def write(self, *args, **kwargs):
"""Write a gridded N-dimensional data object out in specified format.
This function provides the `~.NDDataBase` interface to the astropy
unified I/O layer. This allows easily writing a file in the supported
data formats.
"""
io_registry.write(self, *args, **kwargs)
def write(self, *args, **kwargs):
"""
Write a gridded N-dimensional data object out in specified format.
This function provides the NDDataBase interface to the astropy unified
I/O layer. This allows easily writing a file in the supported data
formats.
"""
io_registry.write(self, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this table to a file
Parameters
----------
target: `str`
filename for output data file
*args
other positional arguments will be passed directly to the
underlying writer method for the given format
format : `str`, optional
format for output data; if not given, an attempt will be made
to automatically identify the format based on the `target`
filename
**kwargs
other keyword arguments will be passed directly to the
underlying writer method for the given format
Raises
------
astropy.io.registry.IORegistryError
if the `format` cannot be automatically identified
Notes
-----"""
return registry.write(self, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this table to a file
Parameters
----------
target: `str`
filename for output data file
*args
other positional arguments will be passed directly to the
underlying writer method for the given format
format : `str`, optional
format for output data; if not given, an attempt will be made
to automatically identify the format based on the `target`
filename
**kwargs
other keyword arguments will be passed directly to the
underlying writer method for the given format
Raises
------
astropy.io.registry.IORegistryError
if the `format` cannot be automatically identified
Notes
-----"""
return registry.write(self, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write the `StarField` table to a file
This utility is essentially a wrapper around
`~astropy.table.Table.write`, see that method for more information
Parameters
----------
target : `str`
filename for output data file
*args : `tuple`, optional
other positional arguments passed to the underlying data writer
for the given format
format : `str`, optional
file format for output data; if not given, the data writer will
attempt to automatically identify the format based on ``target``
**kwargs : `dict`, optional
other keyword arguments passed to the underlying data writer
for the given format
Notes
-----"""
return registry.write(self.table, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this `StateVector` to a file
Parameters
----------
target : `str`
output filename
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this `SegmentList` to a file
Arguments and keywords depend on the output format, see the
online documentation for full details for each format.
Parameters
----------
target : `str`
output filename
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this `SegmentList` to a file
Arguments and keywords depend on the output format, see the
online documentation for full details for each format.
Parameters
----------
target : `str`
output filename
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this `FrequencySeries` to a file
Arguments and keywords depend on the output format, see the
online documentation for full details for each format, the
parameters below are common to most formats.
Parameters
----------
target : `str`
output filename
format : `str`, optional
output format identifier. If not given, the format will be
detected if possible. See below for list of acceptable
formats.
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
def write(self, target, *args, **kwargs):
"""Write this `SpectralVariance` to a file
Arguments and keywords depend on the output format, see the
online documentation for full details for each format, the
parameters below are common to most formats.
Parameters
----------
target : `str`
output filename
format : `str`, optional
output format identifier. If not given, the format will be
detected if possible. See below for list of acceptable
formats.
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
print('fitting ' + str(prior.nsrc) + ' sources \n')
print('using ' + str(prior.snpix) + ' pixels')
from xidplus.numpyro_fit import LOFAR150
fit = LOFAR150.LOFAR_150(prior, num_samples=1000, num_warmup=1000)
samples = fit.get_samples()['src_f']
posterior = xidplus.posterior_numpyro(fit, [prior])
if os.path.exists(
'data/xidplus_results/pybdsf/xidplus_run_{}'.format(n)) == True:
()
else:
os.mkdir('data/xidplus_results/pybdsf/xidplus_run_{}'.format(n))
