def main():
import os
import sys
from optparse import OptionParser
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage = progname + """ input_image output_directory --wn=CTF_WINDOW_SIZE --apix=PIXEL_SIZE --Cs=CS --voltage=VOLATEGE --ac=AMP_CONTRAST --f_start=FREA_START --f_stop=FREQ_STOP --kboot=KBOOT --overlap_x=OVERLAP_X --overlap_y=OVERLAP_Y --edge_x=EDGE_X --edge_y=EDGE_Y --set_ctf_header --MPI --stack_mode --debug
sxcter exists in for both MPI and non-MPI versions.
Milti-Micrograph Mode - Process a set of micrographs in a list file or in a directory:
Specify a micrograph list file name (e.g. output of sxgui_unblur.py or sxgui_cter.py) and output directory as arguments. The file extension must be ".txt".
mpirun -np 16 sxcter.py mic_list.txt outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --MPI
Alternativel, specify micrograph name pattern with wild card [*] enclosed by single quotes ['] or double quotes ["]
(Note: sxgui.py automatically adds single quotes [']) and output directory as arguments.
BDB files can not be selected as input micrographs.
mpirun -np 16 sxcter.py 'Micrographs/mic*.mrc' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --MPI
Single-Micrograph Mode - Process a single micrograph:
Specify micrograph name (without wild card "*") and output directory as arguments.
BDB file can not be selected as input micrograph. Use single processor for this mode.
sxcter.py Micrographs/mic0.mrc outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
Stack Mode - Process a stack (Advanced Option):
Use option --stack_mode, then specify name of stack (without wild card "*") and output directory as arguments.
--wn will be not used with this mode. Use single processor for this mode.
sxcter.py bdb:stack outdir_cter --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --stack_mode
"""
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--wn",
type="int",
default=512,
help=
"CTF window size [pixels]: should be slightly larger than particle box size. used only in micrograph modes. (default 512)"
)
parser.add_option("--apix",
type="float",
default=-1.0,
help="pixel size [A]: (default -1.0)")
parser.add_option(
"--Cs",
type="float",
default=2.0,
help="microscope spherical aberration (Cs) [mm]: (default 2.0)")
parser.add_option("--voltage",
type="float",
default=300.0,
help="microscope voltage [kV]: (default 300.0)")
parser.add_option("--ac",
type="float",
default=10.0,
help="amplitude contrast [%]: (default 10.0)")
parser.add_option(
"--f_start",
type="float",
default=-1.0,
help=
"starting frequency [1/A]: by default determined automatically (default -1.0)"
)
parser.add_option(
"--f_stop",
type="float",
default=-1.0,
help=
"stop frequency [1/A]: by default determined automatically (default -1.0)"
)
parser.add_option(
"--kboot",
type="int",
default=16,
help=
"number of defocus estimates for micrograph: used for error assessment (default 16)"
)
parser.add_option("--overlap_x",
type="int",
default=50,
help="overlap x [%]: (default 50)")
parser.add_option("--overlap_y",
type="int",
default=50,
help="overlap y [%]: (default 50)")
parser.add_option("--edge_x",
type="int",
default=0,
help="edge x [pixels]: (default 0)")
parser.add_option("--edge_y",
type="int",
default=0,
help="edge y [pixels]: (default 0)")
parser.add_option(
"--set_ctf_header",
action="store_true",
default=False,
help=
"set estimated CTF parameters to image header: used only in micrograph modes. (default False)"
)
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version: (default False)")
parser.add_option(
"--stack_mode",
action="store_true",
default=False,
help=
"use stack mode: also set a stack name to input image. this is advanced option. (default False)"
)
parser.add_option("--debug",
action="store_true",
default=False,
help="print out debug info: (default False)")
(options, args) = parser.parse_args(arglist[1:])
if len(args) != 2:
print "see usage " + usage
sys.exit()
# NOTE: 2015/11/27 Toshio Moriya
# Require single quotes (') or double quotes (") for input_image so that
# sys.argv does not automatically expand wild card and create a list of file names
#
input_image = args[0]
output_directory = args[1]
#
# NOTE: 2016/03/17 Toshio Moriya
# cter_mrk() will take care of all error conditions
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv), sys.argv)
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
from morphology import cter_mrk
global_def.BATCH = True
result = cter_mrk(input_image, output_directory, options.wn, pixel_size=options.apix, \
Cs = options.Cs, voltage=options.voltage, wgh=options.ac, \
f_start=options.f_start, f_stop=options.f_stop, kboot=options.kboot, \
overlap_x = options.overlap_x, overlap_y = options.overlap_y, \
edge_x = options.edge_x, edge_y = options.edge_y, \
set_ctf_header = options.set_ctf_header, MPI=options.MPI, \
stack_mode = options.stack_mode, debug_mode = options.debug)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_comm_rank, MPI_COMM_WORLD, mpi_finalize
if mpi_comm_rank(MPI_COMM_WORLD) == 0:
if options.debug:
print "returned value from cter_mrk() := ", result
print "DONE!!!"
