ll = vac[2]['LOGLAM'][:]
eta = vac[2]['ETA'][:]
forest.correc_ivar = interp1d(ll,
eta,
fill_value="extrapolate",
kind="nearest")
vac.close()
except:
print(" Error while reading ivar_calib file {}".format(
args.ivar_calib))
sys.exit(1)
### Apply dust correction
if not args.dust_map is None:
print("applying dust correction")
forest.ebv_map = io.read_dust_map(args.dust_map)
nit = args.nit
log = open(os.path.expandvars(args.log), 'w')
data,ndata,healpy_nside,healpy_pix_ordering = io.read_data(os.path.expandvars(args.in_dir), args.drq, args.mode,\
zmin=args.zqso_min, zmax=args.zqso_max, nspec=args.nspec, log=log,\
keep_bal=args.keep_bal, bi_max=args.bi_max, order=args.order,\
best_obs=args.best_obs, single_exp=args.single_exp, pk1d=args.delta_format )
### Get the lines to veto
usr_mask_obs = None
usr_mask_RF = None
usr_mask_RF_DLA = None
if (args.mask_file is not None):
def main():
# pylint: disable-msg=too-many-locals,too-many-branches,too-many-statements
"""Computes delta field"""
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=('Compute the delta field '
'from a list of spectra'))
parser.add_argument('--out-dir',
type=str,
default=None,
required=True,
help='Output directory')
parser.add_argument('--drq',
type=str,
default=None,
required=True,
help='Catalog of objects in DRQ format')
parser.add_argument('--in-dir',
type=str,
default=None,
required=True,
help='Directory to spectra files')
parser.add_argument('--log',
type=str,
default='input.log',
required=False,
help='Log input data')
parser.add_argument('--iter-out-prefix',
type=str,
default='iter',
required=False,
help='Prefix of the iteration file')
parser.add_argument('--mode',
type=str,
default='pix',
required=False,
help=('Open mode of the spectra files: pix, spec, '
'spcframe, spplate, desi'))
parser.add_argument('--best-obs',
action='store_true',
required=False,
help=('If mode == spcframe, then use only the best '
'observation'))
parser.add_argument(
'--single-exp',
action='store_true',
required=False,
help=('If mode == spcframe, then use only one of the '
'available exposures. If best-obs then choose it '
'among those contributing to the best obs'))
parser.add_argument('--zqso-min',
type=float,
default=None,
required=False,
help='Lower limit on quasar redshift from drq')
parser.add_argument('--zqso-max',
type=float,
default=None,
required=False,
help='Upper limit on quasar redshift from drq')
parser.add_argument('--keep-bal',
action='store_true',
required=False,
help='Do not reject BALs in drq')
parser.add_argument('--bi-max',
type=float,
required=False,
default=None,
help=('Maximum CIV balnicity index in drq (overrides '
'--keep-bal)'))
parser.add_argument('--lambda-min',
type=float,
default=3600.,
required=False,
help='Lower limit on observed wavelength [Angstrom]')
parser.add_argument('--lambda-max',
type=float,
default=5500.,
required=False,
help='Upper limit on observed wavelength [Angstrom]')
parser.add_argument('--lambda-rest-min',
type=float,
default=1040.,
required=False,
help='Lower limit on rest frame wavelength [Angstrom]')
parser.add_argument('--lambda-rest-max',
type=float,
default=1200.,
required=False,
help='Upper limit on rest frame wavelength [Angstrom]')
parser.add_argument('--rebin',
type=int,
default=3,
required=False,
help=('Rebin wavelength grid by combining this number '
'of adjacent pixels (ivar weight)'))
parser.add_argument('--npix-min',
type=int,
default=50,
required=False,
help='Minimum of rebined pixels')
parser.add_argument('--dla-vac',
type=str,
default=None,
required=False,
help='DLA catalog file')
parser.add_argument('--dla-mask',
type=float,
default=0.8,
required=False,
help=('Lower limit on the DLA transmission. '
'Transmissions below this number are masked'))
parser.add_argument('--absorber-vac',
type=str,
default=None,
required=False,
help='Absorber catalog file')
parser.add_argument(
'--absorber-mask',
type=float,
default=2.5,
required=False,
help=('Mask width on each side of the absorber central '
'observed wavelength in units of '
'1e4*dlog10(lambda)'))
parser.add_argument('--mask-file',
type=str,
default=None,
required=False,
help=('Path to file to mask regions in lambda_OBS and '
'lambda_RF. In file each line is: region_name '
'region_min region_max (OBS or RF) [Angstrom]'))
parser.add_argument('--optical-depth',
type=str,
default=None,
required=False,
nargs='*',
help=('Correct for the optical depth: tau_1 gamma_1 '
'absorber_1 tau_2 gamma_2 absorber_2 ...'))
