def test_init_by_type():
# LLSSurvey
system = pyasu.class_by_type('LLS')((0.*u.deg, 0.*u.deg),
2.0, None, NHI=17.9)
assert isinstance(system, LLSSystem)
# DLASurvey
system = pyasu.class_by_type('DLA')((0.*u.deg, 0.*u.deg),
2.5, None, NHI=20.55)
assert isinstance(system, DLASystem)
def test_init_by_type():
# LLSSurvey
system = pyasu.class_by_type('LLS')((0.*u.deg, 0.*u.deg),
2.0, None, NHI=17.9)
assert isinstance(system, LLSSystem)
# DLASurvey
system = pyasu.class_by_type('DLA')((0.*u.deg, 0.*u.deg),
2.5, None, NHI=20.55)
assert isinstance(system, DLASystem)
def from_flist(cls, flist, tree=None, **kwargs):
""" Read from list of .dat files (historical JXP format)
Parameters
----------
flist : str
ASCII file including list of .dat files
tree : str, optional
Path to .dat files
kwargs :
Passed to __init__
"""
if tree is None:
tree = ''
# Load up (if possible)
data = ascii.read(tree + flist,
data_start=0,
guess=False,
format='no_header')
slf = cls(**kwargs)
slf.tree = tree
slf.flist = flist
# Load up
slf.dat_files = list(data['col1'])
# Generate IGMSys list
for dat_file in slf.dat_files:
slf._abs_sys.append(
class_by_type(slf.abs_type).from_datfile(dat_file,
tree=slf.tree))
print('Read {:d} files from {:s} in the tree {:s}'.format(
slf.nsys, slf.flist, slf.tree))
return slf
def from_flist(cls, flist, tree=None, **kwargs):
""" Read from list of .dat files (historical JXP format)
Parameters
----------
flist : str
ASCII file including list of .dat files
tree : str, optional
Path to .dat files
kwargs :
Passed to __init__
"""
if tree is None:
tree = ''
# Load up (if possible)
data = ascii.read(tree+flist, data_start=0,
guess=False, format='no_header')
slf = cls(**kwargs)
slf.tree = tree
slf.flist = flist
# Load up
slf.dat_files = list(data['col1'])
# Generate IGMSys list
for dat_file in slf.dat_files:
slf._abs_sys.append(class_by_type(slf.abs_type).from_datfile(dat_file, tree=slf.tree))
print('Read {:d} files from {:s} in the tree {:s}'.format(
slf.nsys, slf.flist, slf.tree))
return slf
def build_abs_sys_from_dict(self, abssys_name, **kwargs):
""" Build an AbsSystem from the _dict
The item in self._abs_sys is filled and
the systems is also returned
Parameters
----------
abssys_name : str
Needs to match a key in the dict
**kwargs
Passed to components_from_dict()
Returns
-------
abs_sys : AbsSystem
"""
# Index
idx = self.sys_idx(abssys_name)
# Instantiate
abssys = class_by_type(self.abs_type).from_dict(
self._dict[abssys_name], coord=self.coords[idx], **kwargs)
# Fill
if len(self._abs_sys) == 0:
self.init_abs_sys()
self._abs_sys[idx] = abssys
# Return too
return abssys
def from_sfits(cls, summ_fits, **kwargs):
"""Generate the Survey from a summary FITS file
Handles SPEC_FILES too.
