def prepare_outdir_log(outdir='.', verbose=False, is_main=True):
"""
Prepares output directory and sets up log file.
Arguments:
outdir : Output directory
verbose : (boolean) Whether to write to screen
is_main : (boolean) If using multiple cores, some tasks only need to be performed once, not by all cores
Returns:
log : instance of Logger class
verbose : (boolean) New version of Logger can write to screen simultaneously
"""
# Create directory if it doesn't exist
if is_main:
if os.path.isdir(outdir):
sxprint("Writing to output directory: %s" % outdir)
else:
sxprint("Created output directory: %s" % outdir)
os.makedirs(
outdir) # os.mkdir() can only operate one directory deep
sp_global_def.write_command(outdir)
logname = "log_" + datetime.now().strftime("%Y%m%d_%H%M%S") + ".txt"
logname = os.path.join(outdir, logname)
#if global_def.LOGFILE:
#global_def.LOGFILE = logname
#print('LOGFILE', global_def.LOGFILE)
#exit()
# May be using old version of logger.py
try:
if verbose:
log = Logger(base_logger=BaseLogger_Files(),
base_logger2=BaseLogger_Print(),
file_name=logname)
verbose = False # logger output will be echoed to screen
else:
log = Logger(base_logger=BaseLogger_Files(), file_name=logname)
except TypeError:
if is_main: sxprint("WARNING: Using old sp_logger.py library")
log = Logger(base_logger=BaseLogger_Files()) #, file_name=logname)
logname = 'log.txt'
if is_main: sxprint("Writing log file to %s\n" % logname)
if is_main:
progbase = os.path.basename(__file__).split('.')[0].upper()
#print('progbase', progbase)
#exit()
length = len(progbase) + 4
log.add("\n" + " " * TIMESTAMP_LENGTH + "*" * length + "\n" +
" " * TIMESTAMP_LENGTH + "* " + progbase + " *\n" +
" " * TIMESTAMP_LENGTH + "*" * length)
return log, verbose
def prepare_log(outdir='.', verbose=False, main=True):
"""
Prepare log file.
Arguments:
outdir : Output directory
verbose : (boolean) Whether to write additional information to screen
main : (boolean) Whether main MPI process
Returns:
log : Instance of Logger class
verbose : (boolean) Updates flag to False if Logger class can mirror output to screen
"""
TIMESTAMP_LENGTH = 23
logname = "log_" + datetime.now().strftime("%Y%m%d_%H%M%S") + ".txt"
logname = os.path.join(outdir, logname)
# May be using old version of logger.py
try:
if verbose:
log = Logger(base_logger=BaseLogger_Files(),
base_logger2=BaseLogger_Print(),
file_name=logname)
verbose = False # logger output will be echoed to screen
else:
log = Logger(base_logger=BaseLogger_Files(), file_name=logname)
except TypeError:
print("WARNING: Using old sp_logger.py library")
log = Logger(base_logger=BaseLogger_Files()) #, file_name=logname)
logname = 'log.txt'
print("Writing log file to %s" % logname)
if main:
progbase = os.path.basename(__file__).split('.')[0].upper()
length = len(progbase) + 4
log.add("\n" + " " * TIMESTAMP_LENGTH + "*" * length + "\n" +
" " * TIMESTAMP_LENGTH + "* " + progbase + " *\n" +
" " * TIMESTAMP_LENGTH + "*" * length)
return log, verbose
def main():
progname = os.path.basename(sys.argv[0])
usage = progname + " stack outdir <maskfile> --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translation_step --dst=delta --center=center --maxit=max_iteration --CTF --snr=SNR --Fourvar=Fourier_variance --Ng=group_number --Function=user_function_name --CUDA --GPUID --MPI"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--ir", type="float", default=1, help="inner radius for rotational correlation > 0 (set to 1)")
parser.add_option("--ou", type="float", default=-1, help="outer radius for rotational correlation < nx/2-1 (set to the radius of the particle)")
parser.add_option("--rs", type="float", default=1, help="step between rings in rotational correlation > 0 (set to 1)" )
parser.add_option("--xr", type="string", default="4 2 1 1", help="range for translation search in x direction, search is +/xr ")
parser.add_option("--yr", type="string", default="-1", help="range for translation search in y direction, search is +/yr ")
parser.add_option("--ts", type="string", default="2 1 0.5 0.25",help="step of translation search in both directions")
parser.add_option("--nomirror", action="store_true", default=False, help="Disable checking mirror orientations of images (default False)")
parser.add_option("--dst", type="float", default=0.0, help="delta")
parser.add_option("--center", type="float", default=-1, help="-1.average center method; 0.not centered; 1.phase approximation; 2.cc with Gaussian function; 3.cc with donut-shaped image 4.cc with user-defined reference 5.cc with self-rotated average")
parser.add_option("--maxit", type="float", default=0, help="maximum number of iterations (0 means the maximum iterations is 10, but it will automatically stop should the criterion falls")
parser.add_option("--CTF", action="store_true", default=False, help="use CTF correction during alignment")
parser.add_option("--snr", type="float", default=1.0, help="signal-to-noise ratio of the data (set to 1.0)")
parser.add_option("--Fourvar", action="store_true", default=False, help="compute Fourier variance")
#parser.add_option("--Ng", type="int", default=-1, help="number of groups in the new CTF filteration")
parser.add_option("--function", type="string", default="ref_ali2d", help="name of the reference preparation function (default ref_ali2d)")
#parser.add_option("--CUDA", action="store_true", default=False, help="use CUDA program")
#parser.add_option("--GPUID", type="string", default="", help="ID of GPUs available")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version ")
parser.add_option("--rotational", action="store_true", default=False, help="rotational alignment with optional limited in-plane angle, the parameters are: ir, ou, rs, psi_max, mode(F or H), maxit, orient, randomize")
parser.add_option("--psi_max", type="float", default=180.0, help="psi_max")
parser.add_option("--mode", type="string", default="F", help="Full or Half rings, default F")
parser.add_option("--randomize",action="store_true", default=False, help="randomize initial rotations (suboption of friedel, default False)")
parser.add_option("--orient", action="store_true", default=False, help="orient images such that the average is symmetric about x-axis, for layer lines (suboption of friedel, default False)")
parser.add_option("--template", type="string", default=None, help="2D alignment will be initialized using the template provided (only non-MPI version, default None)")
parser.add_option("--random_method", type="string", default="", help="use SHC or SCF (default standard method)")
(options, args) = parser.parse_args()
if len(args) < 2 or len(args) > 3:
sxprint( "Usage: " + usage )
sxprint( "Please run \'" + progname + " -h\' for detailed options" )
sp_global_def.ERROR( "Invalid number of parameters used. Please see usage information above." )
return
elif(options.rotational):
from sp_applications import ali2d_rotationaltop
sp_global_def.BATCH = True
ali2d_rotationaltop(args[1], args[0], options.randomize, options.orient, options.ir, options.ou, options.rs, options.psi_max, options.mode, options.maxit)
else:
if args[1] == 'None':
outdir = None
else:
outdir = args[1]
if len(args) == 2:
mask = None
else:
mask = args[2]
if sp_global_def.CACHE_DISABLE:
from sp_utilities import disable_bdb_cache
disable_bdb_cache()
sp_global_def.BATCH = True
if options.MPI:
from sp_applications import ali2d_base
from mpi import mpi_comm_size, mpi_comm_rank, MPI_COMM_WORLD
number_of_proc = mpi_comm_size(MPI_COMM_WORLD)
myid = mpi_comm_rank(MPI_COMM_WORLD)
main_node = 0
if(myid == main_node):
import subprocess
from sp_logger import Logger, BaseLogger_Files
# Create output directory
log = Logger(BaseLogger_Files())
log.prefix = os.path.join(outdir)
cmd = "mkdir "+log.prefix
outcome = subprocess.call(cmd, shell=True)
log.prefix += "/"
else:
outcome = 0
log = None
from sp_utilities import bcast_number_to_all
outcome = bcast_number_to_all(outcome, source_node = main_node)
if(outcome == 1):
sp_global_def.ERROR( "Output directory exists, please change the name and restart the program", myid=myid )
dummy = ali2d_base(args[0], outdir, mask, options.ir, options.ou, options.rs, options.xr, options.yr, \
options.ts, options.nomirror, options.dst, \
options.center, options.maxit, options.CTF, options.snr, options.Fourvar, \
options.function, random_method = options.random_method, log = log, \
number_of_proc = number_of_proc, myid = myid, main_node = main_node, mpi_comm = MPI_COMM_WORLD,\
write_headers = True)
else:
sxprint( " Non-MPI is no more in use, try MPI option, please." )
"""
from sp_applications import ali2d
ali2d(args[0], outdir, mask, options.ir, options.ou, options.rs, options.xr, options.yr, \
options.ts, options.nomirror, options.dst, \
options.center, options.maxit, options.CTF, options.snr, options.Fourvar, \
-1, options.function, False, "", options.MPI, \
options.template, random_method = options.random_method)
"""
sp_global_def.BATCH = False
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_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 sp_applications import MPI_start_end
from sp_reconstruction import recons3d_em, recons3d_em_MPI
from sp_reconstruction import recons3d_4nn_MPI, recons3d_4nn_ctf_MPI
from sp_utilities import print_begin_msg, print_end_msg, print_msg
from sp_utilities import read_text_row, get_image, get_im, wrap_mpi_send, wrap_mpi_recv
from sp_utilities import bcast_EMData_to_all, bcast_number_to_all
from sp_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 sp_global_def.CACHE_DISABLE:
from sp_utilities import disable_bdb_cache
disable_bdb_cache()
# Set up global variables related to ERROR function
sp_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: sp_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 mpi.mpi_comm_size(MPI_COMM_WORLD) > 1:
ERROR("Cannot use more than one CPU for symmetry preparation")
if not os.path.exists(current_output_dir):
os.makedirs(current_output_dir)
sp_global_def.write_command(current_output_dir)
from sp_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")
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("sp_cpy.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"
sxprint(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 sp_fundamentals import window2d
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:
sxprint("Usage: " + usage)
sxprint("Please run \'" + progname + " -h\' for detailed options")
ERROR(
"Invalid number of parameters used. Please see usage information above."
)
return
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",
myid=myid)
#if options.VAR and options.SND:
# ERROR( "Only one of var and SND can be set!",myid=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",
myid=myid)
#if options.SND and (options.ave2D or options.ave3D):
# ERROR( "When SND is set, the program cannot output ave2D or ave3D", myid=myid )
#if options.nvec > 0 :
# ERROR( "PCA option not implemented", myid=myid )
#if options.nvec > 0 and options.ave3D == None:
# ERROR( "When doing PCA analysis, one must set ave3D", myid=myid )
if current_decimate > 1.0 or current_decimate < 0.0:
ERROR("Decimate rate should be a value between 0.0 and 1.0",
myid=myid)
if current_window < 0.0:
ERROR("Target window size should be always larger than zero",
myid=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",
myid=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.makedirs(current_output_dir
) # Never delete output_dir in the program!