parser.add_argument('--dust-map',
type=str,
default=None,
required=False,
help=('Path to DRQ catalog of objects for dust map to '
'apply the Schlegel correction'))
parser.add_argument(
'--flux-calib',
type=str,
default=None,
required=False,
help=('Path to previously produced picca_delta.py file '
'to correct for multiplicative errors in the '
'pipeline flux calibration'))
parser.add_argument(
'--ivar-calib',
type=str,
default=None,
required=False,
help=('Path to previously produced picca_delta.py file '
'to correct for multiplicative errors in the '
'pipeline inverse variance calibration'))
parser.add_argument('--eta-min',
type=float,
default=0.5,
required=False,
help='Lower limit for eta')
parser.add_argument('--eta-max',
type=float,
default=1.5,
required=False,
help='Upper limit for eta')
parser.add_argument('--vlss-min',
type=float,
default=0.,
required=False,
help='Lower limit for variance LSS')
parser.add_argument('--vlss-max',
type=float,
default=0.3,
required=False,
help='Upper limit for variance LSS')
parser.add_argument('--delta-format',
type=str,
default=None,
required=False,
help='Format for Pk 1D: Pk1D')
parser.add_argument('--use-ivar-as-weight',
action='store_true',
default=False,
help=('Use ivar as weights (implemented as eta = 1, '
'sigma_lss = fudge = 0)'))
parser.add_argument('--use-constant-weight',
action='store_true',
default=False,
help=('Set all the delta weights to one (implemented '
'as eta = 0, sigma_lss = 1, fudge = 0)'))
parser.add_argument('--order',
type=int,
default=1,
required=False,
help=('Order of the log10(lambda) polynomial for the '
'continuum fit, by default 1.'))
parser.add_argument('--nit',
type=int,
default=5,
required=False,
help=('Number of iterations to determine the mean '
'continuum shape, LSS variances, etc.'))
parser.add_argument('--nproc',
type=int,
default=None,
required=False,
help='Number of processors')
parser.add_argument('--nspec',
type=int,
default=None,
required=False,
help='Maximum number of spectra to read')
parser.add_argument('--use-mock-continuum',
action='store_true',
default=False,
help='use the mock continuum for computing the deltas')
parser.add_argument('--spall',
type=str,
default=None,
required=False,
help=('Path to spAll file'))
parser.add_argument('--metadata',
type=str,
default=None,
required=False,
help=('Name for table containing forests metadata'))
t0 = time.time()
args = parser.parse_args()
# setup forest class variables
Forest.log_lambda_min = np.log10(args.lambda_min)
Forest.log_lambda_max = np.log10(args.lambda_max)
Forest.log_lambda_min_rest_frame = np.log10(args.lambda_rest_min)
Forest.log_lambda_max_rest_frame = np.log10(args.lambda_rest_max)
Forest.rebin = args.rebin
Forest.delta_log_lambda = args.rebin * 1e-4
# minumum dla transmission
Forest.dla_mask_limit = args.dla_mask
Forest.absorber_mask_width = args.absorber_mask
# Find the redshift range
if args.zqso_min is None:
args.zqso_min = max(0., args.lambda_min / args.lambda_rest_max - 1.)
userprint("zqso_min = {}".format(args.zqso_min))
if args.zqso_max is None:
args.zqso_max = max(0., args.lambda_max / args.lambda_rest_min - 1.)