Parameters
----------
summ_fits : str or Table or QTable
Summary FITS file
**kwargs : dict
passed to __init__
"""
# Init
slf = cls(**kwargs)
# Read
if isinstance(summ_fits, Table):
systems = summ_fits
else:
systems = QTable.read(summ_fits)
nsys = len(systems)
# Dict
kdict = dict(NHI=['NHI', 'logNHI'],
sig_NHI=['sig(logNHI)', 'SIGNHI'],
name=['Name'], vlim=['vlim'],
zabs=['Z_LLS', 'ZABS', 'zabs'],
zem=['Z_QSO', 'QSO_ZEM'],
RA=['RA'], Dec=['DEC', 'Dec'])
# Parse the Table
inputs = {}
for key in kdict.keys():
vals, tag = lsio.get_table_column(kdict[key], [systems],idx=0)
if vals is not None:
inputs[key] = vals
# vlim
if 'vlim' not in inputs.keys():
default_vlim = [-1000, 1000.]* u.km / u.s
inputs['vlim'] = [default_vlim]*nsys
# Generate
for kk in range(nsys):
# Generate keywords
kwargs = {}
args = {}
for key in inputs.keys():
if key in ['vlim', 'zabs', 'RA', 'Dec']:
args[key] = inputs[key][kk]
else:
kwargs[key] = inputs[key][kk]
# Instantiate
abssys = class_by_type(slf.abs_type)((args['RA'], args['Dec']), args['zabs'], args['vlim'], **kwargs)
# spec_files
try:
abssys.spec_files += systems[kk]['SPEC_FILES'].tolist()
except (KeyError, AttributeError):
pass
slf._abs_sys.append(abssys)
# Mask
slf.init_mask()
# Return
return slf
def from_dict(cls, idict, **kwargs):
""" Instantiate from a dict
Parameters
----------
idict : dict
Required keys are:
'RA' -- float (deg)
'DEC' -- float(deg)
'zem' -- float
'name' -- str
'components' -- list
Other keys are added as attributes to the IgmSightline object
Returns
-------
"""
if 'linelist' not in kwargs.keys():
from linetools.lists.linelist import LineList
ism = LineList('ISM')
kwargs['linelist'] = ism
from pyigm.abssys.utils import class_by_type
ism = LineList('ISM')
kwargs['linelist'] = ism
# Load ISM to speed things up
if 'meta' in idict.keys():
meta = idict['meta']
else:
meta = idict
# Components -- backwards compatability
if 'cmps' in idict.keys():
idict['components'] = idict['cmps'].copy()
# Instantiate
slf = cls(SkyCoord(ra=meta['RA'], dec=meta['DEC'], unit='deg'),
zem=meta['zem'],
name=meta['JNAME'],
**kwargs)
# Other
for key in idict.keys():
if key in [
'RA', 'DEC', 'zem', 'name', 'components', 'meta', 'cmps'
]:
continue
else:
setattr(slf, key, idict[key])
add_comps_from_dict(slf, idict, **kwargs)
# Systems
if 'systems' in idict.keys():
for key in idict['systems'].keys():
asys = class_by_type(
idict['systems'][key]['abs_type']).from_dict(
idict['systems'][key], **kwargs)
slf._abssystems.append(asys)
# Return
return slf
def load_sys_files(inp, type, ref=None, sys_path=False, **kwargs):
""" Load up a set of SYS files from the hard-drive (JSON files)
Parameters
----------
inp : str
Name of JSON tarball or if sys_path=True then the path to a folder of JSON files
type : str
type of IGMSystem, e.g. LLS
ref : str, optional
Reference label
sys_path : str, optional
indicates that inp is a path to a set of JSON SYS files
otherwise, inp should be the filename of a tarball of JSON files
Returns
-------
survey : IGMSurvey
"""
import tarfile
#
survey = class_by_type(type)(ref=ref)
system = pyasu.class_by_type(type)
if sys_path:
# Individual files
files = glob.glob(inp+'*.json')
files.sort()
for ifile in files:
tdict = ltu.loadjson(ifile)
abssys = system.from_dict(tdict)
survey._abs_sys.append(abssys)
else: # tarball
print('Loading systems from {:s}'.format(inp))
tar = tarfile.open(inp)
