if child.returncode != 0:
sp_global_def.sxprint(
'Process failed for image {0}.\nPlease make sure that the unblur path is correct\nand check the respective logfile.'
.format(file_path))
log.write('Time => {0:.2f} for command: {1}'.format(
time.time() - start, execute_command))
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
if my_mpi_proc_id == mpi_print_id:
idx = idx + 1
total_time = time.time() - start_unblur
average_time = total_time / float(idx)
sp_global_def.sxprint(
'{0: 6.2f}% => Elapsed time: {1: 6.2f}min | Estimated total time: {2: 6.2f}min | Time per micrograph: {3: 5.2f}min/mic'
.format(
100 * idx / float(max_nima),
total_time / float(60),
(max_nima) * average_time / float(60),
average_time / float(60),
))
if __name__ == '__main__':
sp_global_def.print_timestamp('Start')
sp_global_def.BATCH = True
main(parse_args())
sp_global_def.BATCH = False
sp_global_def.print_timestamp('Finish')
mpi.mpi_finalize()
if cryolo_train_path:
cryolo_ex_pth = cryolo_train_path
if not fine_tune:
command = [
cryolo_ex_pth, "-c=config_yolo.json", warmup_argument,
gpu_argument, early_stop, gpu_fraction_arg
]
if num_cpu != -1:
command.append(num_cpu_arg)
subprocess.check_call(command)
warmup_argument = "-w=0"
command = [
cryolo_ex_pth, "-c=config_yolo.json", warmup_argument, gpu_argument,
early_stop, gpu_fraction_arg
]
if fine_tune:
command.append(fine_tune_argument)
if num_cpu != -1:
command.append(num_cpu_arg)
subprocess.check_call(command)
if __name__ == "__main__":
sp_global_def.print_timestamp("Start")
sp_global_def.write_command()
main()
sp_global_def.print_timestamp("Finish")
def main():
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = optparse.os.path.basename(arglist[0])
usage = progname + " stack --params='parm1 parm2 parm3 ...' --zero --one --set=number --randomize --rand_alpha --import=file --export=file --print --backup --suffix --restore --delete"
parser = optparse.OptionParser(usage, version=sp_global_def.SPARXVERSION)
parser.add_option("--params",
type="string",
default=None,
help="parameter list")
parser.add_option("--zero",
action="store_true",
default=False,
help="set parameter to zero")
parser.add_option("--one",
action="store_true",
default=False,
help="set parameter to one")
parser.add_option("--set",
type="float",
default=0.0,
help="set parameter to a value (different from 0.0)")
parser.add_option("--randomize",
action="store_true",
default=False,
help="set parameter to randomized value")
parser.add_option("--rand_alpha",
action="store_true",
default=False,
help="set all angles to randomized value")
parser.add_option("--import",
type="string",
dest="fimport",
default=None,
help="import parameters from file")
parser.add_option("--export",
type="string",
dest="fexport",
default=None,
help="export parameters to file")
parser.add_option("--print",
action="store_true",
dest="fprint",
default=False,
help="print parameters")
parser.add_option("--backup",
action="store_true",
default=False,
help="backup parameters")
parser.add_option("--suffix",
type="string",
default="_backup",
help="suffix for xform name in backup")
parser.add_option("--restore",
action="store_true",
default=False,
help="restore parameters")
parser.add_option("--delete",
action="store_true",
default=False,
help="delete parameters")
parser.add_option(
"--consecutive",
action="store_true",
default=False,
help="set selected parameter to consecutive integers starting from 0")
parser.add_option(
"--list",
type="string",
default=None,
help=
"Indices list containing the same amount of rows as the import file")
(options, args) = parser.parse_args(arglist[1:])
if not options.fprint:
sp_global_def.print_timestamp("Start")
sp_global_def.write_command()
if len(args) != 1:
sp_global_def.sxprint("Usage: " + usage)
sp_global_def.ERROR(
"Invalid number of parameters provided. Please see usage information above."
)
return
if options.params == None:
sp_global_def.sxprint("Usage: " + usage)
sp_global_def.ERROR(
"No parameters provided. Please see usage information above.")
return
if sp_global_def.CACHE_DISABLE:
pass #IMPORTIMPORTIMPORT from sp_utilities import disable_bdb_cache
sp_utilities.disable_bdb_cache()
pass #IMPORTIMPORTIMPORT from sp_applications import header
sp_applications.header(args[0], options.params, options.zero, options.one, options.set, options.randomize, options.rand_alpha, options.fimport, options.fexport, \
options.fprint, options.backup, options.suffix, options.restore, options.delete, options.consecutive, options.list)
if not options.fprint:
sp_global_def.print_timestamp("Finish")