userprint("zqso_max = {}".format(args.zqso_max))
#-- Create interpolators for mean quantities, such as
#-- Large-scale structure variance : var_lss
#-- Pipeline ivar correction error: eta
#-- Pipeline ivar correction term : fudge
#-- Mean continuum : mean_cont
log_lambda_temp = (Forest.log_lambda_min + np.arange(2) *
(Forest.log_lambda_max - Forest.log_lambda_min))
log_lambda_rest_frame_temp = (
Forest.log_lambda_min_rest_frame + np.arange(2) *
(Forest.log_lambda_max_rest_frame - Forest.log_lambda_min_rest_frame))
Forest.get_var_lss = interp1d(log_lambda_temp,
0.2 + np.zeros(2),
fill_value="extrapolate",
kind="nearest")
Forest.get_eta = interp1d(log_lambda_temp,
np.ones(2),
fill_value="extrapolate",
kind="nearest")
Forest.get_fudge = interp1d(log_lambda_temp,
np.zeros(2),
fill_value="extrapolate",
kind="nearest")
Forest.get_mean_cont = interp1d(log_lambda_rest_frame_temp,
1 + np.zeros(2))
#-- Check that the order of the continuum fit is 0 (constant) or 1 (linear).
if args.order:
if (args.order != 0) and (args.order != 1):
userprint(("ERROR : invalid value for order, must be eqal to 0 or"
"1. Here order = {:d}").format(args.order))
sys.exit(12)
#-- Correct multiplicative pipeline flux calibration
if args.flux_calib is not None:
hdu = fitsio.read(args.flux_calib, ext=1)
stack_log_lambda = hdu['loglam']
stack_delta = hdu['stack']
w = (stack_delta != 0.)
Forest.correct_flux = interp1d(stack_log_lambda[w],
stack_delta[w],
fill_value="extrapolate",
kind="nearest")
#-- Correct multiplicative pipeline inverse variance calibration
if args.ivar_calib is not None:
hdu = fitsio.read(args.ivar_calib, ext=2)
log_lambda = hdu['loglam']
eta = hdu['eta']
Forest.correct_ivar = interp1d(log_lambda,
eta,
fill_value="extrapolate",
kind="nearest")
### Apply dust correction
if not args.dust_map is None:
userprint("applying dust correction")
Forest.extinction_bv_map = io.read_dust_map(args.dust_map)
log_file = open(os.path.expandvars(args.log), 'w')
# Read data
(data, num_data, nside,
healpy_pix_ordering) = io.read_data(os.path.expandvars(args.in_dir),
args.drq,
args.mode,
z_min=args.zqso_min,
z_max=args.zqso_max,
max_num_spec=args.nspec,
log_file=log_file,
keep_bal=args.keep_bal,
bi_max=args.bi_max,
best_obs=args.best_obs,
single_exp=args.single_exp,
pk1d=args.delta_format,
spall=args.spall)
#-- Add order info
for pix in data:
for forest in data[pix]:
if not forest is None:
forest.order = args.order
### Read masks
if args.mask_file is not None:
args.mask_file = os.path.expandvars(args.mask_file)
try:
mask = Table.read(args.mask_file,
names=('type', 'wave_min', 'wave_max', 'frame'),
format='ascii')
mask['log_wave_min'] = np.log10(mask['wave_min'])
mask['log_wave_max'] = np.log10(mask['wave_max'])
except (OSError, ValueError):
userprint(("ERROR: Error while reading mask_file "
"file {}").format(args.mask_file))
sys.exit(1)
else:
mask = Table(names=('type', 'wave_min', 'wave_max', 'frame',
'log_wave_min', 'log_wave_max'))
### Mask lines
for healpix in data:
for forest in data[healpix]:
forest.mask(mask)
### Mask absorbers
if not args.absorber_vac is None:
userprint("INFO: Adding absorbers")
absorbers = io.read_absorbers(args.absorber_vac)
num_absorbers = 0
for healpix in data:
for forest in data[healpix]:
if forest.thingid in absorbers:
for lambda_absorber in absorbers[forest.thingid]:
forest.add_absorber(lambda_absorber)
num_absorbers += 1
log_file.write("Found {} absorbers in forests\n".format(num_absorbers))