img_per_grp = options.img_per_grp
#nvec = options.nvec
radiuspca = options.radiuspca
from sp_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",
myid=myid)
except:
ERROR(
"Input stack is not prepared for symmetry, please follow instructions",
myid=myid)
from sp_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",
myid=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")
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 sp_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 sp_projection import prep_vol, prgs
from sp_statistics import im_diff
from sp_utilities import get_im, model_circle, get_params_proj, set_params_proj
from sp_utilities import get_ctf, generate_ctf
from sp_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 sp_utilities import bcast_number_to_all, bcast_list_to_all, send_EMData, recv_EMData
from sp_utilities import set_params_proj, get_params_proj, params_3D_2D, get_params2D, set_params2D, compose_transform2
from sp_utilities import model_blank, nearest_proj, model_circle, write_text_row, wrap_mpi_gatherv
from sp_applications import pca
from sp_statistics import avgvar, avgvar_ctf, ccc
from sp_filter import filt_tanl
from sp_morphology import threshold, square_root
from sp_projection import project, prep_vol, prgs
from sets import Set
from sp_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 sp_applications import prepare_2d_forPCA
from sp_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 sp_utilities import pad
from sp_filter import filt_ctf
from sp_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([str(entry) for entry in 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 sp_fundamentals import fpol
from sp_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 sp_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 sp_fundamentals import fpol
from sp_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 sp_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 sp_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")
if RUNNING_UNDER_MPI:
sp_global_def.MPI = False
sp_global_def.BATCH = False
def main():
from sp_logger import Logger, BaseLogger_Files
arglist = []
i = 0
while (i < len(sys.argv)):
if sys.argv[i] == '-p4pg':
i = i + 2
elif sys.argv[i] == '-p4wd':
i = i + 2
else:
arglist.append(sys.argv[i])
i = i + 1
progname = os.path.basename(arglist[0])
usage = progname + " stack outdir <mask> --focus=3Dmask --radius=outer_radius --delta=angular_step" +\
"--an=angular_neighborhood --maxit=max_iter --CTF --sym=c1 --function=user_function --independent=indenpendent_runs --number_of_images_per_group=number_of_images_per_group --low_pass_filter=.25 --seed=random_seed"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--focus",
type="string",
default='',
help="bineary 3D mask for focused clustering ")
parser.add_option(
"--ir",
type="int",
default=1,
help="inner radius for rotational correlation > 0 (set to 1)")
parser.add_option(
"--radius",
type="int",
default=-1,
help=
"particle radius in pixel for rotational correlation <nx-1 (set to the radius of the particle)"
)
parser.add_option("--maxit",
type="int",
default=25,
help="maximum number of iteration")
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 ")
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='0.25',
help=
"step size of the translation search in both directions direction, search is -xr, -xr+ts, 0, xr-ts, xr "
)
parser.add_option("--delta",
type="string",
default='2',
help="angular step of reference projections")
parser.add_option("--an",
type="string",
default='-1',
help="angular neighborhood for local searches")
parser.add_option(
"--center",
type="int",
default=0,
help=
"0 - if you do not want the volume to be centered, 1 - center the volume using cog (default=0)"
)
parser.add_option(
"--nassign",
type="int",
default=1,
help=
"number of reassignment iterations performed for each angular step (set to 3) "
)
parser.add_option(
"--nrefine",
type="int",
default=0,
help=
"number of alignment iterations performed for each angular step (set to 0)"
)
parser.add_option("--CTF",
action="store_true",
default=False,
help="do CTF correction during clustring")
parser.add_option(
"--stoprnct",
type="float",
default=3.0,
help="Minimum percentage of assignment change to stop the program")
parser.add_option("--sym",
type="string",
default='c1',
help="symmetry of the structure ")
parser.add_option("--function",
type="string",
default='do_volume_mrk05',
help="name of the reference preparation function")
parser.add_option("--independent",
type="int",
default=3,
help="number of independent run")
parser.add_option("--number_of_images_per_group",
type="int",
default=1000,
help="number of groups")
parser.add_option(
"--low_pass_filter",
type="float",
default=-1.0,
help=
"absolute frequency of low-pass filter for 3d sorting on the original image size"
)
parser.add_option("--nxinit",
type="int",
default=64,
help="initial image size for sorting")
parser.add_option("--unaccounted",
action="store_true",
default=False,
help="reconstruct the unaccounted images")
parser.add_option(
"--seed",
type="int",
default=-1,
help="random seed for create initial random assignment for EQ Kmeans")
parser.add_option("--smallest_group",
type="int",
default=500,
help="minimum members for identified group")
parser.add_option("--sausage",
action="store_true",
default=False,
help="way of filter volume")
parser.add_option("--chunk0",
type="string",
default='',
help="chunk0 for computing margin of error")
parser.add_option("--chunk1",
type="string",
default='',
help="chunk1 for computing margin of error")
parser.add_option(
"--PWadjustment",
type="string",
default='',
help=
"1-D power spectrum of PDB file used for EM volume power spectrum correction"
)
parser.add_option(
"--protein_shape",
type="string",
default='g',
help=
"protein shape. It defines protein preferred orientation angles. Currently it has g and f two types "
)
parser.add_option(
"--upscale",
type="float",
default=0.5,
help=" scaling parameter to adjust the power spectrum of EM volumes")
parser.add_option("--wn",
type="int",
default=0,
help="optimal window size for data processing")
parser.add_option(
"--interpolation",
type="string",
default="4nn",
help="3-d reconstruction interpolation method, two options trl and 4nn"
)
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 1 or len(args) > 4:
sxprint("Usage: " + usage)
sxprint("Please run \'" + progname + " -h\' for detailed options")
ERROR(
"Invalid number of parameters used. Please see usage information above."
)
return
else:
if len(args) > 2:
mask_file = args[2]
else:
mask_file = None
orgstack = args[0]
masterdir = args[1]
sp_global_def.BATCH = True
#---initialize MPI related variables
nproc = mpi.mpi_comm_size(mpi.MPI_COMM_WORLD)
myid = mpi.mpi_comm_rank(mpi.MPI_COMM_WORLD)
mpi_comm = mpi.MPI_COMM_WORLD
main_node = 0
# import some utilities
from sp_utilities import get_im, bcast_number_to_all, cmdexecute, write_text_file, read_text_file, wrap_mpi_bcast, get_params_proj, write_text_row
from sp_applications import recons3d_n_MPI, mref_ali3d_MPI, Kmref_ali3d_MPI
from sp_statistics import k_means_match_clusters_asg_new, k_means_stab_bbenum
from sp_applications import mref_ali3d_EQ_Kmeans, ali3d_mref_Kmeans_MPI
# Create the main log file
from sp_logger import Logger, BaseLogger_Files
if myid == main_node:
log_main = Logger(BaseLogger_Files())
log_main.prefix = masterdir + "/"
else:
log_main = None
#--- fill input parameters into dictionary named after Constants
Constants = {}
Constants["stack"] = args[0]
Constants["masterdir"] = masterdir
Constants["mask3D"] = mask_file
Constants["focus3Dmask"] = options.focus
Constants["indep_runs"] = options.independent
Constants["stoprnct"] = options.stoprnct
Constants[
"number_of_images_per_group"] = options.number_of_images_per_group
Constants["CTF"] = options.CTF
Constants["maxit"] = options.maxit
Constants["ir"] = options.ir
Constants["radius"] = options.radius
Constants["nassign"] = options.nassign
Constants["rs"] = options.rs
Constants["xr"] = options.xr
Constants["yr"] = options.yr
Constants["ts"] = options.ts
Constants["delta"] = options.delta
Constants["an"] = options.an
Constants["sym"] = options.sym
Constants["center"] = options.center
Constants["nrefine"] = options.nrefine
#Constants["fourvar"] = options.fourvar
Constants["user_func"] = options.function
Constants[
"low_pass_filter"] = options.low_pass_filter # enforced low_pass_filter
#Constants["debug"] = options.debug
Constants["main_log_prefix"] = args[1]
#Constants["importali3d"] = options.importali3d
Constants["myid"] = myid
Constants["main_node"] = main_node
Constants["nproc"] = nproc
Constants["log_main"] = log_main
Constants["nxinit"] = options.nxinit
Constants["unaccounted"] = options.unaccounted
Constants["seed"] = options.seed
Constants["smallest_group"] = options.smallest_group
Constants["sausage"] = options.sausage
Constants["chunk0"] = options.chunk0
Constants["chunk1"] = options.chunk1
Constants["PWadjustment"] = options.PWadjustment
Constants["upscale"] = options.upscale
Constants["wn"] = options.wn
Constants["3d-interpolation"] = options.interpolation
Constants["protein_shape"] = options.protein_shape
# -----------------------------------------------------
#
# Create and initialize Tracker dictionary with input options
Tracker = {}
Tracker["constants"] = Constants
Tracker["maxit"] = Tracker["constants"]["maxit"]
Tracker["radius"] = Tracker["constants"]["radius"]
#Tracker["xr"] = ""
#Tracker["yr"] = "-1" # Do not change!
#Tracker["ts"] = 1
#Tracker["an"] = "-1"
#Tracker["delta"] = "2.0"
#Tracker["zoom"] = True
#Tracker["nsoft"] = 0
#Tracker["local"] = False
#Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
Tracker["upscale"] = Tracker["constants"]["upscale"]
#Tracker["upscale"] = 0.5
Tracker[
"applyctf"] = False # Should the data be premultiplied by the CTF. Set to False for local continuous.
#Tracker["refvol"] = None
Tracker["nxinit"] = Tracker["constants"]["nxinit"]
#Tracker["nxstep"] = 32
Tracker["icurrentres"] = -1
#Tracker["ireachedres"] = -1
#Tracker["lowpass"] = 0.4
#Tracker["falloff"] = 0.2
#Tracker["inires"] = options.inires # Now in A, convert to absolute before using
Tracker["fuse_freq"] = 50 # Now in A, convert to absolute before using
#Tracker["delpreviousmax"] = False
#Tracker["anger"] = -1.0
#Tracker["shifter"] = -1.0
#Tracker["saturatecrit"] = 0.95
#Tracker["pixercutoff"] = 2.0
#Tracker["directory"] = ""
#Tracker["previousoutputdir"] = ""
#Tracker["eliminated-outliers"] = False
#Tracker["mainiteration"] = 0
#Tracker["movedback"] = False
#Tracker["state"] = Tracker["constants"]["states"][0]
#Tracker["global_resolution"] =0.0
Tracker["orgstack"] = orgstack
#--------------------------------------------------------------------
# import from utilities
from sp_utilities import sample_down_1D_curve, get_initial_ID, remove_small_groups, print_upper_triangular_matrix, print_a_line_with_timestamp
from sp_utilities import print_dict, get_resolution_mrk01, partition_to_groups, partition_independent_runs, get_outliers
from sp_utilities import merge_groups, save_alist, margin_of_error, get_margin_of_error, do_two_way_comparison, select_two_runs, get_ali3d_params
from sp_utilities import counting_projections, unload_dict, load_dict, get_stat_proj, create_random_list, get_number_of_groups, recons_mref
from sp_utilities import apply_low_pass_filter, get_groups_from_partition, get_number_of_groups, get_complementary_elements_total, update_full_dict
from sp_utilities import count_chunk_members, set_filter_parameters_from_adjusted_fsc, get_two_chunks_from_stack
####------------------------------------------------------------------
#
# Get the pixel size; if none, set to 1.0, and the original image size
from sp_utilities import get_shrink_data_huang
if (myid == main_node):
line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
sxprint((line + "Initialization of 3-D sorting"))
a = get_im(orgstack)
nnxo = a.get_xsize()
if (Tracker["nxinit"] > nnxo):
sp_global_def.ERROR(
"Image size less than minimum permitted $d" %
Tracker["nxinit"])
nnxo = -1
else:
if Tracker["constants"]["CTF"]:
i = a.get_attr('ctf')
pixel_size = i.apix
fq = pixel_size / Tracker["fuse_freq"]
else:
pixel_size = 1.0
# No pixel size, fusing computed as 5 Fourier pixels
fq = 5.0 / nnxo
del a
else:
nnxo = 0
fq = 0.0
pixel_size = 1.0
nnxo = bcast_number_to_all(nnxo, source_node=main_node)
if (nnxo < 0):
return
pixel_size = bcast_number_to_all(pixel_size, source_node=main_node)
fq = bcast_number_to_all(fq, source_node=main_node)
if Tracker["constants"]["wn"] == 0:
Tracker["constants"]["nnxo"] = nnxo
else:
Tracker["constants"]["nnxo"] = Tracker["constants"]["wn"]
nnxo = Tracker["constants"]["nnxo"]
Tracker["constants"]["pixel_size"] = pixel_size
Tracker["fuse_freq"] = fq
del fq, nnxo, pixel_size
if (Tracker["constants"]["radius"] < 1):
Tracker["constants"][
"radius"] = Tracker["constants"]["nnxo"] // 2 - 2
elif ((2 * Tracker["constants"]["radius"] + 2) >
Tracker["constants"]["nnxo"]):
sp_global_def.ERROR("Particle radius set too large!", myid=myid)
####-----------------------------------------------------------------------------------------
# Master directory
if myid == main_node:
if masterdir == "":
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir = "master_sort3d" + timestring
li = len(masterdir)
cmd = "{} {}".format("mkdir -p", masterdir)
os.system(cmd)
else:
li = 0
li = mpi.mpi_bcast(li, 1, mpi.MPI_INT, main_node,
mpi.MPI_COMM_WORLD)[0]
if li > 0:
masterdir = mpi.mpi_bcast(masterdir, li, mpi.MPI_CHAR, main_node,
mpi.MPI_COMM_WORLD)
import string
masterdir = string.join(masterdir, "")
if myid == main_node:
print_dict(Tracker["constants"],
"Permanent settings of 3-D sorting program")
######### create a vstack from input stack to the local stack in masterdir
# stack name set to default
Tracker["constants"]["stack"] = "bdb:" + masterdir + "/rdata"
Tracker["constants"]["ali3d"] = os.path.join(masterdir,
"ali3d_init.txt")
Tracker["constants"]["ctf_params"] = os.path.join(
masterdir, "ctf_params.txt")
Tracker["constants"]["partstack"] = Tracker["constants"][
"ali3d"] # also serves for refinement
if myid == main_node:
total_stack = EMUtil.get_image_count(Tracker["orgstack"])
else:
total_stack = 0
total_stack = bcast_number_to_all(total_stack, source_node=main_node)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
from time import sleep
while not os.path.exists(masterdir):
sxprint("Node ", myid, " waiting...")
