def sanity_checks(command_args, input_vol):
if os.path.isfile(
os.path.join(command_args.output_dir,
command_args.prefix + '_mask.hdf')):
if not command_args.override:
global_def.ERROR(
'sxmask',
'Output mask already exists! Please provide the override option if you want to override the existing mask.',
1)
if command_args.second_mask_shape in ('cylinder', 'sphere'):
nx = input_vol.get_xsize()
ny = input_vol.get_ysize()
nz = input_vol.get_zsize()
if command_args.s_radius > nx // 2 or \
command_args.s_radius > ny // 2:
global_def.ERROR(
'sxmask',
'Provided radius is larger than input image dimensions!', 1)
if command_args.second_mask_shape is not None:
nx = input_vol.get_xsize()
ny = input_vol.get_ysize()
nz = input_vol.get_zsize()
if command_args.s_nx > nx or \
command_args.s_ny > ny or \
command_args.s_nz > nz:
global_def.ERROR(
'sxmask',
'Provided s_nx, s_ny, s_nz mask dimension is larger than input image dimensions!',
1)
def import_partres_file(partres_file):
"""
Import the information from a SPHIRE partres file.
Arguments:
partres_file - Partres file name
Returns:
Array containing the ctf information.
"""
with open(partres_file, 'r') as r:
number_of_columns = len(r.readline().split())
if number_of_columns == 22:
columns = [0, 1, 2, 3, 6, 7, 17, 19, 20, 21]
dtype_import_list = [
('defocus', float),
('cs', float),
('voltage', float),
('pixel_size', float),
('astig_amp', float),
('astig_angle', float),
('max_resolution', float),
('amplitude_contrast', float),
('phase_shift', float),
('micrograph_name', '|S1000'),
]
dtype_output_list = [
('_rlnDefocusU', float),
('_rlnDefocusV', float),
('_rlnDefocusAngle', float),
('_rlnMicrographName', '|S1000'),
('_rlnDetectorPixelSize', float),
('_rlnMagnification', float),
('_rlnCtfMaxResolution', float),
('_rlnPhaseShift', float),
('_rlnAmplitudeContrast', float),
('_rlnSphericalAberration', float),
('_rlnVoltage', float),
]
else:
global_def.ERROR('Number of columns in partres file not known: {0}'.format(number_of_columns), 'sxsphire2relion', 1)
assert len(columns) == len(dtype_import_list)
partres_import_array = np.genfromtxt(partres_file, dtype=dtype_import_list, usecols=columns)
partres_array = np.empty(partres_import_array.shape[0], sorted(dtype_output_list))
partres_array['_rlnDefocusU'] = (20000 * partres_import_array['defocus'] - 10000 * partres_import_array['astig_amp']) / 2
partres_array['_rlnDefocusV'] = 20000 * partres_import_array['defocus'] - partres_array['_rlnDefocusU']
partres_array['_rlnDefocusAngle'] = 45 - partres_import_array['astig_angle']
partres_array['_rlnMicrographName'] = partres_import_array['micrograph_name']
partres_array['_rlnAmplitudeContrast'] = partres_import_array['amplitude_contrast'] / 100
partres_array['_rlnVoltage'] = partres_import_array['voltage']
partres_array['_rlnSphericalAberration'] = partres_import_array['cs']
partres_array['_rlnPhaseShift'] = partres_import_array['phase_shift']
partres_array['_rlnDetectorPixelSize'] = partres_import_array['pixel_size']
partres_array['_rlnMagnification'] = 10000
partres_array['_rlnCtfMaxResolution'] = 1 / partres_import_array['max_resolution']
return partres_array
def sanity_checks(args):
"""
Check if the settings are valid.
Arguments:
args - Command line arguments parsed via argparse
Returns:
Output file name
"""
file_exists_check = [
args.particle_stack,
args.partres_file,
args.params_2d_file,
args.params_3d_file,
args.params_3d_index_file,
args.list,
args.exlist,
]
stack_dependency_check = [
args.params_2d_file,
args.params_3d_file,
args.params_3d_index_file,
args.list,
args.exlist,
]
if not args.particle_stack and not args.partres_file:
global_def.ERROR(
'Particle_stack or partres_file option needs to be present!'.format(option),
'sxsphire2relion',
1
)
for option in stack_dependency_check:
if option and not args.particle_stack:
global_def.ERROR(
'{0} requires particle stack option!'.format(option),
'sxsphire2relion',
1
)
for idx, option in enumerate(file_exists_check):
if option:
if option.startswith('bdb:'):
if '#' in option:
raw_dirnames, basename = option.split('#')
dirnames = raw_dirnames[4:]
else:
dirnames = os.path.dirname(option[4:])
if not dirnames:
dirnames = '.'
basename = os.path.basename(option[4:])
option = '{0}/EMAN2DB/{1}.bdb'.format(dirnames,basename)
if not os.path.isfile(option):
global_def.ERROR(
'{0} stack must exist!'.format(option),
'sxsphire2relion',
1
)
if args.list and args.exlist:
global_def.ERROR(
'Arguments list and exlist cannot be used at the same time.',
'sxsphire2relion',
1
)
if args.params_2d_file and args.params_3d_file:
global_def.ERROR(
'Arguments params_2d_file and params_3d_file cannot be used at the same time.',
'sxsphire2relion',
1
)
if args.params_3d_index_file and not args.params_3d_file:
global_def.ERROR(
'Arguments params_3d_index_file requires params_3d_file to be set.',
'sxsphire2relion',
1
)
if args.params_3d_chunk_files and not args.params_3d_file:
global_def.ERROR(
'Arguments params_3d_chunk_files requires params_3d_file to be set.',
'sxsphire2relion',
1
)
try:
os.mkdir(args.output_dir)
except OSError:
pass
output_path = os.path.join(args.output_dir, args.output_name)
if os.path.exists(output_path) and args.force:
pass
elif os.path.exists(output_path) and not args.force:
global_def.ERROR(
'Output file {0} must not exist! Use the --force flag to overwrite existing files'.format(output_path),
'sxsphire2relion',
1
)
else:
pass
return output_path
import subprocess
import glob
import re
import global_def
import os
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('submission_command', type=str, help='Submission command, e.g., qsub, qsub -V, sbatch, bash')
parser.add_argument('input_run_dir', type=str, help='Directory containin the pipeline submission files')
parser.add_argument('--hold_flag', type=str, default=None, help='Hold flag for the submission command, e.g. -hold_jid')
parser.add_argument('--first_hold_number', type=str, default=None, help='Wait number of an already running job')
args = parser.parse_args()
global_def.BATCH = True
if not os.path.exists(args.input_run_dir):
global_def.ERROR('Input directory does not exist!', 'sxbatch.py', 1)
qsub_dict = {
'qsub': re.compile('Your job (\w+)'),
'sbatch': re.compile('Submitted batch job (\w+)'),
}
if args.submission_command.split()[0] not in qsub_dict and args.hold_flag:
global_def.ERROR('Qsub return output not known! Please contact the SPHIRE authors!', 'sxbatch.py', 1)
if args.first_hold_number:
prev_hold = args.first_hold_number
else:
prev_hold = 'aaa'
for idx, file_name in enumerate(sorted(glob.glob('{0}/*'.format(args.input_run_dir)))):
command = args.submission_command.split()
if args.hold_flag and (idx != 0 or args.first_hold_number):