mpi_finalize()
else:
if options.debug:
print "returned value from cter_mrk() := ", result
print "DONE!!!"
def main():
program_name = os.path.basename(sys.argv[0])
usage = program_name + """ input_image_path output_directory --selection_list=selection_list --wn=CTF_WINDOW_SIZE --apix=PIXEL_SIZE --Cs=CS --voltage=VOLTAGE --ac=AMP_CONTRAST --f_start=FREA_START --f_stop=FREQ_STOP --vpp --kboot=KBOOT --overlap_x=OVERLAP_X --overlap_y=OVERLAP_Y --edge_x=EDGE_X --edge_y=EDGE_Y --check_consistency --stack_mode --debug_mode
Automated estimation of CTF parameters with error assessment.
All Micrographs Mode - Process all micrographs in a directory:
Specify a list of input micrographs using a wild card (*), called here input micrographs path pattern.
Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc).
Running from the command line requires enclosing the string by single quotes (') or double quotes (").
sxgui.py will automatically adds single quotes to the string.
BDB files can not be selected as input micrographs.
Then, specify output directory where all outputs should be saved.
In this mode, all micrographs matching the path pattern will be processed.
mpirun -np 16 sxcter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
Selected Micrographs Mode - Process all micrographs in a selection list file:
In addition to input micrographs path pattern and output directry arguments,
specify a name of micrograph selection list text file using --selection_list option
(e.g. output of sxgui_unblur.py or sxgui_cter.py). The file extension must be ".txt".
In this mode, only micrographs in the selection list which matches the file name part of the pattern (ignoring the directory paths) will be processed.
If a micrograph name in the selection list does not exists in the directory specified by the micrograph path pattern, processing of the micrograph will be skipped.
mpirun -np 16 sxcter.py './mic*.hdf' outdir_cter --selection_list=mic_list.txt --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
Single Micrograph Mode - Process a single micrograph:
In addition to input micrographs path pattern and output directry arguments,
specify a single micrograph name using --selection_list option.
In this mode, only the specified single micrograph will be processed.
If this micrograph name does not matches the file name part of the pattern (ignoring the directory paths), the process will exit without processing it.
If this micrograph name matches the file name part of the pattern but does not exists in the directory which specified by the micrograph path pattern, again the process will exit without processing it.
Use single processor for this mode.
sxcter.py './mic*.hdf' outdir_cter --selection_list=mic0.hdf --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
Stack Mode - Process a particle stack (Not supported by SPHIRE GUI))::
Use --stack_mode option, then specify the path of particle stack file (without wild card "*") and output directory as arguments.
This mode ignores --selection_list, --wn --overlap_x, --overlap_y, --edge_x, and --edge_y options.
Use single processor for this mode. Not supported by SPHIRE GUI (sxgui.py).