sleep(5)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
if myid == main_node:
log_main.add("Sphire sort3d ")
log_main.add("the sort3d master directory is " + masterdir)
#####
###----------------------------------------------------------------------------------
# Initial data analysis and handle two chunk files
from random import shuffle
# Compute the resolution
#### make chunkdir dictionary for computing margin of error
import sp_user_functions
user_func = sp_user_functions.factory[Tracker["constants"]
["user_func"]]
chunk_dict = {}
chunk_list = []
if myid == main_node:
chunk_one = read_text_file(Tracker["constants"]["chunk0"])
chunk_two = read_text_file(Tracker["constants"]["chunk1"])
else:
chunk_one = 0
chunk_two = 0
chunk_one = wrap_mpi_bcast(chunk_one, main_node)
chunk_two = wrap_mpi_bcast(chunk_two, main_node)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
######################## Read/write bdb: data on main node ############################
if myid == main_node:
if (orgstack[:4] == "bdb:"):
cmd = "{} {} {}".format(
"e2bdb.py", orgstack,
"--makevstack=" + Tracker["constants"]["stack"])
else:
cmd = "{} {} {}".format("sp_cpy.py", orgstack,
Tracker["constants"]["stack"])
junk = cmdexecute(cmd)
cmd = "{} {} {}".format(
"sp_header.py --params=xform.projection",
"--export=" + Tracker["constants"]["ali3d"], orgstack)
junk = cmdexecute(cmd)
cmd = "{} {} {}".format(
"sp_header.py --params=ctf",
"--export=" + Tracker["constants"]["ctf_params"], orgstack)
junk = cmdexecute(cmd)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
########-----------------------------------------------------------------------------
Tracker["total_stack"] = total_stack
Tracker["constants"]["total_stack"] = total_stack
Tracker["shrinkage"] = float(
Tracker["nxinit"]) / Tracker["constants"]["nnxo"]
Tracker[
"radius"] = Tracker["constants"]["radius"] * Tracker["shrinkage"]
if Tracker["constants"]["mask3D"]:
Tracker["mask3D"] = os.path.join(masterdir, "smask.hdf")
else:
Tracker["mask3D"] = None
if Tracker["constants"]["focus3Dmask"]:
Tracker["focus3D"] = os.path.join(masterdir, "sfocus.hdf")
else:
Tracker["focus3D"] = None
if myid == main_node:
if Tracker["constants"]["mask3D"]:
mask_3D = get_shrink_3dmask(Tracker["nxinit"],
Tracker["constants"]["mask3D"])
mask_3D.write_image(Tracker["mask3D"])
if Tracker["constants"]["focus3Dmask"]:
mask_3D = get_shrink_3dmask(
Tracker["nxinit"], Tracker["constants"]["focus3Dmask"])
st = Util.infomask(mask_3D, None, True)
if (st[0] == 0.0):
ERROR(
"Incorrect focused mask, after binarize all values zero"
)
mask_3D.write_image(Tracker["focus3D"])
del mask_3D
if Tracker["constants"]["PWadjustment"] != '':
PW_dict = {}
nxinit_pwsp = sample_down_1D_curve(
Tracker["constants"]["nxinit"], Tracker["constants"]["nnxo"],
Tracker["constants"]["PWadjustment"])
Tracker["nxinit_PW"] = os.path.join(masterdir, "spwp.txt")
if myid == main_node:
write_text_file(nxinit_pwsp, Tracker["nxinit_PW"])
PW_dict[Tracker["constants"]
["nnxo"]] = Tracker["constants"]["PWadjustment"]
PW_dict[Tracker["constants"]["nxinit"]] = Tracker["nxinit_PW"]
Tracker["PW_dict"] = PW_dict
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
#-----------------------From two chunks to FSC, and low pass filter-----------------------------------------###
for element in chunk_one:
chunk_dict[element] = 0
for element in chunk_two:
chunk_dict[element] = 1
chunk_list = [chunk_one, chunk_two]
Tracker["chunk_dict"] = chunk_dict
Tracker["P_chunk0"] = len(chunk_one) / float(total_stack)
Tracker["P_chunk1"] = len(chunk_two) / float(total_stack)
### create two volumes to estimate resolution
if myid == main_node:
for index in range(2):
write_text_file(
chunk_list[index],
os.path.join(masterdir, "chunk%01d.txt" % index))
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
vols = []
for index in range(2):
data, old_shifts = get_shrink_data_huang(
Tracker,
Tracker["constants"]["nxinit"],
os.path.join(masterdir, "chunk%01d.txt" % index),
Tracker["constants"]["partstack"],
myid,
main_node,
nproc,
preshift=True)
vol = recons3d_4nn_ctf_MPI(myid=myid,
prjlist=data,
symmetry=Tracker["constants"]["sym"],
finfo=None)
if myid == main_node:
vol.write_image(os.path.join(masterdir, "vol%d.hdf" % index))
vols.append(vol)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
if myid == main_node:
low_pass, falloff, currentres = get_resolution_mrk01(
vols, Tracker["constants"]["radius"],
Tracker["constants"]["nxinit"], masterdir, Tracker["mask3D"])
if low_pass > Tracker["constants"]["low_pass_filter"]:
low_pass = Tracker["constants"]["low_pass_filter"]
else:
low_pass = 0.0
falloff = 0.0
currentres = 0.0
bcast_number_to_all(currentres, source_node=main_node)
bcast_number_to_all(low_pass, source_node=main_node)
bcast_number_to_all(falloff, source_node=main_node)
Tracker["currentres"] = currentres
Tracker["falloff"] = falloff
if Tracker["constants"]["low_pass_filter"] == -1.0:
Tracker["low_pass_filter"] = min(
.45, low_pass / Tracker["shrinkage"]) # no better than .45
else:
Tracker["low_pass_filter"] = min(
.45,
Tracker["constants"]["low_pass_filter"] / Tracker["shrinkage"])
Tracker["lowpass"] = Tracker["low_pass_filter"]
Tracker["falloff"] = .1
Tracker["global_fsc"] = os.path.join(masterdir, "fsc.txt")
############################################################################################
if myid == main_node:
log_main.add("The command-line inputs are as following:")
log_main.add(
"**********************************************************")
for a in sys.argv:
if myid == main_node: log_main.add(a)
if myid == main_node:
log_main.add("number of cpus used in this run is %d" %
Tracker["constants"]["nproc"])
log_main.add(
"**********************************************************")
from sp_filter import filt_tanl
### START 3-D sorting
if myid == main_node:
log_main.add("----------3-D sorting program------- ")
log_main.add(
"current resolution %6.3f for images of original size in terms of absolute frequency"
% Tracker["currentres"])
log_main.add("equivalent to %f Angstrom resolution" %
(Tracker["constants"]["pixel_size"] /
Tracker["currentres"] / Tracker["shrinkage"]))
log_main.add("the user provided enforced low_pass_filter is %f" %
Tracker["constants"]["low_pass_filter"])
#log_main.add("equivalent to %f Angstrom resolution"%(Tracker["constants"]["pixel_size"]/Tracker["constants"]["low_pass_filter"]))
for index in range(2):
filt_tanl(
get_im(os.path.join(masterdir, "vol%01d.hdf" % index)),
Tracker["low_pass_filter"],
Tracker["falloff"]).write_image(
os.path.join(masterdir, "volf%01d.hdf" % index))
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
from sp_utilities import get_input_from_string
delta = get_input_from_string(Tracker["constants"]["delta"])
delta = delta[0]
from sp_utilities import even_angles
n_angles = even_angles(delta, 0, 180)
this_ali3d = Tracker["constants"]["ali3d"]
sampled = get_stat_proj(Tracker, delta, this_ali3d)
if myid == main_node:
nc = 0
for a in sampled:
if len(sampled[a]) > 0:
nc += 1
log_main.add("total sampled direction %10d at angle step %6.3f" %
(len(n_angles), delta))
log_main.add(
"captured sampled directions %10d percentage covered by data %6.3f"
% (nc, float(nc) / len(n_angles) * 100))
number_of_images_per_group = Tracker["constants"][
"number_of_images_per_group"]
if myid == main_node:
log_main.add("user provided number_of_images_per_group %d" %
number_of_images_per_group)
Tracker["number_of_images_per_group"] = number_of_images_per_group
number_of_groups = get_number_of_groups(total_stack,
number_of_images_per_group)
Tracker["number_of_groups"] = number_of_groups
generation = 0
partition_dict = {}
full_dict = {}
workdir = os.path.join(masterdir, "generation%03d" % generation)
Tracker["this_dir"] = workdir
if myid == main_node:
log_main.add("---- generation %5d" % generation)
log_main.add("number of images per group is set as %d" %
number_of_images_per_group)
log_main.add("the initial number of groups is %10d " %
number_of_groups)
cmd = "{} {}".format("mkdir", workdir)
os.system(cmd)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
list_to_be_processed = list(range(Tracker["constants"]["total_stack"]))
Tracker["this_data_list"] = list_to_be_processed
create_random_list(Tracker)
#################################
full_dict = {}
for iptl in range(Tracker["constants"]["total_stack"]):
full_dict[iptl] = iptl
Tracker["full_ID_dict"] = full_dict
#################################
for indep_run in range(Tracker["constants"]["indep_runs"]):
Tracker["this_particle_list"] = Tracker["this_indep_list"][
indep_run]
ref_vol = recons_mref(Tracker)
if myid == main_node:
log_main.add("independent run %10d" % indep_run)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
Tracker["this_data_list"] = list_to_be_processed
Tracker["total_stack"] = len(Tracker["this_data_list"])
Tracker["this_particle_text_file"] = os.path.join(
workdir,
"independent_list_%03d.txt" % indep_run) # for get_shrink_data
if myid == main_node:
write_text_file(Tracker["this_data_list"],
Tracker["this_particle_text_file"])
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
outdir = os.path.join(workdir, "EQ_Kmeans%03d" % indep_run)
ref_vol = apply_low_pass_filter(ref_vol, Tracker)
mref_ali3d_EQ_Kmeans(ref_vol, outdir,
Tracker["this_particle_text_file"], Tracker)
partition_dict[indep_run] = Tracker["this_partition"]
Tracker["partition_dict"] = partition_dict
Tracker["total_stack"] = len(Tracker["this_data_list"])
Tracker["this_total_stack"] = Tracker["total_stack"]
###############################
do_two_way_comparison(Tracker)
###############################
ref_vol_list = []
from time import sleep
number_of_ref_class = []
for igrp in range(len(Tracker["two_way_stable_member"])):
Tracker["this_data_list"] = Tracker["two_way_stable_member"][igrp]
Tracker["this_data_list_file"] = os.path.join(
workdir, "stable_class%d.txt" % igrp)
if myid == main_node:
write_text_file(Tracker["this_data_list"],
Tracker["this_data_list_file"])
data, old_shifts = get_shrink_data_huang(
Tracker,
Tracker["nxinit"],
Tracker["this_data_list_file"],
Tracker["constants"]["partstack"],
myid,
main_node,
nproc,
preshift=True)
volref = recons3d_4nn_ctf_MPI(myid=myid,
prjlist=data,
symmetry=Tracker["constants"]["sym"],
finfo=None)
ref_vol_list.append(volref)
number_of_ref_class.append(len(Tracker["this_data_list"]))
if myid == main_node:
log_main.add("group %d members %d " %
(igrp, len(Tracker["this_data_list"])))
Tracker["number_of_ref_class"] = number_of_ref_class
nx_of_image = ref_vol_list[0].get_xsize()
if Tracker["constants"]["PWadjustment"]:
Tracker["PWadjustment"] = Tracker["PW_dict"][nx_of_image]
else:
Tracker["PWadjustment"] = Tracker["constants"][
"PWadjustment"] # no PW adjustment
if myid == main_node:
for iref in range(len(ref_vol_list)):
refdata = [None] * 4
refdata[0] = ref_vol_list[iref]
refdata[1] = Tracker
refdata[2] = Tracker["constants"]["myid"]
refdata[3] = Tracker["constants"]["nproc"]
volref = user_func(refdata)
volref.write_image(os.path.join(workdir, "volf_stable.hdf"),
iref)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
Tracker["this_data_list"] = Tracker["this_accounted_list"]
outdir = os.path.join(workdir, "Kmref")
empty_group, res_groups, final_list = ali3d_mref_Kmeans_MPI(
ref_vol_list, outdir, Tracker["this_accounted_text"], Tracker)
Tracker["this_unaccounted_list"] = get_complementary_elements(
list_to_be_processed, final_list)
if myid == main_node:
log_main.add("the number of particles not processed is %d" %
len(Tracker["this_unaccounted_list"]))
write_text_file(Tracker["this_unaccounted_list"],
Tracker["this_unaccounted_text"])
update_full_dict(Tracker["this_unaccounted_list"], Tracker)
#######################################
number_of_groups = len(res_groups)
vol_list = []
number_of_ref_class = []
for igrp in range(number_of_groups):
data, old_shifts = get_shrink_data_huang(
Tracker,
Tracker["constants"]["nnxo"],
os.path.join(outdir, "Class%d.txt" % igrp),
Tracker["constants"]["partstack"],
myid,
main_node,
nproc,
preshift=True)
volref = recons3d_4nn_ctf_MPI(myid=myid,
prjlist=data,
symmetry=Tracker["constants"]["sym"],
finfo=None)
vol_list.append(volref)
if (myid == main_node):
npergroup = len(
read_text_file(os.path.join(outdir, "Class%d.txt" % igrp)))
else:
npergroup = 0
npergroup = bcast_number_to_all(npergroup, main_node)
number_of_ref_class.append(npergroup)
Tracker["number_of_ref_class"] = number_of_ref_class
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
nx_of_image = vol_list[0].get_xsize()
if Tracker["constants"]["PWadjustment"]:
Tracker["PWadjustment"] = Tracker["PW_dict"][nx_of_image]
else:
Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
if myid == main_node:
for ivol in range(len(vol_list)):
refdata = [None] * 4
refdata[0] = vol_list[ivol]
refdata[1] = Tracker
refdata[2] = Tracker["constants"]["myid"]
refdata[3] = Tracker["constants"]["nproc"]
volref = user_func(refdata)
volref.write_image(
os.path.join(workdir, "volf_of_Classes.hdf"), ivol)
log_main.add("number of unaccounted particles %10d" %
len(Tracker["this_unaccounted_list"]))
log_main.add("number of accounted particles %10d" %
len(Tracker["this_accounted_list"]))
Tracker["this_data_list"] = Tracker[
"this_unaccounted_list"] # reset parameters for the next round calculation
Tracker["total_stack"] = len(Tracker["this_unaccounted_list"])
