0: last_ring = int(onx/2) - 2
mask2D = model_circle(last_ring,onx,onx) - model_circle(ali3d_options.ir,onx,onx)
if(shrinkage < 1.0):
# get the new size
masks2D = resample(mask2D, shrinkage)
nx = masks2D.get_xsize()
masks2D = model_circle(int(last_ring*shrinkage+0.5),nx,nx) - model_circle(max(int(ali3d_options.ir*shrinkage+0.5),1),nx,nx)
nima = len(projdata)
oldshifts = [0.0,0.0]*nima
for im in xrange(nima):
#data[im].set_attr('ID', list_of_particles[im])
ctf_applied = projdata[im].get_attr_default('ctf_applied', 0)
phi,theta,psi,sx,sy = get_params_proj(projdata[im])
projdata[im] = fshift(projdata[im], sx, sy)
set_params_proj(projdata[im],[phi,theta,psi,0.0,0.0])
# For local SHC set anchor
#if(nsoft == 1 and an[0] > -1):
# set_params_proj(data[im],[phi,tetha,psi,0.0,0.0], "xform.anchor")
oldshifts[im] = [sx,sy]
if ali3d_options.CTF :
ctf_params = projdata[im].get_attr("ctf")
if ctf_applied == 0:
st = Util.infomask(projdata[im], mask2D, False)
projdata[im] -= st[0]
projdata[im] = filt_ctf(projdata[im], ctf_params)
projdata[im].set_attr('ctf_applied', 1)
if(shrinkage < 1.0):
#phi,theta,psi,sx,sy = get_params_proj(projdata[im])
projdata[im] = resample(projdata[im], shrinkage)
st = Util.infomask(projdata[im], None, True)
projdata[im] -= st[0]
st = Util.infomask(projdata[im], masks2D, True)
projdata[im] /= st[1]
#sx *= shrinkage
#sy *= shrinkage
#set_params_proj(projdata[im], [phi,theta,psi,sx,sy])
if ali3d_options.CTF :
ctf_params.apix /= shrinkage
projdata[im].set_attr('ctf', ctf_params)
else:
st = Util.infomask(projdata[im], None, True)
projdata[im] -= st[0]
st = Util.infomask(projdata[im], mask2D, True)
projdata[im] /= st[1]
del mask2D
if(shrinkage < 1.0): del masks2D
"""
if(paramsdict["delpreviousmax"]):
for i in xrange(len(projdata)):
try: projdata[i].del_attr("previousmax")
except: pass
"""
if(myid == main_node):
print_dict(paramsdict,"3D alignment parameters")
print(" => actual lowpass : "******" => actual init lowpass : "******" => PW adjustment : ",ali3d_options.pwreference)
print(" => partids : ",partids)
print(" => partstack : ",partstack)
if(ali3d_options.fl > 0.46): ERROR("Low pass filter in 3D alignment > 0.46 on the scale of shrank data","sxcenter_projections",1,myid)
# Run alignment command, it returns params per CPU
params = center_projections_3D(projdata, paramsdict["refvol"], \
ali3d_options, onx, shrinkage, \
mpi_comm = MPI_COMM_WORLD, myid = myid, main_node = main_node, log = log )
del log, projdata
params = wrap_mpi_gatherv(params, main_node, MPI_COMM_WORLD)
# store params
if(myid == main_node):
for im in xrange(nima):
params[im][0] = params[im][0]/shrinkage +oldshifts[im][0]
params[im][1] = params[im][1]/shrinkage +oldshifts[im][1]
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
print(line,"Executed successfully: ","3D alignment"," number of images:%7d"%len(params))
write_text_row(params, os.path.join(outputdir,"params.txt") )
def main():
def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
# the final ali2d parameters already combine shifts operation first and rotation operation second for parameters converted from 3D
if mirror:
m = 1
alpha, sx, sy, scalen = compose_transform2(0, s2x, s2y, 1.0, 540.0-psi, 0, 0, 1.0)
else:
m = 0
alpha, sx, sy, scalen = compose_transform2(0, s2x, s2y, 1.0, 360.0-psi, 0, 0, 1.0)
return alpha, sx, sy, m
progname = os.path.basename(sys.argv[0])
usage = progname + " prj_stack --ave2D= --var2D= --ave3D= --var3D= --img_per_grp= --fl= --aa= --sym=symmetry --CTF"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--output_dir", type="string" , default="./", help="Output directory")
parser.add_option("--ave2D", type="string" , default=False, help="Write to the disk a stack of 2D averages")
parser.add_option("--var2D", type="string" , default=False, help="Write to the disk a stack of 2D variances")
parser.add_option("--ave3D", type="string" , default=False, help="Write to the disk reconstructed 3D average")
parser.add_option("--var3D", type="string" , default=False, help="Compute 3D variability (time consuming!)")
parser.add_option("--img_per_grp", type="int" , default=100, help="Number of neighbouring projections.(Default is 100)")
parser.add_option("--no_norm", action="store_true", default=False, help="Do not use normalization.(Default is to apply normalization)")
#parser.add_option("--radius", type="int" , default=-1 , help="radius for 3D variability" )
parser.add_option("--npad", type="int" , default=2 , help="Number of time to pad the original images.(Default is 2 times padding)")
parser.add_option("--sym" , type="string" , default="c1", help="Symmetry. (Default is no symmetry)")
parser.add_option("--fl", type="float" , default=0.0, help="Low pass filter cutoff in absolute frequency (0.0 - 0.5) and is applied to decimated images. (Default - no filtration)")
parser.add_option("--aa", type="float" , default=0.02 , help="Fall off of the filter. Use default value if user has no clue about falloff (Default value is 0.02)")
parser.add_option("--CTF", action="store_true", default=False, help="Use CFT correction.(Default is no CTF correction)")
#parser.add_option("--MPI" , action="store_true", default=False, help="use MPI version")
#parser.add_option("--radiuspca", type="int" , default=-1 , help="radius for PCA" )
#parser.add_option("--iter", type="int" , default=40 , help="maximum number of iterations (stop criterion of reconstruction process)" )
#parser.add_option("--abs", type="float" , default=0.0 , help="minimum average absolute change of voxels' values (stop criterion of reconstruction process)" )
#parser.add_option("--squ", type="float" , default=0.0 , help="minimum average squared change of voxels' values (stop criterion of reconstruction process)" )
parser.add_option("--VAR" , action="store_true", default=False, help="Stack of input consists of 2D variances (Default False)")
parser.add_option("--decimate", type ="float", default=0.25, help="Image decimate rate, a number less than 1. (Default is 0.25)")
parser.add_option("--window", type ="int", default=0, help="Target image size relative to original image size. (Default value is zero.)")
