def main(args):
from astropy import coordinates
from astropy import units as u
from ESOAsg import archive_observations
from ESOAsg import msgs
from ESOAsg.ancillary import cleaning_lists
ra_list = cleaning_lists.from_element_to_list(args.ra_degree,
element_type=float)
dec_list = cleaning_lists.from_element_to_list(args.dec_degree,
element_type=float)
if args.radius is None:
radius = None
else:
radius = cleaning_lists.from_element_to_list(args.radius,
element_type=float)[0]
instruments = cleaning_lists.from_element_to_list(args.instruments,
element_type=str)
data_types = cleaning_lists.from_element_to_list(args.data_types,
element_type=str)
msgs.start()
for ra, dec in zip(ra_list, dec_list):
position = coordinates.SkyCoord(ra=ra * u.degree,
dec=dec * u.degree,
frame='fk5')
msgs.newline()
msgs.info('Query for ESO archival data around the position: {}'.format(
position.to_string('hmsdms')))
result_from_query = archive_observations.query_from_radec(
position,
radius=radius,
instruments=instruments,
data_types=data_types,
verbose=False)
if len(result_from_query['dp_id']) > 0:
archive_observations.download(result_from_query['dp_id'])
msgs.end()
EXAMPLES = r"""
Example:
fix_muse_p197.py --input_fits
"""
if __name__ == '__main__':
args = parse_arguments()
# getting fits names
input_fits = np.str(args.input_fits[0])
if args.output_fits is None:
output_fits = input_fits.replace('.fits', '_fixed.fits')
else:
output_fits = np.str(args.output_fits[0])
msgs.start()
hdul_original = fits.open(input_fits)
msgs.work('Updating checksum and datasum')
hdul[0].add_datasum()
hdul[1].add_datasum()
hdul[0].add_checksum(override_datasum=True)
hdul[1].add_checksum(override_datasum=True)
msgs.work('Flushing changes.')
hdul.flush()
hdul.close()
def main(args):
import numpy as np
import os
import shutil
from astropy.coordinates import SkyCoord
from astropy.coordinates import name_resolve
from astropy import units as u
from astropy.io import fits
from ESOAsg.ancillary import cleaning_lists
from ESOAsg.core import fitsfiles
from ESOAsg import msgs
# Cleaning input lists
input_fits_files = cleaning_lists.make_list_of_fits_files(args.input_fits)
# Make whitelight images
if args.whitelight:
make_whitelight_image = True
else:
make_whitelight_image = False
# Creating output list
if args.suffix is None:
overwrite = False
msgs.warning('The file will overwrite the input files')
else:
overwrite = True
suffix_string = cleaning_lists.make_string(args.suffix)
output_fits_files = cleaning_lists.make_list_of_fits_files_and_append_suffix(
input_fits_files, suffix=suffix_string)
if make_whitelight_image:
output_whitelight_files = cleaning_lists.make_list_of_fits_files_and_append_suffix(
input_fits_files, suffix=suffix_string + '_WL')
else:
output_whitelight_files = [None] * len(input_fits_files)
'''
# reference
if args.referenc is not None:
reference = str(args.referenc[0])
else:
reference = str(' ')
# fluxcal
if args.fluxcal == 'ABSOLUTE':
fluxcal = 'ABSOLUTE'
elif args.fluxcal == 'UNCALIBRATED':
fluxcal = 'UNCALIBRATED'
else:
msgs.error('Possible values for fluxcal are: `ABSOLUTE` or `UNCALIBRATED`')
# abmaglim
if args.abmaglim is not None:
abmaglim = args.abmaglim
assert isinstance(abmaglim, (int, np.float_)), 'ABMAGLIM must be a float'
if abmaglim < 0:
msgs.error('ABMAGLIM must be positive')
else:
abmaglim = np.float_(-1.)