Tracker["this_total_stack"] = Tracker["total_stack"]
number_of_groups = get_number_of_groups(
len(Tracker["this_unaccounted_list"]), number_of_images_per_group)
Tracker["number_of_groups"] = number_of_groups
while number_of_groups >= 2:
generation += 1
partition_dict = {}
workdir = os.path.join(masterdir, "generation%03d" % generation)
Tracker["this_dir"] = workdir
if myid == main_node:
log_main.add("*********************************************")
log_main.add("----- generation %5d " %
generation)
log_main.add("number of images per group is set as %10d " %
number_of_images_per_group)
log_main.add("the number of groups is %10d " %
number_of_groups)
log_main.add(" number of particles for clustering is %10d" %
Tracker["total_stack"])
cmd = "{} {}".format("mkdir", workdir)
os.system(cmd)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
create_random_list(Tracker)
for indep_run in range(Tracker["constants"]["indep_runs"]):
Tracker["this_particle_list"] = Tracker["this_indep_list"][
indep_run]
ref_vol = recons_mref(Tracker)
if myid == main_node:
log_main.add("independent run %10d" % indep_run)
outdir = os.path.join(workdir, "EQ_Kmeans%03d" % indep_run)
Tracker["this_data_list"] = Tracker["this_unaccounted_list"]
#ref_vol=apply_low_pass_filter(ref_vol,Tracker)
mref_ali3d_EQ_Kmeans(ref_vol, outdir,
Tracker["this_unaccounted_text"], Tracker)
partition_dict[indep_run] = Tracker["this_partition"]
Tracker["this_data_list"] = Tracker["this_unaccounted_list"]
Tracker["total_stack"] = len(Tracker["this_unaccounted_list"])
Tracker["partition_dict"] = partition_dict
Tracker["this_total_stack"] = Tracker["total_stack"]
total_list_of_this_run = Tracker["this_unaccounted_list"]
###############################
do_two_way_comparison(Tracker)
###############################
ref_vol_list = []
number_of_ref_class = []
for igrp in range(len(Tracker["two_way_stable_member"])):
Tracker["this_data_list"] = Tracker["two_way_stable_member"][
igrp]
Tracker["this_data_list_file"] = os.path.join(
workdir, "stable_class%d.txt" % igrp)
if myid == main_node:
write_text_file(Tracker["this_data_list"],
Tracker["this_data_list_file"])
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
data, old_shifts = get_shrink_data_huang(
Tracker,
Tracker["constants"]["nxinit"],
Tracker["this_data_list_file"],
Tracker["constants"]["partstack"],
myid,
main_node,
nproc,
preshift=True)
volref = recons3d_4nn_ctf_MPI(
myid=myid,
prjlist=data,
symmetry=Tracker["constants"]["sym"],
finfo=None)
#volref = filt_tanl(volref, Tracker["constants"]["low_pass_filter"],.1)
if myid == main_node:
volref.write_image(os.path.join(workdir, "vol_stable.hdf"),
iref)
#volref = resample(volref,Tracker["shrinkage"])
ref_vol_list.append(volref)
number_of_ref_class.append(len(Tracker["this_data_list"]))
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
Tracker["number_of_ref_class"] = number_of_ref_class
Tracker["this_data_list"] = Tracker["this_accounted_list"]
outdir = os.path.join(workdir, "Kmref")
empty_group, res_groups, final_list = ali3d_mref_Kmeans_MPI(
ref_vol_list, outdir, Tracker["this_accounted_text"], Tracker)
# calculate the 3-D structure of original image size for each group
number_of_groups = len(res_groups)
Tracker["this_unaccounted_list"] = get_complementary_elements(
total_list_of_this_run, final_list)
if myid == main_node:
log_main.add("the number of particles not processed is %d" %
len(Tracker["this_unaccounted_list"]))
write_text_file(Tracker["this_unaccounted_list"],
Tracker["this_unaccounted_text"])
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
update_full_dict(Tracker["this_unaccounted_list"], Tracker)
vol_list = []
for igrp in range(number_of_groups):
data, old_shifts = get_shrink_data_huang(
Tracker,
Tracker["constants"]["nnxo"],
os.path.join(outdir, "Class%d.txt" % igrp),
Tracker["constants"]["partstack"],
myid,
main_node,
nproc,
preshift=True)
volref = recons3d_4nn_ctf_MPI(
myid=myid,
prjlist=data,
symmetry=Tracker["constants"]["sym"],
finfo=None)
vol_list.append(volref)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
nx_of_image = ref_vol_list[0].get_xsize()
if Tracker["constants"]["PWadjustment"]:
Tracker["PWadjustment"] = Tracker["PW_dict"][nx_of_image]
else:
Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
if myid == main_node:
for ivol in range(len(vol_list)):
refdata = [None] * 4
refdata[0] = vol_list[ivol]
refdata[1] = Tracker
refdata[2] = Tracker["constants"]["myid"]
refdata[3] = Tracker["constants"]["nproc"]
volref = user_func(refdata)
volref.write_image(
os.path.join(workdir, "volf_of_Classes.hdf"), ivol)
log_main.add("number of unaccounted particles %10d" %
len(Tracker["this_unaccounted_list"]))
log_main.add("number of accounted particles %10d" %
len(Tracker["this_accounted_list"]))
del vol_list
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
number_of_groups = get_number_of_groups(
len(Tracker["this_unaccounted_list"]),
number_of_images_per_group)
Tracker["number_of_groups"] = number_of_groups
Tracker["this_data_list"] = Tracker["this_unaccounted_list"]
Tracker["total_stack"] = len(Tracker["this_unaccounted_list"])
if Tracker["constants"]["unaccounted"]:
data, old_shifts = get_shrink_data_huang(
Tracker,
Tracker["constants"]["nnxo"],
Tracker["this_unaccounted_text"],
Tracker["constants"]["partstack"],
myid,
main_node,
nproc,
preshift=True)
volref = recons3d_4nn_ctf_MPI(myid=myid,
prjlist=data,
symmetry=Tracker["constants"]["sym"],
finfo=None)
nx_of_image = volref.get_xsize()
if Tracker["constants"]["PWadjustment"]:
Tracker["PWadjustment"] = Tracker["PW_dict"][nx_of_image]
else:
Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
if (myid == main_node):
refdata = [None] * 4
refdata[0] = volref
refdata[1] = Tracker
refdata[2] = Tracker["constants"]["myid"]
refdata[3] = Tracker["constants"]["nproc"]
volref = user_func(refdata)
#volref = filt_tanl(volref, Tracker["constants"]["low_pass_filter"],.1)
volref.write_image(
os.path.join(workdir, "volf_unaccounted.hdf"))
# Finish program
if myid == main_node: log_main.add("sxsort3d finishes")
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
return
def main():
from time import sleep
from sp_logger import Logger, BaseLogger_Files
arglist = []
i = 0
while( i < len(sys.argv) ):
if sys.argv[i]=='-p4pg':
i = i+2
elif sys.argv[i]=='-p4wd':
i = i+2
else:
arglist.append( sys.argv[i] )
i = i+1
progname = os.path.basename(arglist[0])
usage = progname + " stack outdir <mask> --focus=3Dmask --radius=outer_radius --delta=angular_step" +\
"--an=angular_neighborhood --maxit=max_iter --CTF --sym=c1 --function=user_function --independent=indenpendent_runs --number_of_images_per_group=number_of_images_per_group --low_pass_filter=.25 --seed=random_seed"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--focus", type="string", default=None, help="3D mask for focused clustering ")
parser.add_option("--ir", type= "int", default= 1, help="inner radius for rotational correlation > 0 (set to 1)")
parser.add_option("--radius", type= "int", default=-1, help="outer radius for rotational correlation <nx-1 (set to the radius of the particle)")
parser.add_option("--maxit", type= "int", default=50, help="maximum number of iteration")
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 ")
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='0.25', help="step size of the translation search in both directions direction, search is -xr, -xr+ts, 0, xr-ts, xr ")
parser.add_option("--delta", type="string", default='2', help="angular step of reference projections")
parser.add_option("--an", type="string", default='-1', help="angular neighborhood for local searches")
parser.add_option("--center", type="int", default=0, help="0 - if you do not want the volume to be centered, 1 - center the volume using cog (default=0)")
parser.add_option("--nassign", type="int", default=1, help="number of reassignment iterations performed for each angular step (set to 3) ")
parser.add_option("--nrefine", type="int", default=0, help="number of alignment iterations performed for each angular step (set to 1) ")
parser.add_option("--CTF", action="store_true", default=False, help="Consider CTF correction during the alignment ")
parser.add_option("--stoprnct", type="float", default=3.0, help="Minimum percentage of assignment change to stop the program")
parser.add_option("--sym", type="string", default='c1', help="symmetry of the structure ")
parser.add_option("--function", type="string", default='do_volume_mrk05', help="name of the reference preparation function")
parser.add_option("--independent", type="int", default= 3, help="number of independent run")
parser.add_option("--number_of_images_per_group", type='int', default=1000, help="number of images per groups")
parser.add_option("--low_pass_filter", type="float", default=-1.0, help="absolute frequency of low-pass filter for 3d sorting on the original image size" )
parser.add_option("--nxinit", type="int", default=64, help="initial image size for sorting" )
parser.add_option("--unaccounted", action="store_true", default=False, help="reconstruct the unaccounted images")
parser.add_option("--seed", type="int", default=-1, help="random seed for create initial random assignment for EQ Kmeans")
parser.add_option("--smallest_group", type="int", default=500, help="minimum members for identified group" )
parser.add_option("--previous_run1", type="string", default='', help="two previous runs" )
parser.add_option("--previous_run2", type="string", default='', help="two previous runs" )
parser.add_option("--group_size_for_unaccounted", type="int", default=500, help="size for unaccounted particles" )
parser.add_option("--chunkdir", type="string", default='', help="chunkdir for computing margin of error")
parser.add_option("--sausage", action="store_true", default=False, help="way of filter volume")
parser.add_option("--PWadjustment", type="string", default='', help="1-D power spectrum of PDB file used for EM volume power spectrum correction")
parser.add_option("--protein_shape", type="string", default='g', help="protein shape. It defines protein preferred orientation angles. Currently it has g and f two types ")
parser.add_option("--upscale", type="float", default=0.5, help=" scaling parameter to adjust the power spectrum of EM volumes")
parser.add_option("--wn", type="int", default=0, help="optimal window size for data processing")
parser.add_option("--interpolation", type="string", default="4nn", help="3-d reconstruction interpolation method, two options, trl and 4nn")
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 1 or len(args) > 4:
sxprint("Usage: " + usage)
sxprint("Please run \'" + progname + " -h\' for detailed options")
ERROR( "Invalid number of parameters used. Please see usage information above." )
return
else:
if len(args)>2:
mask_file = args[2]
else:
mask_file = None
orgstack =args[0]
masterdir =args[1]
sp_global_def.BATCH = True
#---initialize MPI related variables
nproc = mpi.mpi_comm_size( mpi.MPI_COMM_WORLD )
myid = mpi.mpi_comm_rank( mpi.MPI_COMM_WORLD )
mpi_comm = mpi.MPI_COMM_WORLD
main_node = 0
# Create the main log file
from sp_logger import Logger,BaseLogger_Files
if myid ==main_node:
log_main=Logger(BaseLogger_Files())
log_main.prefix=masterdir+"/"
else:
log_main = None
#--- fill input parameters into dictionary named after Constants
Constants ={}
Constants["stack"] =args[0]
Constants["masterdir"] =masterdir
Constants["mask3D"] =mask_file
Constants["focus3Dmask"] =options.focus
Constants["indep_runs"] =options.independent
Constants["stoprnct"] =options.stoprnct
Constants["number_of_images_per_group"] =options.number_of_images_per_group
Constants["CTF"] =options.CTF
Constants["maxit"] =options.maxit
Constants["ir"] =options.ir
Constants["radius"] =options.radius
Constants["nassign"] =options.nassign
Constants["rs"] =options.rs
Constants["xr"] =options.xr
Constants["yr"] =options.yr
Constants["ts"] =options.ts
Constants["delta"] =options.delta
Constants["an"] =options.an
Constants["sym"] =options.sym
Constants["center"] =options.center
Constants["nrefine"] =options.nrefine
Constants["user_func"] =options.function
Constants["low_pass_filter"] =options.low_pass_filter # enforced low_pass_filter
Constants["main_log_prefix"] =args[1]
#Constants["importali3d"] =options.importali3d
Constants["myid"] =myid
Constants["main_node"] =main_node
Constants["nproc"] =nproc
Constants["log_main"] =log_main
Constants["nxinit"] =options.nxinit
Constants["unaccounted"] =options.unaccounted
Constants["seed"] =options.seed
Constants["smallest_group"] =options.smallest_group
Constants["previous_runs"] =options.previous_run1+" "+options.previous_run2
Constants["sausage"] =options.sausage
Constants["chunkdir"] =options.chunkdir
Constants["PWadjustment"] =options.PWadjustment
Constants["upscale"] =options.upscale
Constants["wn"] =options.wn
Constants["3d-interpolation"] =options.interpolation
Constants["protein_shape"] =options.protein_shape
#Constants["frequency_stop_search"] =options.frequency_stop_search
#Constants["scale_of_number"] =options.scale_of_number
# -------------------------------------------------------------
#
# Create and initialize Tracker dictionary with input options
Tracker = {}
Tracker["constants"] = Constants
Tracker["maxit"] = Tracker["constants"]["maxit"]
Tracker["radius"] = Tracker["constants"]["radius"]
#Tracker["xr"] = ""
#Tracker["yr"] = "-1" # Do not change!
