def initialize_processing(paramfile, run_no):
''' Initialize processing for a set of images
:param paramfile: text file with IOTA parameters
:param run_no: number of the processing run
:return: info: INFO object
params: IOTA params
'''
try:
phil, _ = inp.get_input_phil(paramfile=paramfile)
except Exception as e:
msg = 'IOTA_PROC_ERROR: Cannot import IOTA parameters! {}'.format(e)
return False, msg
else:
params = phil.extract()
# Reconstruct integration base path and get info object
int_base = os.path.join(params.output, 'integration/{:03d}'.format(run_no))
try:
info_file = os.path.join(int_base, 'proc.info')
info = ProcInfo.from_json(filepath=info_file)
except Exception as e:
msg = 'IOTA_PROC_ERROR: Cannot import INFO object! {}'.format(e)
return False, msg
# Generate input list and input base
if not hasattr(info, 'input_list'):
info.generate_input_list(params=params)
common_pfx = os.path.abspath(
os.path.dirname(os.path.commonprefix(info.input_list)))
input_base = common_pfx
if os.path.isdir(os.path.abspath(params.input[0])):
new_common_pfx = os.path.commonprefix([os.path.abspath(params.input[0]), common_pfx])
if new_common_pfx not in ('', '.'):
input_base = new_common_pfx
# Generate subfolder paths
paths = dict(obj_base=os.path.join(int_base, 'image_objects'),
fin_base=os.path.join(int_base, 'final'),
log_base=os.path.join(int_base, 'logs'),
viz_base=os.path.join(int_base, 'visualization'),
tmp_base=os.path.join(int_base, 'tmp'),
input_base=input_base)
# FIXME: ordering of items in dictionaries changes depending on python version
for bkey, bvalue in paths.items():
if bkey == "input_base": # I think this is what the original code wanted to do
continue
if not os.path.isdir(bvalue):
os.makedirs(bvalue)
info.update(paths)
# Generate filepaths for various info files
info_files = dict(
obj_list_file=os.path.join(info.tmp_base, 'finished_objects.lst'),
idx_file=os.path.join(info.int_base, 'observations.pickle')
)
info.update(info_files)
# Initialize stat containers
info = generate_stat_containers(info=info, params=params)
# Initialize main log
util.main_log(info.logfile, '{:*^80} \n'.format(' IOTA MAIN LOG '))
util.main_log(info.logfile, '{:-^80} \n'.format(' SETTINGS FOR THIS RUN '))
util.main_log(info.logfile, info.iota_phil)
util.main_log(info.logfile, '{:-^80} \n'.format('BACKEND SETTINGS'))
util.main_log(info.logfile, info.target_phil)
info.export_json()
return info, params
def initialize_processing(paramfile, run_no):
"""Initialize processing for a set of images.
:param paramfile: text file with IOTA parameters
:param run_no: number of the processing run
:return: info: INFO object
params: IOTA params
"""
try:
phil, _ = inp.get_input_phil(paramfile=paramfile)
except Exception as e:
msg = "IOTA_PROC_ERROR: Cannot import IOTA parameters! {}".format(e)
return False, msg
else:
params = phil.extract()
# Reconstruct integration base path and get info object
int_base = os.path.join(params.output, "integration/{:03d}".format(run_no))
try:
info_file = os.path.join(int_base, "proc.info")
info = ProcInfo.from_json(filepath=info_file)
except Exception as e:
msg = "IOTA_PROC_ERROR: Cannot import INFO object! {}".format(e)
return False, msg
# Generate input list and input base
if not hasattr(info, "input_list"):
info.generate_input_list(params=params)
filepath_list = []
for item in info.input_list:
if isinstance(item, list) or isinstance(item, tuple):
fp = [i for i in item if os.path.exists(str(i))]
if fp and len(fp) == 1:
filepath_list.append(fp[0])
else:
if os.path.exists(item):
filepath_list.append(item)
common_pfx = os.path.abspath(
os.path.dirname(os.path.commonprefix(filepath_list)))
input_base = common_pfx
if os.path.isdir(os.path.abspath(params.input[0])):
new_common_pfx = os.path.commonprefix(
[os.path.abspath(params.input[0]), common_pfx])
if new_common_pfx not in ("", "."):
input_base = new_common_pfx
# Generate subfolder paths
paths = dict(
obj_base=os.path.join(int_base, "image_objects"),
fin_base=os.path.join(int_base, "final"),
log_base=os.path.join(int_base, "logs"),
dials_log_base=os.path.join(int_base, "logs/dials_logs"),
viz_base=os.path.join(int_base, "visualization"),
tmp_base=os.path.join(int_base, "tmp"),
input_base=input_base,
)
for bkey, bvalue in paths.items():
if bkey == "input_base":
continue
if not os.path.isdir(bvalue):
os.makedirs(bvalue)
info.update(paths)
# Generate filepaths for various info files
info_files = dict(
obj_list_file=os.path.join(info.tmp_base, "finished_objects.lst"),
idx_file=os.path.join(info.int_base, "observations.pickle"),
)
info.update(info_files)
# Initialize stat containers
info = generate_stat_containers(info=info, params=params)
# Initialize main log
util.main_log(info.logfile, "{:*^80} \n".format(" IOTA MAIN LOG "))
util.main_log(info.logfile, "{:-^80} \n".format(" SETTINGS FOR THIS RUN "))
util.main_log(info.logfile, info.iota_phil)
util.main_log(info.logfile, "{:-^80} \n".format("BACKEND SETTINGS"))
util.main_log(info.logfile, info.target_phil)
info.export_json()
return info, params