def source_to_unknowns(source, write=False, verbose=True, min_ampl=0.):
"""
Parameters
----------
source
write
min_ampl : float (optional)
Minimum amplitude for a new UNKNOWN
Returns
-------
"""
# Load
src_dict = load_source.load(source)
U_lines = src_dict['U_lines']
# Cut on amplitude
print("Cutting UNKNOWNs on min_ampl")
U_lines = U_lines[U_lines['amplitude'] > min_ampl]
src_dict['U_lines'] = U_lines
# UNKNWN lines
if U_lines is None:
return
# Unique ions
uions = arcl_utils.unique_ions(source, src_dict=src_dict)
# Check against 'complete' NIST and our line lists
mask, _ = arcl_utils.vette_unkwn_against_lists(U_lines,
uions,
verbose=verbose)
if np.sum(mask) == 0:
return
if not os.path.isfile(unk_file): # Generate?
if write:
print("Generating line list:\n {:s}".format(unk_file))
unknwn_list = create_line_list(U_lines[mask > 0],
source['File'],
source['Instr'],
unknown=True,
ions=uions)
arcl_io.write_line_list(unknwn_list, unk_file)
else: # Update
unknwn_list, updated = update_uline_list(U_lines[mask > 0],
source['File'],
source['Instr'], uions)
if write and updated:
arcl_io.write_line_list(unknwn_list, unk_file)
# Return
return unknwn_list
def source_to_line_lists(source, write=False, llist_dict=None):
"""
Parameters
----------
source
write
scratch : bool, optional
Build from scratch -- EXPERTS ONLY
Returns
-------
"""
if llist_dict is None: # For building without writing
llist_dict = {}
# Parse
src_dict = load_source.load(source)
# Check
if src_dict['ID_lines'] is None:
print("No IDs in source: {:s}".format(source['File']))
return llist_dict
# Unique ions
uions = arcl_utils.unique_ions(source, src_dict=src_dict)
# Loop on ID ions
for ion in uions:
ion_file = llist_path + '{:s}_lines.dat'.format(ion)
# Parse
idx = src_dict['ID_lines']['ion'] == ion
sub_tbl = src_dict['ID_lines'][idx]
# Generate?
if (not os.path.isfile(ion_file)) and (ion not in llist_dict.keys()):
# New
llist_dict[ion] = create_line_list(sub_tbl, source['File'],
source['Instr'])
if not write:
print("Would generate line list:\n {:s}".format(ion_file))
else:
print("Generating line list:\n {:s}".format(ion_file))
arcl_io.write_line_list(llist_dict[ion], ion_file)
else:
if ion not in llist_dict.keys():
raise KeyError(
"You are trying to build from scratch but didn't remove {:s}"
.format(ion_file))
llist_dict[ion], updated = update_line_list(
llist_dict[ion], sub_tbl, source['File'], source['Instr'])
# Write
if write and updated:
arcl_io.write_line_list(llist_dict[ion], ion_file)
# Return
return llist_dict
def by_hand(llist_dict, write=False):
"""
Returns
-------
"""
# By-hand
print("=============================================================")
print("Adding lines by hand!")
print("=============================================================")
handIDs = arcl_io.load_by_hand()
uhions = np.unique(handIDs['ion'].data)
# Loop on ID ions
for ion in uhions:
# Parse
idx = handIDs['ion'] == ion
sub_tbl = handIDs[idx]
# Update only
llist_dict[ion], updated = update_line_list(llist_dict[ion], sub_tbl, None, None)
if write and updated:
ion_file = llist_path+'{:s}_lines.dat'.format(ion)
arcl_io.write_line_list(llist_dict[ion], ion_file)
def purge_unknowns(line_list, write=False, tol_llist=2., verbose=True):
line_dict = defs.lines()
# Load
unknwns = arcl_io.load_unknown_list([], all=True)
mask = np.array([True] * len(unknwns))
updated = False
# Loop
for ss, row in enumerate(unknwns):
dwv = np.abs(line_list['wave'] - row['wave'])
imin = np.argmin(np.abs(dwv))
# Match?
if dwv[imin] < tol_llist:
line_flag = line_dict[line_list['ion'][imin]]
if row['line_flag'] % (2 * line_flag) >= line_flag:
mask[ss] = False
updated = True
if verbose:
print("Will purge UNKNOWN line \n {}".format(row))
print("Matched to \n {}".format(line_list[imin]))
# Write?
if write and updated:
arcl_io.write_line_list(unknwns[mask], unk_file)