def init_default_param(self, dic_param):
"""Initialise the parameters as defined in the input dictionary
Hardcoded in init_musepipe.py
"""
for key in dic_param.keys():
if self.verbose:
mpipe.print_info(
"Default initialisation of attribute {0}".format(key))
setattr(self, key, dic_param[key])
def _set_cpu(self, first_cpu=0, ncpu=24, list_cpu=None) :
"""Setting the cpu format for calling the esorex command
"""
if (list_cpu is None) | (len(list_cpu) < 1):
self.list_cpu = "{0}-{1}".format(first_cpu, first_cpu + ncpu - 1)
else :
self.list_cpu = "{0}".format(list_cpu[0])
for i in range(1, len(list_cpu)) :
self.list_cpu += ":{0}".format(list_cpu[i])
if self.verbose:
mpipe.print_info("LIST_CPU: {0}".format(self.list_cpu))
def __init__(self, galaxyname=None, pointing=1):
if galaxyname not in MUSEPIPE_sample.keys():
mpipe.print_error(
"ERROR: no Galaxy named {gal} in the defined sample".format(
gal=galaxyname))
return
mpipe.print_info("Initialising Target {name}".format(name=galaxyname))
self.targetname = galaxyname
self.info_pointings = MUSEPIPE_sample[galaxyname]
if pointing not in self.info_pointings.keys():
mpipe.print_error(
"ERROR: no pointing {pointing} for the Galaxy".format(
pointing))
return
self.pointing = pointing
self.run = self.info_pointings[pointing]
def write_sof(self, sof_filename, sof_folder=None, new=False, verbose=None) :
"""Feeding an sof file with input filenames from a dictionary
"""
# Setting the default SOF folder if not provided
if sof_folder is None : sof_folder = self.paths.sof
# Removing the extension of the file if already set
if not sof_filename.lower().endswith(".sof") :
sof_filename = sof_filename + ".sof"
sof = joinpath(sof_folder, sof_filename)
# If new file, start from scratch (overwrite)
if new :
sof_file = open(sof, "w+")
if verbose :
mpipe.print_info("Writing in file {0}".format(sof))
# if not new, then append
else :
sof_file = open(sof, "a")
if verbose :
mpipe.print_info("Appending in file {0}".format(sof))
# Use dictionary to write up the lines
for key in self._sofdict.keys() :
for item in self._sofdict[key] :
text_to_write = "{0} {1}\n".format(item, key)
sof_file.write(text_to_write)
if verbose :
mpipe.print_info(text_to_write)
sof_file.close()
# Returning the current sof as relative path
self.current_sof = mpipe.normpath(os.path.relpath(sof))
def read_param_file(self, filename, dic_param):
"""Reading an input parameter initialisation file
"""
# Testing existence of filename
if not os.path.isfile(filename):
mpipe.print_info(
("ERROR: input parameter {inputname} cannot be found. "
"We will use the default hardcoded in the "
"init_musepipe.py module").format(inputname=filename))
return
# If it exists, open and read it
f_param = open(filename)
lines = f_param.readlines()
# Dummy dictionary to see which items are not initialised
dummy_dic_param = copy.copy(dic_param)
for line in lines:
if line[0] in ["#", "%"]: continue
sline = line.split()
if sline[0] in dic_param.keys():
if self.verbose:
mpipe.print_info("Initialisation of attribute {0}".format(
sline[0]))
setattr(self, sline[0], sline[1])
# Here we drop the item which was initialised
val = dummy_dic_param.pop(sline[0])
else:
continue
# Set of non initialised folders
not_initialised_param = dummy_dic_param.keys()
# Listing them as warning and using the hardcoded default
for key in not_initialised_param:
mpipe.print_info(("WARNING: parameter {param} not initialised "
"We will use the default hardcoded value from "
"init_musepipe.py").format(param=key))
setattr(self, key, dic_param[key])