#Tracker["ts"] = 1
#Tracker["an"] = "-1"
#Tracker["delta"] = "2.0"
#Tracker["zoom"] = True
#Tracker["nsoft"] = 0
#Tracker["local"] = False
Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
Tracker["upscale"] = Tracker["constants"]["upscale"]
Tracker["applyctf"] = False # Should the data be premultiplied by the CTF. Set to False for local continuous.
#Tracker["refvol"] = None
Tracker["nxinit"] = Tracker["constants"]["nxinit"]
#Tracker["nxstep"] = 32
Tracker["icurrentres"] = -1
#Tracker["ireachedres"] = -1
Tracker["lowpass"] = Tracker["constants"]["low_pass_filter"]
Tracker["falloff"] = 0.1
#Tracker["inires"] = options.inires # Now in A, convert to absolute before using
Tracker["fuse_freq"] = 50 # Now in A, convert to absolute before using
#Tracker["delpreviousmax"]= False
#Tracker["anger"] = -1.0
#Tracker["shifter"] = -1.0
#Tracker["saturatecrit"] = 0.95
#Tracker["pixercutoff"] = 2.0
#Tracker["directory"] = ""
#Tracker["previousoutputdir"] = ""
#Tracker["eliminated-outliers"] = False
#Tracker["mainiteration"] = 0
#Tracker["movedback"] = False
#Tracker["state"] = Tracker["constants"]["states"][0]
#Tracker["global_resolution"] = 0.0
Tracker["orgstack"] = orgstack
#--------------------------------------------------------------------
# import from utilities
from sp_utilities import sample_down_1D_curve,get_initial_ID,remove_small_groups,print_upper_triangular_matrix,print_a_line_with_timestamp
from sp_utilities import convertasi,prepare_ptp,print_dict,get_resolution_mrk01,partition_to_groups,partition_independent_runs,get_outliers
from sp_utilities import merge_groups, save_alist, margin_of_error, get_margin_of_error, do_two_way_comparison, select_two_runs, get_ali3d_params
from sp_utilities import counting_projections, unload_dict, load_dict, get_stat_proj, create_random_list, get_number_of_groups, recons_mref
from sp_utilities import apply_low_pass_filter, get_groups_from_partition, get_number_of_groups, get_complementary_elements_total, update_full_dict
from sp_utilities import count_chunk_members, set_filter_parameters_from_adjusted_fsc, get_two_chunks_from_stack
####------------------------------------------------------------------
# another part
from sp_utilities import get_class_members, remove_small_groups, get_number_of_groups, get_stable_members_from_two_runs
from sp_utilities import two_way_comparison_single, get_leftover_from_stable, get_initial_ID, Kmeans_exhaustive_run
from sp_utilities import print_a_line_with_timestamp, split_a_group
#
# Get the pixel size; if none, set to 1.0, and the original image size
from sp_utilities import get_shrink_data_huang
from time import sleep
import sp_user_functions
user_func = sp_user_functions.factory[Tracker["constants"]["user_func"]]
if(myid == main_node):
line = ''
sxprint((line+"Initialization of 3-D sorting"))
a = get_im(Tracker["orgstack"])
nnxo = a.get_xsize()
if( Tracker["nxinit"] > nnxo ):
ERROR( "Image size less than minimum permitted $d"%Tracker["nxinit"] )
nnxo = -1 # we break here, so not sure what this is supposed to accomplish
return
else:
if Tracker["constants"]["CTF"]:
i = a.get_attr('ctf')
pixel_size = i.apix
fq = pixel_size/Tracker["fuse_freq"]
else:
pixel_size = 1.0
# No pixel size, fusing computed as 5 Fourier pixels
fq = 5.0/nnxo
del a
else:
nnxo = 0
fq = 0.0
pixel_size = 1.0
nnxo = bcast_number_to_all(nnxo, source_node = main_node)
if( nnxo < 0 ):
return
pixel_size = bcast_number_to_all(pixel_size, source_node = main_node)
fq = bcast_number_to_all(fq, source_node = main_node)
if Tracker["constants"]["wn"]==0:
Tracker["constants"]["nnxo"] = nnxo
else:
Tracker["constants"]["nnxo"] = Tracker["constants"]["wn"]
nnxo= Tracker["constants"]["wn"]
Tracker["constants"]["pixel_size"] = pixel_size
Tracker["fuse_freq"] = fq
del fq, nnxo, pixel_size
if(Tracker["constants"]["radius"] < 1):
Tracker["constants"]["radius"] = Tracker["constants"]["nnxo"]//2-2
elif((2*Tracker["constants"]["radius"] +2) > Tracker["constants"]["nnxo"]):
ERROR( "Particle radius set too large!", myid=myid )
return
####-----------------------------------------------------------------------------------------
# create the master directory
if myid == main_node:
if masterdir =="":
timestring = strftime("_%d_%b_%Y_%H_%M_%S", localtime())
masterdir ="master_sort3d"+timestring
li =len(masterdir)
else:
li = 0
cmd="{} {}".format("mkdir -p", masterdir)
os.system(cmd)
sp_global_def.write_command(masterdir)
else:
li=0
li = mpi.mpi_bcast( li, 1, mpi.MPI_INT, main_node, mpi.MPI_COMM_WORLD )[0]
if li>0:
masterdir = mpi.mpi_bcast( masterdir, li,MPI_CHAR, main_node, mpi.MPI_COMM_WORLD )
masterdir = string.join(masterdir,"")
####--- masterdir done!
if myid == main_node:
print_dict(Tracker["constants"],"Permanent settings of 3-D sorting program")
from time import sleep
while not os.path.exists(masterdir): # Be sure each proc is able to access the created dir
sxprint("Node ",myid," waiting...")
sleep(5)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
######### create a vstack from input stack to the local stack in masterdir
# stack name set to default
Tracker["constants"]["stack"] = "bdb:"+masterdir+"/rdata"
Tracker["constants"]["ali3d"] = os.path.join(masterdir, "ali3d_init.txt")
Tracker["constants"]["partstack"] = Tracker["constants"]["ali3d"]
Tracker["constants"]["ctf_params"] = os.path.join(masterdir, "ctf_params.txt")
######
if myid == main_node:
if(Tracker["orgstack"][:4] == "bdb:"): cmd = "{} {} {}".format("e2bdb.py", Tracker["orgstack"],"--makevstack="+Tracker["constants"]["stack"])
else: cmd = "{} {} {}".format("sp_cpy.py", orgstack, Tracker["constants"]["stack"])
cmdexecute(cmd)
cmd = "{} {} {} {} ".format("sp_header.py", Tracker["constants"]["stack"],"--params=xform.projection","--export="+Tracker["constants"]["ali3d"])
cmdexecute(cmd)
cmd = "{} {} {} {} ".format("sp_header.py", Tracker["constants"]["stack"],"--params=ctf","--export="+Tracker["constants"]["ctf_params"])
cmdexecute(cmd)
#keepchecking = False
total_stack = EMUtil.get_image_count(Tracker["orgstack"])
else:
total_stack =0
total_stack = bcast_number_to_all(total_stack, source_node = main_node)
"""
if myid==main_node:
from EMAN2db import db_open_dict
OB = db_open_dict(orgstack)
DB = db_open_dict(Tracker["constants"]["stack"])
for i in xrange(total_stack):
DB[i] = OB[i]
OB.close()
DB.close()
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
if myid==main_node:
params= []
for i in xrange(total_stack):
e=get_im(orgstack,i)
phi,theta,psi,s2x,s2y = get_params_proj(e)
params.append([phi,theta,psi,s2x,s2y])
write_text_row(params,Tracker["constants"]["ali3d"])
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
"""
#Tracker["total_stack"] = total_stack
Tracker["constants"]["total_stack"] = total_stack
Tracker["shrinkage"] = float(Tracker["nxinit"])/Tracker["constants"]["nnxo"]
#####------------------------------------------------------------------------------
if Tracker["constants"]["mask3D"]:
Tracker["mask3D"] = os.path.join(masterdir,"smask.hdf")
else:Tracker["mask3D"] = None
if Tracker["constants"]["focus3Dmask"]: Tracker["focus3D"]=os.path.join(masterdir,"sfocus.hdf")
else: Tracker["focus3D"] = None
if myid ==main_node:
if Tracker["constants"]["mask3D"]:
get_shrink_3dmask(Tracker["nxinit"],Tracker["constants"]["mask3D"]).write_image(Tracker["mask3D"])
if Tracker["constants"]["focus3Dmask"]:
mask_3D = get_shrink_3dmask(Tracker["nxinit"],Tracker["constants"]["focus3Dmask"])
st = Util.infomask(mask_3D, None, True)
if( st[0] == 0.0 ):
ERROR( "sxrsort3d","incorrect focused mask, after binarize all values zero" )
mask_3D.write_image(Tracker["focus3D"])
del mask_3D
if Tracker["constants"]["PWadjustment"]:
PW_dict={}
nxinit_pwsp=sample_down_1D_curve(Tracker["constants"]["nxinit"],Tracker["constants"]["nnxo"],Tracker["constants"]["PWadjustment"])
Tracker["nxinit_PW"] = os.path.join(masterdir,"spwp.txt")
if myid ==main_node:
write_text_file(nxinit_pwsp,Tracker["nxinit_PW"])
PW_dict[Tracker["constants"]["nnxo"]] =Tracker["constants"]["PWadjustment"]
PW_dict[Tracker["constants"]["nxinit"]] =Tracker["nxinit_PW"]
Tracker["PW_dict"] = PW_dict
###----------------------------------------------------------------------------------
####--------------------------- Extract the previous results #####################################################
from random import shuffle
if myid ==main_node:
log_main.add(" Sphire rsort3d ")
log_main.add("extract stable groups from two previous runs")
stable_member_list = get_stable_members_from_two_runs(Tracker["constants"]["previous_runs"], Tracker["constants"]["total_stack"], log_main)
Tracker["this_unaccounted_list"], new_stable_P1 = get_leftover_from_stable(stable_member_list, Tracker["constants"]["total_stack"], Tracker["constants"]["smallest_group"])
Tracker["this_unaccounted_list"].sort()
Tracker["total_stack"] = len(Tracker["this_unaccounted_list"])
log_main.add("new stable is %d"%len(new_stable_P1))
else:
Tracker["total_stack"] = 0
Tracker["this_unaccounted_list"] = 0
stable_member_list =0
stable_member_list = wrap_mpi_bcast(stable_member_list, main_node)
Tracker["total_stack"] = bcast_number_to_all(Tracker["total_stack"], source_node = main_node)
left_one_from_old_two_runs = wrap_mpi_bcast(Tracker["this_unaccounted_list"], main_node)
if myid ==main_node:
write_text_file(left_one_from_old_two_runs, os.path.join(masterdir,"unaccounted_from_two_previous_runs.txt"))
sxprint(" Extracting results of two previous runs is done!")