### Add optical depth contribution
if not args.optical_depth is None:
userprint(("INFO: Adding {} optical"
"depths").format(len(args.optical_depth) // 3))
assert len(args.optical_depth) % 3 == 0
for index in range(len(args.optical_depth) // 3):
tau = float(args.optical_depth[3 * index])
gamma = float(args.optical_depth[3 * index + 1])
lambda_rest_frame = constants.ABSORBER_IGM[args.optical_depth[
3 * index + 2]]
userprint(
("INFO: Adding optical depth for tau = {}, gamma = {}, "
"lambda_rest_frame = {} A").format(tau, gamma,
lambda_rest_frame))
for healpix in data:
for forest in data[healpix]:
forest.add_optical_depth(tau, gamma, lambda_rest_frame)
### Mask DLAs
if not args.dla_vac is None:
userprint("INFO: Adding DLAs")
np.random.seed(0)
dlas = io.read_dlas(args.dla_vac)
num_dlas = 0
for healpix in data:
for forest in data[healpix]:
if forest.thingid in dlas:
for dla in dlas[forest.thingid]:
forest.add_dla(dla[0], dla[1], mask)
num_dlas += 1
log_file.write("Found {} DLAs in forests\n".format(num_dlas))
## Apply cuts
log_file.write(
("INFO: Input sample has {} "
"forests\n").format(np.sum([len(forest)
for forest in data.values()])))
remove_keys = []
for healpix in data:
forests = []
for forest in data[healpix]:
if ((forest.log_lambda is None)
or len(forest.log_lambda) < args.npix_min):
log_file.write(("INFO: Rejected {} due to forest too "
"short\n").format(forest.thingid))
continue
if np.isnan((forest.flux * forest.ivar).sum()):
log_file.write(("INFO: Rejected {} due to nan "
"found\n").format(forest.thingid))
continue
if (args.use_constant_weight
and (forest.flux.mean() <= 0.0 or forest.mean_snr <= 1.0)):
log_file.write(("INFO: Rejected {} due to negative mean or "
"too low SNR found\n").format(forest.thingid))
continue
forests.append(forest)
log_file.write("{} {}-{}-{} accepted\n".format(
forest.thingid, forest.plate, forest.mjd, forest.fiberid))
data[healpix][:] = forests
if len(data[healpix]) == 0:
remove_keys += [healpix]
for healpix in remove_keys:
del data[healpix]
num_forests = np.sum([len(forest) for forest in data.values()])
log_file.write(("INFO: Remaining sample has {} "
"forests\n").format(num_forests))
userprint(f"Remaining sample has {num_forests} forests")
# Sanity check: all forests must have the attribute log_lambda
for healpix in data:
for forest in data[healpix]:
assert forest.log_lambda is not None
t1 = time.time()
tmin = (t1 - t0) / 60
userprint('INFO: time elapsed to read data', tmin, 'minutes')
# compute fits to the forests iteratively
# (see equations 2 to 4 in du Mas des Bourboux et al. 2020)
num_iterations = args.nit
for iteration in range(num_iterations):
context = multiprocessing.get_context('fork')
pool = context.Pool(processes=args.nproc)
userprint(
f"Continuum fitting: starting iteration {iteration} of {num_iterations}"
)
#-- Sorting healpix pixels before giving to pool (for some reason)
pixels = np.array([k for k in data])
sort = pixels.argsort()
sorted_data = [data[k] for k in pixels[sort]]
data_fit_cont = pool.map(cont_fit, sorted_data)
for index, healpix in enumerate(pixels[sort]):
data[healpix] = data_fit_cont[index]
userprint(
f"Continuum fitting: ending iteration {iteration} of {num_iterations}"
)
pool.close()
if iteration < num_iterations - 1:
#-- Compute mean continuum (stack in rest-frame)
(log_lambda_rest_frame, mean_cont,
mean_cont_weight) = prep_del.compute_mean_cont(data)
w = mean_cont_weight > 0.
