def fors_photometry(aligned_phot: List[str],
master_sky_flat_img: str,
output_dir: str,
output_filename: str = None,
chip_num: int = 1,
sof_name: str = "photometry.sof"):
sof_name = u.sanitise_file_ext(sof_name, ".sof")
old_dir = os.getcwd()
os.chdir(output_dir)
sof_path = os.path.join(output_dir, sof_name)
phot_table = select_phot_table(chip_num)
sof(
{
"MASTER_SKY_FLAT_IMG": [master_sky_flat_img],
"ALIGNED_PHOT": aligned_phot,
"PHOT_TABLE": [os.path.join(fors2_calib_path, phot_table)],
}, sof_path)
u.system_command_verbose(
f"{eso_bin_path} fors_photometry --fite=one {sof_path}")
master_path = os.path.join(output_dir, "phot_coeff_table.fits")
if output_filename is not None:
final_path = os.path.join(output_dir, output_filename)
shutil.move(master_path, final_path)
else:
final_path = master_path
os.chdir(old_dir)
return final_path
def disco(
redux_dir: str,
tags: list = None,
expression: str = None,
output: str = None,
file_glob: str = "*_skySubtracted.fits",
refcat: str = None,
refcat_format: str = None, #"ascii.csv",
refcat_ra: str = None,
refcat_dec: str = None,
ignore_objcat: bool = False):
# Switch working directory to reduction directory.
pwd = os.getcwd()
os.chdir(redux_dir)
ds_str = build_data_select_str(tags=tags,
expression=expression,
file_glob=file_glob)
sys_str = f"disco `{ds_str}`"
if output is not None:
if os.path.isfile(output):
os.remove(output)
sys_str += f" -o {output}"
if refcat is not None:
if refcat_ra is not None or refcat_dec is not None:
filename = os.path.split(refcat)[-1]
refcat_tbl = Table.read(refcat, format=refcat_format)
if refcat_ra is not None:
refcat_tbl["RA"] = refcat_tbl[refcat_ra]
refcat_tbl.remove_column(refcat_ra)
if refcat_dec is not None:
refcat_tbl["DEC"] = refcat_tbl[refcat_dec]
refcat_tbl.remove_column(refcat_dec)
refcat_tbl.write(os.path.join(redux_dir, filename), overwrite=True)
refcat = filename
sys_str += f" --refcat_columns RA,DEC"
sys_str += f" --refcat {refcat}"
if refcat_format is not None:
sys_str += f" --refcat_format {refcat_format}"
if ignore_objcat:
sys_str += " --ignore_objcat"
u.system_command_verbose(sys_str)
os.chdir(pwd)
def source_extractor(
image_path: str,
output_dir: str = None,
configuration_file: str = None,
parameters_file: str = None,
catalog_name: str = None,
copy_params: bool = True,
template_image_path: str = None,
**configs):
"""
:param configs: Any source-extractor (sextractor) parameter, normally read via the config file but that can be
overridden by passing to the shell command, can be given here.
"""
if "gain" in configs:
configs["gain"] = u.check_quantity(number=configs["gain"], unit=gain_unit).to(gain_unit).value
old_dir = os.getcwd()
if output_dir is None:
output_dir = os.getcwd()
else:
u.mkdir_check(output_dir)
os.chdir(output_dir)
if copy_params:
os.system(f"cp {os.path.join(p.path_to_config_psfex(), '*')} .")
sys_str = "source-extractor "
if template_image_path is not None:
sys_str += f"{template_image_path},"
sys_str += image_path + " "
if configuration_file is not None:
sys_str += f" -c {configuration_file}"
if catalog_name is None:
image_name = os.path.split(image_path)[-1]
catalog_name = f"{image_name}.cat"
sys_str += f" -CATALOG_NAME {catalog_name}"
if parameters_file is not None:
sys_str += f" -PARAMETERS_NAME {parameters_file}"
for param in configs:
sys_str += f" -{param.upper()} {configs[param]}"
u.system_command_verbose(sys_str, error_on_exit_code=True)
catalog_path = os.path.join(output_dir, catalog_name)
os.chdir(old_dir)
return catalog_path
def fors_bias(bias_frames: List[str],
output_dir: str,
output_filename: str = None,
sof_name: str = "bias.sof"):
sof_name = u.sanitise_file_ext(sof_name, ".sof")
old_dir = os.getcwd()
os.chdir(output_dir)
sof_path = os.path.join(output_dir, sof_name)
sof({"BIAS": bias_frames}, sof_path)
u.system_command_verbose(f"{eso_bin_path} fors_bias {sof_path}")
master_path = os.path.join(output_dir, "master_bias.fits")
if output_filename is not None:
final_path = os.path.join(output_dir, output_filename)
shutil.move(master_path, final_path)
else:
final_path = master_path
os.chdir(old_dir)
return final_path
def fors_zeropoint(
standard_img: str,
master_bias: str,
master_sky_flat_img: str,
output_dir: str,
output_filename: str = None,
chip_num: int = 1,
sof_name: str = "zeropoint.sof",
flux_std_imgs: List[str] = fors_flux_std_imgs,
):
sof_name = u.sanitise_file_ext(sof_name, ".sof")
old_dir = os.getcwd()
os.chdir(output_dir)
sof_path = os.path.join(output_dir, sof_name)
phot_table = select_phot_table(chip_num)
sof(
{
"STANDARD_IMG": [standard_img],
"MASTER_BIAS": [master_bias],
"MASTER_SKY_FLAT_IMG": [master_sky_flat_img],
"FLX_STD_IMG":
list(
map(lambda f: os.path.join(fors2_calib_path, f),
flux_std_imgs)),
"PHOT_TABLE": [os.path.join(fors2_calib_path, phot_table)],
}, sof_path)
u.system_command_verbose(f"{eso_bin_path} fors_zeropoint {sof_path}")
master_path = os.path.join(output_dir, "aligned_phot.fits")
std_path = os.path.join(output_dir, "standard_reduced_img.fits")
if output_filename is not None:
final_path = os.path.join(output_dir, output_filename)
shutil.move(master_path, final_path)
else:
final_path = master_path
os.chdir(old_dir)
return final_path, std_path
def fors_img_sky_flat(flat_frames: List[str],
master_bias: str,
output_dir: str,
output_filename: str = None,
sof_name: str = "flat.sof"):
sof_name = u.sanitise_file_ext(sof_name, ".sof")
old_dir = os.getcwd()
os.chdir(output_dir)
sof_path = os.path.join(output_dir, sof_name)
sof({
"SKY_FLAT_IMG": flat_frames,
"MASTER_BIAS": [master_bias],
}, sof_path)
u.system_command_verbose(f"{eso_bin_path} fors_img_sky_flat {sof_path}")
master_path = os.path.join(output_dir, "master_sky_flat_img.fits")
if output_filename is not None:
final_path = os.path.join(output_dir, output_filename)
shutil.move(master_path, final_path)
else:
final_path = master_path
os.chdir(old_dir)
return final_path
def data_select(redux_dir: str,
directory: str,
file_glob: str = "*.fits",
tags: list = None,
expression: str = None,
output: str = None):
# Switch working directory to reduction directory.
pwd = os.getcwd()
os.chdir(redux_dir)
sys_str = build_data_select_str(directory=directory,
file_glob=file_glob,
tags=tags,
expression=expression,
output=output)
u.system_command_verbose(sys_str)
data_list = None
if output is not None:
with open(output) as data_file:
data_list = data_file.read()
os.chdir(pwd)
return data_list