#################################### Estimate resolution----------------------#############
#### make chunkdir dictionary for computing margin of error
chunk_list = []
if Tracker["constants"]["chunkdir"] !="": ##inhere previous random assignment of odd and even
if myid == main_node:
chunk_one = read_text_file(os.path.join(Tracker["constants"]["chunkdir"],"chunk0.txt"))
chunk_two = read_text_file(os.path.join(Tracker["constants"]["chunkdir"],"chunk1.txt"))
else:
chunk_one = 0
chunk_two = 0
chunk_one = wrap_mpi_bcast(chunk_one, main_node)
chunk_two = wrap_mpi_bcast(chunk_two, main_node)
else: ## if traces are lost, then creating new random assignment of odd, even particles
chunks = list(range(Tracker["constants"]["total_stack"]))
shuffle(chunks)
chunk_one =chunks[0:Tracker["constants"]["total_stack"]//2]
chunk_two =chunks[Tracker["constants"]["total_stack"]//2:Tracker["constants"]["total_stack"]]
chunk_one = wrap_mpi_bcast(chunk_one, main_node)
chunk_two = wrap_mpi_bcast(chunk_two, main_node)
###### Fill chunk ID into headers when calling get_shrink_data_huang
if myid ==main_node:
sxprint(" random odd and even assignment done !")
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
#------------------------------------------------------------------------------
Tracker["chunk_dict"] = {}
for element in chunk_one: Tracker["chunk_dict"][element] = 0
for element in chunk_two: Tracker["chunk_dict"][element] = 1
Tracker["P_chunk0"] = len(chunk_one)/float(Tracker["constants"]["total_stack"])
Tracker["P_chunk1"] = len(chunk_two)/float(Tracker["constants"]["total_stack"])
### create two volumes to estimate resolution
if myid == main_node:
write_text_file(chunk_one, os.path.join(masterdir,"chunk0.txt"))
write_text_file(chunk_two, os.path.join(masterdir,"chunk1.txt"))
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
vols = []
for index in range(2):
data1,old_shifts1 = get_shrink_data_huang(Tracker,Tracker["constants"]["nxinit"], os.path.join(masterdir,"chunk%d.txt"%index), Tracker["constants"]["partstack"], myid, main_node, nproc, preshift = True)
vol1 = recons3d_4nn_ctf_MPI(myid=myid, prjlist=data1, symmetry=Tracker["constants"]["sym"], finfo=None)
if myid ==main_node:
vol1_file_name = os.path.join(masterdir, "vol%d.hdf"%index)
vol1.write_image(vol1_file_name)
vols.append(vol1)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
if myid ==main_node:
low_pass, falloff, currentres = get_resolution_mrk01(vols, Tracker["constants"]["radius"]*Tracker["shrinkage"], Tracker["constants"]["nxinit"], masterdir,Tracker["mask3D"])
if low_pass > Tracker["constants"]["low_pass_filter"]: low_pass = Tracker["constants"]["low_pass_filter"]
else:
low_pass = 0.0
falloff = 0.0
currentres = 0.0
currentres = bcast_number_to_all(currentres,source_node = main_node)
low_pass = bcast_number_to_all(low_pass,source_node = main_node)
falloff = bcast_number_to_all(falloff,source_node = main_node)
Tracker["currentres"] = currentres
####################################################################
Tracker["falloff"] = falloff
if Tracker["constants"]["low_pass_filter"] == -1.0:
Tracker["low_pass_filter"] = low_pass*Tracker["shrinkage"]
else:
Tracker["low_pass_filter"] = Tracker["constants"]["low_pass_filter"]/Tracker["shrinkage"]
Tracker["lowpass"] = Tracker["low_pass_filter"]
Tracker["falloff"] = 0.1
Tracker["global_fsc"] = os.path.join(masterdir,"fsc.txt")
##################################################################
if myid ==main_node:
log_main.add("The command-line inputs are :")
log_main.add("**********************************************************")
for a in sys.argv:
log_main.add(a)
log_main.add("**********************************************************")
from sp_filter import filt_tanl
##################### START 3-D sorting ##########################
if myid ==main_node:
log_main.add("----------3-D sorting program------- ")
log_main.add("current resolution %6.3f for images of original size in terms of absolute frequency"%Tracker["currentres"])
log_main.add("equivalent to %f Angstrom resolution"%(round((Tracker["constants"]["pixel_size"]/Tracker["currentres"]/Tracker["shrinkage"]),4)))
filt_tanl(get_im(os.path.join(masterdir, "vol0.hdf")), Tracker["low_pass_filter"], 0.1).write_image(os.path.join(masterdir, "volf0.hdf"))
filt_tanl(get_im(os.path.join(masterdir, "vol1.hdf")), Tracker["low_pass_filter"], 0.1).write_image(os.path.join(masterdir, "volf1.hdf"))
sxprint(" random odd and even assignment done !")
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
## ---------------------------------------------------------------------------------------------########
## Stop program and output results when the leftover from two sort3d runs is not sufficient for a new run ########
## --------------------------------------------------- --------------------------------------- ######
Tracker["number_of_groups"] = get_number_of_groups(len(left_one_from_old_two_runs), Tracker["constants"]["number_of_images_per_group"])
if Tracker["number_of_groups"] <=1 : # programs finishes
if myid == main_node:
log_main.add("the unaccounted ones are no sufficient for a simple two-group run, output results!")
log_main.add("this implies your two sort3d runs already achieved high reproducibale ratio. ")
log_main.add("Or your number_of_images_per_group is too large ")
log_main.add("the final reproducibility is %f"%((Tracker["constants"]["total_stack"]-len(Tracker["this_unaccounted_list"]))/float(Tracker["constants"]["total_stack"])))
for i in range(len(stable_member_list)): write_text_file(stable_member_list[i], os.path.join(masterdir,"P2_final_class%d.txt"%i))
mask3d = get_im(Tracker["constants"]["mask3D"])
else:
mask3d = model_blank(Tracker["constants"]["nnxo"],Tracker["constants"]["nnxo"],Tracker["constants"]["nnxo"])
bcast_EMData_to_all(mask3d, myid, main_node)
for igrp in range(len(stable_member_list)):
#name_of_class_file = os.path.join(masterdir, "P2_final_class%d.txt"%igrp)
data, old_shifts = get_shrink_data_huang(Tracker,Tracker["constants"]["nnxo"], os.path.join(masterdir, "P2_final_class%d.txt"%igrp), Tracker["constants"]["partstack"], myid, main_node, nproc,preshift = True)
if Tracker["constants"]["CTF"]:
volref, fscc = rec3D_two_chunks_MPI(data, 1.0, Tracker["constants"]["sym"], mask3d,os.path.join(masterdir,"resolution_%02d.txt"%igrp), myid, main_node, index =-1, npad=2)
else:
sxprint("Missing CTF flag!")
return
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
#nx_of_image=volref.get_xsize()
if Tracker["constants"]["PWadjustment"] : Tracker["PWadjustment"] = Tracker["PW_dict"][Tracker["constants"]["nnxo"]]
else: Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
if myid ==main_node:
try:
lowpass = search_lowpass(fscc)
falloff = 0.1
except:
lowpass = 0.4
falloff = 0.1
log_main.add(" lowpass and falloff from fsc are %f %f"%(lowpass, falloff))
lowpass = round(lowpass,4)
falloff = round(min(0.1,falloff),4)
Tracker["lowpass"] = lowpass
Tracker["falloff"] = falloff
refdata = [None]*4
refdata[0] = volref
refdata[1] = Tracker
refdata[2] = Tracker["constants"]["myid"]
refdata[3] = Tracker["constants"]["nproc"]
volref = user_func(refdata)
cutoff = Tracker["constants"]["pixel_size"]/lowpass
log_main.add("%d vol low pass filer %f %f cut to %f Angstrom"%(igrp,Tracker["lowpass"],Tracker["falloff"],cutoff))
volref.write_image(os.path.join(masterdir,"volf_final%d.hdf"%igrp))
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
return
else: # Continue clustering on unaccounted ones that produced by two_way comparison of two previous runs
#########################################################################################################################
#if Tracker["constants"]["number_of_images_per_group"] ==-1: # Estimate number of images per group from delta, and scale up
# or down by scale_of_number
# number_of_images_per_group = int(Tracker["constants"]["scale_of_number"]*len(n_angles))
#
#########################################################################################################################P2
if myid ==main_node:
sxprint(" Now continue clustering on accounted ones because they can make at least two groups!")