log_lambda_cont = log_lambda_rest_frame[w]
new_cont = Forest.get_mean_cont(log_lambda_cont) * mean_cont[w]
Forest.get_mean_cont = interp1d(log_lambda_cont,
new_cont,
fill_value="extrapolate")
#-- Compute observer-frame mean quantities (var_lss, eta, fudge)
if not (args.use_ivar_as_weight or args.use_constant_weight):
(log_lambda, eta, var_lss, fudge, num_pixels, var_pipe_values,
var_delta, var2_delta, count, num_qso, chi2_in_bin, error_eta,
error_var_lss, error_fudge) = prep_del.compute_var_stats(
data, (args.eta_min, args.eta_max),
(args.vlss_min, args.vlss_max))
w = num_pixels > 0
Forest.get_eta = interp1d(log_lambda[w],
eta[w],
fill_value="extrapolate",
kind="nearest")
Forest.get_var_lss = interp1d(log_lambda[w],
var_lss[w],
fill_value="extrapolate",
kind="nearest")
Forest.get_fudge = interp1d(log_lambda[w],
fudge[w],
fill_value="extrapolate",
kind="nearest")
else:
num_bins = 10 # this value is arbitrary
log_lambda = (
Forest.log_lambda_min + (np.arange(num_bins) + .5) *
(Forest.log_lambda_max - Forest.log_lambda_min) / num_bins)
if args.use_ivar_as_weight:
userprint(("INFO: using ivar as weights, skipping eta, "
"var_lss, fudge fits"))
eta = np.ones(num_bins)
var_lss = np.zeros(num_bins)
fudge = np.zeros(num_bins)
else:
userprint(("INFO: using constant weights, skipping eta, "
"var_lss, fudge fits"))
eta = np.zeros(num_bins)
var_lss = np.ones(num_bins)
fudge = np.zeros(num_bins)
error_eta = np.zeros(num_bins)
error_var_lss = np.zeros(num_bins)
error_fudge = np.zeros(num_bins)
chi2_in_bin = np.zeros(num_bins)
num_pixels = np.zeros(num_bins)
var_pipe_values = np.zeros(num_bins)
var_delta = np.zeros((num_bins, num_bins))
var2_delta = np.zeros((num_bins, num_bins))
count = np.zeros((num_bins, num_bins))
num_qso = np.zeros((num_bins, num_bins))
Forest.get_eta = interp1d(log_lambda,
eta,
fill_value='extrapolate',
kind='nearest')
Forest.get_var_lss = interp1d(log_lambda,
var_lss,
fill_value='extrapolate',
kind='nearest')
Forest.get_fudge = interp1d(log_lambda,
fudge,
fill_value='extrapolate',
kind='nearest')
### Read metadata from forests and export it
if not args.metadata is None:
tab_cont = get_metadata(data)
tab_cont.write(args.metadata, format="fits", overwrite=True)
stack_log_lambda, stack_delta, stack_weight = prep_del.stack(data)
### Save iter_out_prefix
results = fitsio.FITS(args.iter_out_prefix + ".fits.gz",
'rw',
clobber=True)
header = {}
header["NSIDE"] = nside
header["PIXORDER"] = healpy_pix_ordering
header["FITORDER"] = args.order
results.write([stack_log_lambda, stack_delta, stack_weight],
names=['loglam', 'stack', 'weight'],
header=header,
extname='STACK')
results.write([log_lambda, eta, var_lss, fudge, num_pixels],
names=['loglam', 'eta', 'var_lss', 'fudge', 'nb_pixels'],
extname='WEIGHT')
results.write([
log_lambda_rest_frame,
Forest.get_mean_cont(log_lambda_rest_frame), mean_cont_weight
],
names=['loglam_rest', 'mean_cont', 'weight'],
extname='CONT')
var_pipe_values = np.broadcast_to(var_pipe_values.reshape(1, -1),
var_delta.shape)
results.write(
[var_pipe_values, var_delta, var2_delta, count, num_qso, chi2_in_bin],
names=['var_pipe', 'var_del', 'var2_del', 'count', 'nqsos', 'chi2'],
extname='VAR')
results.close()
### Compute deltas and format them
get_stack_delta = interp1d(stack_log_lambda[stack_weight > 0.],
stack_delta[stack_weight > 0.],
kind="nearest",
fill_value="extrapolate")
deltas = {}
data_bad_cont = []
for healpix in sorted(data.keys()):
for forest in data[healpix]:
if not forest.bad_cont is None:
continue
#-- Compute delta field from flux, continuum and various quantites
get_delta_from_forest(forest, get_stack_delta, Forest.get_var_lss,
Forest.get_eta, Forest.get_fudge,
args.use_mock_continuum)
