def fits_table_all(input_path: str,
output_path: str = "",
science_only: bool = True):
"""
Produces and writes to disk a table of .fits files in the given path, with the vital statistics of each. Intended
only for use with raw ESO data.
:param input_path:
:param output_path:
:param science_only: If True, we are writing a list for a folder that also contains calibration files, which we want
to ignore.
:return:
"""
# If there's no trailing slash in the paths, add one.
u.check_trailing_slash(output_path)
if output_path == "":
output_path = input_path + "fits_table.csv"
elif output_path[-4:] != ".csv":
if output_path[-1] == "/":
output_path = output_path + "fits_table.csv"
else:
output_path = output_path + ".csv"
print('Writing table of fits files to: \n', output_path)
files = os.listdir(input_path)
files.sort()
files_fits = list(filter(lambda x: x[-5:] == '.fits', files))
# Create list of dictionaries to be used as the output data
output = []
ids = string.ascii_lowercase
if len(ids) < len(files_fits):
ids = ids + string.ascii_uppercase
if len(ids) < len(files_fits):
ids = ids + string.digits
for i, f in enumerate(files_fits):
data = {}
file = fits.open(input_path + f)
header = file[0].header
for key in header:
data[key] = header[key]
if 'ESO TEL AIRM END' in data and 'ESO TEL AIRM START' in data:
data['AIRMASS'] = (float(data['ESO TEL AIRM END']) +
float(data['ESO TEL AIRM START'])) / 2
if science_only and 'SCIENCE' in data['ESO DPR CATG']:
output.append(data)
elif not science_only:
output.append(data)
file.close()
output.sort(key=lambda a: a['ARCFILE'])
out_file = pd.DataFrame(output)
out_file.to_csv(output_path)
return out_file
def check_for_config():
u.mkdir_check(config_dir)
p = load_params(config_file)
if p is None:
config_text = pkg_resources.resource_string(
__name__, os.path.join("..", f"param",
"config_template.yaml")).decode()
print(type(config_text))
config_text = config_text.replace(
"proj_dir: <some_directory>/craft-optical-followup/",
f"proj_dir: {os.getcwd()}/")
with open(config_file, "w") as cfg:
cfg.write(config_text)
print(f"No config file was detected at {config_file}.")
print(f"A fresh config file has been created at '{config_file}'")
print(
"In this file, please set 'top_data_dir' to a valid path in which to store all "
"data products of this package (This may require a large amount of space.)."
)
print("You may also like to specify an alternate param_dir")
input("\nOnce you have edited this file, press any key to proceed.")
p = load_params(config_file)
else:
for param in p:
p[param] = u.check_trailing_slash(p[param])
save_params(config_file, p)
yaml_to_json(config_file)
return p
def main(path):
print(f"\nExecuting Python script plot_fwhms.py, with path {path}\n")
path = check_trailing_slash(path)
outputs = p.tabulate_output_values(path=path, output=path + "output_values.csv")
plt.plot(range(len(outputs)), outputs["_fwhm_arcsec"])
plt.ylabel("FWHM")
plt.xlabel("Frame")
plt.title(f"FWHM in {path}")
plt.savefig(path + "fwhm.png")
def check_for_config():
p = load_params('param/config.yaml')
if p is None:
print("No config.yaml file found.")
else:
for param in p:
p[param] = u.check_trailing_slash(p[param])
save_params('param/config.yaml', p)
yaml_to_json('param/config.yaml')
return p
def tabulate_output_values(path: str, output: str = None):
path = u.check_trailing_slash(path=path)
outputs = []
for file in filter(lambda filename: 'output_values.yaml' in filename,
os.listdir(path)):
output_values = load_params(file=path + file)
output_values["filename"] = file
outputs.append(output_values)
outputs = tbl.Table(outputs)
if output is not None:
output = u.sanitise_file_ext(filename=output, ext='.csv')
outputs.write(output)
outputs.sort(keys="filename")
return outputs
def main(data_dir, data_title, origin, destination, all_synths):
print("\nExecuting Python script pipeline_fors2/5-background_subtract.py, with:")
print(f"\tepoch {data_title}")
print(f"\torigin directory {origin}")
print(f"\tdestination directory {destination}")
print()
methods = ["ESO backgrounds only", "SExtractor backgrounds only", "polynomial fit", "Gaussian fit", "median value"]
if all_synths:
frame = 56
method = "polynomial fit"
degree = 5
do_mask = True
local = True
global_sub = False
trim_image = False
recorrect_subbed = True
eso_back = False
else:
frame = 200