P2_partitions = []
number_of_P2_runs = 2 # Notice P2 start from two P1 runs
### input list_to_be_processed
import copy
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
for iter_P2_run in range(number_of_P2_runs): # two runs such that one can obtain reproducibility
list_to_be_processed = left_one_from_old_two_runs[:]#Tracker["this_unaccounted_list"][:]
Tracker["this_unaccounted_list"] = left_one_from_old_two_runs[:]
if myid == main_node : new_stable1 = new_stable_P1[:]
total_stack = len(list_to_be_processed) # This is the input from two P1 runs
#number_of_images_per_group = Tracker["constants"]["number_of_images_per_group"]
P2_run_dir = os.path.join(masterdir, "P2_run%d"%iter_P2_run)
Tracker["number_of_groups"] = get_number_of_groups(total_stack, Tracker["constants"]["number_of_images_per_group"])
if myid == main_node:
cmd="{} {}".format("mkdir", P2_run_dir)
os.system(cmd)
log_main.add("----------------P2 independent run %d--------------"%iter_P2_run)
log_main.add("user provided number_of_images_per_group %d"%Tracker["constants"]["number_of_images_per_group"])
sxprint("----------------P2 independent run %d--------------"%iter_P2_run)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
#
#Tracker["number_of_groups"] = get_number_of_groups(total_stack,Tracker["constants"]["number_of_images_per_group"])
generation = 0
if myid == main_node:
log_main.add("number of groups is %d"%Tracker["number_of_groups"])
log_main.add("total stack %d"%total_stack)
while( Tracker["number_of_groups"]>=2 ):
partition_dict = {}
full_dict = {}
workdir = os.path.join(P2_run_dir,"generation%03d"%generation)
Tracker["this_dir"] = workdir
if myid ==main_node:
cmd="{} {}".format("mkdir", workdir)
os.system(cmd)
log_main.add("---- generation %5d"%generation)
log_main.add("number of images per group is set as %d"%Tracker["constants"]["number_of_images_per_group"])
log_main.add("the initial number of groups is %d "%Tracker["number_of_groups"])
log_main.add(" the number to be processed in this generation is %d"%len(list_to_be_processed))
sxprint("---- generation %5d"%generation)
#core=read_text_row(Tracker["constants"]["ali3d"],-1)
#write_text_row(core, os.path.join(workdir,"node%d.txt"%myid))
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
Tracker["this_data_list"] = list_to_be_processed # leftover of P1 runs
Tracker["total_stack"] = len(list_to_be_processed)
create_random_list(Tracker)
###------ For super computer ##############
update_full_dict(list_to_be_processed, Tracker)
###----
##### ----------------Independent runs for EQ-Kmeans ------------------------------------
for indep_run in range(Tracker["constants"]["indep_runs"]):
Tracker["this_particle_list"] = Tracker["this_indep_list"][indep_run]
ref_vol = recons_mref(Tracker)
if myid ==main_node: log_main.add("independent run %10d"%indep_run)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
#this_particle_text_file = # for get_shrink_data
if myid ==main_node:
write_text_file(list_to_be_processed, os.path.join(workdir, "independent_list_%03d.txt"%indep_run))
mref_ali3d_EQ_Kmeans(ref_vol, os.path.join(workdir, "EQ_Kmeans%03d"%indep_run), os.path.join(workdir, "independent_list_%03d.txt"%indep_run), Tracker)
partition_dict[indep_run] = Tracker["this_partition"]
del ref_vol
Tracker["partition_dict"] = partition_dict
Tracker["this_total_stack"] = Tracker["total_stack"]
do_two_way_comparison(Tracker)
##############################
if myid ==main_node: log_main.add("Now calculate stable volumes")
if myid ==main_node:
for igrp in range(len(Tracker["two_way_stable_member"])):
Tracker["this_data_list"] = Tracker["two_way_stable_member"][igrp]
write_text_file(Tracker["this_data_list"], os.path.join(workdir,"stable_class%d.txt"%igrp))
Tracker["this_data_list_file"] = -1
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
###
number_of_ref_class = []
ref_vol_list = []
for igrp in range(len(Tracker["two_way_stable_member"])):
data, old_shifts = get_shrink_data_huang(Tracker,Tracker["nxinit"], os.path.join(workdir, "stable_class%d.txt"%igrp), Tracker["constants"]["partstack"], myid, main_node, nproc, preshift = True)
volref = recons3d_4nn_ctf_MPI(myid=myid,prjlist=data,symmetry=Tracker["constants"]["sym"],finfo = None)
ref_vol_list.append(volref)
number_of_ref_class.append(len(Tracker["this_data_list"]))
if myid ==main_node:
log_main.add("group %d members %d "%(igrp,len(Tracker["this_data_list"])))
#ref_vol_list=apply_low_pass_filter(ref_vol_list,Tracker)
for iref in range(len(ref_vol_list)): ref_vol_list[iref].write_image(os.path.join(workdir,"vol_stable.hdf"),iref)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
################################
Tracker["number_of_ref_class"] = number_of_ref_class
Tracker["this_data_list"] = Tracker["this_accounted_list"]
outdir = os.path.join(workdir, "Kmref")
empty_groups,res_classes,final_list = ali3d_mref_Kmeans_MPI(ref_vol_list, outdir, os.path.join(workdir,"Accounted.txt"), Tracker)
Tracker["this_unaccounted_list"] = get_complementary_elements(list_to_be_processed,final_list)
if myid == main_node: log_main.add("the number of particles not processed is %d"%len(Tracker["this_unaccounted_list"]))
update_full_dict(Tracker["this_unaccounted_list"], Tracker)
if myid == main_node: write_text_file(Tracker["this_unaccounted_list"], Tracker["this_unaccounted_text"])
Tracker["number_of_groups"] = len(res_classes)
### Update data
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
if myid == main_node:
number_of_ref_class=[]
log_main.add(" Compute volumes of original size")
for igrp in range(Tracker["number_of_groups"]):
if os.path.exists( os.path.join( outdir,"Class%d.txt"%igrp ) ):
new_stable1.append( read_text_file( os.path.join( outdir, "Class%d.txt"%igrp ) ) )
log_main.add(" read Class file %d"%igrp)
number_of_ref_class.append(len(new_stable1))
else: number_of_ref_class = 0
number_of_ref_class = wrap_mpi_bcast(number_of_ref_class,main_node)
################################
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
if myid ==main_node:
vol_list = []
for igrp in range(Tracker["number_of_groups"]):
if myid ==main_node: log_main.add("start vol %d"%igrp)
data,old_shifts = get_shrink_data_huang(Tracker,Tracker["constants"]["nnxo"], os.path.join(outdir,"Class%d.txt"%igrp), Tracker["constants"]["partstack"],myid, main_node, nproc, preshift = True)
volref = recons3d_4nn_ctf_MPI(myid=myid, prjlist = data, symmetry = Tracker["constants"]["sym"],finfo= None)
if myid == main_node:
vol_list.append(volref)
log_main.add(" vol %d is done"%igrp)
Tracker["number_of_ref_class"] = number_of_ref_class
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
generation +=1
#################################
if myid ==main_node:
for ivol in range(len(vol_list)): vol_list[ivol].write_image(os.path.join(workdir, "vol_of_Classes.hdf"),ivol)
filt_tanl(vol_list[ivol],Tracker["constants"]["low_pass_filter"],.1).write_image(os.path.join(workdir, "volf_of_Classes.hdf"),ivol)
log_main.add("number of unaccounted particles %10d"%len(Tracker["this_unaccounted_list"]))
log_main.add("number of accounted particles %10d"%len(Tracker["this_accounted_list"]))
del vol_list
Tracker["this_data_list"] = Tracker["this_unaccounted_list"]
Tracker["total_stack"] = len(Tracker["this_unaccounted_list"])
Tracker["this_total_stack"] = Tracker["total_stack"]
#update_full_dict(complementary)
#number_of_groups = int(float(len(Tracker["this_unaccounted_list"]))/number_of_images_per_group)
del list_to_be_processed
list_to_be_processed = copy.deepcopy(Tracker["this_unaccounted_list"])
Tracker["number_of_groups"] = get_number_of_groups(len(list_to_be_processed),Tracker["constants"]["number_of_images_per_group"])
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
#############################################################################################################################
### Reconstruct the unaccounted is only done once
if (Tracker["constants"]["unaccounted"] and (len(Tracker["this_unaccounted_list"]) != 0)):
data,old_shifts = get_shrink_data_huang(Tracker,Tracker["constants"]["nnxo"],Tracker["this_unaccounted_text"],Tracker["constants"]["partstack"],myid,main_node,nproc,preshift = True)
volref = recons3d_4nn_ctf_MPI(myid=myid, prjlist = data, symmetry=Tracker["constants"]["sym"],finfo=None)
volref = filt_tanl(volref, Tracker["constants"]["low_pass_filter"],.1)
if myid ==main_node: volref.write_image(os.path.join(workdir, "volf_unaccounted.hdf"))
######## Exhaustive Kmeans #############################################
if myid ==main_node:
if len(Tracker["this_unaccounted_list"])>=Tracker["constants"]["smallest_group"]:
new_stable1.append(Tracker["this_unaccounted_list"])
unaccounted = get_complementary_elements_total(Tracker["constants"]["total_stack"], final_list)
Tracker["number_of_groups"] = len(new_stable1)
log_main.add("----------------Exhaustive Kmeans------------------")
log_main.add("number_of_groups is %d"%Tracker["number_of_groups"])
else: Tracker["number_of_groups"] = 0
### prepare references for final K-means
if myid == main_node:
final_list =[]
for alist in new_stable1:
for element in alist:final_list.append(int(element))
unaccounted = get_complementary_elements_total(Tracker["constants"]["total_stack"],final_list)
if len(unaccounted) > Tracker["constants"]["smallest_group"]: # treat unaccounted ones also as a group if it is not too small.
new_stable1.append(unaccounted)
Tracker["number_of_groups"] = len(new_stable1)
for any in unaccounted:final_list.append(any)
log_main.add("total number %d"%len(final_list))
else: final_list = 0
Tracker["number_of_groups"] = bcast_number_to_all(Tracker["number_of_groups"],source_node = main_node)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
final_list = wrap_mpi_bcast(final_list, main_node)
workdir = os.path.join(P2_run_dir,"Exhaustive_Kmeans") # new workdir
if myid==main_node:
os.mkdir(workdir)
write_text_file(final_list, os.path.join(workdir,"final_list.txt"))
else: new_stable1 = 0
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
## Create reference volumes
if myid == main_node:
number_of_ref_class = []
for igrp in range(Tracker["number_of_groups"]):
class_file = os.path.join(workdir,"final_class%d.txt"%igrp)
write_text_file(new_stable1[igrp],class_file)
log_main.add(" group %d number of particles %d"%(igrp,len(new_stable1[igrp])))
number_of_ref_class.append(len(new_stable1[igrp]))
else: number_of_ref_class= 0
number_of_ref_class = wrap_mpi_bcast(number_of_ref_class,main_node)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
ref_vol_list = []
for igrp in range(Tracker["number_of_groups"]):
if myid ==main_node : sxprint(" prepare reference %d"%igrp)
#Tracker["this_data_list_file"] = os.path.join(workdir,"final_class%d.txt"%igrp)
data,old_shifts = get_shrink_data_huang(Tracker, Tracker["nxinit"],os.path.join(workdir,"final_class%d.txt"%igrp), Tracker["constants"]["partstack"], myid,main_node,nproc,preshift = True)
volref = recons3d_4nn_ctf_MPI(myid=myid, prjlist = data, symmetry=Tracker["constants"]["sym"], finfo = None)
#volref = filt_tanl(volref, Tracker["low_pass_filter"],.1)
#if myid == main_node:
# volref.write_image(os.path.join(masterdir,"volf_stable.hdf"),iref)
#volref = resample(volref,Tracker["shrinkage"])
bcast_EMData_to_all(volref, myid, main_node)
ref_vol_list.append(volref)
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
### -------variables used in Kmeans_exhaustive_run-----
Tracker["number_of_ref_class"] = number_of_ref_class
Tracker["this_data_list"] = final_list
Tracker["total_stack"] = len(final_list)
Tracker["this_dir"] = workdir
Tracker["this_data_list_file"] = os.path.join(workdir,"final_list.txt")
KE_group = Kmeans_exhaustive_run(ref_vol_list,Tracker) #
P2_partitions.append(KE_group[:][:])
if myid ==main_node:
log_main.add(" the number of groups after exhaustive Kmeans is %d"%len(KE_group))
for ike in range(len(KE_group)):log_main.add(" group %d number of objects %d"%(ike,len(KE_group[ike])))
del new_stable1
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
if myid == main_node: log_main.add("P2 runs are done, now start two-way comparision to exclude those that are not reproduced ")
reproduced_groups = two_way_comparison_single(P2_partitions[0],P2_partitions[1],Tracker)# Here partition IDs are original indexes.
###### ----------------Reconstruct reproduced groups------------------------#######
######
if myid == main_node:
for index_of_reproduced_groups in range(len(reproduced_groups)):
name_of_class_file = os.path.join(masterdir, "P2_final_class%d.txt"%index_of_reproduced_groups)
write_text_file(reproduced_groups[index_of_reproduced_groups],name_of_class_file)
log_main.add("-------start to reconstruct reproduced volumes individully to orignal size-----------")
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
if Tracker["constants"]["mask3D"]: mask_3d = get_shrink_3dmask(Tracker["constants"]["nnxo"],Tracker["constants"]["mask3D"])
else: mask_3d = None
for igrp in range(len(reproduced_groups)):
data,old_shifts = get_shrink_data_huang(Tracker,Tracker["constants"]["nnxo"],os.path.join(masterdir, "P2_final_class%d.txt"%igrp),Tracker["constants"]["partstack"],myid,main_node,nproc,preshift = True)
#volref = recons3d_4nn_ctf_MPI(myid=myid, prjlist = data, symmetry=Tracker["constants"]["sym"], finfo=None)
if Tracker["constants"]["CTF"]:
volref, fscc = rec3D_two_chunks_MPI(data,1.0,Tracker["constants"]["sym"],mask_3d, \
os.path.join(masterdir,"resolution_%02d.txt"%igrp),myid,main_node,index =-1,npad =2,finfo=None)
else:
sxprint("Missing CTF flag!")