sxcter.py bdb:stack outdir_cter --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --stack_mode
"""
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--selection_list",
type="string",
default=None,
help=
"Micrograph selecting list: Specify path of a micrograph selection list text file for Selected Micrographs Mode. The file extension must be \'.txt\'. Alternatively, the file name of a single micrograph can be specified for Single Micrograph Mode. (default none)"
)
parser.add_option(
"--wn",
type="int",
default=512,
help=
"CTF window size [pixels]: The size should be slightly larger than particle box size. This will be ignored in Stack Mode. (default 512)"
)
parser.add_option(
"--apix",
type="float",
default=-1.0,
help=
"Pixel size [A/Pixels]: The pixel size of input micrograph(s) or images in input particle stack. (default -1.0)"
)
parser.add_option(
"--Cs",
type="float",
default=2.0,
help=
"Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default 2.0)"
)
parser.add_option(
"--voltage",
type="float",
default=300.0,
help=
"Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0)"
)
parser.add_option(
"--ac",
type="float",
default=10.0,
help=
"Amplitude contrast [%]: The typical amplitude contrast is in the range of 7% - 14%. The value mainly depends on the thickness of the ice embedding the particles. (default 10.0)"
)
parser.add_option(
"--f_start",
type="float",
default=-1.0,
help=
"Lowest frequency [1/A]: Lowest frequency to be considered in the CTF estimation. Determined automatically by default. (default -1.0)"
)
parser.add_option(
"--f_stop",
type="float",
default=-1.0,
help=
"Highest frequency [1/A]: Highest frequency to be considered in the CTF estimation. Determined automatically by default. (default -1.0)"
)
parser.add_option(
"--kboot",
type="int",
default=16,
help=
"Number of CTF estimates per micrograph: Used for error assessment. (default 16)"
)
parser.add_option(
"--overlap_x",
type="int",
default=50,
help=
"X overlap [%]: Overlap between the windows in the x direction. This will be ignored in Stack Mode. (default 50)"
)
parser.add_option(
"--overlap_y",
type="int",
default=50,
help=
"Y overlap [%]: Overlap between the windows in the y direction. This will be ignored in Stack Mode. (default 50)"
)
parser.add_option(
"--edge_x",
type="int",
default=0,
help=
"Edge x [pixels]: Defines the edge of the tiling area in the x direction. Normally it does not need to be modified. This will be ignored in Stack Mode. (default 0)"
)
parser.add_option(
"--edge_y",
type="int",
default=0,
help=
"Edge y [pixels]: Defines the edge of the tiling area in the y direction. Normally it does not need to be modified. This will be ignored in Stack Mode. (default 0)"
)
parser.add_option(
"--check_consistency",
action="store_true",
default=False,
help=
"Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False)"
)
parser.add_option(
"--stack_mode",
action="store_true",
default=False,
help=
"Use stack mode: Use a stack as the input. Please set the file path of a stack as the first argument and output directory for the second argument. This is advanced option. Not supported by sxgui. (default False)"
)
parser.add_option(
"--debug_mode",
action="store_true",
default=False,
help="Enable debug mode: Print out debug information. (default False)")
parser.add_option(
"--vpp",
action="store_true",
default=False,
help="Volta Phase Plate - fit smplitude contrast. (default False)")
parser.add_option("--defocus_min",
type="float",
default=0.3,
help="Minimum defocus search [um] (default 0.3)")
parser.add_option("--defocus_max",
type="float",
default=9.0,
help="Maximum defocus search [um] (default 9.0)")
parser.add_option("--defocus_step",
type="float",
default=0.1,
help="Step defocus search [um] (default 0.1)")
parser.add_option("--phase_min",
type="float",
default=5.0,
help="Minimum phase search [degrees] (default 5.0)")
parser.add_option("--phase_max",
type="float",
default=175.0,
help="Maximum phase search [degrees] (default 175.0)")
parser.add_option("--phase_step",
type="float",
default=5.0,
help="Step phase search [degrees] (default 5.0)")
parser.add_option("--pap",
action="store_true",
default=False,
help="Use power spectrum for fitting. (default False)")
(options, args) = parser.parse_args(sys.argv[1:])
# ====================================================================================
# Prepare processing
# ====================================================================================
# ------------------------------------------------------------------------------------
# Set up MPI related variables
# ------------------------------------------------------------------------------------
# Detect if program is running under MPI
RUNNING_UNDER_MPI = "OMPI_COMM_WORLD_SIZE" in os.environ
main_mpi_proc = 0
if RUNNING_UNDER_MPI:
from mpi import mpi_init, mpi_comm_rank, mpi_comm_size, mpi_barrier, MPI_COMM_WORLD
sys.argv = mpi_init(len(sys.argv), sys.argv)
my_mpi_proc_id = mpi_comm_rank(MPI_COMM_WORLD)
n_mpi_procs = mpi_comm_size(MPI_COMM_WORLD)
global_def.MPI = True
else:
my_mpi_proc_id = 0
n_mpi_procs = 1
# ------------------------------------------------------------------------------------
# Set up SPHIRE global definitions
# ------------------------------------------------------------------------------------
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
# Change the name log file for error message
original_logfilename = global_def.LOGFILE