if healpix in deltas:
deltas[healpix].append(forest)
else:
deltas[healpix] = [forest]
data_bad_cont = data_bad_cont + [
forest for forest in data[healpix] if forest.bad_cont is not None
]
for forest in data_bad_cont:
log_file.write("INFO: Rejected {} due to {}\n".format(
forest.thingid, forest.bad_cont))
log_file.write(
("INFO: Accepted sample has {}"
"forests\n").format(np.sum([len(p) for p in deltas.values()])))
t2 = time.time()
tmin = (t2 - t1) / 60
userprint('INFO: time elapsed to fit continuum', tmin, 'minutes')
### Save delta
for healpix in sorted(deltas.keys()):
if args.delta_format == 'Pk1D_ascii':
results = open(args.out_dir + "/delta-{}".format(healpix) + ".txt",
'w')
for delta in deltas[healpix]:
num_pixels = len(delta.delta)
if args.mode == 'desi':
delta_log_lambda = (
(delta.log_lambda[-1] - delta.log_lambda[0]) /
float(len(delta.log_lambda) - 1))
else:
delta_log_lambda = delta.delta_log_lambda
line = '{} {} {} '.format(delta.plate, delta.mjd,
delta.fiberid)
line += '{} {} {} '.format(delta.ra, delta.dec, delta.z_qso)
line += '{} {} {} {} {} '.format(delta.mean_z, delta.mean_snr,
delta.mean_reso,
delta_log_lambda, num_pixels)
for index in range(num_pixels):
line += '{} '.format(delta.delta[index])
for index in range(num_pixels):
line += '{} '.format(delta.log_lambda[index])
for index in range(num_pixels):
line += '{} '.format(delta.ivar[index])
for index in range(num_pixels):
line += '{} '.format(delta.exposures_diff[index])
line += ' \n'
results.write(line)
results.close()
else:
results = fitsio.FITS(args.out_dir + "/delta-{}".format(healpix) +
".fits.gz",
'rw',
clobber=True)
for delta in deltas[healpix]:
header = [
{
'name': 'RA',
'value': delta.ra,
'comment': 'Right Ascension [rad]'
},
{
'name': 'DEC',
'value': delta.dec,
'comment': 'Declination [rad]'
},
{
'name': 'Z',
'value': delta.z_qso,
'comment': 'Redshift'
},
{
'name':
'PMF',
'value':
'{}-{}-{}'.format(delta.plate, delta.mjd,
delta.fiberid)
},
{
'name': 'THING_ID',
'value': delta.thingid,
'comment': 'Object identification'
},
{
'name': 'PLATE',
'value': delta.plate
},
{
'name': 'MJD',
'value': delta.mjd,
'comment': 'Modified Julian date'
},
{
'name': 'FIBERID',
'value': delta.fiberid
},
{
'name': 'ORDER',
'value': delta.order,
'comment': 'Order of the continuum fit'
},
]
if args.delta_format == 'Pk1D':
header += [
{
'name': 'MEANZ',
'value': delta.mean_z,
'comment': 'Mean redshift'
},
{
'name': 'MEANRESO',
'value': delta.mean_reso,
'comment': 'Mean resolution'
},
{
'name': 'MEANSNR',
'value': delta.mean_snr,
'comment': 'Mean SNR'
},
]
if args.mode == 'desi':
delta_log_lambda = (
(delta.log_lambda[-1] - delta.log_lambda[0]) /
float(len(delta.log_lambda) - 1))
else:
delta_log_lambda = delta.delta_log_lambda
header += [{
'name': 'DLL',
'value': delta_log_lambda,
'comment': 'Loglam bin size [log Angstrom]'
}]
exposures_diff = delta.exposures_diff
if exposures_diff is None:
exposures_diff = delta.log_lambda * 0
cols = [
delta.log_lambda, delta.delta, delta.ivar,
exposures_diff
]
names = ['LOGLAM', 'DELTA', 'IVAR', 'DIFF']
units = ['log Angstrom', '', '', '']
comments = [
'Log lambda', 'Delta field', 'Inverse variance',
'Difference'
]
else:
cols = [
delta.log_lambda, delta.delta, delta.weights,
delta.cont
]
names = ['LOGLAM', 'DELTA', 'WEIGHT', 'CONT']
units = ['log Angstrom', '', '', '']
comments = [
'Log lambda', 'Delta field', 'Pixel weights',
'Continuum'
]
results.write(cols,
names=names,
header=header,
comment=comments,
units=units,
extname=str(delta.thingid))
results.close()
t3 = time.time()
tmin = (t3 - t2) / 60
userprint('INFO: time elapsed to write deltas', tmin, 'minutes')
ttot = (t3 - t0) / 60
userprint('INFO: total elapsed time', ttot, 'minutes')
log_file.close()