#parser.add_option("--SND", action="store_true", default=False, help="compute squared normalized differences (Default False)")
#parser.add_option("--nvec", type="int" , default=0 , help="Number of eigenvectors, (Default = 0 meaning no PCA calculated)")
parser.add_option("--symmetrize", action="store_true", default=False, help="Prepare input stack for handling symmetry (Default False)")
parser.add_option("--overhead", type ="float", default=0.5, help="python overhead per CPU.")
(options,args) = parser.parse_args()
#####
from mpi import mpi_init, mpi_comm_rank, mpi_comm_size, mpi_recv, MPI_COMM_WORLD
from mpi import mpi_barrier, mpi_reduce, mpi_bcast, mpi_send, MPI_FLOAT, MPI_SUM, MPI_INT, MPI_MAX
#from mpi import *
from applications import MPI_start_end
from reconstruction import recons3d_em, recons3d_em_MPI
from reconstruction import recons3d_4nn_MPI, recons3d_4nn_ctf_MPI
from utilities import print_begin_msg, print_end_msg, print_msg
from utilities import read_text_row, get_image, get_im, wrap_mpi_send, wrap_mpi_recv
from utilities import bcast_EMData_to_all, bcast_number_to_all
from utilities import get_symt
# This is code for handling symmetries by the above program. To be incorporated. PAP 01/27/2015
from EMAN2db import db_open_dict
# Set up global variables related to bdb cache
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
# Set up global variables related to ERROR function
global_def.BATCH = True
# detect if program is running under MPI
RUNNING_UNDER_MPI = "OMPI_COMM_WORLD_SIZE" in os.environ
if RUNNING_UNDER_MPI: global_def.MPI = True
if options.output_dir =="./": current_output_dir = os.path.abspath(options.output_dir)
else: current_output_dir = options.output_dir
if options.symmetrize :
if RUNNING_UNDER_MPI:
try:
sys.argv = mpi_init(len(sys.argv), sys.argv)
try:
number_of_proc = mpi_comm_size(MPI_COMM_WORLD)
if( number_of_proc > 1 ):
ERROR("Cannot use more than one CPU for symmetry preparation","sx3dvariability",1)
except:
pass
except:
pass
if not os.path.exists(current_output_dir): os.mkdir(current_output_dir)
# Input
#instack = "Clean_NORM_CTF_start_wparams.hdf"
#instack = "bdb:data"
from logger import Logger,BaseLogger_Files
if os.path.exists(os.path.join(current_output_dir, "log.txt")): os.remove(os.path.join(current_output_dir, "log.txt"))
log_main=Logger(BaseLogger_Files())
log_main.prefix = os.path.join(current_output_dir, "./")
instack = args[0]
sym = options.sym.lower()
if( sym == "c1" ):
ERROR("There is no need to symmetrize stack for C1 symmetry","sx3dvariability",1)
line =""
for a in sys.argv:
line +=" "+a
log_main.add(line)
if(instack[:4] !="bdb:"):
#if output_dir =="./": stack = "bdb:data"
stack = "bdb:"+current_output_dir+"/data"
delete_bdb(stack)
junk = cmdexecute("sxcpy.py "+instack+" "+stack)
else: stack = instack
qt = EMUtil.get_all_attributes(stack,'xform.projection')
na = len(qt)
ts = get_symt(sym)
ks = len(ts)
angsa = [None]*na
for k in range(ks):
#Qfile = "Q%1d"%k
#if options.output_dir!="./": Qfile = os.path.join(options.output_dir,"Q%1d"%k)
Qfile = os.path.join(current_output_dir, "Q%1d"%k)
#delete_bdb("bdb:Q%1d"%k)
delete_bdb("bdb:"+Qfile)
#junk = cmdexecute("e2bdb.py "+stack+" --makevstack=bdb:Q%1d"%k)
junk = cmdexecute("e2bdb.py "+stack+" --makevstack=bdb:"+Qfile)
#DB = db_open_dict("bdb:Q%1d"%k)
DB = db_open_dict("bdb:"+Qfile)
for i in range(na):
ut = qt[i]*ts[k]
DB.set_attr(i, "xform.projection", ut)
#bt = ut.get_params("spider")
#angsa[i] = [round(bt["phi"],3)%360.0, round(bt["theta"],3)%360.0, bt["psi"], -bt["tx"], -bt["ty"]]
#write_text_row(angsa, 'ptsma%1d.txt'%k)
#junk = cmdexecute("e2bdb.py "+stack+" --makevstack=bdb:Q%1d"%k)
#junk = cmdexecute("sxheader.py bdb:Q%1d --params=xform.projection --import=ptsma%1d.txt"%(k,k))
DB.close()
#if options.output_dir =="./": delete_bdb("bdb:sdata")
delete_bdb("bdb:" + current_output_dir + "/"+"sdata")
#junk = cmdexecute("e2bdb.py . --makevstack=bdb:sdata --filt=Q")
sdata = "bdb:"+current_output_dir+"/"+"sdata"
print(sdata)
junk = cmdexecute("e2bdb.py " + current_output_dir +" --makevstack="+sdata +" --filt=Q")
#junk = cmdexecute("ls EMAN2DB/sdata*")
#a = get_im("bdb:sdata")
a = get_im(sdata)
a.set_attr("variabilitysymmetry",sym)
#a.write_image("bdb:sdata")
a.write_image(sdata)
else:
from fundamentals import window2d
sys.argv = mpi_init(len(sys.argv), sys.argv)
myid = mpi_comm_rank(MPI_COMM_WORLD)
number_of_proc = mpi_comm_size(MPI_COMM_WORLD)
main_node = 0
shared_comm = mpi_comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL)
myid_on_node = mpi_comm_rank(shared_comm)
no_of_processes_per_group = mpi_comm_size(shared_comm)
masters_from_groups_vs_everything_else_comm = mpi_comm_split(MPI_COMM_WORLD, main_node == myid_on_node, myid_on_node)
color, no_of_groups, balanced_processor_load_on_nodes = get_colors_and_subsets(main_node, MPI_COMM_WORLD, myid, \
shared_comm, myid_on_node, masters_from_groups_vs_everything_else_comm)
overhead_loading = options.overhead*number_of_proc
#memory_per_node = options.memory_per_node
#if memory_per_node == -1.: memory_per_node = 2.*no_of_processes_per_group
keepgoing = 1
current_window = options.window