# frame_arcsec = 30 * units.arcsec
# frame_deg = frame_arcsec.to(units.deg)
eso_back = False
_, method = u.select_option(message="Please select the background subtraction method.", options=methods,
default="polynomial fit")
degree = None
if method == "polynomial fit":
degree = u.user_input(message=f"Please enter the degree of {method} to use:", typ=int, default=3)
elif method == "ESO backgrounds only":
eso_back = True
do_mask = False
if method not in ["ESO backgrounds only", "SExtractor backgrounds only", "median value"]:
do_mask = u.select_yn(message="Mask sources using SExtractor catalogue?", default=True)
if method in ["polynomial fit", "Gaussian fit"]:
local = u.select_yn(message="Use a local fit?", default=True)
else:
local = False
global_sub = False
trim_image = False
recorrect_subbed = False
if local:
global_sub = u.select_yn(message="Subtract local fit from entire image?", default="n")
if not global_sub:
trim_image = u.select_yn(message="Trim images to subtracted region?", default="y")
recorrect_subbed = u.select_yn(message="Re-normalise background of subtracted region?", default="y")
# if not eso_back and method != "SExtractor backgrounds only":
# eso_back = u.select_yn(message="Subtract ESO Reflex fitted backgrounds first?", default=False)
outputs = p.object_output_params(data_title, instrument='FORS2')
data_dir = u.check_trailing_slash(data_dir)
destination = u.check_trailing_slash(destination)
destination = data_dir + destination
u.mkdir_check_nested(destination)
origin = u.check_trailing_slash(origin)
science_origin = data_dir + origin + "science/"
print(science_origin)
filters = outputs['filters']
frb_params = p.object_params_frb(obj=data_title[:-2])
epoch_params = p.object_params_fors2(obj=data_title)
background_origin_eso = ""
if eso_back:
background_origin_eso = data_dir + "/" + origin + "/backgrounds/"
if method == "SExtractor backgrounds only":
background_origin = f"{data_dir}{origin}backgrounds_sextractor/"
elif method == "polynomial fit":
background_origin = f"{destination}backgrounds/" # f"{destination}backgrounds_{method.replace(' ', '')}_degree_{degree}_local_{local}_globalsub_{global_sub}/"
else:
background_origin = f"{destination}backgrounds/" # f"{destination}backgrounds_{method.replace(' ', '')}_local_{local}_globalsub_{global_sub}/"
trimmed_path = ""
if trim_image:
trimmed_path = f"{data_dir}{origin}trimmed_to_background/"
u.mkdir_check_nested(trimmed_path)
ra = frb_params["burst_ra"]
dec = frb_params["burst_dec"]
if all_synths:
ras = epoch_params["test_synths"]["ra"]
decs = epoch_params["test_synths"]["dec"]
else:
ras = [ra]
decs = [dec]
for fil in filters:
trimmed_path_fil = ""
if trim_image:
trimmed_path_fil = f"{trimmed_path}{fil}/"
u.mkdir_check(trimmed_path_fil)
background_fil_dir = f"{background_origin}{fil}/"
u.mkdir_check_nested(background_fil_dir)
science_destination_fil = f"{destination}science/{fil}/"
u.mkdir_check_nested(science_destination_fil)
files = os.listdir(science_origin + fil + "/")
for file_name in files:
if file_name.endswith('.fits'):
new_file = file_name.replace("norm", "bg_sub")
new_path = f"{science_destination_fil}/{new_file}"
print("NEW_PATH:", new_path)
science = science_origin + fil + "/" + file_name
# First subtract ESO Reflex background images
# frame = (frame_deg / f.get_pixel_scale(file=science, astropy_units=True)[1]).to(f.pix).value
if eso_back:
background_eso = background_origin_eso + fil + "/" + file_name.replace("SCIENCE_REDUCED",
"PHOT_BACKGROUND_SCI")
ff.subtract_file(file=science, sub_file=background_eso, output=new_path)
science_image = new_path
if method != "ESO backgrounds only":
print(ra, dec)
print("Science image:", science)
science_image = fits.open(science)
print("Science file:", science_image)
wcs_this = WCS(header=science_image[0].header)
if method == "SExtractor backgrounds only":
background = background_origin + fil + "/" + file_name + "_back.fits"
print("Background image:", background)
else:
if method == "median value":
print(science_image[0].data.shape)
_, background_value, _ = sigma_clipped_stats(science_image[0].data)
background = deepcopy(science_image)
background[0].data = np.full(shape=science_image[0].data.shape, fill_value=background_value)
background_path = background_origin + fil + "/" + file_name.replace("SCIENCE_REDUCED",
"PHOT_BACKGROUND_MEDIAN")
