def fit_one_cube(plt,
ifu,
drpall_file=None,
directory_path=None,
analysis_path=None):
# Grab the required input parameters
config_file = '{0}-{1}.cfg'.format(plt, ifu)
get_config(plt, ifu, config_file, drpall_file=drpall_file)
# Read the datacube
cube = MaNGADataCube.from_config(config_file,
directory_path=directory_path)
# Define how you want to analyze the data
plan = AnalysisPlanSet([
AnalysisPlan(
drpqa_key='SNRG',
bin_key='VOR10', #'HYB10',
continuum_key='MILESHCMPL10',
elmom_key='EMOMMPL10',
elfit_key='EFITMPL10', #'EFITMPL9DB',
spindex_key='INDXEN')
])
# Run it!
return manga_dap(cube,
plan,
verbose=2,
directory_path=directory_path,
analysis_path=analysis_path)
def main(args):
# import warnings
# warnings.simplefilter('error', DeprecationWarning)
from mangadap.config.analysisplan import AnalysisPlan
from mangadap.survey.manga_dap import manga_dap
from mangadap.datacube import DataCube
from mangadap.util.pkg import load_object
# Execute the MaNGA DAP for a single datacube
# - Import the module used to read the datacube
if isinstance(args.cube_module, list) and len(args.cube_module) > 2:
raise ValueError(
'Provided cube module must be one or two strings.')
if isinstance(args.cube_module, str) or len(args.cube_module) == 1:
UserDataCube = load_object(args.cube_module if isinstance(
args.cube_module, str) else args.cube_module[0])
else:
UserDataCube = load_object(args.cube_module[0],
obj=args.cube_module[1])
# - Check that the class is derived from DataCube
if not issubclass(UserDataCube, DataCube):
raise TypeError(
'Defined cube object must subclass from mangadap.datacube.DataCube.'
)
# - Import the module used to set the analysis plan
if isinstance(args.plan_module, list) and len(args.plan_module) > 2:
raise ValueError(
'Provided plan module must be one or two strings.')
if isinstance(args.plan_module, str) or len(args.plan_module) == 1:
UserPlan = load_object(args.plan_module if isinstance(
args.plan_module, str) else args.plan_module[0])
else:
UserPlan = load_object(args.plan_module[0],
obj=args.plan_module[1])
# - Check that the class is derived from AnalysisPlan
if not issubclass(UserPlan, AnalysisPlan):
raise TypeError('Defined plan object must subclass from '
'mangadap.config.analysisplan.AnalysisPlan')
# - Instantiate the datacube object using either the datacube file
# directly or a configuration file
cube = UserDataCube(args.cubefile) if args.config is None \
else UserDataCube.from_config(args.config)
# - Read the analysis plan
plan = UserPlan.default(cube=cube, analysis_path=args.output_path) if args.plan is None \
else UserPlan.from_toml(args.plan, cube=cube, analysis_path=args.output_path)
# - Run the pipeline
status = manga_dap(cube,
plan,
dbg=args.dbg,
log=args.log,
verbose=args.verbose)
def fit_one_cube(plt, ifu, drpall_file=None, directory_path=None, analysis_path=None):
# Grab the required input parameters
obs = get_obsinput(plt, ifu, drpall_file='./data/drpall-v2_4_3.fits')
# Define how you want to analyze the data
plan = AnalysisPlanSet([ AnalysisPlan(drpqa_key='SNRG',
bin_key='VOR10',
continuum_key='GAU-MILESHC',
elmom_key='EMOMM',
elfit_key='EFITM-MIUSCATTHIN',
spindex_key='INDXEN') ])
# Run it!
return manga_dap(obs, plan, verbose=2, directory_path='./data', analysis_path='./output')
def main(args):
# Instantiate the DataCube
# - Try to import the module
try:
CubeModule = importlib.import_module(args.cube_module)
except (ModuleNotFoundError, ImportError) as e:
raise ImportError('Cube module {0} import failed!'.format(
args.cube_module)) from e
# - Try to import the class
UserDataCube = getattr(CubeModule, args.cube_object)
# - Check that the class is derived from DataCube
if not issubclass(UserDataCube, DataCube):
raise TypeError(
'Defined cube object must subclass from mangadap.datacube.DataCube.'
)
# - Instantiate using either the datacube file directly or a
# configuration file
cube = UserDataCube(args.cubefile) if args.config is None \
else UserDataCube.from_config(args.config, drpver=args.drpver,
redux_path=args.redux_path,
directory_path=args.directory_path)
# Read the analysis plan
analysisplan = AnalysisPlanSet.default() if args.plan is None \
else AnalysisPlanSet.from_par_file(args.plan)
# Run the pipeline
status = manga_dap(cube,
analysisplan,
dbg=args.dbg,
log=args.log,
verbose=args.verbose,
drpver=args.drpver,
redux_path=args.redux_path,
directory_path=args.directory_path,
dapver=args.dapver,
analysis_path=args.analysis_path)
'--dap_src',
type=str,
help=
'Top-level directory with the DAP source code; defaults to $MANGADAP_DIR',
default=None)
parser.add_argument(
'-a',
'--analysis_path',
type=str,
help=
'Top-level output directory for the DAP results; defaults to $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER',
default=None)
arg = parser.parse_args()
obspar = ObsInputPar.from_par_file(arg.obs)
analysisplan = AnalysisPlanSet.from_par_file(arg.plan)
status = manga_dap(obspar,
analysisplan,
dbg=arg.dbg,
log=arg.log,
verbose=arg.verbose,
drpver=arg.drpver,
redux_path=arg.redux_path,
directory_path=arg.directory_path,
dapver=arg.dapver,
dapsrc=arg.dap_src,
analysis_path=arg.analysis_path)
print('Elapsed time: {0} seconds'.format(clock() - t))