def test_bad_l0_invalid(tmpdir, caplog):
# Test no valid values
testfile = os.path.join(str(tmpdir), 'sparta.fits')
create_sparta_table(outfile=testfile, L0=1000)
compute_psf_from_sparta(testfile)
assert caplog.records[
1].message == '1/1 : No valid values, skipping this row'
assert caplog.records[2].message == 'No valid values'
def test_reconstruction2(tmpdir):
tbl = create_sparta_table()
# Modify values for the first LGS
tbl.data[0]['LGS1_L0'] = 20
tbl.data[0]['LGS1_SEEING'] = 0.8
tbl.data[0]['LGS1_TUR_GND'] = 0.5
# and give a bad value to the 3rd LGS
tbl.data[0]['LGS3_L0'] = 100
hdul = fits.HDUList([tbl])
# Note: the case when npsflin=1 is tested below with test_script
res = compute_psf_from_sparta(hdul,
npsflin=3,
lmin=500,
lmax=700,
nl=3,
mean_of_lgs=False)
assert len(res) == 5
# check that meta are correctly saved
fit = Table.read(res['FIT_ROWS'])
assert_allclose(fit[fit['lgs_idx'] == 1]['L0'], 20)
assert_allclose(fit[fit['lgs_idx'] != 1]['L0'], 25)
# check fit result
assert_allclose(fit['center'], 20)
assert_allclose(fit[fit['lbda'] == 500]['fwhm'][:, 0], [0.79, 0.86, 0.86],
atol=1e-2)
def test_plot(tmpdir):
import matplotlib
matplotlib.use('agg', force=True)
testfile = os.path.join(str(tmpdir), 'sparta.fits')
create_sparta_table(outfile=testfile, nlines=2)
res = compute_psf_from_sparta(testfile)
outfile = os.path.join(str(tmpdir), 'fitres.fits')
res.writeto(outfile, overwrite=True)
fig = plot_psf(res)
fig.savefig(str(tmpdir.join('fig.png')))
fig = plot_psf(outfile)
fig.savefig(str(tmpdir.join('fig.png')))
def test_bad_l0(tmpdir, caplog):
testfile = os.path.join(str(tmpdir), 'sparta.fits')
create_sparta_table(outfile=testfile, bad_l0=True)
# Note: the case when npsflin=1 is tested below with test_script
res = compute_psf_from_sparta(testfile, lmin=490, lmax=541.76, nl=5)
assert (caplog.records[1].message ==
'1/1 : Using only 3 values out of 4 after outliers rejection')
assert caplog.records[3].message == 'Using three lasers mode'
assert len(res) == 5
# check that meta are correctly saved
fit = Table.read(res['FIT_ROWS'])
assert_allclose(fit['L0'], 25)
# check fit result
assert_allclose(fit['center'], 20)
assert_allclose(fit[1]['lbda'], 502.9, atol=1e-1)
assert_allclose(fit[1]['fwhm'], 0.86, atol=1e-2)
def test_script_with_file(tmpdir):
testfile = os.path.join(str(tmpdir), 'sparta.fits')
create_sparta_table(outfile=testfile)
logfile = os.path.join(str(tmpdir), 'muse_psfr.log')
outfile = os.path.join(str(tmpdir), 'out.fits')
main([testfile, '--no-color', '--logfile', logfile, '--outfile', outfile])
with fits.open(outfile) as hdul:
assert [hdu.name for hdu in hdul] == [
'PRIMARY', 'SPARTA_ATM_DATA', 'FIT_ROWS', 'FIT_MEAN', 'PSF_MEAN'
]
with open(logfile) as f:
lines = f.read().splitlines()
assert lines[2:] == [
'OB None None Airmass 0.00-0.00',
'--------------------------------------------------------------------',
'LBDA 5000 7000 9000', 'FWHM 0.85 0.73 0.62', 'BETA 2.73 2.55 2.23',
'--------------------------------------------------------------------'
]
def test_reconstruction(tmpdir):
tbl = create_sparta_table()
hdul = fits.HDUList([tbl])
# Note: the case when npsflin=1 is tested below with test_script
res = compute_psf_from_sparta(hdul, npsflin=3, lmin=490, lmax=541.76, nl=5)
assert len(res) == 5
# check that meta are correctly saved
fit = Table.read(res['FIT_ROWS'])
assert_allclose(fit['L0'], 25)
# check fit result
assert_allclose(fit['center'], 20)
assert_allclose(fit[1]['lbda'], 502.9, atol=1e-1)
assert_allclose(fit[1]['fwhm'], 0.85, atol=1e-2)
def test_fit_poly(tmpdir):
tbl = create_sparta_table()
hdul = fits.HDUList([tbl])
res = compute_psf_from_sparta(hdul, lmin=500, lmax=900, nl=9)
fit = Table.read(res['FIT_ROWS'])
res = fit_psf_with_polynom(fit['lbda'],
fit['fwhm'][:, 0],
fit['n'],
deg=(5, 5),
output=1)
assert_allclose(res['fwhm_pol'][0], 0.65, atol=1e-2)
assert_allclose(res['beta_pol'][0], 0.78, atol=1e-2)
# fit[1] at 550nm matches roughly res[8] (550.1)
assert_allclose(res['beta_fit'][8], fit[1]['n'], atol=1e-2)
assert_allclose(res['fwhm_fit'][8], fit[1]['fwhm'], atol=1e-2)
def main(args=None):
parser = argparse.ArgumentParser(
description=f'MUSE-PSFR version {__version__}')
addarg = parser.add_argument
addarg('raw', help='observation raw file name', nargs='?')