return
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
fscc = read_text_file(os.path.join(masterdir, "resolution_%02d.txt"%igrp),-1)
nx_of_image = volref.get_xsize()
if Tracker["constants"]["PWadjustment"]: Tracker["PWadjustment"] = Tracker["PW_dict"][nx_of_image]
else: Tracker["PWadjustment"] = Tracker["constants"]["PWadjustment"]
try:
lowpass = search_lowpass(fscc)
falloff = 0.1
except:
lowpass= 0.4
falloff= 0.1
sxprint(lowpass)
lowpass=round(lowpass,4)
falloff=round(min(.1,falloff),4)
Tracker["lowpass"]= lowpass
Tracker["falloff"]= falloff
if myid == main_node:
refdata =[None]*4
refdata[0] = volref
refdata[1] = Tracker
refdata[2] = Tracker["constants"]["myid"]
refdata[3] = Tracker["constants"]["nproc"]
volref = user_func(refdata)
cutoff = Tracker["constants"]["pixel_size"]/lowpass
log_main.add("%d vol low pass filer %f %f cut to %f Angstrom"%(igrp,Tracker["lowpass"],Tracker["falloff"],cutoff))
volref.write_image(os.path.join(masterdir,"volf_final%d.hdf"%igrp))
if myid==main_node: log_main.add(" sxsort3d_P2 finishes. ")
# Finish program
mpi.mpi_barrier( mpi.MPI_COMM_WORLD )
return
def main():
global Tracker, Blockdata
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 = True if options.pw_adjustment=='analytical_model' else False
no_adjustment = True if options.pw_adjustment=='no_adjustment' else False
B_enhance = True if options.pw_adjustment=='bfactor' else False
adjust_to_given_pw2 = True if not (adjust_to_analytic_model or no_adjustment or B_enhance) else False
# mpi
nproc = mpi.mpi_comm_size(mpi.MPI_COMM_WORLD)
myid = mpi.mpi_comm_rank(mpi.MPI_COMM_WORLD)
Blockdata = {}
Blockdata["nproc"] = nproc
Blockdata["myid"] = myid
Blockdata["main_node"] = 0
Blockdata["shared_comm"] = mpi.mpi_comm_split_type(mpi.MPI_COMM_WORLD, mpi.MPI_COMM_TYPE_SHARED, 0, mpi.MPI_INFO_NULL)
Blockdata["myid_on_node"] = mpi.mpi_comm_rank(Blockdata["shared_comm"])
Blockdata["no_of_processes_per_group"] = mpi.mpi_comm_size(Blockdata["shared_comm"])
masters_from_groups_vs_everything_else_comm = mpi.mpi_comm_split( mpi.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.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
sp_global_def.BATCH = True
sp_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.MPI_COMM_WORLD)
if checking_flag ==1:
ERROR( "User provided power spectrum does not exist", myid=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"
sxprint(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.makedirs(masterdir)
else:
if os.path.exists(masterdir): sxprint("%s already exists"%masterdir)
else:
os.makedirs(masterdir)
sp_global_def.write_command(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.mpi_bcast(li,1,mpi.MPI_INT,Blockdata["main_node"],mpi.MPI_COMM_WORLD)[0]
masterdir = mpi.mpi_bcast(masterdir,li,mpi.MPI_CHAR,Blockdata["main_node"],mpi.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"]):
sxprint("Node ", Blockdata["myid"], " waiting...", Tracker["constants"]["masterdir"])
sleep(1)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
if(Blockdata["myid"] == Blockdata["main_node"]):
init_dict = {}
sxprint(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.MPI_COMM_WORLD)
###
do_ctf = True
if options.noctf: do_ctf = False
if(Blockdata["myid"] == Blockdata["main_node"]):
if do_ctf: sxprint("CTF correction is on")
else: sxprint("CTF correction is off")
if options.local_alignment: sxprint("local refinement is on")
else: sxprint("local refinement is off")
if B_enhance: sxprint("Bfactor is to be applied on averages")
elif adjust_to_given_pw2: sxprint("PW of averages is adjusted to a given 1D PW curve")
elif adjust_to_analytic_model: sxprint("PW of averages is adjusted to analytical model")
else: sxprint("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:
sxprint("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.", myid=Blockdata["myid"] )
## 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), myid=Blockdata["myid"] )
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.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.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"]):
sxprint("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:
sxprint("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.MPI_COMM_WORLD)
list_dict = wrap_mpi_bcast(list_dict, Blockdata["main_node"], communicator = mpi.MPI_COMM_WORLD)
memlist = wrap_mpi_bcast(memlist, Blockdata["main_node"], communicator = mpi.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
# distribute workload among mpi processes
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.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)]
data_list = [ None for im in range(navg)]
plist_dict = {}
if Blockdata["myid"] == Blockdata["main_node"]:
if B_enhance:
sxprint("Avg ID B-factor FH1(Res before ali) FH2(Res after ali)")
else:
sxprint("Avg ID FH1(Res before ali) FH2(Res after ali)")
FH_list = [ [0, 0.0, 0.0] for im in range(navg)]
for iavg in range(image_start,image_end):
mlist = EMData.read_images(Tracker["constants"]["orgstack"], list_dict[iavg])
for im in range(len(mlist)):
set_params2D(mlist[im], params_dict[iavg][im], xform = "xform.align2d")
if options.local_alignment:
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
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"])
sxprint(" %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)
sxprint(" %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)
sxprint(" %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
sxprint(strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>", "Refined average %7d"%iavg)
## send to main node to write
mpi.mpi_barrier(mpi.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.MPI_COMM_WORLD)
wrap_mpi_send(FH_list, Blockdata["main_node"], mpi.MPI_COMM_WORLD)
elif cpu_dict[im]!= Blockdata["main_node"] and Blockdata["myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(cpu_dict[im], mpi.MPI_COMM_WORLD)
plist_dict[im] = dummy
dummy = wrap_mpi_recv(cpu_dict[im], mpi.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.MPI_COMM_WORLD)
elif cpu_dict[im]!= Blockdata["main_node"] and Blockdata["myid"] == Blockdata["main_node"]:
dummy = wrap_mpi_recv(cpu_dict[im], mpi.MPI_COMM_WORLD)
FH_list[im] = dummy[im]
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
mpi.mpi_barrier(mpi.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.mpi_barrier(mpi.MPI_COMM_WORLD)
target_xr =3
target_yr =3
if( Blockdata["myid"] == 0):
cmd = "{} {} {} {} {} {} {} {} {} {}".format("sp_chains.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)
return
def main(args):
progname = os.path.basename(sys.argv[0])
usage = progname + " stack [output_directory] --ir=inner_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translational_search_step --delta=angular_step --center=center_type --maxit1=max_iter1 --maxit2=max_iter2 --L2threshold=0.1 --ref_a=S --sym=c1"
usage += """
stack 2D images in a stack file: (default required string)
directory output directory name: into which the results will be written (if it does not exist, it will be created, if it does exist, the results will be written possibly overwriting previous results) (default required string)
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--radius", type="int", default=29, help="radius of the particle: has to be less than < int(nx/2)-1 (default 29)")
parser.add_option("--xr", type="string", default='0', help="range for translation search in x direction: search is +/xr in pixels (default '0')")
parser.add_option("--yr", type="string", default='0', help="range for translation search in y direction: if omitted will be set to xr, search is +/yr in pixels (default '0')")
parser.add_option("--mask3D", type="string", default=None, help="3D mask file: (default sphere)")
parser.add_option("--moon_elimination", type="string", default='', help="elimination of disconnected pieces: two arguments: mass in KDa and pixel size in px/A separated by comma, no space (default none)")
parser.add_option("--ir", type="int", default=1, help="inner radius for rotational search: > 0 (default 1)")
# 'radius' and 'ou' are the same as per Pawel's request; 'ou' is hidden from the user
# the 'ou' variable is not changed to 'radius' in the 'sparx' program. This change is at interface level only for sxviper.
##### XXXXXXXXXXXXXXXXXXXXXX option does not exist in docs XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
parser.add_option("--ou", type="int", default=-1, help=SUPPRESS_HELP)
parser.add_option("--rs", type="int", default=1, help="step between rings in rotational search: >0 (default 1)")
parser.add_option("--ts", type="string", default='1.0', help="step size of the translation search in x-y directions: search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional (default '1.0')")
parser.add_option("--delta", type="string", default='2.0', help="angular step of reference projections: (default '2.0')")
parser.add_option("--center", type="float", default=-1.0, help="centering of 3D template: average shift method; 0: no centering; 1: center of gravity (default -1.0)")
parser.add_option("--maxit1", type="int", default=400, help="maximum number of iterations performed for the GA part: (default 400)")
parser.add_option("--maxit2", type="int", default=50, help="maximum number of iterations performed for the finishing up part: (default 50)")
parser.add_option("--L2threshold", type="float", default=0.03, help="stopping criterion of GA: given as a maximum relative dispersion of volumes' L2 norms: (default 0.03)")
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="point-group symmetry of the structure: (default c1)")
# parser.add_option("--function", type="string", default="ref_ali3d", help="name of the reference preparation function (ref_ali3d by default)")
##### XXXXXXXXXXXXXXXXXXXXXX option does not exist in docs XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
parser.add_option("--function", type="string", default="ref_ali3d", help= SUPPRESS_HELP)
parser.add_option("--nruns", type="int", default=6, help="GA population: aka number of quasi-independent volumes (default 6)")
parser.add_option("--doga", type="float", default=0.1, help="do GA when fraction of orientation changes less than 1.0 degrees is at least doga: (default 0.1)")
##### XXXXXXXXXXXXXXXXXXXXXX option does not exist in docs XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
parser.add_option("--npad", type="int", default= 2, help="padding size for 3D reconstruction (default=2)")
parser.add_option("--fl", type="float", default=0.25, help="cut-off frequency applied to the template volume: using a hyperbolic tangent low-pass filter (default 0.25)")
parser.add_option("--aa", type="float", default=0.1, help="fall-off of hyperbolic tangent low-pass filter: (default 0.1)")
parser.add_option("--pwreference", type="string", default='', help="text file with a reference power spectrum: (default none)")
parser.add_option("--debug", action="store_true", default=False, help="debug info printout: (default False)")
##### XXXXXXXXXXXXXXXXXXXXXX option does not exist in docs XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
parser.add_option("--return_options", action="store_true", dest="return_options", default=False, help = SUPPRESS_HELP)
#parser.add_option("--an", type="string", default= "-1", help="NOT USED angular neighborhood for local searches (phi and theta)")
#parser.add_option("--CTF", action="store_true", default=False, help="NOT USED Consider CTF correction during the alignment ")
#parser.add_option("--snr", type="float", default= 1.0, help="NOT USED Signal-to-Noise Ratio of the data (default 1.0)")
# (options, args) = parser.parse_args(sys.argv[1:])
required_option_list = ['radius']
(options, args) = parser.parse_args(args)
# option_dict = vars(options)
# print parser
if options.return_options:
return parser
if options.moon_elimination == "":
options.moon_elimination = []
else:
options.moon_elimination = list(map(float, options.moon_elimination.split(",")))
# Making sure all required options appeared.
for required_option in required_option_list:
if not options.__dict__[required_option]:
sxprint("\n ==%s== mandatory option is missing.\n"%required_option)
sxprint("Please run '" + progname + " -h' for detailed options")
ERROR( "Missing parameter. Please see above" )
return
if len(args) < 2 or len(args) > 3:
sxprint("Usage: " + usage)
sxprint("Please run \'" + progname + " -h\' for detailed options" )
ERROR( "Invalid number of parameters used. Please see usage information above." )
return
log = Logger(BaseLogger_Files())
# 'radius' and 'ou' are the same as per Pawel's request; 'ou' is hidden from the user
# the 'ou' variable is not changed to 'radius' in the 'sparx' program. This change is at interface level only for sxviper.
options.ou = options.radius
runs_count = options.nruns
mpi_rank = mpi.mpi_comm_rank(mpi.MPI_COMM_WORLD)
mpi_size = mpi.mpi_comm_size(mpi.MPI_COMM_WORLD) # Total number of processes, passed by --np option.
if mpi_rank == 0:
all_projs = EMData.read_images(args[0])
subset = list(range(len(all_projs)))
# if mpi_size > len(all_projs):
# ERROR('Number of processes supplied by --np needs to be less than or equal to %d (total number of images) ' % len(all_projs), 'sxviper', 1)
# mpi.mpi_finalize()
# return
else:
all_projs = None
subset = None
outdir = args[1]
error = 0
if mpi_rank == 0:
if mpi_size % options.nruns != 0:
ERROR( "Number of processes needs to be a multiple of total number of runs. Total runs by default are 3, you can change it by specifying --nruns option.", action=0 )
error = 1
if os.path.exists(outdir):
ERROR( "Output directory \'%s\' exists, please change the name and restart the program"%outdir, action=0 )
error = 1
import sp_global_def
sp_global_def.LOGFILE = os.path.join(outdir, sp_global_def.LOGFILE)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
error = bcast_number_to_all(error, source_node = 0, mpi_comm = mpi.MPI_COMM_WORLD)
if error == 1 :
return
if mpi_rank == 0:
os.makedirs(outdir)
sp_global_def.write_command(outdir)
if outdir[-1] != "/":
outdir += "/"
log.prefix = outdir
# if len(args) > 2:
# ref_vol = get_im(args[2])
# else:
#ref_vol = None
options.user_func = sp_user_functions.factory[options.function]
options.CTF = False
options.snr = 1.0
options.an = -1.0
from sp_multi_shc import multi_shc
out_params, out_vol, out_peaks = multi_shc(all_projs, subset, runs_count, options, mpi_comm=mpi.MPI_COMM_WORLD, log=log)
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 range(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")
sxprint(" => actual lowpass : "******" => actual init lowpass : "******" => PW adjustment : ",ali3d_options.pwreference)
sxprint(" => partids : ",partids)
sxprint(" => partstack : ",partstack)
if(ali3d_options.fl > 0.46):
ERROR("Low pass filter in 3D alignment > 0.46 on the scale of shrank data", myid=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 range(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()) + " =>"
sxprint(line,"Executed successfully: ","3D alignment"," number of images:%7d"%len(params))
write_text_row(params, os.path.join(outputdir,"params.txt") )