'''
msgs.start()
for fits_in, fits_out, image_out in zip(input_fits_files,
output_fits_files,
output_whitelight_files):
if os.path.exists(fits_out):
shutil.copy(fits_out, fits_out.replace('.fit', '_old.fit'))
msgs.warning('{} already exists. Backup created.'.format(fits_out))
if image_out is not None:
if os.path.exists(image_out):
shutil.copy(image_out, image_out.replace('.fit', '_old.fit'))
msgs.warning(
'{} already exists. Backup created.'.format(image_out))
full_hdul = fitsfiles.get_hdul(fits_in)
try:
instrument = full_hdul[0].header['HIERARCH ESO SEQ ARM']
except KeyError:
msgs.error(
'Failed to read the keyword HIERARCH ESO SEQ ARM from the primary header'
)
finally:
if instrument in SUPPORTED_INSTRUMENT:
msgs.info(
'The input file is from SPHERE/{}'.format(instrument))
else:
msgs.warning(
'Instrument SPHERE/{} not supported'.format(instrument))
# ToDo
# These needs to be transformed in objects
if instrument.startswith('IFS'):
msgs.work('Fixing header for SPHERE/{} file {}'.format(
instrument, fits_in))
# Create a copy of the file where there is a primary HDU and data are in the 'DATA" HDU
msgs.work('Reshaping cube into PrimaryHEADER and Data Header')
fitsfiles.new_fits_like(fits_in, [0],
fits_out,
overwrite=overwrite,
fix_header=True)
hdul = fitsfiles.get_hdul(fits_out, 'update', checksum=True)
hdr0 = hdul[0].header
hdr1 = hdul[1].header
# Check for HISTORY
# Primary Header
if 'HISTORY' in hdr0.keys():
history_cards_hdr0 = [
history_card_hdr0 for history_card_hdr0 in hdr0
if history_card_hdr0.startswith('HISTORY')
]
history_values_hdr0 = [
hdr0[history_card_hdr0] for history_card_hdr0 in hdr0
if history_card_hdr0.startswith('HISTORY')
]
for history_card_hdr0, history_value_hdr0 in zip(
history_cards_hdr0, history_values_hdr0):
msgs.work('Cleaning cards: {} = {}'.format(
history_card_hdr0, history_value_hdr0))
del hdr0['HISTORY'][:]
# Data Header
if 'HISTORY' in hdr1.keys():
history_values_hdr1 = hdr1['HISTORY'][:]
for history_number in range(0, len(history_values_hdr1)):
clean_history = cleaning_lists.remove_non_ascii(
history_values_hdr1[history_number])
if len(clean_history) > 0:
hdr1['HISTORY'][history_number] = str(clean_history)
else:
hdr1['HISTORY'][history_number] = str(' ')
# Update cards for headers:
# Updating values with different CARD in the header
cards_input = [
'CRPIX4', 'CRVAL4', 'CTYPE4', 'CUNIT4', 'CD4_4', 'CD1_4',
'CD2_4', 'CD4_1', 'CD4_2'
]
cards_output = [
'CRPIX3', 'CRVAL3', 'CTYPE3', 'CUNIT3', 'CD3_3', 'CD1_3',
'CD2_3', 'CD3_1', 'CD3_2'
]
fitsfiles.transfer_header_cards(hdr1,
hdr1,
cards_input,
output_cards=cards_output,
delete_card=True)
# Remove not used values
cards_to_be_removed_hdr1 = ['CD4_3', 'CD3_4']
for card_to_be_removed_hdr1 in cards_to_be_removed_hdr1:
hdr1.remove(card_to_be_removed_hdr1, ignore_missing=True)
# Transfer cards from HDU1 to the PrimaryHDU
not_to_be_transfer = [
hdr1_card for hdr1_card in hdr1
if hdr1_card.startswith('COMMENT') or hdr1_card.startswith(
'EXTNAME') or hdr1_card.startswith('BITPIX') or
hdr1_card.startswith('NAXIS') or hdr1_card.startswith('CRPIX')
or hdr1_card.startswith('CRVAL') or hdr1_card.startswith(
'CDELT') or hdr1_card.startswith('CTYPE')
or hdr1_card.startswith('CD1_') or hdr1_card.startswith('CD2_')
or hdr1_card.startswith('CD3_') or hdr1_card.startswith(
'CUNIT') or hdr1_card.startswith('CSYER') or hdr1_card.
