def extract_from_file(fname, n_pixels, threshold, fwhmfilt, isolation_radius,
aperture_radius,
region_filename=None):
logger.info('Extracting catalogue from %s', fname)
with open_fits(fname) as infile:
header = infile[0].header
ref_image_id = header['image_id']
source_table = source_detect(fname,
n_pixels=n_pixels,
threshold=threshold,
fwhmfilt=fwhmfilt,
aperture_radius=aperture_radius)
logger.info('Found %s sources', len(source_table))
filtered_source_table = filter_source_table(source_table,
radius=isolation_radius)
logger.info('Keeping %s sources', len(filtered_source_table))
if region_filename is not None:
with RegionFile(region_filename,
aperture_radius=aperture_radius) as rfile:
rfile.add_regions(filtered_source_table, colour='green')
rfile.add_regions(source_table, colour='red')
inc_prescan = image_has_prescan(fname)
logger.debug('Image has prescan: %s', inc_prescan)
for row in filtered_source_table:
yield TransmissionCatalogueEntry(
aperture_radius=aperture_radius,
ref_image_id=int(ref_image_id),
x_coordinate=float(row['X_coordinate']),
y_coordinate=float(row['Y_coordinate']),
inc_prescan=inc_prescan,
flux_adu=float(row['Aper_flux_3']))
def extract_from_file(cls, filename, ref_catalogue, sky_radius_inner,
sky_radius_outer):
with open_fits(filename) as infile:
image_data = infile[0].data
source_flux = photometry_local(
image_data, ref_catalogue.x, ref_catalogue.y,
ref_catalogue.radius[0], sky_radius_inner, sky_radius_outer)
return cls(ref_catalogue.x, ref_catalogue.y, ref_catalogue.radius,
source_flux)
def from_file(cls, filename, cursor, sky_radius_inner, sky_radius_outer):
logger.info('Extracting transmission from %s', filename)
with open_fits(filename) as infile:
header = infile[0].header
image_id = header['image_id']
photometry_results = extract_photometry_results(
filename, cursor, image_id, sky_radius_inner, sky_radius_outer)
photometry_results['image_id'] = image_id
return cls(**photometry_results)
def source_detect(fname, n_pixels, threshold, fwhmfilt, aperture_radius):
logger.info('Running source detect')
logger.debug('n_pixels: %s, threshold: %s', n_pixels, threshold)
with tempfile.NamedTemporaryFile(suffix='.fits') as tfile:
cmd = ['imcore', fname, 'noconf', tfile.name, n_pixels, threshold,
'--noell', '--filtfwhm', fwhmfilt, '--rcore', aperture_radius]
str_cmd = list(map(str, cmd))
logger.debug('Running command [%s]', ' '.join(str_cmd))
sp.check_call(str_cmd)
tfile.seek(0)
with open_fits(tfile.name) as infile:
return infile[1].data
def get_refcat_id(filename):
logger.debug("Extracting reference image id from {filename}".format(filename=filename))
with open_fits(filename) as infile:
header = infile[0].header
try:
return header["agrefimg"]
except KeyError:
logger.exception(
"""No autoguider reference image found in file %s.
Assuming this is ok and continuing.""",
filename,
)
raise NoAutoguider