# Next do background fitting.
else:
background = deepcopy(science_image)
background[0].data = np.zeros(background[0].data.shape)
background_path = background_origin + fil + "/" + file_name.replace("SCIENCE_REDUCED",
"PHOT_BACKGROUND_FITTED")
for i, ra in enumerate(ras):
dec = decs[i]
x, y = wcs_this.all_world2pix(ra, dec, 0)
print(x, y)
bottom, top, left, right = ff.subimage_edges(data=science_image[0].data, x=x, y=y,
frame=frame)
if do_mask:
# Produce a pixel mask that roughly masks out the true sources in the image so that
# they don't get fitted.
mask_max = 10
_, pixel_scale = ff.get_pixel_scale(science_image)
sextractor = Table.read(
f"{data_dir}analysis/sextractor/4-divided_by_exp_time/{fil}/{file_name.replace('.fits', '_psf-fit.cat')}",
format='ascii.sextractor')
weights = np.ones(shape=science_image[0].data.shape)
for obj in filter(
lambda o: left < o["X_IMAGE"] < right and bottom < o["Y_IMAGE"] < top,
sextractor):
mask_rad = min(int(obj["A_WORLD"] * obj["KRON_RADIUS"] / pixel_scale), mask_max)
x_prime = int(np.round(obj["X_IMAGE"]))
y_prime = int(np.round(obj["Y_IMAGE"]))
weights[y_prime - mask_rad:y_prime + mask_rad,
x_prime - mask_rad:x_prime + mask_rad] = 0.0
plt.imshow(weights, origin="lower")
plt.savefig(
background_origin + fil + "/" + file_name.replace("norm.fits", "mask.png"))
else:
weights = None
background_this = fit_background_fits(image=science_image,
model_type=method[:method.find(" ")],
deg=degree, local=local,
global_sub=global_sub,
centre_x=x, centre_y=y, frame=frame,
weights=weights)
background[0].data += background_this[0].data
if recorrect_subbed:
offset = get_median_background(image=science,
ra=epoch_params["renormalise_centre_ra"],
dec=epoch_params["renormalise_centre_dec"], frame=50,
show=False,
output=new_path[
:new_path.find("bg_sub")] + "renorm_patch_")
print("RECORRECT_SUBBED:", recorrect_subbed)
print("SUBTRACTING FROM BACKGROUND:", offset)
print(bottom, top, left, right)
print(background[0].data[bottom:top, left:right].shape)
print(np.median(background[0].data[bottom:top, left:right]))
background[0].data[bottom:top, left:right] -= offset
print(np.median(background[0].data[bottom:top, left:right]))
if trim_image:
print("TRIMMED_PATH_FIL:", trimmed_path_fil)
science_image = ff.trim_file(path=science_image, left=left, right=right, top=top,
bottom=bottom,
new_path=trimmed_path_fil + file_name.replace(
"norm.fits",
"trimmed_to_back.fits"))
print("Science after trim:", science_image)
background = ff.trim_file(path=background, left=left, right=right, top=top,
bottom=bottom,
new_path=background_path)
print("Writing background to:")
print(background_path)
background.writeto(background_path, overwrite=True)
print("SCIENCE:", science_image)
print("BACKGROUND:", background)
subbed = ff.subtract_file(file=science_image, sub_file=background, output=new_path)
# # TODO: check if regions overlap
#
# plt.hist(subbed[0].data[int(y - frame + 1):int(y + frame - 1),
# int(x - frame + 1):int(x + frame - 1)].flatten(),
# bins=10)
# plt.savefig(new_path[:new_path.find("bg_sub")] + "histplot.png")
# plt.close()
copyfile(data_dir + "/" + origin + "/" + data_title + ".log", destination + data_title + ".log")
u.write_log(path=destination + data_title + ".log",
action=f'Backgrounds subtracted using 4-background_subtract.py with method {method}\n')
if not quiet:
print('Saving parameter file to ' + output)
for param in p:
if type(p[param]) is date:
p[param] = str(p[param])
with open(output, 'w') as fj:
json.dump(p, fj)
return p
config = check_for_config()
param_path = u.check_trailing_slash(config['param_dir'])
def path_or_params_obj(obj: Union[dict, str],
instrument: str = 'FORS2',
quiet: bool = False):
if type(obj) is str:
return obj, object_params_instrument(obj,
instrument=instrument,
quiet=quiet)
elif type(obj) is dict:
params = obj
obj = params[
'data_title'] # TODO: This is broken since you removed data_title from epoch params.
return obj, params
def fits_table(input_path: str,
output_path: str = "",
science_only: bool = True):
"""
Produces and writes to disk a table of .fits files in the given path, with the vital statistics of each. Intended
only for use with raw ESO data.
:param input_path:
:param output_path:
:param science_only: If True, we are writing a list for a folder that also contains calibration files, which we want
to ignore.