startswith('HDUCLAS') or hdr1_card.startswith('XTENSION')
or hdr1_card.startswith('PCOUNT') or hdr1_card.startswith(
'GCOUNT') or hdr1_card.startswith('HDUDOC') or hdr1_card.
startswith('HDUVER') or hdr1_card.startswith('HISTORY')
]
cards_to_be_transfer = []
for hdr1_card in hdr1:
if hdr1_card not in not_to_be_transfer:
cards_to_be_transfer.append(hdr1_card)
fitsfiles.transfer_header_cards(hdr1,
hdr0,
cards_to_be_transfer,
with_comment=True,
delete_card=True)
# Try to guess coordinates
if 'CRVAL1' not in hdr1.keys():
msgs.warning('CRVAL position keywords not preset')
if 'OBJECT' in hdr0.keys():
try:
object_coordinate = SkyCoord.from_name(
str(hdr0['OBJECT']).strip())
ra_obj, dec_obj = object_coordinate.ra.degree, object_coordinate.dec.degree
if 'RA' in hdr0.keys() and 'DEC' in hdr0.keys():
pointing_coordinate = SkyCoord(float(hdr0['RA']),
float(hdr0['DEC']),
unit='deg')
msgs.work(
'Testing from separation from pointing position'
)
separation = object_coordinate.separation(
pointing_coordinate).arcsec
if separation < 120.:
msgs.info('Object - Pointing separation is {}'.
format(separation))
msgs.info(
'Updating CRVAL1 = {}'.format(ra_obj))
msgs.info(
'Updating CRVAL2 = {}'.format(dec_obj))
hdr1['CRVAL1'] = ra_obj
hdr1['CRVAL2'] = dec_obj
msgs.work('Updating CUNIT')
hdr1['CUNIT1'] = 'deg'
hdr1['CUNIT2'] = 'deg'
msgs.work('Updating CTYPE')
hdr1['CTYPE1'] = 'RA---TAN'
hdr1['CTYPE2'] = 'DEC--TAN'
msgs.work('Updating CRPIX')
hdr1['CRPIX1'] = float(
hdul[1].data.shape[2]) / 2.
hdr1['CRPIX2'] = float(
hdul[1].data.shape[1]) / 2.
msgs.info('Updating CD1 and CD2')
hdr1['CD1_1'] = 2.06E-06
hdr1['CD2_2'] = 2.06E-06
hdr1['CD1_2'] = 0.
hdr1['CD2_1'] = 0.
msgs.work('Updating RA, DEC')
hdr0['RA'] = ra_obj
hdr0.comments[
'RA'] = object_coordinate.ra.to_string(
u.hour)
hdr0['DEC'] = dec_obj
hdr0.comments[
'DEC'] = object_coordinate.dec.to_string(
u.degree, alwayssign=True)
else:
msgs.warning(
'Object - Pointing separation is {}'.