for member in tar.getmembers():
if '.' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Extract
f = tar.extractfile(member)
tdict = json.load(f)
# Add keys (for backwards compatability)
if ('NHI' in tdict.keys()) and ('flag_NHI' not in tdict.keys()):
tdict['flag_NHI'] = 1
# Generate
abssys = system.from_dict(tdict, chk_sep=False, **kwargs) # Consider use_coord=True as default
survey._abs_sys.append(abssys)
tar.close()
# Return
return survey
def load_sys_files(inp, type, ref=None, sys_path=False, **kwargs):
""" Load up a set of SYS files from the hard-drive (JSON files)
Parameters
----------
inp : str
type : str
type of IGMSystem, e.g. LLS
ref : str, optional
Reference label
sys_path : str, optional
indicates that inp is a path to a set of JSON SYS files
otherwise, inp should be the filename of a tarball of JSON files
Returns
-------
survey : IGMSurvey
"""
import tarfile
#
survey = class_by_type(type)(ref=ref)
system = pyasu.class_by_type(type)
if sys_path:
# Individual files
files = glob.glob(inp+'*.json')
files.sort()
for ifile in files:
tdict = ltu.loadjson(ifile)
abssys = system.from_dict(tdict)
survey._abs_sys.append(abssys)
else: # tarball
print('Loading systems from {:s}'.format(inp))
tar = tarfile.open(inp)
for member in tar.getmembers():
if '.' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Extract
f = tar.extractfile(member)
tdict = json.load(f)
# Add keys (for backwards compatability)
if ('NHI' in tdict.keys()) and ('flag_NHI' not in tdict.keys()):
tdict['flag_NHI'] = 1
# Generate
abssys = system.from_dict(tdict, chk_sep=False, **kwargs) # Consider use_coord=True as default
survey._abs_sys.append(abssys)
tar.close()
# Return
return survey
def load_sys_files(inp, type, sys_path=False):
""" Load up a set of SYS files from the hard-drive (JSON files)
Parameters
----------
inp : str
type : str
type of IGMSystem
sys_path : str, optional
indicates that inp is a path to a set of SYS files
otherwise, it should be the filename of a tarball
Returns
-------
survey : IGMSurvey
"""
import tarfile
#
survey = class_by_type(type)(ref='HD-LLS')
system = pyasu.class_by_type(type)
if sys_path:
# Individual files
files = glob.glob(inp+'*.json')
files.sort()
for ifile in files:
tdict = ltu.loadjson(ifile)
abssys = system.from_dict(tdict)
survey._abs_sys.append(abssys)
else: # tarball
print('Loading systems from {:s}'.format(inp))
tar = tarfile.open(inp)
for member in tar.getmembers():
if '.' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Extract
f = tar.extractfile(member)
tdict = json.load(f)
# Generate
abssys = system.from_dict(tdict)
survey._abs_sys.append(abssys)
# Return
return survey
def build_abs_sys_from_data(self, row):
""" Build an AbsSystem from the _data
The item in self._abs_sys is filled and
the system is also returned
Parameters
----------
row : int
Row of the _data table
Ignores any masking -- this may change
Returns
-------
abs_sys : AbsSystem
"""
# vlim -- may make optional
vlim = self._data['vlim'][row]
if self._data['vlim'].unit is not None:
vlim *= self._data['vlim'].unit
else:
vlim = vlim * u.km / u.s
# skwargs
skwargs = {}
for key in ['NHI', 'sig_NHI', 'name', 'zem']:
if key in self._data.keys():
skwargs[key] = self._data[key][row]
# Instantiate
abssys = class_by_type(self.abs_type)(self.coords[row],
self._data['zabs'][row], vlim,
**skwargs)
# Fill
if len(self._abs_sys) == 0:
self.init_abs_sys()