:return:
"""
# If there's no trailing slash in the paths, add one.
input_path = u.check_trailing_slash(input_path)
if output_path == "":
output_path = input_path + "fits_table.csv"
elif output_path[-4:] != ".csv":
if output_path[-1] == "/":
output_path = output_path + "fits_table.csv"
else:
output_path = output_path + ".csv"
print('Writing table of fits files to: \n', output_path)
files = os.listdir(input_path)
files.sort()
files_fits = []
# Keep only the relevant fits files
for f in files:
if f[-5:] == ".fits":
files_fits.append(f)
# Create list of dictionaries to be used as the output data
output = []
ids = string.ascii_lowercase
if len(ids) < len(files_fits):
ids = ids + string.ascii_uppercase
if len(ids) < len(files_fits):
ids = ids + string.digits
for i, f in enumerate(files_fits):
data = {}
file = fits.open(input_path + f)
header = file[0].header
data['identifier'] = f
if science_only and ('ESO DPR CATG' not in header
or 'SCIENCE' not in header['ESO DPR CATG']):
continue
if len(ids) >= len(files_fits):
data['id'] = ids[i]
if "OBJECT" in header:
data['object'] = header["OBJECT"]
if "ESO OBS NAME" in header:
data['obs_name'] = header["ESO OBS NAME"]
if "EXPTIME" in header:
data['exp_time'] = header["EXPTIME"]
if "AIRMASS" in header:
data['airmass'] = header["AIRMASS"]
elif "ESO TEL AIRM START" in header and "ESO TEL AIRM END":
data['airmass'] = (header["ESO TEL AIRM START"] +
header["ESO TEL AIRM END"]) / 2
if "CRVAL1" in header:
data['ref_ra'] = header["CRVAL1"]
if "CRVAL2" in header:
data['ref_dec'] = header["CRVAL2"]
if "CRPIX1" in header:
data['ref_pix_x'] = header["CRPIX1"]
if "CRPIX2" in header:
data['ref_pix_y'] = header["CRPIX2"]
if "EXTNAME" in header:
data['chip'] = header["EXTNAME"]
elif "ESO DET CHIP1 ID" in header:
if header["ESO DET CHIP1 ID"] == 'CCID20-14-5-3':
data['chip'] = 'CHIP1'
if header["ESO DET CHIP1 ID"] == 'CCID20-14-5-6':
data['chip'] = 'CHIP2'
if "GAIN" in header:
data['gain'] = header["GAIN"]
if "INSTRUME" in header:
data['instrument'] = header["INSTRUME"]
if "ESO TEL AIRM START" in header:
data['airmass_start'] = header["ESO TEL AIRM START"]
if "ESO TEL AIRM END" in header:
data['airmass_end'] = header["ESO TEL AIRM END"]
if "ESO INS OPTI3 NAME" in header:
data['collimater'] = header["ESO INS OPTI3 NAME"]
if "ESO INS OPTI5 NAME" in header:
data['filter1'] = header["ESO INS OPTI5 NAME"]
if "ESO INS OPTI6 NAME" in header:
data['filter2'] = header["ESO INS OPTI6 NAME"]
if "ESO INS OPTI7 NAME" in header:
data['filter3'] = header["ESO INS OPTI7 NAME"]
if "ESO INS OPTI9 NAME" in header:
data['filter4'] = header["ESO INS OPTI9 NAME"]
if "ESO INS OPTI10 NAME" in header:
data['filter5'] = header["ESO INS OPTI10 NAME"]
if "ESO INS OPTI8 NAME" in header:
data['camera'] = header["ESO INS OPTI8 NAME"]
if "NAXIS1" in header:
data['pixels_x'] = header["NAXIS1"]
if "NAXIS2" in header:
data['pixels_y'] = header["NAXIS2"]
if "SATURATE" in header:
data['saturate'] = header["SATURATE"]
if "MJD-OBS" in header:
data['mjd_obs'] = header["MJD-OBS"]
output.append(data)
file.close()
output.sort(key=lambda a: a['identifier'])
out_file = pd.DataFrame(output)
out_file.to_csv(output_path)
return out_file
p = load_params(file=yaml_file)
u.debug_print(1, 'Saving parameter file to ' + output)
for param in p:
if type(p[param]) is date:
p[param] = str(p[param])
with open(output, 'w') as fj:
json.dump(p, fj)
return p
config = check_for_config()
param_dir = u.check_trailing_slash(config['param_dir'])
project_path = u.check_trailing_slash(config['proj_dir'])
data_path = u.check_trailing_slash(config["top_data_dir"])
furby_path = None
if "furby_dir" in config and config["furby_dir"] is not None:
furby_path = u.check_trailing_slash(config["furby_dir"])
def get_project_git_hash(short: bool = False):
return u.get_git_hash(directory=project_path, short=short)
def path_or_params_obj(obj: Union[dict, str],
instrument: str = 'FORS2',
quiet: bool = False):
if type(obj) is str:
