def setup_rundirs(prefix, scan, conf_dir, **kwargs):
"""
Concludes the experiment directory, creates main configuration files, and calls function to copy other configuration files.
Parameters
----------
prefix : str
prefix to name of the experiment/data reconstruction
scan : str
a range of scans to prepare data from
conf_dir : str
directory from where the configuration files will be copied
specfile : str
optional, from kwargs, specfile configuration to write to config file
copy_prep : bool
optional, from kwargs, if sets to true, the prepared file is also copied
Returns
-------
nothing
"""
id = prefix + '_' + scan
if not os.path.isdir(conf_dir):
print('configured directory ' + conf_dir + ' does not exist')
return
main_conf = os.path.join(conf_dir, 'config')
if not os.path.isfile(main_conf):
print('the configuration directory does not contain "config" file')
return
if not ver.ver_config_prep(main_conf):
return
try:
with open(main_conf, 'r') as f:
config_map = cfg.Config(f.read())
except Exception as e:
print('Please check the configuration file ' + main_conf +
'. Cannot parse ' + str(e))
return
try:
working_dir = config_map.working_dir.strip()
except:
working_dir = os.getcwd()
experiment_dir = os.path.join(working_dir, id)
if not os.path.exists(experiment_dir):
os.makedirs(experiment_dir)
# copy config_data, config_rec, cofig_disp files from cofig directory into the experiment conf directory
experiment_conf_dir = os.path.join(experiment_dir, 'conf')
if not os.path.exists(experiment_conf_dir):
os.makedirs(experiment_conf_dir)
# here we want the command line to be used if present, so need to check if None was passed or not.
if 'specfile' in kwargs:
specfile = kwargs['specfile']
if specfile is None:
try:
specfile = config_map.specfile.strip()
except:
print("Specfile not in config or command line")
# Based on params passed to this function create a temp config file and then copy it to the experiment dir.
experiment_main_config = os.path.join(experiment_conf_dir, 'config')
conf_map = {}
conf_map['working_dir'] = '"' + working_dir + '"'
conf_map['experiment_id'] = '"' + prefix + '"'
conf_map['scan'] = '"' + scan + '"'
if specfile is not None:
conf_map['specfile'] = '"' + specfile + '"'
temp_file = os.path.join(experiment_conf_dir, 'temp')
with open(temp_file, 'a') as f:
for key in conf_map:
value = conf_map[key]
if len(value) > 0:
f.write(key + ' = ' + conf_map[key] + '\n')
f.close()
if not ver.ver_config(temp_file):
print('please check the entered parameters. Cannot save this format')
else:
shutil.copy(temp_file, experiment_main_config)
os.remove(temp_file)
copy_conf(conf_dir, experiment_conf_dir)
if 'copy_prep' in kwargs:
copy_prep = kwargs['copy_prep']
if copy_prep:
# use abspath to get rid of trailing dir sep if it is there
other_exp_dir = os.path.split(os.path.abspath(conf_dir))[0]
new_exp_dir = os.path.split(os.path.abspath(experiment_conf_dir))[0]
# get case of single scan or summed
prep_dir_list = glob.glob(os.path.join(other_exp_dir, 'prep'),
recursive=True)
for dir in prep_dir_list:
shutil.copytree(dir, os.path.join(new_exp_dir, 'prep'))
# get case of split scans
prep_dir_list = glob.glob(os.path.join(other_exp_dir, "scan*/prep"),
recursive=True)
for dir in prep_dir_list:
scandir = os.path.basename(os.path.split(dir)[0])
shutil.copytree(dir, os.path.join(new_exp_dir, *(scandir, 'prep')))
return experiment_dir
def create_exp(prefix, scan, working_dir, **args):
"""
Concludes experiment name, creates directory, and "conf" subdirectory with initial configuration files.
Parameters
----------
prefix : str
a literal ID of the experiment
scan : str
string indicating scan number, or scan range
ex1: 5
ex2: 67 - 89
working_dir : str
directory where the file will be saved
specfile : str
optional, name of specfile that was saved during the experiment
Returns
-------
experiment_dir : str
directory where the new experiment is located
"""
id = prefix + '_' + scan
if not os.path.isdir(working_dir):
print('working directory ' + working_dir + ' does not exist')
return
experiment_dir = os.path.join(working_dir, id)
if not os.path.exists(experiment_dir):
os.makedirs(experiment_dir)
else:
print('experiment with this id already exists')
return experiment_dir
experiment_conf_dir = os.path.join(experiment_dir, 'conf')
if not os.path.exists(experiment_conf_dir):
os.makedirs(experiment_conf_dir)
# Based on params passed to this function create a temp config file and then copy it to the experiment dir.
experiment_main_config = os.path.join(experiment_conf_dir, 'config')
conf_map = {}
conf_map['working_dir'] = '"' + working_dir + '"'
conf_map['experiment_id'] = '"' + prefix + '"'
conf_map['scan'] = '"' + scan + '"'
if 'specfile' in args:
conf_map['specfile'] = '"' + args['specfile'] + '"'
if 'beamline' in args:
conf_map['beamline'] = '"' + args['beamline'] + '"'
temp_file = os.path.join(experiment_conf_dir, 'temp')
with open(temp_file, 'a') as f:
for key in conf_map:
value = conf_map[key]
if len(value) > 0:
f.write(key + ' = ' + conf_map[key] + '\n')
f.close()
if not ver.ver_config(temp_file):
print('please check the entered parameters. Cannot save this format')
else:
shutil.copy(temp_file, experiment_main_config)
os.remove(temp_file)
# create simple configuration for each phase
create_conf_prep(experiment_conf_dir)
create_conf_data(experiment_conf_dir)
create_conf_rec(experiment_conf_dir)
create_conf_disp(experiment_conf_dir)
return experiment_dir
def write_conf(conf_map, dir, file):
"""
It creates configuration file from the parameters included in dictionary, verifies, and saves in the configuration directory.
Parameters
----------
conf_map : dict
dictionary containing configuration parameters
dir : str
a directory where the configuration file will be saved
file : str
name of the configuration file to save
Returns
-------
nothing
"""
# create "temp" file first, verify it, and if ok, copy to a configuration file
if not os.path.exists(dir):
os.makedirs(dir)
conf_file = os.path.join(dir, file)
temp_file = os.path.join(dir, 'temp')
if os.path.isfile(temp_file):
os.remove(temp_file)
with open(temp_file, 'a') as f:
for key in conf_map:
value = conf_map[key]
if len(value) > 0:
f.write(key + ' = ' + conf_map[key] + '\n')
f.close()
if file == 'config':
if not ver.ver_config(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the main window. Cannot save this format'
)
return False
elif file == 'config_prep':
if not ver.ver_config_prep(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Data prep tab. Cannot save this format'
)
return False
elif file == 'config_data':
if not ver.ver_config_data(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Data tab. Cannot save this format'
)
return False
elif file.endswith('config_rec'):
if not ver.ver_config_rec(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Reconstruction tab. Cannot save this format'
)
return False
elif file == 'config_disp':
if not ver.ver_config_disp(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Display tab. Cannot save this format'
)
return False
# copy if verified
shutil.copy(temp_file, conf_file)
os.remove(temp_file)
return True