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 master_build(write=False, nsources=None, plots=True, verbose=True):
""" Master loop to build the line lists
Parameters
----------
check_only : bool, optional
Only check to see what would be created, i.e. do not execute
nsources : int, optional
Mainly for step-by-step build
plots : bool, optional
Generate plots, if write=True too
"""
# Load sources
sources = arcl_io.load_source_table()
if nsources is not None:
sources = sources[0:nsources]
# Loop on sources
for source in sources:
print("=============================================================")
print("Working on source {:s}".format(source['File']))
print("=============================================================")
# Load line table
ID_lines, U_lines = load_source.load(source['File'], source['Format'],
source['Lines'].split(','),
plot=plots, wvmnx=[source['wvmin'], source['wvmax']])
# Lines (Double check)
src_lines = source['Lines'].split(',')
if ID_lines is None:
uions = src_lines
else:
# Check
uions = np.unique(ID_lines['ion'].data)
for src_line in src_lines:
if src_line not in uions.tolist():
raise ValueError("Line {:s} not found in ID_lines".format(src_line))
# Loop on ID ions
for ion in uions:
# Parse
idx = ID_lines['ion'] == ion
sub_tbl = ID_lines[idx]
# Generate?
ion_file = llist_path+'{:s}_lines.dat'.format(ion)
if not os.path.isfile(ion_file):
if not write:
print("Would generate line list:\n {:s}".format(ion_file))
else:
print("Generating line list:\n {:s}".format(ion_file))
create_line_list(sub_tbl, source['File'],
source['Instr'], ion_file)
else:
update_line_list(sub_tbl, source['File'],
source['Instr'], ion_file, write=write)
def main(args=None):
""" Run
Parameters
----------
args
Returns
-------
"""
# Grab arguments
pargs = parser(options=args)
import numpy as np
from astropy.table import vstack
from arclines import build_lists
from arclines import io as arcl_io
from arclines import load_source
from arclines import plots as arcl_plots
from arclines import utils as arcl_utils
print("=============================================================")
print("This script is for EXPERTS ONLY")
print("Continue only if you know what you are doing")
print("This script adds only the *last* source listed")
print("Otherwise exit")
print("=============================================================")
if not pargs.skip_stop:
pdb.set_trace()
# Load sources
sources = arcl_io.load_source_table()
source = sources[-1]
# Load line lists
uions = arcl_utils.unique_ions(source)
llist_dict = {}
for ion in uions:
try:
llist_dict[ion] = arcl_io.load_line_list(ion, use_ion=True)
except IOError:
print("No linelist found for ion={:s}. Will create one".format(ion))
# IDs
print("=============================================================")
print("Working on adding IDs from source {:s}".format(source['File']))
print("=============================================================")
llist_dict = build_lists.source_to_line_lists(source, write=pargs.write,
llist_dict=llist_dict)
# Create line list
ll = []
for key in llist_dict.keys():
ll.append(llist_dict[key])
line_lists = vstack(ll)
# Purge unknowns
print("=============================================================")
print("Purging UNKNOWNs")
print("=============================================================")
build_lists.purge_unknowns(line_lists, write=pargs.write)
print("=============================================================")
print("Working on adding Unknowns from source {:s}".format(source['File']))
print("=============================================================")
if not pargs.no_unknowns:
unknwns = build_lists.source_to_unknowns(source, write=pargs.write)
unknwns.remove_column('line_flag')
else:
unknwns = None
if unknwns is not None:
ll.append(unknwns)
# Loop to my loop
print("=============================================================")
print("Working on plot for {:s}".format(source['File']))
print("=============================================================")
# Load
src_dict = load_source.load(source)
uions = arcl_utils.unique_ions(source, src_dict=src_dict)
src_dict['uions'] = uions
# Outfile
iext = source['File'].rfind('.')
outfile = source['File'][:iext]+'.pdf'
title = source['File'][:iext]
#
arcl_plots.show_source(src_dict, line_lists, outfile, title=title, clobber=True)