xidplus.save(
[prior], posterior,
'data/xidplus_results/pybdsf/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.pkl'
.format(n, n))
LOFAR_cat = cat.create_LOFAR_cat(posterior, prior, 0)
LOFAR_cat = Table.read(LOFAR_cat)
with serialize_method_as(LOFAR_cat, None):
registry.write(
LOFAR_cat,
'data/xidplus_results/pybdsf/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.fits'
.format(n, n),
format='fits',
overwrite=True)
def __call__(self, *args, **kwargs):
serialize_method = kwargs.pop('serialize_method', None)
instance = self._instance
with serialize_method_as(instance, serialize_method):
registry.write(instance, *args, **kwargs)
def __call__(self, *args, serialize_method=None, **kwargs):
instance = self._instance
with serialize_method_as(instance, serialize_method):
registry.write(instance, *args, **kwargs)
posterior = xidplus.posterior_stan(fit, [prior250, prior350, prior500])
priors = [prior250, prior350, prior500]
import xidplus.catalogue as cat
SPIRE_cat = cat.create_SPIRE_cat(posterior, priors[0], priors[1], priors[2])
SPIRE_cat = Table.read(SPIRE_cat)
mask = [SPIRE_cat['HELP_ID'][i] in ids for i in range(len(SPIRE_cat))]
SPIRE_cat = SPIRE_cat[mask]
if os.path.exists('data/fir/v0_7/SPIRE/xidplus_run_{}'.format(taskid)) == True:
()
else:
os.mkdir('data/fir/v0_7/SPIRE/xidplus_run_{}'.format(taskid))
xidplus.save([prior250, prior350, prior500], posterior,
'data/fir/v0_7/SPIRE/xidplus_run_{}/lofar_xidplus_fir_{}'.format(
taskid, taskid))
#the next couple of lines are an alternative way to save astropy table since the Table.write method is currently broken
with serialize_method_as(SPIRE_cat, None):
registry.write(
SPIRE_cat,
'data/fir/v0_7/SPIRE/xidplus_run_{}/lofar_xidplus_fir_{}.fits'.format(
taskid, taskid),
format='fits',
overwrite=True)
#Table.write(SPIRE_cat,'data/fir/v0_7/SPIRE/xidplus_run_{}/lofar_xidplus_fir_{}.fits'.format(taskid,taskid),overwrite=True)
time1 = time.time()
print('total time taken = {}'.format(time1 - time0))
def __call__(self, *args, serialize_method=None, **kwargs):
registry.write(self._instance, *args, **kwargs)
def __call__(self, format, *args, **kwargs):
return io_registry.write(self._instance,
None,
*args,
format=format,
**kwargs)
posterior = xidplus.posterior_stan(fit, [prior100, prior160])
priors = [prior100, prior160]
import xidplus.catalogue as cat
PACS_cat = cat.create_PACS_cat(posterior, priors[0], priors[1])
PACS_cat = Table.read(PACS_cat)
mask = [PACS_cat['help_id'][i] in ids for i in range(len(PACS_cat))]
PACS_cat = PACS_cat[mask]
if os.path.exists(
'data/fir/PACS_no_lofar/xidplus_run_{}'.format(taskid)) == True:
()
else:
os.mkdir('data/fir/PACS_no_lofar/xidplus_run_{}'.format(taskid))
xidplus.save(
[prior100, prior160], posterior,
'data/fir/PACS_no_lofar/xidplus_run_{}/lofar_xidplus_fir_{}'.format(
taskid, taskid))
#the next couple of lines are an alternative way to save astropy table since the Table.write method is currently broken
with serialize_method_as(PACS_cat, None):
registry.write(
PACS_cat,
'data/fir/PACS_no_lofar/xidplus_run_{}/lofar_xidplus_fir_{}.fits'.
format(taskid, taskid),
format='fits',
overwrite=True)
#Table.write(PACS_cat,'data/fir/PACS/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.fits'.format(taskid,taskid),overwrite=True)
else:
prfs.append(psf_dirty[0])
pinds.append(np.arange(0,prfs[m].shape[0],1))
prior.set_prfs(prfs,pinds,pinds)
prior.get_pointing_matrix_multiple_prf()
prior.upper_lim_map()
print('fitting '+ str(prior.nsrc)+' sources \n')
print('using ' + str(prior.snpix) + ' pixels')
from xidplus.numpyro_fit import LOFAR150
fit=LOFAR150.LOFAR_150(prior,num_samples=1000,num_warmup=1000)
samples = fit.get_samples()['src_f']
posterior = xidplus.posterior_numpyro(fit,[prior])
if os.path.exists('data/xidplus_results/random_positions/xidplus_run_{}'.format(n))==True:()
else:
os.mkdir('data/xidplus_results/random_positions/xidplus_run_{}'.format(n))
xidplus.save([prior],posterior,'data/xidplus_results/random_positions/xidplus_run_{}/random_positions_{}.pkl'.format(n,n))
LOFAR_cat=cat.create_LOFAR_cat(posterior,prior)
LOFAR_cat = Table.read(LOFAR_cat)
with serialize_method_as(LOFAR_cat, None):
registry.write(LOFAR_cat,'data/xidplus_results/random_positions/xidplus_run_{}/random_positions_cat_{}.fits'.format(n,n),format='fits',overwrite=True)
def write(self, target, *args, **kwargs):
"""Write a `ChannelList` to a file
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
def __call__(self, *args, **kwargs):
registry.write(self._instance, *args, **kwargs)
prior500.upper_lim_map()
print('fitting '+ str(prior250.nsrc)+' sources \n')
print('using ' + str(prior250.snpix)+', '+ str(prior350.snpix)+' and '+ str(prior500.snpix)+' pixels')
