def test_fpack(solved_fits_file):
new_file = solved_fits_file.replace('solved', 'solved_copy')
copy_file = shutil.copyfile(solved_fits_file, new_file)
info = os.stat(copy_file)
assert info.st_size > 0.
uncompressed = fits_utils.funpack(copy_file, verbose=True)
assert os.stat(uncompressed).st_size > info.st_size
compressed = fits_utils.fpack(uncompressed, verbose=True)
assert os.stat(compressed).st_size == info.st_size
os.remove(copy_file)
def test_no_overwrite_fpack(solved_fits_file):
new_file = solved_fits_file.replace('solved', 'solved_copy')
copy_file = shutil.copyfile(solved_fits_file, new_file)
# Unpack the file. This removes the packed version.
uncompressed = fits_utils.funpack(copy_file)
# Copy file again so now the packed version exists alongside unpacked.
copy_file = shutil.copyfile(solved_fits_file, new_file)
# Deny overwriting gives error.
with pytest.raises(FileExistsError):
_ = fits_utils.fpack(uncompressed, overwrite=False)
# Default is overwrite=True.
compressed = fits_utils.fpack(uncompressed)
# Cleanup test.
for file in [copy_file, uncompressed, compressed]:
with suppress(FileNotFoundError):
os.remove(file)
def _lookup_via_sextractor(fits_file, sextractor_params=None, *args, **kwargs):
# Write the sextractor catalog to a file
base_dir = os.path.dirname(fits_file)
source_dir = os.path.join(base_dir, 'sextractor')
os.makedirs(source_dir, exist_ok=True)
img_id = os.path.splitext(os.path.basename(fits_file))[0]
source_file = os.path.join(source_dir, f'point_sources_{img_id}.cat')
# sextractor can't handle compressed data
if fits_file.endswith('.fz'):
fits_file = fits_utils.funpack(fits_file)
logger.info("Point source catalog: {}".format(source_file))
if not os.path.exists(source_file) or kwargs.get('force_new', False):
logger.info("No catalog found, building from sextractor")
# Build catalog of point sources
sextractor = shutil.which('sextractor')
if sextractor is None:
sextractor = shutil.which('sex')
if sextractor is None:
raise Exception('sextractor not found')
if sextractor_params is None:
sextractor_params = [
'-c',
'{}/PIAA/resources/conf_files/sextractor/panoptes.sex'.format(
os.getenv('PANDIR')),
'-CATALOG_NAME',
source_file,
]
logger.info("Running sextractor...")
cmd = [sextractor, *sextractor_params, fits_file]
logger.info(cmd)
try:
subprocess.run(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
timeout=60,
check=True)
except subprocess.CalledProcessError as e:
raise Exception("Problem running sextractor: {}".format(e))
# Read catalog
logger.info('Building detected source table')
point_sources = Table.read(source_file, format='ascii.sextractor')
# Remove the point sources that sextractor has flagged
# if 'FLAGS' in point_sources.keys():
# point_sources = point_sources[point_sources['FLAGS'] == 0]
# point_sources.remove_columns(['FLAGS'])
# Rename columns
point_sources.rename_column('XPEAK_IMAGE', 'x')
point_sources.rename_column('YPEAK_IMAGE', 'y')
# Filter point sources near edge
# w, h = data[0].shape
w, h = (3476, 5208)
stamp_size = 60
logger.info('Trimming sources near edge')
top = point_sources['y'] > stamp_size
bottom = point_sources['y'] < w - stamp_size
left = point_sources['x'] > stamp_size
right = point_sources['x'] < h - stamp_size
point_sources = point_sources[top & bottom & right & left].to_pandas()
point_sources.columns = [
'ra',
'dec',
'x',
'y',
'x_image',
'y_image',
'background',
'flux_best',
'fluxerr_best',
'mag_best',
'magerr_best',
'flux_max',
'fwhm_image',
'flags',
]
logger.info(f'Returning {len(point_sources)} sources')
return point_sources
def _lookup_via_sextractor(fits_file, sextractor_params=None, *args, **kwargs):
# Write the sextractor catalog to a file
base_dir = os.path.dirname(fits_file)
source_dir = os.path.join(base_dir, 'sextractor')
os.makedirs(source_dir, exist_ok=True)
img_id = os.path.splitext(os.path.basename(fits_file))[0]
source_file = os.path.join(source_dir, f'point_sources_{img_id}.cat')
# sextractor can't handle compressed data
if fits_file.endswith('.fz'):
fits_file = fits_utils.funpack(fits_file)
logger.info("Point source catalog: {}".format(source_file))
if not os.path.exists(source_file) or kwargs.get('force_new', False):
logger.info("No catalog found, building from sextractor")
# Build catalog of point sources
sextractor = shutil.which('sextractor')
if sextractor is None:
sextractor = shutil.which('sex')
if sextractor is None:
raise Exception('sextractor not found')
if sextractor_params is None:
sextractor_params = [
'-c', '{}/PIAA/resources/conf_files/sextractor/panoptes.sex'.format(
os.getenv('PANDIR')),
'-CATALOG_NAME', source_file,
]
logger.info("Running sextractor...")
cmd = [sextractor, *sextractor_params, fits_file]
logger.info(cmd)
try:
subprocess.run(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
timeout=60,
check=True)
except subprocess.CalledProcessError as e:
raise Exception("Problem running sextractor: {}".format(e))
# Read catalog
logger.info('Building detected source table')
point_sources = Table.read(source_file, format='ascii.sextractor')
# Remove the point sources that sextractor has flagged
# if 'FLAGS' in point_sources.keys():
# point_sources = point_sources[point_sources['FLAGS'] == 0]
# point_sources.remove_columns(['FLAGS'])
# Rename columns
point_sources.rename_column('XPEAK_IMAGE', 'x')
point_sources.rename_column('YPEAK_IMAGE', 'y')
# Filter point sources near edge
# w, h = data[0].shape
w, h = (3476, 5208)
stamp_size = 60
logger.info('Trimming sources near edge')
top = point_sources['y'] > stamp_size
bottom = point_sources['y'] < w - stamp_size
left = point_sources['x'] > stamp_size
right = point_sources['x'] < h - stamp_size
point_sources = point_sources[top & bottom & right & left].to_pandas()
point_sources.columns = [
'ra', 'dec',
'x', 'y',
'x_image', 'y_image',
'background',
'flux_best', 'fluxerr_best',
'mag_best', 'magerr_best',
'flux_max',
'fwhm_image',
'flags',
]
logger.info(f'Returning {len(point_sources)} sources')
return point_sources