def initialize_single_image(img, paramfile, output_file=None, output_dir=None,
min_bragg=10):
phil, _ = inp.get_input_phil(paramfile=paramfile)
params = phil.extract()
params.input = [img]
params.mp.n_processors = 1
params.data_selection.image_triage.minimum_Bragg_peaks = min_bragg
info = ProcInfo.from_args(iota_phil=phil.as_str(),
paramfile=paramfile)
# Initialize output
if output_file is not None:
if output_dir is not None:
output = os.path.join(os.path.abspath(output_dir), output_file)
else:
output = os.path.abspath(output_file)
else:
output = None
info.obj_list_file = output
info.generate_input_list(params=params)
info = generate_stat_containers(info=info, params=params)
return info, params
def initialize_new_run(phil, input_dict=None, target_phil=None):
''' Create base integration folder; safe phil, input, and info to file '''
try:
params = phil.extract()
int_base, run_no = util.set_base_dir(dirname='integration',
out_dir=params.output,
get_run_no=True)
if not os.path.isdir(int_base):
os.makedirs(int_base)
# Create input list file and populate param input line
if input_dict:
if len(input_dict['imagepaths']) >= 10:
input_list_file = os.path.join(int_base, 'input.lst')
with open(input_list_file, 'w') as lf:
for f in input_dict['imagefiles']:
lf.write('{}\n'.format(f))
params.input = [input_list_file]
else:
input_list_file = None
params.input = input_dict['imagepaths']
else:
input_list_file = None
# Generate default backend PHIL, write to file, and update params
target_fp = os.path.join(int_base,'target.phil')
if target_phil:
target_phil = inp.write_phil(phil_str=target_phil,
dest_file=target_fp,
write_target_file=True)
else:
if params.cctbx_xfel.target:
target_phil = inp.write_phil(phil_file=params.cctbx_xfel.target,
dest_file=target_fp,
write_target_file=True)
else:
method = params.advanced.processing_backend
target_phil, _ = inp.write_defaults(method=method,
write_param_file=False,
filepath=target_fp)
params.cctbx_xfel.target = target_fp
# Save PHIL for this run in base integration folder
paramfile = os.path.join(int_base, 'iota_r{}.param'.format(run_no))
phil = phil.format(python_object=params)
with open(paramfile, 'w') as philf:
philf.write(phil.as_str())
# Initialize main log
logfile = os.path.abspath(os.path.join(int_base, 'iota.log'))
# Initialize proc.info object and save to file
info = ProcInfo.from_args(
iota_phil=phil.as_str(),
target_phil=target_phil.as_str(),
int_base=int_base,
input_list_file=input_list_file,
info_file=os.path.join(int_base, 'proc.info'),
cluster_info_file=os.path.join(int_base, 'cluster.info'),
paramfile=paramfile,
logfile=logfile,
run_number=run_no,
description=params.description,
status='initialized',
have_results=False,
errors=[],
init_proc=False)
info.export_json()
return True, info, 'IOTA_XTERM_INIT: Initialization complete!'
except Exception as e:
import traceback
traceback.print_exc()
msg = 'IOTA_INIT_ERROR: Could not initialize run! {}'.format(e)
return False, None, msg
def initialize_new_run(phil, input_dict=None, target_phil=None):
''' Create base integration folder; safe phil, input, and info to file '''
try:
params = phil.extract()
int_base, run_no = util.set_base_dir(dirname='integration',
out_dir=params.output,
get_run_no=True)
if not os.path.isdir(int_base):
os.makedirs(int_base)
# Create input list file and populate param input line
if input_dict:
if len(input_dict['imagepaths']) >= 25:
input_list_file = os.path.join(int_base, 'input.lst')
with open(input_list_file, 'w') as lf:
for f in input_dict['imagefiles']:
lf.write('{}\n'.format(f))
params.input = [input_list_file]
else:
# If there are too many imagefiles, re-constitute the "glob" format
# by matching filepaths and replacing non-matching characters with
# asterisks
if len(input_dict['imagefiles']) >= 25:
input_paths = []
for path in input_dict['imagepaths']:
fileset = [
os.path.basename(i)
for i in input_dict['imagefiles'] if path in i
]
zips = [list(set(i)) for i in zip(*fileset)]
chars = [i[0] if len(i) == 1 else '*' for i in zips]
fname = ''.join(chars)
while "*" * 2 in fname:
fname = fname.replace("*" * 2, "*")
input_paths.append(os.path.join(path, fname))
params.input = input_paths
else:
params.input = input_dict['imagefiles']
input_list_file = None
else:
input_list_file = None
# Generate default backend PHIL, write to file, and update params
target_fp = os.path.join(int_base, 'target.phil')
if target_phil:
target_phil = inp.write_phil(phil_str=target_phil,
dest_file=target_fp,
write_target_file=True)
else:
if params.cctbx_xfel.target:
target_phil = inp.write_phil(
phil_file=params.cctbx_xfel.target,
dest_file=target_fp,
write_target_file=True)
else:
method = params.advanced.processing_backend
target_phil, _ = inp.write_defaults(method=method,
write_param_file=False,
filepath=target_fp)
params.cctbx_xfel.target = target_fp
# Save PHIL for this run in base integration folder
paramfile = os.path.join(int_base, 'iota_r{}.param'.format(run_no))
phil = phil.format(python_object=params)
with open(paramfile, 'w') as philf:
philf.write(phil.as_str())
# Initialize main log
logfile = os.path.abspath(os.path.join(int_base, 'iota.log'))
# Initialize proc.info object and save to file
info = ProcInfo.from_args(
iota_phil=phil.as_str(),
target_phil=target_phil.as_str(),
int_base=int_base,
input_list_file=input_list_file,
info_file=os.path.join(int_base, 'proc.info'),
cluster_info_file=os.path.join(int_base, 'cluster.info'),
paramfile=paramfile,
logfile=logfile,
run_number=run_no,
description=params.description,
status='initialized',
have_results=False,
errors=[],
init_proc=False)
info.export_json()
return True, info, 'IOTA_XTERM_INIT: Initialization complete!'
except Exception as e:
msg = 'IOTA_INIT_ERROR: Could not initialize run! {}'.format(e)
return False, None, msg