global_def.LOGFILE = os.path.splitext(
program_name)[0] + '_' + original_logfilename + '.txt'
# ------------------------------------------------------------------------------------
# Check error conditions of arguments and options, then prepare variables for arguments
# ------------------------------------------------------------------------------------
input_image_path = None
output_directory = None
# not a real while, an if with the opportunity to use break when errors need to be reported
error_status = None
while True:
# --------------------------------------------------------------------------------
# Check the number of arguments. If OK, then prepare variables for them
# --------------------------------------------------------------------------------
if len(args) != 2:
error_status = (
"Please check usage for number of arguments.\n Usage: " +
usage + "\n" + "Please run %s -h for help." % (program_name),
getframeinfo(currentframe()))
break
# NOTE: 2015/11/27 Toshio Moriya
# Require single quotes (') or double quotes (") when input micrograph pattern is give for input_image_path
# so that sys.argv does not automatically expand wild card and create a list of file names
#
input_image_path = args[0]
output_directory = args[1]
# --------------------------------------------------------------------------------
# NOTE: 2016/03/17 Toshio Moriya
# cter_mrk() will take care of all the error conditions
# --------------------------------------------------------------------------------
break
if_error_then_all_processes_exit_program(error_status)
# Toshio, please see how to make it informative
assert input_image_path != None, " directory missing input_image_path"
assert output_directory != None, " directory missing output_directory"
if options.vpp == False:
wrong_params = False
import string as str
vpp_options = [
"--defocus_min", "--defocus_max", "--defocus_step", "--phase_min",
"--phase_max", "--phase_step"
]
for command_token in sys.argv:
for vppo in vpp_options:
if str.find(command_token, vppo) > -1: wrong_params = True
if wrong_params: break
if wrong_params: break
if wrong_params:
ERROR(
"Some options are valid only for Volta Phase Plate command %s"
% command_token, "sxcter", 1, my_mpi_proc_id)
if my_mpi_proc_id == main_mpi_proc:
command_line = ""
for command_token in sys.argv:
command_line += command_token + " "
print(" ")
print("Shell line command:")
print(command_line)
if options.vpp:
vpp_options = [
options.defocus_min, options.defocus_max, options.defocus_step,
options.phase_min, options.phase_max, options.phase_step
]
from morphology import cter_vpp
result = cter_vpp(input_image_path, output_directory,
options.selection_list, options.wn, options.apix,
options.Cs, options.voltage, options.ac,
options.f_start, options.f_stop, options.kboot,
options.overlap_x, options.overlap_y, options.edge_x,
options.edge_y, options.check_consistency,
options.stack_mode, options.debug_mode, program_name,
vpp_options, RUNNING_UNDER_MPI, main_mpi_proc,
my_mpi_proc_id, n_mpi_procs)
elif options.pap:
from morphology import cter_pap
result = cter_pap(input_image_path, output_directory,
options.selection_list, options.wn, options.apix,
options.Cs, options.voltage, options.ac,
options.f_start, options.f_stop, options.kboot,
options.overlap_x, options.overlap_y, options.edge_x,
options.edge_y, options.check_consistency,
options.stack_mode, options.debug_mode, program_name,
RUNNING_UNDER_MPI, main_mpi_proc, my_mpi_proc_id,
n_mpi_procs)
else:
from morphology import cter_mrk
result = cter_mrk(input_image_path, output_directory,
options.selection_list, options.wn, options.apix,
options.Cs, options.voltage, options.ac,
options.f_start, options.f_stop, options.kboot,
options.overlap_x, options.overlap_y, options.edge_x,
options.edge_y, options.check_consistency,
options.stack_mode, options.debug_mode, program_name,
RUNNING_UNDER_MPI, main_mpi_proc, my_mpi_proc_id,
n_mpi_procs)
if RUNNING_UNDER_MPI:
mpi_barrier(MPI_COMM_WORLD)
if main_mpi_proc == my_mpi_proc_id:
if options.debug_mode:
print("Returned value from cter_mrk() := ", result)
print(" ")
print("DONE!!!")
print(" ")
# ====================================================================================
# Clean up
# ====================================================================================
# ------------------------------------------------------------------------------------
# Reset SPHIRE global definitions
# ------------------------------------------------------------------------------------
global_def.LOGFILE = original_logfilename
# ------------------------------------------------------------------------------------
# Clean up MPI related variables
# ------------------------------------------------------------------------------------
if RUNNING_UNDER_MPI:
mpi_barrier(MPI_COMM_WORLD)
from mpi import mpi_finalize
mpi_finalize()
sys.stdout.flush()
sys.exit(0)
def main():
import os
import sys
from optparse import OptionParser
arglist = []
for arg in sys.argv:
arglist.append( arg )
progname = os.path.basename(arglist[0])
usage = progname + """ input_image output_directory --wn=CTF_WINDOW_SIZE --apix=PIXEL_SIZE --Cs=CS --voltage=VOLATEGE --ac=AMP_CONTRAST --f_start=FREA_START --f_stop=FREQ_STOP --kboot=KBOOT --overlap_x=OVERLAP_X --overlap_y=OVERLAP_Y --edge_x=EDGE_X --edge_y=EDGE_Y --set_ctf_header --MPI --stack_mode --debug
sxcter exists in for both MPI and non-MPI versions.