current_decimate = options.decimate
if len(args) == 1: stack = args[0]
else:
print(( "usage: " + usage))
print(( "Please run '" + progname + " -h' for detailed options"))
return 1
t0 = time()
# obsolete flags
options.MPI = True
#options.nvec = 0
options.radiuspca = -1
options.iter = 40
options.abs = 0.0
options.squ = 0.0
if options.fl > 0.0 and options.aa == 0.0:
ERROR("Fall off has to be given for the low-pass filter", "sx3dvariability", 1, myid)
#if options.VAR and options.SND:
# ERROR("Only one of var and SND can be set!", "sx3dvariability", myid)
if options.VAR and (options.ave2D or options.ave3D or options.var2D):
ERROR("When VAR is set, the program cannot output ave2D, ave3D or var2D", "sx3dvariability", 1, myid)
#if options.SND and (options.ave2D or options.ave3D):
# ERROR("When SND is set, the program cannot output ave2D or ave3D", "sx3dvariability", 1, myid)
#if options.nvec > 0 :
# ERROR("PCA option not implemented", "sx3dvariability", 1, myid)
#if options.nvec > 0 and options.ave3D == None:
# ERROR("When doing PCA analysis, one must set ave3D", "sx3dvariability", 1, myid)
if current_decimate>1.0 or current_decimate<0.0:
ERROR("Decimate rate should be a value between 0.0 and 1.0", "sx3dvariability", 1, myid)
if current_window < 0.0:
ERROR("Target window size should be always larger than zero", "sx3dvariability", 1, myid)
if myid == main_node:
img = get_image(stack, 0)
nx = img.get_xsize()
ny = img.get_ysize()
if(min(nx, ny) < current_window): keepgoing = 0
keepgoing = bcast_number_to_all(keepgoing, main_node, MPI_COMM_WORLD)
if keepgoing == 0: ERROR("The target window size cannot be larger than the size of decimated image", "sx3dvariability", 1, myid)
import string
options.sym = options.sym.lower()
# if global_def.CACHE_DISABLE:
# from utilities import disable_bdb_cache
# disable_bdb_cache()
# global_def.BATCH = True
if myid == main_node:
if not os.path.exists(current_output_dir): os.mkdir(current_output_dir)# Never delete output_dir in the program!
img_per_grp = options.img_per_grp
#nvec = options.nvec
radiuspca = options.radiuspca
from logger import Logger,BaseLogger_Files
#if os.path.exists(os.path.join(options.output_dir, "log.txt")): os.remove(os.path.join(options.output_dir, "log.txt"))
log_main=Logger(BaseLogger_Files())
log_main.prefix = os.path.join(current_output_dir, "./")
if myid == main_node:
line = ""
for a in sys.argv: line +=" "+a
log_main.add(line)
log_main.add("-------->>>Settings given by all options<<<-------")
log_main.add("Symmetry : %s"%options.sym)
log_main.add("Input stack : %s"%stack)
log_main.add("Output_dir : %s"%current_output_dir)
if options.ave3D: log_main.add("Ave3d : %s"%options.ave3D)
if options.var3D: log_main.add("Var3d : %s"%options.var3D)
if options.ave2D: log_main.add("Ave2D : %s"%options.ave2D)
if options.var2D: log_main.add("Var2D : %s"%options.var2D)
if options.VAR: log_main.add("VAR : True")
else: log_main.add("VAR : False")
if options.CTF: log_main.add("CTF correction : True ")
else: log_main.add("CTF correction : False ")
log_main.add("Image per group : %5d"%options.img_per_grp)
log_main.add("Image decimate rate : %4.3f"%current_decimate)
log_main.add("Low pass filter : %4.3f"%options.fl)
current_fl = options.fl
if current_fl == 0.0: current_fl = 0.5
log_main.add("Current low pass filter is equivalent to cutoff frequency %4.3f for original image size"%round((current_fl*current_decimate),3))
log_main.add("Window size : %5d "%current_window)
log_main.add("sx3dvariability begins")
symbaselen = 0
if myid == main_node:
nima = EMUtil.get_image_count(stack)
img = get_image(stack)
nx = img.get_xsize()
ny = img.get_ysize()
nnxo = nx
nnyo = ny
if options.sym != "c1" :
imgdata = get_im(stack)
try:
i = imgdata.get_attr("variabilitysymmetry").lower()
if(i != options.sym):
ERROR("The symmetry provided does not agree with the symmetry of the input stack", "sx3dvariability", 1, myid)
except:
ERROR("Input stack is not prepared for symmetry, please follow instructions", "sx3dvariability", 1, myid)
from utilities import get_symt
i = len(get_symt(options.sym))
if((nima/i)*i != nima):
ERROR("The length of the input stack is incorrect for symmetry processing", "sx3dvariability", 1, myid)
symbaselen = nima/i
else: symbaselen = nima
else:
nima = 0
nx = 0
ny = 0
nnxo = 0
nnyo = 0
nima = bcast_number_to_all(nima)
nx = bcast_number_to_all(nx)
ny = bcast_number_to_all(ny)
nnxo = bcast_number_to_all(nnxo)
nnyo = bcast_number_to_all(nnyo)
if current_window > max(nx, ny):
ERROR("Window size is larger than the original image size", "sx3dvariability", 1)
if current_decimate == 1.:
if current_window !=0:
nx = current_window
ny = current_window
else:
if current_window == 0:
nx = int(nx*current_decimate+0.5)
ny = int(ny*current_decimate+0.5)
else:
nx = int(current_window*current_decimate+0.5)
ny = nx
symbaselen = bcast_number_to_all(symbaselen)
# check FFT prime number
from fundamentals import smallprime
is_fft_friendly = (nx == smallprime(nx))
if not is_fft_friendly:
if myid == main_node:
log_main.add("The target image size is not a product of small prime numbers")
log_main.add("Program adjusts the input settings!")