from xidplus.stan_fit import SPIRE
fit=SPIRE.all_bands(prior250,prior350,prior500,iter=1000)
posterior=xidplus.posterior_stan(fit,[prior250,prior350,prior500])
priors = [prior250,prior350,prior500]
import xidplus.catalogue as cat
SPIRE_cat=cat.create_SPIRE_cat(posterior,priors[0],priors[1],priors[2])
SPIRE_cat = Table.read(SPIRE_cat)
#mask = ['ILTJ' in SPIRE_cat['HELP_ID'][i] for i in range(len(SPIRE_cat)) if SPIRE_cat['RA'][i] in ras]
mask = [SPIRE_cat['HELP_ID'][i] in ids for i in range(len(SPIRE_cat))]
SPIRE_cat = SPIRE_cat[mask]
if os.path.exists('data/fir/SPIRE_no_lofar/xidplus_run_{}'.format(taskid))==True:()
else:
os.mkdir('data/fir/SPIRE_no_lofar/xidplus_run_{}'.format(taskid))
xidplus.save([prior250,prior350,prior500],posterior,'data/fir/SPIRE_no_lofar/xidplus_run_{}/lofar_xidplus_fir_{}_rerun'.format(taskid,taskid))
#the next couple of lines are an alternative way to save astropy table since the Table.write method is currently broken
with serialize_method_as(SPIRE_cat, None):
registry.write(SPIRE_cat,'data/fir/SPIRE_no_lofar/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.fits'.format(taskid,taskid),format='fits')
#Table.write(SPIRE_cat,'data/fir/SPIRE/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.fits'.format(taskid,taskid),format='fits',overwrite=True)
def write(self, target, *args, **kwargs):
"""Write a `ChannelList` to a file
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
else:
prfs.append(psf_dirty[0])
pinds.append(np.arange(0,prfs[m].shape[0],1))
prior.set_prfs(prfs,pinds,pinds)
prior.get_pointing_matrix_multiple_prf()
prior.upper_lim_map()
print('fitting '+ str(prior.nsrc)+' sources \n')
print('using ' + str(prior.snpix) + ' pixels')
from xidplus.numpyro_fit import LOFAR150
fit=LOFAR150.LOFAR_150(prior,num_samples=1000,num_warmup=1000)
samples = fit.get_samples()['src_f']
posterior = xidplus.posterior_numpyro(fit,[prior])
if os.path.exists('data/xidplus_results/injected_sources/xidplus_run_{}'.format(n))==True:()
else:
os.mkdir('data/xidplus_results/injected_sources/xidplus_run_{}'.format(n))
xidplus.save([prior],posterior,'data/xidplus_results/injected_sources/xidplus_run_{}/injected_sources_{}.pkl'.format(n,n))
LOFAR_cat=cat.create_LOFAR_cat(posterior,prior)
LOFAR_cat = Table.read(LOFAR_cat)
with serialize_method_as(LOFAR_cat, None):
registry.write(LOFAR_cat,'data/xidplus_results/injected_sources/xidplus_run_{}/injected_sources_cat_{}.fits'.format(n,n),format='fits',overwrite=True)
def write(self, target, *args, **kwargs):
"""Write this `DataQualityFlag` to file
Notes
-----"""
return io_registry.write(self, target, *args, **kwargs)
def __call__(self, *args, **kwargs):
registry.write(self._instance, *args, **kwargs)
posterior = xidplus.posterior_stan(fit, [prior250])
priors = [prior250]
import xidplus.catalogue as cat
MIPS_cat = cat.create_MIPS_cat(posterior, priors[0], 0)
MIPS_cat = Table.read(MIPS_cat)
mask = [MIPS_cat['help_id'][i] in ids for i in range(len(MIPS_cat))]
MIPS_cat = MIPS_cat[mask]
if os.path.exists('data/fir/v0_7/MIPS/xidplus_run_{}'.format(taskid)) == True:
()
else:
os.mkdir('data/fir/v0_7/MIPS/xidplus_run_{}'.format(taskid))
#the next couple of lines are an alternative way to save astropy table since the Table.write method is currently broken
with serialize_method_as(MIPS_cat, None):
registry.write(
MIPS_cat,
'data/fir/v0_7/MIPS/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.fits'.
format(taskid, taskid),
format='fits',
overwrite=True)
#Table.write(MIPS_cat,'data/fir/MIPS/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.fits'.format(taskid,taskid),overwrite=True)
xidplus.save(
[prior250], posterior,
'data/fir/v0_7/MIPS/xidplus_run_{}/lofar_xidplus_fir_{}_rerun.pkl'.format(
taskid, taskid))
print('fitting ' + str(prior.nsrc) + ' sources \n')
print('using ' + str(prior.snpix) + ' pixels')
from xidplus.numpyro_fit import LOFAR150
fit = LOFAR150.LOFAR_150(prior, num_samples=1000, num_warmup=1000)
samples = fit.get_samples()['src_f']
posterior = xidplus.posterior_numpyro(fit, [prior])
if os.path.exists(
'data/xidplus_results/pybdsf_components/xidplus_run_{}'.format(
n)) == True:
()
else:
os.mkdir('data/xidplus_results/pybdsf_components/xidplus_run_{}'.format(n))
xidplus.save(
[prior], posterior,
'data/xidplus_results/pybdsf_components/xidplus_run_{}/LOFAR_{}_run_components_restoring_beam.pkl'
.format(n, n))
LOFAR_cat = cat.create_LOFAR_cat(posterior, prior)
LOFAR_cat = Table.read(LOFAR_cat)
with serialize_method_as(LOFAR_cat, None):
registry.write(
LOFAR_cat,
'data/xidplus_results/pybdsf_components/xidplus_run_{}/LOFAR_{}_run_components_restoring_beam'
.format(n, n),
format='fits',
overwrite=True)
