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")