Milti-Micrograph Mode - Process a set of micrographs in a list file or in a directory:
Specify a micrograph list file name (e.g. output of sxgui_unblur.py or sxgui_cter.py) and output directory as arguments. The file extension must be ".txt".
mpirun -np 16 sxcter.py mic_list.txt outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --MPI
Alternativel, specify micrograph name pattern with wild card [*] enclosed by single quotes ['] or double quotes ["]
(Note: sxgui.py automatically adds single quotes [']) and output directory as arguments.
BDB files can not be selected as input micrographs.
mpirun -np 16 sxcter.py 'Micrographs/mic*.mrc' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --MPI
Single-Micrograph Mode - Process a single micrograph:
Specify micrograph name (without wild card "*") and output directory as arguments.
BDB file can not be selected as input micrograph. Use single processor for this mode.
sxcter.py Micrographs/mic0.mrc outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
Stack Mode - Process a stack (Advanced Option):
Use option --stack_mode, then specify name of stack (without wild card "*") and output directory as arguments.
--wn will be not used with this mode. Use single processor for this mode.
sxcter.py bdb:stack outdir_cter --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --stack_mode
"""
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--wn", type="int", default=512, help="CTF window size [pixels]: should be slightly larger than particle box size. used only in micrograph modes. (default 512)")
parser.add_option("--apix", type="float", default=-1.0, help="pixel size [A]: (default -1.0)")
parser.add_option("--Cs", type="float", default=2.0, help="microscope spherical aberration (Cs) [mm]: (default 2.0)")
parser.add_option("--voltage", type="float", default=300.0, help="microscope voltage [kV]: (default 300.0)")
parser.add_option("--ac", type="float", default=10.0, help="amplitude contrast [%]: (default 10.0)")
parser.add_option("--f_start", type="float", default=-1.0, help="starting frequency [1/A]: by default determined automatically (default -1.0)")
parser.add_option("--f_stop", type="float", default=-1.0, help="stop frequency [1/A]: by default determined automatically (default -1.0)")
parser.add_option("--kboot", type="int", default=16, help="number of defocus estimates for micrograph: used for error assessment (default 16)")
parser.add_option("--overlap_x", type="int", default=50, help="overlap x [%]: (default 50)")
parser.add_option("--overlap_y", type="int", default=50, help="overlap y [%]: (default 50)")
parser.add_option("--edge_x", type="int", default=0, help="edge x [pixels]: (default 0)")
parser.add_option("--edge_y", type="int", default=0, help="edge y [pixels]: (default 0)")
parser.add_option("--set_ctf_header", action="store_true", default=False, help="set estimated CTF parameters to image header: used only in micrograph modes. (default False)")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version: (default False)")
parser.add_option("--stack_mode", action="store_true", default=False, help="use stack mode: also set a stack name to input image. this is advanced option. (default False)")
parser.add_option("--debug", action="store_true", default=False, help="print out debug info: (default False)")
(options, args) = parser.parse_args(arglist[1:])
if len(args) != 2:
print "see usage " + usage
sys.exit()
# NOTE: 2015/11/27 Toshio Moriya
# Require single quotes (') or double quotes (") for input_image so that
# sys.argv does not automatically expand wild card and create a list of file names
#
input_image = args[0]
output_directory = args[1]
#
# NOTE: 2016/03/17 Toshio Moriya
# cter_mrk() will take care of all error conditions
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv), sys.argv)
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
from morphology import cter_mrk
global_def.BATCH = True
result = cter_mrk(input_image, output_directory, options.wn, pixel_size=options.apix, \
Cs = options.Cs, voltage=options.voltage, wgh=options.ac, \
f_start=options.f_start, f_stop=options.f_stop, kboot=options.kboot, \
overlap_x = options.overlap_x, overlap_y = options.overlap_y, \
edge_x = options.edge_x, edge_y = options.edge_y, \
set_ctf_header = options.set_ctf_header, MPI=options.MPI, \
stack_mode = options.stack_mode, debug_mode = options.debug)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_comm_rank, MPI_COMM_WORLD, mpi_finalize
if mpi_comm_rank(MPI_COMM_WORLD) == 0:
if options.debug:
print "returned value from cter_mrk() := ", result
print "DONE!!!"
mpi_finalize()
else:
if options.debug:
print "returned value from cter_mrk() := ", result
print "DONE!!!"