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redmapper.py
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redmapper.py
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"""
redMaPPer catalog class.
"""
from __future__ import division, print_function
import os
import functools
from astropy.io import fits
from astropy.cosmology import FlatLambdaCDM
from GCR import BaseGenericCatalog
__all__ = ['RedmapperCatalog', 'RedMapperLegacyCatalog']
class FitsFile(object):
def __init__(self, path):
self._path = path
self._file_handle = fits.open(self._path, mode='readonly', memmap=True, lazy_load_hdus=True)
self.data = self._file_handle[1].data #pylint: disable=E1101
def __del__(self):
del self.data
del self._file_handle[1].data #pylint: disable=E1101
self._file_handle.close()
del self._file_handle
class RedmapperCatalog(BaseGenericCatalog):
"""
redMaPPer cluster catalog class. Uses generic quantity and filter mechanisms
defined by BaseGenericCatalog class.
"""
def _subclass_init(self, catalog_root_dir,
catalog_path_template,
use_cache=True,
**kwargs): #pylint: disable=W0221
if not os.path.isdir(catalog_root_dir):
raise RuntimeError("Catalog directory %s does not exist." % (catalog_root_dir))
self._catalog_path_template = {k: os.path.join(catalog_root_dir, v) for k, v in catalog_path_template.items()}
cosmology = kwargs.get('cosmology', {})
cosmo_astropy_allowed = FlatLambdaCDM.__init__.__code__.co_varnames[1:]
cosmo_astropy = {k: v for k, v in cosmology.items() if k in cosmo_astropy_allowed}
self.cosmology = FlatLambdaCDM(**cosmo_astropy)
for k, v in cosmology.items():
if k not in cosmo_astropy_allowed:
setattr(self.cosmology, k, v)
self.lightcone = kwargs.get('lightcone')
self.sky_area = kwargs.get('sky_area')
self.cache = dict() if use_cache else None
self._members_only = kwargs.get('members_only')
self._quantity_modifiers = self._generate_quantity_modifiers()
def _generate_quantity_modifiers(self):
quantity_modifiers = {
'cluster_id_member': 'members/mem_match_id',
'id_member': 'members/id',
'ra_member': 'members/ra',
'dec_member': 'members/dec',
'refmag_member': 'members/refmag',
'refmag_err_member': 'members/refmag_err',
'redshift_true_member': 'members/zspec',
'p_member': 'members/p',
'pfree_member': 'members/pfree',
'theta_i_member': 'members/theta_i',
'theta_r_member': 'members/theta_r',
}
# Add magnitudes
for i, band in enumerate(['g', 'r', 'i', 'z', 'y']):
quantity_modifiers['mag_%s_lsst_member' % (band)] = 'members/mag/%d' % (i)
quantity_modifiers['magerr_%s_lsst_member' % (band)] = 'members/mag_err/%d' % (i)
if not self._members_only:
quantity_modifiers.update({
'cluster_id': 'clusters/mem_match_id',
'ra': 'clusters/ra',
'dec': 'clusters/dec',
'redshift': 'clusters/z_lambda',
'redshift_err': 'clusters/z_lambda_e',
'richness': 'clusters/lambda',
'richness_err': 'clusters/lambda_e',
'scaleval': 'clusters/scaleval',
'redshift_true_cg': 'clusters/cg_spec_z',
'maskfrac': 'clusters/maskfrac',
})
# add centrals
for i in range(5):
quantity_modifiers['ra_cen_%d' % (i)] = 'clusters/ra_cent/%d' % (i)
quantity_modifiers['dec_cen_%d' % (i)] = 'clusters/dec_cent/%d' % (i)
quantity_modifiers['p_cen_%d' % (i)] = 'clusters/p_cen/%d' % (i)
quantity_modifiers['id_cen_%d' % (i)] = 'clusters/id_cent/%d' % (i)
return quantity_modifiers
def _iter_native_dataset(self, native_filters=None):
if native_filters is not None:
raise RuntimeError("*native_filters* not supported")
yield functools.partial(self._native_quantity_getter)
def _generate_native_quantity_list(self):
native_quantities = set()
for subset in self._catalog_path_template.keys():
if self._members_only and subset == 'clusters':
continue
f = self._open_dataset(subset)
for name, (dt, _) in f.data.dtype.fields.items():
if dt.shape:
for i in range(dt.shape[0]):
native_quantities.add('/'.join((subset, name, str(i))))
else:
native_quantities.add('/'.join((subset, name)))
return native_quantities
def _open_dataset(self, subset):
path = self._catalog_path_template[subset]
if self.cache is None:
return FitsFile(path)
if subset not in self.cache:
self.cache[subset] = FitsFile(path)
return self.cache[subset]
def _native_quantity_getter(self, native_quantity):
native_quantity = native_quantity.split('/')
if len(native_quantity) not in (2, 3):
raise RuntimeError('something wrong with the native_quantity {}'.format(native_quantity))
subset = native_quantity.pop(0)
column = native_quantity.pop(0)
data = self._open_dataset(subset).data[column]
if native_quantity:
data = data[:,int(native_quantity.pop(0))]
return data.byteswap().newbyteorder()
class RedMapperLegacyCatalog(RedmapperCatalog):
"""
Legacy redMaPPer cluster catalog class.
"""
def _generate_quantity_modifiers(self):
quantity_modifiers = {
'galaxy_id' : 'members/ID',
'cluster_id_member' : 'members/MEM_MATCH_ID',
'ra' : 'members/RA',
'dec' : 'members/DEC',
'redshift_true' : 'members/Z',
'redshift' : 'members/ZRED',
'p_mem' : 'members/P',
'p_free' : 'members/PFREE',
}
# add magnitudes
for i, band in enumerate(['u','g','r','i','z']):
quantity_modifiers['mag_{}_lsst'.format(band)] = 'members/MODEL_MAG/{}'.format(i)
quantity_modifiers['magerr_{}_lsst'.format(band)] = 'members/MODEL_MAGERR/{}'.format(i)
if not self._members_only:
quantity_modifiers.update({
'cluster_id' : 'clusters/MEM_MATCH_ID',
'ra_cluster' : 'clusters/RA',
'dec_cluster' : 'clusters/DEC',
'redshift_cluster' : 'clusters/Z_LAMBDA',
'redshift_true_cluster':'clusters/Z',
'p_cen' : 'clusters/P_BCG',
'richness' : 'clusters/LAMBDA_CHISQ',
'halo_id' : 'clusters/MEM_MATCH_ID',
'halo_mass' : 'clusters/M200',
'lim_limmag_dered' : 'clusters/LIM_LIMMAG_DERED',
'scaleval' : 'clusters/SCALEVAL',
})
return quantity_modifiers