def cigalerun(config, noise='none', overwrite='True'):
''' run CIGALE'''
os.chdir(cigale_dir())
configuration = config.configuration
if os.path.isfile(os.path.join(cigale_dir(), 'pcigale.ini')):
if configuration:
analysis_module = get_module(configuration['analysis_method'])
analysis_module.process(configuration)
if os.path.exists('noise_%s' % noise):
if overwrite != 'True':
print('*** CAUTION: Result folder already exists ***')
shutil.rmtree('out')
else:
shutil.rmtree('noise_%s' % noise)
os.rename('out', 'noise_%s' % noise)
else:
os.rename('out', 'noise_%s' % noise)
else:
print('*** You need to generate CIGALE ini file! ***')
def run(photometry_table,
zcol,
data_file="cigale_in.fits",
config_file="pcigale.ini",
wait_for_input=False,
plot=True,
outdir='out',
compare_obs_model=False,
**kwargs):
"""
Input parameters and then run CIGALE.
Args:
photometry_table (astropy Table):
A table from some photometric catalog with magnitudes and
error measurements. Currently supports
DES, DECaLS, SDSS, Pan-STARRS and WISE
zcol (str):
Name of the column with redshift estimates.
data_file (str, optional):
Root name for the photometry data file generated used as input to CIGALE
config_file (str, optional):
Root name for the file where CIGALE's configuration is generated
wait_for_input (bool, optional):
If true, waits for the user to finish editing the auto-generated config file
before running.
plot (bool, optional):
Plots the best fit SED if true
cores (int, optional):
Number of CPU cores to be used. Defaults
to all cores on the system.
outdir (str, optional):
Path to the many outputs of CIGALE
If not supplied, the outputs will appear in a folder named out/
compare_obs_model (bool, optional):
If True compare the input observed fluxes with the model fluxes
This writes a Table to outdir named 'photo_observed_model.dat'
kwargs: These are passed into gen_cigale_in() and _initialise()
save_sed (bool, optional):
Save the best fit SEDs to disk for each galaxy.
variables (str or list, optional):
A single galaxy property name to save to results
or a list of variable names. Names must belong
to the list defined in the CIGALE documentation.
sed_modules (list of 'str', optional):
A list of SED modules to be used in the
PDF analysis. If this is being input, there
should be a corresponding correct dict
for sed_modules_params.
sed_module_params (dict, optional):
A dict containing parameter values for
the input SED modules. Better not use this
unless you know exactly what you're doing.
"""
gen_cigale_in(photometry_table,
zcol,
infile=data_file,
overwrite=True,
**kwargs)
_initialise(data_file, config_file=config_file, **kwargs)
if wait_for_input:
input("Edit the generated config file {:s} and press any key to run.".
format(config_file))
cigconf = Configuration(config_file)
analysis_module = get_module(cigconf.configuration['analysis_method'])
analysis_module.process(cigconf.configuration)
if plot:
try:
from pcigale_plots import sed # This modifies the backend to Agg so I hide it here
old_version = True
except ImportError:
from pcigale_plots.plot_types.sed import sed
old_version = False
if old_version:
import pcigale
#warnings.warn("You are using CIGALE version {:s}, for which support is deprecated. Please update to 2020.0 or higher.".format(pcigale.__version__))
sed(cigconf, "mJy", True)
else:
# TODO: Let the user customize the plot.
series = [
'stellar_attenuated', 'stellar_unattenuated', 'dust', 'agn',
'model'
]
sed(cigconf, "mJy", True, (False, False), (False, False), series,
"pdf", "out")
# Set back to a GUI
import matplotlib
matplotlib.use('TkAgg')
# Rename the default output directory?
if outdir != 'out':
try:
os.system("rm -rf {}".format(outdir))
os.system("mv out {:s}".format(outdir))
except:
print("Invalid output directory path. Output stored in out/")
# Move input files into outdir too
os.system("mv {:s} {:s}".format(data_file, outdir))
os.system("mv {:s} {:s}".format(config_file, outdir))
os.system("mv {:s}.spec {:s}".format(config_file, outdir))
# Compare?
if compare_obs_model:
#Generate an observation/model flux comparison table.
with Database() as base:
filters = OrderedDict([
(name, base.get_filter(name))
for name in cigconf.configuration['bands']
if not (name.endswith('_err') or name.startswith('line'))
])
filters_wl = np.array(
[filt.pivot_wavelength for filt in filters.values()])
mods = Table.read(outdir + '/results.fits')
try:
obs = Table.read(
os.path.join(outdir, cigconf.configuration['data_file']))
except:
print(
"Something went wrong here. Astropy was unable to read the observations table. Please ensure it is in the fits format."
)
return
for model, obj in zip(mods, obs):
photo_obs_model = Table()
photo_obs_model['lambda_filter'] = [
wl / 1000 for wl in filters_wl
]
photo_obs_model['model_flux'] = np.array(
[model["best." + filt] for filt in filters.keys()])
photo_obs_model['observed_flux'] = np.array(
[obj[filt] for filt in filters.keys()])
photo_obs_model['observed_flux_err'] = np.array(
[obj[filt + '_err'] for filt in filters.keys()])
photo_obs_model.write(outdir + "/photo_observed_model_" +
str(model['id']) + ".dat",
format="ascii",
overwrite=True)
#import pdb; pdb.set_trace()
return