format(separation))
msgs.warning(
'This is suspicious, CRVAL not updated')
except name_resolve.NameResolveError:
msgs.warning('Object {} not recognized'.format(
str(hdr0['OBJECT']).strip()))
msgs.warning('CRVAL not updated')
# Updating file prodcatg
msgs.work('Updating PRODCATG to SCIENCE.CUBE.IFS')
hdr0['PRODCATG'] = str('SCIENCE.CUBE.IFS')
# Some more updates
msgs.work('Setting NAXIS = 0 in primary header')
hdr0['NAXIS'] = 0
if 'OBSTECH' not in hdr0.keys():
msgs.warning('OBSTECH missing')
if 'ESO PRO TECH' in hdr0.keys():
msgs.info('Deriving OBSTECH from HIERARCH ESO PRO TECH')
msgs.work('Updating OBSTECH to {}'.format(
str(hdr0['HIERARCH ESO PRO TECH'])))
hdr0['OBSTECH'] = str(hdr0['HIERARCH ESO PRO TECH'])
if 'EXPTIME' not in hdr0.keys():
msgs.warning('EXPTIME missing')
if 'ESO DET SEQ1 REALDIT' in hdr0.keys(
) and 'ESO DET NDIT' in hdr0.keys():
msgs.info('Deriving EXPTIME and TEXPTIME as REALDIT * DIT')
hdr0['EXPTIME'] = hdr0[
'HIERARCH ESO DET SEQ1 REALDIT'] * hdr0[
'HIERARCH ESO DET NDIT']
hdr0['TEXPTIME'] = hdr0[
'HIERARCH ESO DET SEQ1 REALDIT'] * hdr0[
'HIERARCH ESO DET NDIT']
msgs.work('Updating EXPTIME to {}'.format(
str(hdr0['EXPTIME'])))
msgs.work('Updating TEXPTIME to {}'.format(
str(hdr0['TEXPTIME'])))
if 'WAVELMIN' not in hdr0.keys():
msgs.warning('WAVELMIN missing')
z_pixel = np.arange(int(hdul[1].data.shape[0]))
z_wave = float(
hdr1['CRVAL3']) + (z_pixel * float(hdr1['CD3_3']))
if str(hdr1['CUNIT3']).strip().upper() == 'MICRONS':
msgs.info('Deriving WAVELMIN and WAVELMAX from CRVAL1')
z_wave = z_wave * 1000. # convert to nanometers
hdr0['WAVELMIN'] = np.nanmin(z_wave)
hdr0['WAVELMAX'] = np.nanmax(z_wave)
msgs.work('Updating WAVELMIN to {}'.format(
str(hdr0['WAVELMIN'])))
msgs.work('Updating WAVELMAX to {}'.format(
str(hdr0['WAVELMAX'])))
else:
msgs.warning(
'Unknown units {}. WAVELMIN and WAVELMAX not calculated'
.format(str(hdr1['CUNIT3'])))
if 'SPEC_RES' not in hdr0.keys():
msgs.warning('SPEC_RES missing')
if 'WAVELMAX' in hdr0.keys():
msgs.info('Deriving SPEC_RES from WAVELMAX')
if (float(hdr0['WAVELMAX']) > 1300.) and (float(
hdr0['WAVELMAX']) < 1400.):
hdr0['SPEC_RES'] = 50.
msgs.work('Updating SPEC_RES to {}'.format(
str(hdr0['SPEC_RES'])))
elif (float(hdr0['WAVELMAX']) > 1600.) and (float(
hdr0['WAVELMAX']) < 1700.):
hdr0['SPEC_RES'] = 30.
msgs.work('Updating SPEC_RES to {}'.format(
str(hdr0['SPEC_RES'])))
else:
msgs.warning('WAVELMAX = {} is not in the expected ' /
+ 'range of possible values'.format(
str(hdr0['WAVELMAX'])))
if 'PROGID' not in hdr0.keys():
msgs.warning('PROG_ID missing')
if 'ESO OBS PROG ID' in hdr0.keys():
msgs.info('Deriving PROG_ID from HIERARCH ESO OBS PROG ID')
msgs.work('Updating PROG_ID to {}'.format(
str(hdr0['HIERARCH ESO OBS PROG ID'])))
hdr0['PROG_ID'] = str(hdr0['HIERARCH ESO OBS PROG ID'])
if 'MJD-END' not in hdr0.keys():
msgs.warning('MJD-END missing')
if 'TEXPTIME' in hdr0.keys():
msgs.info('Deriving MJD-END from MJD-OBS and TEXPTIME')
texptime_sec = float(hdr0['TEXPTIME'])
texptime_day = texptime_sec / (60. * 60. * 24.)
mjdend = float(hdr0['MJD-OBS']) + texptime_day
fitsfiles.add_header_card(hdr0, 'MJD-END', mjdend,
'End of observation')
msgs.work('MJD-OBS = {} and TEXPTIME = {} days'.format(
str(hdr0['MJD-OBS']), str(texptime_day)))
msgs.work('Updating MJD-END to {}'.format(
str(hdr0['MJD-END'])))
# Remove not used values
cards_to_be_removed_hdr0 = ['ERRDATA', 'QUALDATA', 'SCIDATA']
for card_to_be_removed_hdr0 in cards_to_be_removed_hdr0:
hdr0.remove(card_to_be_removed_hdr0, ignore_missing=True)
cards_to_be_removed_hdr1 = ['HDUCLASS3']
for card_to_be_removed_hdr1 in cards_to_be_removed_hdr1:
hdr1.remove(card_to_be_removed_hdr1, ignore_missing=True)
# Updating the FITS file definition comment line
hdr0.add_comment(
" FITS (Flexible Image Transport System) format is defined in 'Astronomy"
+ " and "
"Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H",
after='EXTEND')
if 'COMMENT' in hdr1.keys():
comment_values_hdr1 = hdr1['COMMENT'][:]
for index, comment_value_hdr1 in enumerate(
comment_values_hdr1):
msgs.work('Removing COMMENT card : {}'.format(
comment_value_hdr1))
hdr1.remove('COMMENT', ignore_missing=True, remove_all=True)
# Creating white light image keyword:
if make_whitelight_image:
fitsfiles.add_header_card(
hdr0, 'ASSON1',
image_out.split('/')[-1],
'ANCILLARY.IMAGE.WHITELIGHT filename')
msgs.work('Updating ASSON1 to {}'.format(hdr0['ASSON1']))
# Actually creating the white-light image
if make_whitelight_image:
msgs.info('Making white light image')
image_hdu = fits.PrimaryHDU()
image_hdul = fits.HDUList([image_hdu])
if str(hdr1['CUNIT3']).strip().upper() == 'MICRONS':
to_ang = 10000.
else:
msgs.error('Spectral unit: {} not recognized'.format(
hdr1['CUNIT3']))
delta_wave_bin = hdr1['CD3_3']
image_hdul.append(
fits.ImageHDU(
to_ang * delta_wave_bin *
np.nansum(hdul[1].data, axis=0, dtype=np.float_)))
image_hdr0 = image_hdul[0].header
image_hdr1 = image_hdul[1].header
card_for_image0 = [
'WAVELMIN', 'WAVELMAX', 'OBJECT', 'TELESCOP', 'INSTRUME',
'RADECSYS', 'RA', 'DEC', 'EQUINOX'
]
fitsfiles.transfer_header_cards(hdr0,
image_hdr0,
card_for_image0,
with_comment=True,
delete_card=False)
image_hdr0['PRODCATG'] = str('ANCILLARY.IMAGE.WHITELIGHT')
card_for_image1 = [
'CRPIX1', 'CRPIX2', 'CRVAL1', 'CRVAL2', 'CUNIT1', 'CUNIT2',
'NAXIS1', 'NAXIS2', 'EXTNAME', 'CD1_1', 'CD1_2', 'CD2_1',
'CD2_2', 'CTYPE1', 'CTYPE2'
]
fitsfiles.transfer_header_cards(hdr1,
image_hdr1,
card_for_image1,
with_comment=True,
delete_card=False)
# Update checksum and datasum
msgs.work('Updating checksum and datasum')
hdul[0].add_checksum(override_datasum=False)
hdul[1].add_datasum()
hdul[1].add_checksum(override_datasum=True)
hdul.flush(output_verify='fix')
hdul.close()
msgs.info('File {} produced.'.format(fits_out))
if make_whitelight_image:
image_hdul[0].add_datasum()
image_hdul[1].add_datasum()
image_hdul[0].add_checksum(override_datasum=True)
image_hdul[1].add_checksum(override_datasum=True)
image_hdul.writeto(image_out,
overwrite=True,
output_verify='fix')
msgs.info('Image {} produced.'.format(image_out))
elif instrument.startswith('IRDIS'):
msgs.work('Fixing header for SPHERE/{} file {}'.format(
instrument, fits_in))
hdr = fitsfiles.header_from_fits_file(fits_in)
if 'ESO DPR TECH' in hdr.keys():
if str(hdr['ESO DPR TECH']).strip(
) == 'IMAGE,DUAL,CORONOGRAPHY':
msgs.work('Working with {} as observing technique'.format(
str(hdr['ESO DPR TECH']).strip()))
elif 'DUAL' in str(hdr['ESO DPR TECH']).strip():
msgs.error('{} needs to be tested'.format(
str(hdr['ESO DPR TECH']).strip()))
else:
msgs.error('Only DUAL imaging currently implemented')
else:
msgs.error('Cannot recognize the observing technique')
# defining the two fits_out files:
fits_out_index = [0, 1]
fits_out_files = []
for index in fits_out_index:
fits_out_file = fits_out.replace('.fit',
'_' + str(index) + '.fit')
if os.path.exists(fits_out_file):
shutil.copy(fits_out_file,
fits_out_file.replace('.fit', '_old.fit'))
msgs.warning(
'{} already exists. Backup created.'.format(fits_out))
fitsfiles.new_fits_like(fits_in, [0],
fits_out_file,
overwrite=overwrite,
fix_header=True,
empty_primary_hdu=False)
fits_out_files.append(fits_out_file)
for index, fits_out_file in zip(fits_out_index, fits_out_files):
hdul = fitsfiles.get_hdul(fits_out_file,
'update',
checksum=True)
hdr0 = hdul[0].header
hdul[0].data = hdul[0].data[index, :, :]
# Check for HISTORY
# Primary Header
if 'HISTORY' in hdr0.keys():
history_cards_hdr0 = [
history_card_hdr0 for history_card_hdr0 in hdr0
if history_card_hdr0.startswith('HISTORY')
]
history_values_hdr0 = [
hdr0[history_card_hdr0] for history_card_hdr0 in hdr0
if history_card_hdr0.startswith('HISTORY')
]
for history_card_hdr0, history_value_hdr0 in zip(
history_cards_hdr0, history_values_hdr0):
msgs.work('Cleaning cards: {} = {}'.format(
history_card_hdr0, history_value_hdr0))
del hdr0['HISTORY'][:]
# Try to guess coordinates
if 'CRVAL1' not in hdr0.keys():
msgs.warning('CRVAL position keywords not preset')
if 'OBJECT' in hdr0.keys():
try:
object_coordinate = SkyCoord.from_name(
str(hdr0['OBJECT']).strip())
ra_obj, dec_obj = object_coordinate.ra.degree, object_coordinate.dec.degree
if 'RA' in hdr0.keys() and 'DEC' in hdr0.keys():
pointing_coordinate = SkyCoord(
float(hdr0['RA']),
float(hdr0['DEC']),
unit='deg')
msgs.work(
'Testing from separation from pointing position'
)
separation = object_coordinate.separation(
pointing_coordinate).arcsec
if separation < 120.:
msgs.info(
'Object - Pointing separation is {}'.
format(separation))
msgs.info(
'Updating CRVAL1 = {}'.format(ra_obj))
msgs.info(
'Updating CRVAL2 = {}'.format(dec_obj))
hdr0['CRVAL1'] = ra_obj
hdr0['CRVAL2'] = dec_obj
msgs.work('Updating CUNIT')
hdr0['CUNIT1'] = 'deg'
hdr0['CUNIT2'] = 'deg'
msgs.work('Updating CTYPE')
hdr0['CTYPE1'] = 'RA---TAN'
hdr0['CTYPE2'] = 'DEC--TAN'
msgs.work('Updating CRPIX')
hdr0['CRPIX1'] = float(
hdul[0].data.shape[1]) / 2.
hdr0['CRPIX2'] = float(
hdul[0].data.shape[0]) / 2.
msgs.info('Updating CD1 and CD2')
hdr0['CD1_1'] = hdr0[
'PIXSCAL'] * 2.778E-4 / 1000.
hdr0['CD2_2'] = hdr0[
'PIXSCAL'] * 2.778E-4 / 1000.
hdr0['CD1_2'] = 0.
hdr0['CD2_1'] = 0.
msgs.work('Updating RA, DEC')
hdr0['RA'] = ra_obj
hdr0.comments[
'RA'] = object_coordinate.ra.to_string(
u.hour)
hdr0['DEC'] = dec_obj
hdr0.comments[
'DEC'] = object_coordinate.dec.to_string(
u.degree, alwayssign=True)
else:
msgs.warning(
'Object - Pointing separation is {}'.
format(separation))
msgs.warning(
'This is suspicious, CRVAL not updated'
)
except name_resolve.NameResolveError:
msgs.warning('Object {} not recognized'.format(
str(hdr0['OBJECT']).strip()))
msgs.warning('CRVAL not updated')
# Updating file prodcatg
msgs.work('Updating PRODCATG to SCIENCE.IMAGE')
hdr0['PRODCATG'] = str('SCIENCE.IMAGE')
if 'PROGID' not in hdr0.keys():
msgs.warning('PROG_ID missing')
if 'ESO OBS PROG ID' in hdr0.keys():
msgs.info(
'Deriving PROG_ID from HIERARCH ESO OBS PROG ID')
msgs.work('Updating PROG_ID to {}'.format(
str(hdr0['HIERARCH ESO OBS PROG ID'])))
hdr0['PROG_ID'] = str(hdr0['HIERARCH ESO OBS PROG ID'])
# Update checksum and datasum
msgs.work('Updating checksum and datasum')
hdul[0].add_checksum(override_datasum=False)
hdul.flush(output_verify='fix')
hdul.close()
else:
msgs.warning(
'The Instrument {} is not supported \nThe file {} will not be processed'
.format(instrument, fits_in))
msgs.end()
'''
def main(args):
from ESOAsg.ancillary import astro
from ESOAsg.ancillary import cleaning_lists
from ESOAsg.ancillary import polygons
from ESOAsg import archive_science_portal
from ESOAsg import archive_observations
from ESOAsg import msgs
# Cleaning input lists
input_fits_files = cleaning_lists.make_list_of_fits_files(args.input_fits)
instruments = cleaning_lists.from_element_to_list(args.instruments,
element_type=str)
data_types = cleaning_lists.from_element_to_list(args.data_types,
element_type=str)
# Cleaning input values
confidence_level = cleaning_lists.from_element_to_list(
args.confidence_level, element_type=float)[0]
maxrec = cleaning_lists.from_element_to_list(args.maxrec,
element_type=int)[0]
max_vertices = cleaning_lists.from_element_to_list(args.max_vertices,
element_type=int)[0]
# Cleaning bool
show_figure = args.show_sky
# Show link
show_asp = args.asp_link
# Download data
download_data = args.download_data
msgs.start()
for fits_file in input_fits_files:
msgs.info(' ')
msgs.info('Working on file: {}'.format(fits_file))
msgs.info(' ')
contours = astro.contours_from_gw_bayestar(
fits_file, credible_level=confidence_level)
astro.show_contours_from_gw_bayestar(
fits_file,
contours=contours,
cmap='afmhot',
contours_color='white',
show_figure=show_figure,
matplotlib_backend=STARTING_MATPLOTLIB_BACKEND)
polygons_list = polygons.contours_to_polygons(
contours, max_vertices=max_vertices)
if show_asp:
msgs.info('Opening links to ASP')
archive_science_portal.query_from_polygons(polygons=polygons_list,
open_link=True)
results_from_query = archive_observations.query_from_polygons(
polygons=polygons_list,
maxrec=maxrec,
instruments=instruments,
data_types=data_types,
verbose=False)
msgs.info(' ')
if download_data:
if results_from_query is None:
msgs.warning('No data retrieved')
elif isinstance(results_from_query, list):
for idx_poly, result_from_query in enumerate(
results_from_query):
msgs.info(
'Downloading data for polygon N.{}'.format(idx_poly +
1))
archive_observations.download(result_from_query['dp_id'])
else:
msgs.info('Downloading data')
archive_observations.download(results_from_query['dp_id'])
msgs.info(' ')
msgs.end()