addarg('--values',
help='values of seeing, GL, L0, to use instead of the '
'raw file, comma-separated')
addarg('--logfile', default='muse_psfr.log', help='name of log file')
addarg('-o',
'--outfile',
help='name of a FITS file in which the results '
'are saved: table with individual and mean Moffat fits, and mean '
'reconstructed PSF')
addarg('--njobs',
default=-1,
type=int,
help='number of parallel jobs '
'(by default use all CPUs)')
addarg('--verbose', '-v', action='store_true', help='verbose flag')
addarg('--no-color', action='store_true', help='no color in output')
addarg('--plot', action='store_true', help='plot reconstructed psf')
addarg('--version', action='version', version='%(prog)s ' + __version__)
args = parser.parse_args(args)
logger.info('MUSE-PSFR version %s', __version__)
if args.values:
values = [float(x) for x in args.values.split(',')]
if len(values) != 3:
sys.exit('--values must contain a list of 3 comma-separated '
'values for seeing, GL, and L0')
header_line = None
rawf = io.BytesIO()
create_sparta_table(outfile=rawf,
seeing=values[0],
GL=values[1],
L0=values[2])
rawf.seek(0)
else:
if args.raw is None:
sys.exit('no input file provided')
rawf = args.raw
hdr = fits.getheader(rawf)
header_line = ('OB %s %s Airmass %.2f-%.2f' %
(hdr.get('HIERARCH ESO OBS NAME'), hdr.get('DATE'),
hdr.get('HIERARCH ESO TEL AIRM START',
0), hdr.get('HIERARCH ESO TEL AIRM END', 0)))
logger.info(header_line)
logger.info('Computing PSF Reconstruction from Sparta data')
if args.verbose:
_logger = logging.getLogger('muse_psfr')
_logger.setLevel("DEBUG")
_logger.handlers[0].setLevel("DEBUG")
res = compute_psf_from_sparta(rawf,
lmin=500,
lmax=900,
nl=3,
n_jobs=args.njobs,
plot=args.plot)
if res:
data = res['FIT_MEAN'].data
lbda, fwhm, beta = data['lbda'], data['fwhm'][:, 0], data['n']
else:
sys.exit('No results')
f = io.StringIO()
if header_line:
f.write(header_line + '\n')
f.write('-' * 68 + '\n')
try:
import colorama # noqa
except ImportError:
args.no_color = True
lbda *= 10
if args.no_color:
f.write('LBDA %.0f %.0f %.0f\n' % tuple(lbda))
f.write('FWHM %.2f %.2f %.2f\n' % tuple(fwhm))
f.write('BETA %.2f %.2f %.2f\n' % tuple(beta))
else:
from colorama import Fore, Back, Style
RED, GREEN, BLUE = Fore.RED, Fore.GREEN, Fore.BLUE
begin_style = Back.BLACK + Style.BRIGHT + Fore.WHITE
end_style = Fore.RESET + Style.NORMAL + Back.RESET
f.write(
f'{begin_style}'
f'LBDA {BLUE}{lbda[0]:.0f} {GREEN}{lbda[1]:.0f} {RED}{lbda[2]:.0f}'
f'{end_style}\n'
f'{begin_style}'
f'FWHM {BLUE}{fwhm[0]:.2f} {GREEN}{fwhm[1]:.2f} {RED}{fwhm[2]:.2f}'
f'{end_style}\n'
f'{begin_style}'
f'BETA {BLUE}{beta[0]:.2f} {GREEN}{beta[1]:.2f} {RED}{beta[2]:.2f}'
f'{end_style}\n')
f.write(Style.RESET_ALL)
f.write('-' * 68 + '\n')
f.seek(0)
for line in f:
logger.info(line.rstrip('\n'))
if args.logfile is not None:
f.seek(0)
with open(args.logfile, 'a') as fd:
fd.write('\nFile: {}\n'.format(args.raw))
fd.write(f.read())
logger.info('Results saved to %s' % args.logfile)
if args.outfile is not None:
res.writeto(args.outfile, overwrite=True)
logger.info('FITS file saved to %s' % args.outfile)
