def parse_par(args, molecule, isos, d_refs):
"""
Parse the input .par file, args.par_file, into normalized .states and
.trans files, checking for the existence of the relevant sources and
not outputing duplicates. All transitions encountered are written to
the .trans file, even if they're already in the database - duplicate-
handling is done upon staging the upload.
NB the input .par file must be in order of increasing wavenumber
(an error is raised if this is found not to be the case).
"""
# get all of the states for this molecule currently in the database
# as their string representations - these are the keys to the db_stateIDs
# dictionary, with the corresponding database State ids as their values
db_stateIDs = {}
for state in State.objects.filter(iso__in=isos):
db_stateIDs[state.str_rep()] = state.id
vprint('%d existing states for %s read in from database'\
% (len(db_stateIDs), molecule.ordinary_formula))
vprint('Creating .trans and .states files...')
vprint('%s\n-> %s\n %s'\
% (args.par_file, args.trans_file, args.states_file))
if not args.overwrite:
# the .trans and .states files should not already exist
for filename in (args.trans_file, args.states_file):
if os.path.exists(filename):
vprint('File exists:\n%s\nAborting.' % filename, 5)
sys.exit(1)
# read the lines and rstrip them of the EOL characters. We don't lstrip
# because we keep the space in front of molec_ids 1-9
vprint('reading .par lines from %s ...' % args.par_file)
lines = [x.rstrip() for x in open(args.par_file, 'r').readlines()]
ntrans = len(lines)
vprint('%d lines read in' % ntrans)
# find out the state ID at which we can start adding states
try:
first_stateID = State.objects.all().order_by('-id')[0].id + 1
except IndexError:
# no states in the database yet, so let's start at 1
first_stateID = 1
vprint('new states will be added with ids starting at %d' % first_stateID)
fo_s = open(args.states_file, 'w')
fo_t = open(args.trans_file, 'w')
start_time = time.time()
stateID = first_stateID
last_nu = 0. # the previous wavenumber read in
percent_done = 0; percent_increment = 1 # for the progress indicator
for i, line in enumerate(lines):
# progress indicator, as a percentage
percent = float(i)/ntrans * 100.
if percent - percent_done > percent_increment:
vprint('%d %%' % percent_done, 1)
percent_done += percent_increment
# parse the par_line into a HITRANTransition object
trans = HITRANTransition.parse_par_line(line)
if trans is None:
# blank or comment line
continue
# check our wavenumbers are in order
if trans.nu.val < last_nu:
vprint('Error: %s transitions file isn\'t ordered by nu.'\
% args.trans_file, 5)
sys.exit(1)
last_nu = trans.nu.val
# set the global (ie database-wide) ID for the isotopologue in
# the transition and its upper and lower state objects
trans.global_iso_id = args.global_iso_ids[
(trans.molec_id, trans.local_iso_id)]
trans.statep.global_iso_id = trans.global_iso_id
trans.statepp.global_iso_id = trans.global_iso_id
# first deal with the upper state: get its string representation ...
statep_str_rep = trans.statep.str_rep()
# ... and see if it's in our dictionary:
if statep_str_rep in db_stateIDs.keys():
# the upper state is already in the database: set the
# corresponding state ID in the transition object
trans.stateIDp = db_stateIDs[statep_str_rep]
else:
# the upper state is new: assign it an ID and save it
trans.stateIDp = trans.statep.id = stateID
db_stateIDs[statep_str_rep] = stateID
stateID += 1
print >>fo_s, statep_str_rep
# next deal with the lower state: get its string representation ...
statepp_str_rep = trans.statepp.str_rep()
# ... and see if it's in our dictionary:
if statepp_str_rep in db_stateIDs.keys():
# the lower state is already in the database: set the
# corresponding state ID in the transition object
trans.stateIDpp = db_stateIDs[statepp_str_rep]
else:
# the lower state is new: assign it an ID and save it
trans.stateIDpp = trans.statepp.id = stateID
db_stateIDs[statepp_str_rep] = stateID
stateID += 1
print >>fo_s, statepp_str_rep
# check that the references for this transition's parameters are in
# the tables hitranmeta_refs_map and hitranmeta_source - if they
# aren't this is fatal, so we exit
for j, prm_name in enumerate(['nu', 'S', 'gamma_air', 'gamma_self',
'n_air', 'delta_air']):
# the reference fields of the par_line are at character
# positions 134-146 of the 160-byte par_line, in 2-character fields
iref = int(trans.par_line[133+2*j:135+2*j])
# work out which Source in hitranmeta_source this reference id
# is pointing to, using the hitranmeta_refs_map table to map it
# to a primary key in the hitranmeta_source table.
if iref == 0:
# don't worry about missing 0 refs (which default to the
# HITRAN 1986 paper)
source_id = HITRAN1986_SOURCEID
else:
# form a HITRAN-style source identifier as
# <molecule_name>-<prm_name>-<id>, for looking up in the
# hitranmeta_refs_map table
sref = '%s-%s-%d' % (molecule.ordinary_formula,
prm_name, iref)
# we can't use '+' in XML attributes, so replace with 'p'
sref = sref.replace('+', 'p')
if sref not in d_refs.keys():
# Oops - missing reference: bail.
print 'missing reference for %s in hitranmeta_refs_map'\
' table' % sref
sys.exit(1)
# all's well - we have a valid source_id
source_id = d_refs[sref].source_id
# TODO avoid exec here
# Assign the source_id to the parameter object
if prm_name == 'S':
exec('trans.Sw.source_id = %d' % source_id)
exec('trans.A.source_id = %d' % source_id)
else:
try:
exec('trans.%s.source_id = %d' % (prm_name, source_id))
except AttributeError:
# no parameter object exists for prm_name; this can
# happen if e.g. delta_air=0. and none was created, but
# it's fine- we just move on
pass
# write the transition to the .trans file, *even if it is already
# in the database* - this is checked for on upload
print >>fo_t, trans.to_str(trans_fields, ',')
fo_t.close()
fo_s.close()
vprint('%d new or updated states were identified'\
% (stateID-first_stateID))
end_time = time.time()
vprint('%d transitions and %d states in %.1f secs'\
% (len(lines), len(db_stateIDs), end_time - start_time))
sys.path.append(hitran_path)
os.environ['DJANGO_SETTINGS_MODULE'] = 'settings'
from hitranmeta.models import *
isos = Iso.objects.all()
abundances = {}
for iso in isos:
abundances['%2d%1d' % (iso.molecule_id, iso.isoID)] = iso.abundance
par_dir = os.path.join(HOME, 'research/HITRAN/HITRAN2008/HITRAN2008/'\
'By-Molecule/Uncompressed-files')
par_name = sys.argv[1]
par_path = os.path.join(par_dir, par_name)
lines = [x.rstrip() for x in open(par_path, 'r').readlines()]
for i,line in enumerate(lines):
trans = HITRANTransition.parse_par_line(line)
if trans is None:
# blank or comment line
continue
if trans.gp is None:
print 'unassigned line at %12.6f' % trans.nu.val
continue
A = calc_A(trans.nu.val, trans.Elower, trans.gp, trans.Sw.val, Q, T,
abundances[trans.par_line[:3]])
if trans.par_line[25:35] != '%10.3E' % A:
#print trans.par_line[25:35], '%10.3E' % A
print '%10.3E %10.3E' % (trans.A.val, A)
#if i > 10:
# sys.exit(0)