self._abs_sys[row] = abssys
# Return too
return abssys
def load_sys_files(inp,
type,
ref=None,
sys_path=False,
build_abs_sys=False,
**kwargs):
""" Load up a set of SYS files from the hard-drive (JSON files)
Parameters
----------
inp : str
Name of JSON tarball or if sys_path=True then the path to a folder of JSON files
type : str
type of IGMSystem, e.g. LLS
ref : str, optional
Reference label
sys_path : str, optional
indicates that inp is a path to a set of JSON SYS files
otherwise, inp should be the filename of a tarball of JSON files
build_abs_sys : bool, optional
Build a list of AbsSystem's? Can always be instantiated later
**kwargs :
Passed to system
Returns
-------
survey : IGMSurvey
"""
import tarfile
#
survey = class_by_type(type)(ref=ref)
system = pyasu.class_by_type(type)
if sys_path:
pdb.set_trace() # THIS NEEDS TO BE UPDATED AS WAS DONE FOR THE TARBALL
# Individual files
files = glob.glob(inp + '*.json')
files.sort()
for ifile in files:
tdict = ltu.loadjson(ifile)
abssys = system.from_dict(tdict, linelist=llist)
survey._abs_sys.append(abssys)
else: # tarball
print('Loading systems from {:s}'.format(inp))
tar = tarfile.open(inp, 'r:gz')
for member in tar.getmembers():
if '.' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Extract
f = tar.extractfile(member)
f = f.read()
f = f.decode('utf-8')
tdict = json.loads(f)
# Add keys (for backwards compatability)
if ('NHI' in tdict.keys()) and ('flag_NHI' not in tdict.keys()):
tdict['flag_NHI'] = 1
# Add to list of dicts
survey._dict[tdict['Name']] = tdict
tar.close()
# Mask
survey.init_mask()
# Set coordinates
ras = [survey._dict[key]['RA'] for key in survey._dict.keys()]
decs = [survey._dict[key]['DEC'] for key in survey._dict.keys()]
survey.coords = SkyCoord(ra=ras, dec=decs, unit='deg')
# Build AbsSystem objects?
if build_abs_sys:
survey.build_all_abs_sys(linelist=llist)
# Generate the data table
print("Building the data Table from the internal dict")
survey.data_from_dict()
# Return
return survey
def from_sfits(cls, summ_fits, **kwargs):
"""Generate the Survey from a summary FITS file or Table
Handles SPEC_FILES too.
Parameters
----------
summ_fits : str or Table or QTable
Summary FITS file
**kwargs : dict
passed to __init__
"""
# Init
slf = cls(**kwargs)
# Read
if isinstance(summ_fits, Table):
systems = summ_fits
else:
systems = QTable.read(summ_fits)
nsys = len(systems)
# Dict
kdict = dict(NHI=['NHI', 'logNHI'],
sig_NHI=['sig(logNHI)', 'SIGNHI', 'NHI_ERR'],
name=['Name'],
vlim=['vlim'],
zabs=['Z_LLS', 'ZABS', 'zabs'],
zem=['Z_QSO', 'QSO_ZEM', 'ZEM'],
RA=['RA'],
Dec=['DEC', 'Dec'])
# Parse the Table
inputs = {}
for key in kdict.keys():
vals, tag = lsio.get_table_column(kdict[key], [systems], idx=0)
if vals is not None:
inputs[key] = vals
# vlim
if 'vlim' not in inputs.keys():
default_vlim = [-1000, 1000.] * u.km / u.s
inputs['vlim'] = [default_vlim] * nsys
# Generate
for kk in range(nsys):
# Generate keywords
kwargs = {}
args = {}
for key in inputs.keys():
if key in ['vlim', 'zabs', 'RA', 'Dec']:
args[key] = inputs[key][kk]
else:
kwargs[key] = inputs[key][kk]
# Instantiate
abssys = class_by_type(slf.abs_type)((args['RA'], args['Dec']),
args['zabs'], args['vlim'],
**kwargs)
# spec_files
try:
abssys.spec_files += systems[kk]['SPEC_FILES'].tolist()
except (KeyError, AttributeError):
pass
slf._abs_sys.append(abssys)
# Mask
slf.init_mask()
# Return
return slf