### two cases
if current_decimate == 1.:
nx = smallprime(nx)
ny = nx
current_window = nx # update
if myid == main_node:
log_main.add("The window size is updated to %d."%current_window)
else:
if current_window == 0:
nx = smallprime(int(nx*current_decimate+0.5))
current_decimate = float(nx)/nnxo
ny = nx
if (myid == main_node):
log_main.add("The decimate rate is updated to %f."%current_decimate)
else:
nx = smallprime(int(current_window*current_decimate+0.5))
ny = nx
current_window = int(nx/current_decimate+0.5)
if (myid == main_node):
log_main.add("The window size is updated to %d."%current_window)
if myid == main_node:
log_main.add("The target image size is %d"%nx)
if radiuspca == -1: radiuspca = nx/2-2
if myid == main_node: log_main.add("%-70s: %d\n"%("Number of projection", nima))
img_begin, img_end = MPI_start_end(nima, number_of_proc, myid)
"""
if options.SND:
from projection import prep_vol, prgs
from statistics import im_diff
from utilities import get_im, model_circle, get_params_proj, set_params_proj
from utilities import get_ctf, generate_ctf
from filter import filt_ctf
imgdata = EMData.read_images(stack, range(img_begin, img_end))
if options.CTF:
vol = recons3d_4nn_ctf_MPI(myid, imgdata, 1.0, symmetry=options.sym, npad=options.npad, xysize=-1, zsize=-1)
else:
vol = recons3d_4nn_MPI(myid, imgdata, symmetry=options.sym, npad=options.npad, xysize=-1, zsize=-1)
bcast_EMData_to_all(vol, myid)
volft, kb = prep_vol(vol)
mask = model_circle(nx/2-2, nx, ny)
varList = []
for i in xrange(img_begin, img_end):
phi, theta, psi, s2x, s2y = get_params_proj(imgdata[i-img_begin])
ref_prj = prgs(volft, kb, [phi, theta, psi, -s2x, -s2y])
if options.CTF:
ctf_params = get_ctf(imgdata[i-img_begin])
ref_prj = filt_ctf(ref_prj, generate_ctf(ctf_params))
diff, A, B = im_diff(ref_prj, imgdata[i-img_begin], mask)
diff2 = diff*diff
set_params_proj(diff2, [phi, theta, psi, s2x, s2y])
varList.append(diff2)
mpi_barrier(MPI_COMM_WORLD)
"""
if options.VAR: # 2D variance images have no shifts
#varList = EMData.read_images(stack, range(img_begin, img_end))
from EMAN2 import Region
for index_of_particle in range(img_begin,img_end):
image = get_im(stack, index_of_proj)
if current_window > 0: varList.append(fdecimate(window2d(image,current_window,current_window), nx,ny))
else: varList.append(fdecimate(image, nx,ny))
else:
from utilities import bcast_number_to_all, bcast_list_to_all, send_EMData, recv_EMData
from utilities import set_params_proj, get_params_proj, params_3D_2D, get_params2D, set_params2D, compose_transform2
from utilities import model_blank, nearest_proj, model_circle, write_text_row, wrap_mpi_gatherv
from applications import pca
from statistics import avgvar, avgvar_ctf, ccc
from filter import filt_tanl
from morphology import threshold, square_root
from projection import project, prep_vol, prgs
from sets import Set
from utilities import wrap_mpi_recv, wrap_mpi_bcast, wrap_mpi_send
import numpy as np
if myid == main_node:
t1 = time()
proj_angles = []
aveList = []
tab = EMUtil.get_all_attributes(stack, 'xform.projection')
for i in range(nima):
t = tab[i].get_params('spider')
phi = t['phi']
theta = t['theta']
psi = t['psi']
x = theta
if x > 90.0: x = 180.0 - x
x = x*10000+psi
proj_angles.append([x, t['phi'], t['theta'], t['psi'], i])
t2 = time()
log_main.add( "%-70s: %d\n"%("Number of neighboring projections", img_per_grp))
log_main.add("...... Finding neighboring projections\n")
log_main.add( "Number of images per group: %d"%img_per_grp)
log_main.add( "Now grouping projections")
proj_angles.sort()
proj_angles_list = np.full((nima, 4), 0.0, dtype=np.float32)
for i in range(nima):
proj_angles_list[i][0] = proj_angles[i][1]
proj_angles_list[i][1] = proj_angles[i][2]
proj_angles_list[i][2] = proj_angles[i][3]
proj_angles_list[i][3] = proj_angles[i][4]
else: proj_angles_list = 0
proj_angles_list = wrap_mpi_bcast(proj_angles_list, main_node, MPI_COMM_WORLD)
proj_angles = []
for i in range(nima):
proj_angles.append([proj_angles_list[i][0], proj_angles_list[i][1], proj_angles_list[i][2], int(proj_angles_list[i][3])])
del proj_angles_list
proj_list, mirror_list = nearest_proj(proj_angles, img_per_grp, range(img_begin, img_end))
all_proj = Set()
for im in proj_list:
for jm in im:
all_proj.add(proj_angles[jm][3])
all_proj = list(all_proj)
index = {}
for i in range(len(all_proj)): index[all_proj[i]] = i
mpi_barrier(MPI_COMM_WORLD)
if myid == main_node:
log_main.add("%-70s: %.2f\n"%("Finding neighboring projections lasted [s]", time()-t2))
log_main.add("%-70s: %d\n"%("Number of groups processed on the main node", len(proj_list)))
log_main.add("Grouping projections took: %12.1f [m]"%((time()-t2)/60.))
log_main.add("Number of groups on main node: ", len(proj_list))
mpi_barrier(MPI_COMM_WORLD)
if myid == main_node:
log_main.add("...... Calculating the stack of 2D variances \n")
# Memory estimation. There are two memory consumption peaks
# peak 1. Compute ave, var;
# peak 2. Var volume reconstruction;
# proj_params = [0.0]*(nima*5)
aveList = []
varList = []
#if nvec > 0: eigList = [[] for i in range(nvec)]
dnumber = len(all_proj)# all neighborhood set for assigned to myid
pnumber = len(proj_list)*2. + img_per_grp # aveList and varList
tnumber = dnumber+pnumber
vol_size2 = nx**3*4.*8/1.e9
vol_size1 = 2.*nnxo**3*4.*8/1.e9
proj_size = nnxo*nnyo*len(proj_list)*4.*2./1.e9 # both aveList and varList
orig_data_size = nnxo*nnyo*4.*tnumber/1.e9
reduced_data_size = nx*nx*4.*tnumber/1.e9
full_data = np.full((number_of_proc, 2), -1., dtype=np.float16)
full_data[myid] = orig_data_size, reduced_data_size
if myid != main_node: wrap_mpi_send(full_data, main_node, MPI_COMM_WORLD)
if myid == main_node:
for iproc in range(number_of_proc):
if iproc != main_node:
dummy = wrap_mpi_recv(iproc, MPI_COMM_WORLD)
full_data[np.where(dummy>-1)] = dummy[np.where(dummy>-1)]
del dummy
mpi_barrier(MPI_COMM_WORLD)
full_data = wrap_mpi_bcast(full_data, main_node, MPI_COMM_WORLD)
# find the CPU with heaviest load
minindx = np.argsort(full_data, 0)
heavy_load_myid = minindx[-1][1]
total_mem = sum(full_data)
if myid == main_node:
if current_window == 0:
log_main.add("Nx: current image size = %d. Decimated by %f from %d"%(nx, current_decimate, nnxo))
else:
log_main.add("Nx: current image size = %d. Windowed to %d, and decimated by %f from %d"%(nx, current_window, current_decimate, nnxo))
log_main.add("Nproj: number of particle images.")
log_main.add("Navg: number of 2D average images.")
log_main.add("Nvar: number of 2D variance images.")
log_main.add("Img_per_grp: user defined image per group for averaging = %d"%img_per_grp)
log_main.add("Overhead: total python overhead memory consumption = %f"%overhead_loading)
log_main.add("Total memory) = 4.0*nx^2*(nproj + navg +nvar+ img_per_grp)/1.0e9 + overhead: %12.3f [GB]"%\
(total_mem[1] + overhead_loading))
del full_data
mpi_barrier(MPI_COMM_WORLD)
if myid == heavy_load_myid:
log_main.add("Begin reading and preprocessing images on processor. Wait... ")
ttt = time()
#imgdata = EMData.read_images(stack, all_proj)
imgdata = [ None for im in range(len(all_proj))]
for index_of_proj in range(len(all_proj)):
#image = get_im(stack, all_proj[index_of_proj])
if( current_window > 0): imgdata[index_of_proj] = fdecimate(window2d(get_im(stack, all_proj[index_of_proj]),current_window,current_window), nx, ny)
else: imgdata[index_of_proj] = fdecimate(get_im(stack, all_proj[index_of_proj]), nx, ny)
if (current_decimate> 0.0 and options.CTF):
ctf = imgdata[index_of_proj].get_attr("ctf")
ctf.apix = ctf.apix/current_decimate
imgdata[index_of_proj].set_attr("ctf", ctf)
if myid == heavy_load_myid and index_of_proj%100 == 0:
log_main.add(" ...... %6.2f%% "%(index_of_proj/float(len(all_proj))*100.))
mpi_barrier(MPI_COMM_WORLD)
if myid == heavy_load_myid:
log_main.add("All_proj preprocessing cost %7.2f m"%((time()-ttt)/60.))
log_main.add("Wait untill reading on all CPUs done...")
'''
imgdata2 = EMData.read_images(stack, range(img_begin, img_end))
if options.fl > 0.0:
for k in xrange(len(imgdata2)):
imgdata2[k] = filt_tanl(imgdata2[k], options.fl, options.aa)
if options.CTF:
vol = recons3d_4nn_ctf_MPI(myid, imgdata2, 1.0, symmetry=options.sym, npad=options.npad, xysize=-1, zsize=-1)
else:
vol = recons3d_4nn_MPI(myid, imgdata2, symmetry=options.sym, npad=options.npad, xysize=-1, zsize=-1)
if myid == main_node:
vol.write_image("vol_ctf.hdf")
print_msg("Writing to the disk volume reconstructed from averages as : %s\n"%("vol_ctf.hdf"))
del vol, imgdata2
mpi_barrier(MPI_COMM_WORLD)
'''
from applications import prepare_2d_forPCA
from utilities import model_blank
from EMAN2 import Transform
if not options.no_norm:
mask = model_circle(nx/2-2, nx, nx)
if options.CTF:
from utilities import pad
from filter import filt_ctf
from filter import filt_tanl
if myid == heavy_load_myid:
log_main.add("Start computing 2D aveList and varList. Wait...")
ttt = time()
inner=nx//2-4
outer=inner+2
xform_proj_for_2D = [ None for i in range(len(proj_list))]
for i in range(len(proj_list)):
ki = proj_angles[proj_list[i][0]][3]
if ki >= symbaselen: continue
mi = index[ki]
dpar = Util.get_transform_params(imgdata[mi], "xform.projection", "spider")
phiM, thetaM, psiM, s2xM, s2yM = dpar["phi"],dpar["theta"],dpar["psi"],-dpar["tx"]*current_decimate,-dpar["ty"]*current_decimate
grp_imgdata = []
for j in range(img_per_grp):
mj = index[proj_angles[proj_list[i][j]][3]]
cpar = Util.get_transform_params(imgdata[mj], "xform.projection", "spider")
alpha, sx, sy, mirror = params_3D_2D_NEW(cpar["phi"], cpar["theta"],cpar["psi"], -cpar["tx"]*current_decimate, -cpar["ty"]*current_decimate, mirror_list[i][j])
if thetaM <= 90:
if mirror == 0: alpha, sx, sy, scale = compose_transform2(alpha, sx, sy, 1.0, phiM - cpar["phi"], 0.0, 0.0, 1.0)
else: alpha, sx, sy, scale = compose_transform2(alpha, sx, sy, 1.0, 180-(phiM - cpar["phi"]), 0.0, 0.0, 1.0)
else:
if mirror == 0: alpha, sx, sy, scale = compose_transform2(alpha, sx, sy, 1.0, -(phiM- cpar["phi"]), 0.0, 0.0, 1.0)
else: alpha, sx, sy, scale = compose_transform2(alpha, sx, sy, 1.0, -(180-(phiM - cpar["phi"])), 0.0, 0.0, 1.0)
imgdata[mj].set_attr("xform.align2d", Transform({"type":"2D","alpha":alpha,"tx":sx,"ty":sy,"mirror":mirror,"scale":1.0}))
grp_imgdata.append(imgdata[mj])
if not options.no_norm:
for k in range(img_per_grp):
ave, std, minn, maxx = Util.infomask(grp_imgdata[k], mask, False)
grp_imgdata[k] -= ave
grp_imgdata[k] /= std
if options.fl > 0.0:
for k in range(img_per_grp):
grp_imgdata[k] = filt_tanl(grp_imgdata[k], options.fl, options.aa)
# Because of background issues, only linear option works.
if options.CTF: ave, var = aves_wiener(grp_imgdata, SNR = 1.0e5, interpolation_method = "linear")
else: ave, var = ave_var(grp_imgdata)
# Switch to std dev
# threshold is not really needed,it is just in case due to numerical accuracy something turns out negative.
var = square_root(threshold(var))
set_params_proj(ave, [phiM, thetaM, 0.0, 0.0, 0.0])
set_params_proj(var, [phiM, thetaM, 0.0, 0.0, 0.0])
aveList.append(ave)
varList.append(var)
xform_proj_for_2D[i] = [phiM, thetaM, 0.0, 0.0, 0.0]
'''
if nvec > 0:
eig = pca(input_stacks=grp_imgdata, subavg="", mask_radius=radiuspca, nvec=nvec, incore=True, shuffle=False, genbuf=True)
for k in range(nvec):
set_params_proj(eig[k], [phiM, thetaM, 0.0, 0.0, 0.0])
eigList[k].append(eig[k])
"""
if myid == 0 and i == 0:
for k in xrange(nvec):
eig[k].write_image("eig.hdf", k)
"""
'''
if (myid == heavy_load_myid) and (i%100 == 0):
log_main.add(" ......%6.2f%% "%(i/float(len(proj_list))*100.))
del imgdata, grp_imgdata, cpar, dpar, all_proj, proj_angles, index
if not options.no_norm: del mask
if myid == main_node: del tab
# At this point, all averages and variances are computed
mpi_barrier(MPI_COMM_WORLD)
if (myid == heavy_load_myid):
log_main.add("Computing aveList and varList took %12.1f [m]"%((time()-ttt)/60.))
xform_proj_for_2D = wrap_mpi_gatherv(xform_proj_for_2D, main_node, MPI_COMM_WORLD)
if (myid == main_node):
write_text_row(xform_proj_for_2D, os.path.join(current_output_dir, "params.txt"))
del xform_proj_for_2D
mpi_barrier(MPI_COMM_WORLD)
if options.ave2D:
from fundamentals import fpol
from applications import header
if myid == main_node:
log_main.add("Compute ave2D ... ")
km = 0
for i in range(number_of_proc):
if i == main_node :
for im in range(len(aveList)):
aveList[im].write_image(os.path.join(current_output_dir, options.ave2D), km)
km += 1
else:
nl = mpi_recv(1, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
nl = int(nl[0])
for im in range(nl):
ave = recv_EMData(i, im+i+70000)
"""
nm = mpi_recv(1, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
nm = int(nm[0])
members = mpi_recv(nm, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
ave.set_attr('members', map(int, members))
members = mpi_recv(nm, MPI_FLOAT, i, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
ave.set_attr('pix_err', map(float, members))
members = mpi_recv(3, MPI_FLOAT, i, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
ave.set_attr('refprojdir', map(float, members))
"""
tmpvol=fpol(ave, nx, nx,1)
tmpvol.write_image(os.path.join(current_output_dir, options.ave2D), km)
km += 1
else:
mpi_send(len(aveList), 1, MPI_INT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
for im in range(len(aveList)):
send_EMData(aveList[im], main_node,im+myid+70000)
"""
members = aveList[im].get_attr('members')
mpi_send(len(members), 1, MPI_INT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
mpi_send(members, len(members), MPI_INT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
members = aveList[im].get_attr('pix_err')
mpi_send(members, len(members), MPI_FLOAT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
try:
members = aveList[im].get_attr('refprojdir')
mpi_send(members, 3, MPI_FLOAT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
except:
mpi_send([-999.0,-999.0,-999.0], 3, MPI_FLOAT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
"""
if myid == main_node:
header(os.path.join(current_output_dir, options.ave2D), params='xform.projection', fimport = os.path.join(current_output_dir, "params.txt"))
mpi_barrier(MPI_COMM_WORLD)
if options.ave3D:
from fundamentals import fpol
t5 = time()
if myid == main_node: log_main.add("Reconstruct ave3D ... ")
ave3D = recons3d_4nn_MPI(myid, aveList, symmetry=options.sym, npad=options.npad)
bcast_EMData_to_all(ave3D, myid)
if myid == main_node:
if current_decimate != 1.0: ave3D = resample(ave3D, 1./current_decimate)
ave3D = fpol(ave3D, nnxo, nnxo, nnxo) # always to the orignal image size
set_pixel_size(ave3D, 1.0)
ave3D.write_image(os.path.join(current_output_dir, options.ave3D))
log_main.add("Ave3D reconstruction took %12.1f [m]"%((time()-t5)/60.0))
log_main.add("%-70s: %s\n"%("The reconstructed ave3D is saved as ", options.ave3D))
mpi_barrier(MPI_COMM_WORLD)
del ave, var, proj_list, stack, alpha, sx, sy, mirror, aveList
'''
if nvec > 0:
for k in range(nvec):
if myid == main_node:log_main.add("Reconstruction eigenvolumes", k)
cont = True
ITER = 0
mask2d = model_circle(radiuspca, nx, nx)
while cont:
#print "On node %d, iteration %d"%(myid, ITER)
eig3D = recons3d_4nn_MPI(myid, eigList[k], symmetry=options.sym, npad=options.npad)
bcast_EMData_to_all(eig3D, myid, main_node)
if options.fl > 0.0:
eig3D = filt_tanl(eig3D, options.fl, options.aa)
if myid == main_node:
eig3D.write_image(os.path.join(options.outpout_dir, "eig3d_%03d.hdf"%(k, ITER)))
Util.mul_img( eig3D, model_circle(radiuspca, nx, nx, nx) )
eig3Df, kb = prep_vol(eig3D)
del eig3D
cont = False
icont = 0
for l in range(len(eigList[k])):
phi, theta, psi, s2x, s2y = get_params_proj(eigList[k][l])
proj = prgs(eig3Df, kb, [phi, theta, psi, s2x, s2y])
cl = ccc(proj, eigList[k][l], mask2d)
if cl < 0.0:
icont += 1
cont = True
eigList[k][l] *= -1.0
u = int(cont)
u = mpi_reduce([u], 1, MPI_INT, MPI_MAX, main_node, MPI_COMM_WORLD)
icont = mpi_reduce([icont], 1, MPI_INT, MPI_SUM, main_node, MPI_COMM_WORLD)
if myid == main_node:
u = int(u[0])
log_main.add(" Eigenvector: ",k," number changed ",int(icont[0]))
else: u = 0
u = bcast_number_to_all(u, main_node)
cont = bool(u)
ITER += 1
del eig3Df, kb
mpi_barrier(MPI_COMM_WORLD)
del eigList, mask2d
'''
if options.ave3D: del ave3D
if options.var2D:
from fundamentals import fpol
from applications import header
if myid == main_node:
log_main.add("Compute var2D...")
km = 0
for i in range(number_of_proc):
if i == main_node :
for im in range(len(varList)):
tmpvol=fpol(varList[im], nx, nx,1)
tmpvol.write_image(os.path.join(current_output_dir, options.var2D), km)
km += 1
else:
nl = mpi_recv(1, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
nl = int(nl[0])
for im in range(nl):
ave = recv_EMData(i, im+i+70000)
tmpvol=fpol(ave, nx, nx,1)
tmpvol.write_image(os.path.join(current_output_dir, options.var2D), km)
km += 1
else:
mpi_send(len(varList), 1, MPI_INT, main_node, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
for im in range(len(varList)):
send_EMData(varList[im], main_node, im+myid+70000)# What with the attributes??
mpi_barrier(MPI_COMM_WORLD)
if myid == main_node:
from applications import header
header(os.path.join(current_output_dir, options.var2D), params = 'xform.projection',fimport = os.path.join(current_output_dir, "params.txt"))
mpi_barrier(MPI_COMM_WORLD)
if options.var3D:
if myid == main_node: log_main.add("Reconstruct var3D ...")
t6 = time()
# radiusvar = options.radius
# if( radiusvar < 0 ): radiusvar = nx//2 -3
res = recons3d_4nn_MPI(myid, varList, symmetry = options.sym, npad=options.npad)
#res = recons3d_em_MPI(varList, vol_stack, options.iter, radiusvar, options.abs, True, options.sym, options.squ)
if myid == main_node:
from fundamentals import fpol
if current_decimate != 1.0: res = resample(res, 1./current_decimate)
res = fpol(res, nnxo, nnxo, nnxo)
set_pixel_size(res, 1.0)
res.write_image(os.path.join(current_output_dir, options.var3D))
log_main.add("%-70s: %s\n"%("The reconstructed var3D is saved as ", options.var3D))
log_main.add("Var3D reconstruction took %f12.1 [m]"%((time()-t6)/60.0))
log_main.add("Total computation time %f12.1 [m]"%((time()-t0)/60.0))
log_main.add("sx3dvariability finishes")
from mpi import mpi_finalize
mpi_finalize()
if RUNNING_UNDER_MPI: global_def.MPI = False
global_def.BATCH = False
def found_outliers(list_of_projection_indices, outlier_percentile, rviper_iter, masterdir, bdb_stack_location,
outlier_index_threshold_method, angle_threshold):
# sxheader.py bdb:nj --consecutive --params=OID
import numpy as np
mainoutputdir = masterdir + DIR_DELIM + NAME_OF_MAIN_DIR + ("%03d" + DIR_DELIM) %(rviper_iter)
# if this data analysis step was already performed in the past then return
for check_run in list_of_projection_indices:
if not (os.path.exists(mainoutputdir + DIR_DELIM + NAME_OF_RUN_DIR + "%03d"%(check_run) + DIR_DELIM + "rotated_reduced_params.txt")):
break
else:
return
print "identify_outliers"
projs = []
for i1 in list_of_projection_indices:
projs.append(read_text_row(mainoutputdir + NAME_OF_RUN_DIR + "%03d"%(i1) + DIR_DELIM + "params.txt"))
# ti1, ti3, out = find_common_subset(projs, 1.0)
subset, avg_diff_per_image, rotated_params = find_common_subset(projs, target_threshold = 0)
# subset, avg_diff_per_image, rotated_params = find_common_subset(projs, target_threshold = 1.0)
error_values_and_indices = []
for i in xrange(len(avg_diff_per_image)):
error_values_and_indices.append([avg_diff_per_image[i], i])
del subset, avg_diff_per_image
error_values_and_indices.sort()
if outlier_index_threshold_method == "discontinuity_in_derivative":
outlier_index_threshold = find_index_of_discontinuity_in_derivative([i[0] for i in error_values_and_indices],
list_of_projection_indices, mainoutputdir, outlier_percentile)
elif outlier_index_threshold_method == "percentile":
outlier_index_threshold = outlier_percentile * (len(error_values_and_indices) - 1)/ 100.0
elif outlier_index_threshold_method == "angle_measure":
error_values = [i[0] for i in error_values_and_indices]
outlier_index_threshold = min(range(len(error_values)), key=lambda i: abs(error_values[i]-angle_threshold))
elif outlier_index_threshold_method == "use all images":
outlier_index_threshold = len(error_values_and_indices)
index_keep_images = [i[1] for i in error_values_and_indices[:outlier_index_threshold]]
index_outliers = [i[1] for i in error_values_and_indices[outlier_index_threshold:]]
# print "error_values_and_indices: %f"%error_values_and_indices
print "index_outliers: ", index_outliers
import copy
reversed_sorted_index_outliers = copy.deepcopy(index_outliers)
reversed_sorted_index_outliers.sort(reverse=True)
for k in xrange(len(projs)):
for l in reversed_sorted_index_outliers:
del rotated_params[k][l]
index_outliers.sort()
index_keep_images.sort()
write_text_file(index_outliers, mainoutputdir + "this_iteration_index_outliers.txt")
write_text_file(index_keep_images, mainoutputdir + "this_iteration_index_keep_images.txt")
#if len(index_outliers) < 3:
#return False
if len(index_outliers) > 0:
cmd = "{} {} {} {}".format("e2bdb.py ", bdb_stack_location + "_%03d"%(rviper_iter - 1), "--makevstack=" + bdb_stack_location + "_outliers_%03d"%(rviper_iter), "--list=" + mainoutputdir + "this_iteration_index_outliers.txt")
cmdexecute(cmd)
cmd = "{} {} {} {}".format("e2bdb.py ", bdb_stack_location + "_%03d"%(rviper_iter - 1), "--makevstack=" + bdb_stack_location + "_%03d"%(rviper_iter), "--list=" + mainoutputdir + "this_iteration_index_keep_images.txt")
cmdexecute(cmd)
dat = EMData.read_images(bdb_stack_location + "_%03d"%(rviper_iter - 1))
write_text_file([dat[i].get_attr("original_image_index") for i in index_outliers],mainoutputdir + "index_outliers.txt")
write_text_file([dat[i].get_attr("original_image_index") for i in index_keep_images],mainoutputdir + "index_keep_images.txt")
print "index_outliers:: " + str(index_outliers)
# write rotated param files
for i1 in range(len(list_of_projection_indices)):
write_text_row(rotated_params[i1], mainoutputdir + NAME_OF_RUN_DIR + "%03d"%(list_of_projection_indices[i1]) + DIR_DELIM + "rotated_reduced_params.txt")
return True
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():
from utilities import get_input_from_string
progname = os.path.basename(sys.argv[0])
usage = (
progname
+ " stack output_average --radius=particle_radius --xr=xr --yr=yr --ts=ts --thld_err=thld_err --num_ali=num_ali --fl=fl --aa=aa --CTF --verbose --stables"
)
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--radius", type="int", default=-1, help=" particle radius for alignment")
parser.add_option(
"--xr",
type="string",
default="2 1",
help="range for translation search in x direction, search is +/xr (default 2,1)",
)
parser.add_option(
"--yr",
type="string",
default="-1",
help="range for translation search in y direction, search is +/yr (default = same as xr)",
)
parser.add_option(
"--ts",
type="string",
default="1 0.5",
help="step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional (default: 1,0.5)",
)
parser.add_option("--thld_err", type="float", default=0.75, help="threshld of pixel error (default = 0.75)")
parser.add_option(
"--num_ali", type="int", default=5, help="number of alignments performed for stability (default = 5)"
)
parser.add_option("--maxit", type="int", default=30, help="number of iterations for each xr (default = 30)")
parser.add_option(
"--fl",
type="float",
default=0.3,
help="cut-off frequency of hyperbolic tangent low-pass Fourier filter (default = 0.3)",
)
parser.add_option(
"--aa", type="float", default=0.2, help="fall-off of hyperbolic tangent low-pass Fourier filter (default = 0.2)"
)
parser.add_option("--CTF", action="store_true", default=False, help="Use CTF correction during the alignment ")
parser.add_option(
"--verbose", action="store_true", default=False, help="print individual pixel error (default = False)"
)
parser.add_option(
"--stables",
action="store_true",
default=False,
help="output the stable particles number in file (default = False)",
)
parser.add_option(
"--method", type="string", default=" ", help="SHC (standard method is default when flag is ommitted)"
)
(options, args) = parser.parse_args()
if len(args) != 1 and len(args) != 2:
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options"
else:
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
from applications import within_group_refinement, ali2d_ras
from pixel_error import multi_align_stability
from utilities import write_text_file, write_text_row
global_def.BATCH = True
xrng = get_input_from_string(options.xr)
if options.yr == "-1":
yrng = xrng
else:
yrng = get_input_from_string(options.yr)
step = get_input_from_string(options.ts)
class_data = EMData.read_images(args[0])
nx = class_data[0].get_xsize()
ou = options.radius
num_ali = options.num_ali
if ou == -1:
ou = nx / 2 - 2
from utilities import model_circle, get_params2D, set_params2D
mask = model_circle(ou, nx, nx)
if options.CTF:
from filter import filt_ctf
for im in xrange(len(class_data)):
# Flip phases
class_data[im] = filt_ctf(class_data[im], class_data[im].get_attr("ctf"), binary=1)
for im in class_data:
im.set_attr("previousmax", -1.0e10)
try:
t = im.get_attr("xform.align2d") # if they are there, no need to set them!
except:
try:
t = im.get_attr("xform.projection")
d = t.get_params("spider")
set_params2D(im, [0.0, -d["tx"], -d["ty"], 0, 1.0])
except:
set_params2D(im, [0.0, 0.0, 0.0, 0, 1.0])
all_ali_params = []
for ii in xrange(num_ali):
ali_params = []
if options.verbose:
ALPHA = []
SX = []
SY = []
MIRROR = []
if xrng[0] == 0.0 and yrng[0] == 0.0:
avet = ali2d_ras(
class_data,
randomize=True,
ir=1,
ou=ou,
rs=1,
step=1.0,
dst=90.0,
maxit=options.maxit,
check_mirror=True,
FH=options.fl,
FF=options.aa,
)
else:
avet = within_group_refinement(
class_data,
mask,
True,
1,
ou,
1,
xrng,
yrng,
step,
90.0,
maxit=options.maxit,
FH=options.fl,
FF=options.aa,
method=options.method,
)
from utilities import info
# print " avet ",info(avet)
for im in class_data:
alpha, sx, sy, mirror, scale = get_params2D(im)
ali_params.extend([alpha, sx, sy, mirror])
if options.verbose:
ALPHA.append(alpha)
SX.append(sx)
SY.append(sy)
MIRROR.append(mirror)
all_ali_params.append(ali_params)
if options.verbose:
write_text_file([ALPHA, SX, SY, MIRROR], "ali_params_run_%d" % ii)
"""
avet = class_data[0]
from utilities import read_text_file
all_ali_params = []
for ii in xrange(5):
temp = read_text_file( "ali_params_run_%d"%ii,-1)
uuu = []
for k in xrange(len(temp[0])):
uuu.extend([temp[0][k],temp[1][k],temp[2][k],temp[3][k]])
all_ali_params.append(uuu)
"""
stable_set, mir_stab_rate, pix_err = multi_align_stability(
all_ali_params, 0.0, 10000.0, options.thld_err, options.verbose, 2 * ou + 1
)
print "%4s %20s %20s %20s %30s %6.2f" % (
"",
"Size of set",
"Size of stable set",
"Mirror stab rate",
"Pixel error prior to pruning the set above threshold of",
options.thld_err,
)
print "Average stat: %10d %20d %20.2f %15.2f" % (len(class_data), len(stable_set), mir_stab_rate, pix_err)
if len(stable_set) > 0:
if options.stables:
stab_mem = [[0, 0.0, 0] for j in xrange(len(stable_set))]
for j in xrange(len(stable_set)):
stab_mem[j] = [int(stable_set[j][1]), stable_set[j][0], j]
write_text_row(stab_mem, "stable_particles.txt")
stable_set_id = []
particle_pixerr = []
for s in stable_set:
stable_set_id.append(s[1])
particle_pixerr.append(s[0])
from fundamentals import rot_shift2D
avet.to_zero()
l = -1
print "average parameters: angle, x-shift, y-shift, mirror"
for j in stable_set_id:
l += 1
print " %4d %4d %12.2f %12.2f %12.2f %1d" % (
l,
j,
stable_set[l][2][0],
stable_set[l][2][1],
stable_set[l][2][2],
int(stable_set[l][2][3]),
)
avet += rot_shift2D(
class_data[j], stable_set[l][2][0], stable_set[l][2][1], stable_set[l][2][2], stable_set[l][2][3]
)
avet /= l + 1
avet.set_attr("members", stable_set_id)
avet.set_attr("pix_err", pix_err)
avet.set_attr("pixerr", particle_pixerr)
avet.write_image(args[1])
global_def.BATCH = False
