Merge pull request #86 from LSSTDESC/sso_initial

Sso initial

cfg/object_types.yaml

@@ -1,102 +1,109 @@
 #  Yaml fragment to be incorporated into configs
 object_types :
-  galaxy :
-      file_template : 'galaxy_(?P<healpix>\d+).parquet'
-      flux_file_template : 'galaxy_flux_(?P<healpix>\d+).parquet'
-      data_file_type : parquet
-      area_partition :
-        { type: healpix, ordering : ring, nside : 32}
-      composite :
-        bulge : required
-        disk  : required
-        knots : optional
-      attribute_aliases :
-        size_knots_true : size_disk_true
-        size_minor_knots_true : size_minor_disk_true
-  bulge_basic :
-      subtype : bulge
-      parent : galaxy
-      sed_model : tophat
-      internal_extinction : CCM
-      MW_extinction : F19
-      spatial_model : sersic2D
-  disk_basic :
-      subtype : disk
-      parent : galaxy
-      sed_model : tophat
-      internal_extinction : CCM
-      MW_extinction : F19
-      spatial_model :  sersic2D
-  knots_basic :
-      subtype : knots
-      parent : galaxy
-      sed_model : tophat
-      internal_extinction : CCM
-      MW_extinction : F19
-      spatial_model :  knots
-  diffsky_galaxy :
-      file_template : 'galaxy_(?P<healpix>\d+).parquet'
-      flux_file_template : 'galaxy_flux_(?P<healpix>\d+).parquet'
-      sed_file_template : 'galaxy_sed_(?P<healpix>\d+).hdf5'
-      data_file_type : parquet
-      area_partition :
-        { type: healpix, ordering : ring, nside : 32}
-      composite :
-        bulge : required
-        disk  : required
-        knots : optional
-  diffsky_bulge :
-      subtype : bulge
-      parent : diffsky_galaxy
-      sed_model : TBD
-      internal_extinction : CCM
-      MW_extinction : F19
-      spatial_model : sersic2D
-  diffsky_disk :
-      subtype : disk
-      parent : diffsky_galaxy
-      sed_model : TBD
-      internal_extinction : CCM
-      MW_extinction : F19
-      spatial_model :  sersic2D
-  diffsky_knots :
-      subtype : knots
-      parent : diffsky_galaxy
-      sed_model : TBD
-      internal_extinction : CCM
-      MW_extinction : F19
-      spatial_model :  knots
+  galaxy:
+      file_template: 'galaxy_(?P<healpix>\d+).parquet'
+      flux_file_template: 'galaxy_flux_(?P<healpix>\d+).parquet'
+      data_file_type: parquet
+      area_partition:
+        { type: healpix, ordering: ring, nside: 32}
+      composite:
+        bulge: required
+        disk:  required
+        knots: optional
+      attribute_aliases:
+        size_knots_true: size_disk_true
+        size_minor_knots_true: size_minor_disk_true
+  bulge_basic:
+      subtype: bulge
+      parent: galaxy
+      sed_model: tophat
+      internal_extinction: CCM
+      MW_extinction: F19
+      spatial_model: sersic2D
+  disk_basic:
+      subtype: disk
+      parent: galaxy
+      sed_model: tophat
+      internal_extinction: CCM
+      MW_extinction: F19
+      spatial_model:  sersic2D
+  knots_basic:
+      subtype: knots
+      parent: galaxy
+      sed_model: tophat
+      internal_extinction: CCM
+      MW_extinction: F19
+      spatial_model:  knots
+  diffsky_galaxy:
+      file_template: 'galaxy_(?P<healpix>\d+).parquet'
+      flux_file_template: 'galaxy_flux_(?P<healpix>\d+).parquet'
+      sed_file_template: 'galaxy_sed_(?P<healpix>\d+).hdf5'
+      data_file_type: parquet
+      area_partition:
+        { type: healpix, ordering: ring, nside: 32}
+      composite:
+        bulge: required
+        disk : required
+        knots: optional
+  diffsky_bulge:
+      subtype: bulge
+      parent: diffsky_galaxy
+      sed_model: TBD
+      internal_extinction: CCM
+      MW_extinction: F19
+      spatial_model: sersic2D
+  diffsky_disk:
+      subtype: disk
+      parent: diffsky_galaxy
+      sed_model: TBD
+      internal_extinction: CCM
+      MW_extinction: F19
+      spatial_model:  sersic2D
+  diffsky_knots:
+      subtype: knots
+      parent: diffsky_galaxy
+      sed_model: TBD
+      internal_extinction: CCM
+      MW_extinction: F19
+      spatial_model:  knots
 
-  star :
-      file_template : 'pointsource_(?P<healpix>\d+).parquet'
-      flux_file_template : 'pointsource_flux_(?P<healpix>\d+).parquet'
-      data_file_type : parquet
-      area_partition :
-        { type: healpix, ordering : ring, nside : 32}
-      sed_model : file_nm
-      sed_file_root_env_var : SIMS_SED_LIBRARY_DIR
-      MW_extinction : F19
-      internal_extinction : None
-  sncosmo :
-      file_template : 'pointsource_(?P<healpix>\d+).parquet'
-      data_file_type : parquet
-      area_partition :
-        { type: healpix, ordering : ring, nside : 32}
+  star:
+      file_template: 'pointsource_(?P<healpix>\d+).parquet'
+      flux_file_template: 'pointsource_flux_(?P<healpix>\d+).parquet'
+      data_file_type: parquet
+      area_partition:
+        { type: healpix, ordering: ring, nside: 32}
+      sed_model: file_nm
+      sed_file_root_env_var: SIMS_SED_LIBRARY_DIR
+      MW_extinction: F19
+      internal_extinction: None
+  sncosmo:
+      file_template: 'pointsource_(?P<healpix>\d+).parquet'
+      data_file_type: parquet
+      area_partition:
+        { type: healpix, ordering: ring, nside: 32}
 
-      sed_model : sncosmo
-      MW_extinction : F19
-      internal_extinction : None
-  gaia_star :
-      data_file_type : butler_refcat
-      butler_parameters :
-        collections : HSC/defaults
-        dstype : gaia_dr2_20200414
-      area_partition : None
-      sed_method : use_lut
-  snana :
-      file_template : 'snana_(?P<healpix>\d+).parquet'
-      data_file_type : parquet
-      area_partition :
-        { type: healpix, ordering : ring, nside : 32}
-      sed_model : snana
-      internal_extinction : None
+      sed_model: sncosmo
+      MW_extinction: F19
+      internal_extinction: None
+  gaia_star:
+      data_file_type: butler_refcat
+      butler_parameters:
+        collections: HSC/defaults
+        dstype: gaia_dr2_20200414
+      area_partition: None
+      sed_method: use_lut
+  snana:
+      file_template: 'snana_(?P<healpix>\d+).parquet'
+      data_file_type: parquet
+      area_partition:
+        { type: healpix, ordering: ring, nside: 32}
+      sed_model: snana
+      internal_extinction: None
+  sso:
+      file_template: 'sso_(?P<healpix>\d+).parquet'
+      flux_file_template: 'sso_flux_(?P<healpix>\d+).parquet'
+      data_file_type: parquet
+      area_partition:
+        { type: healpix, ordering: ring, nside: 32}
+      sed_model: dbfile_angstrom_flambda

skycatalogs/catalog_creator.py

@@ -24,6 +24,7 @@
 from .utils.creator_utils import make_MW_extinction_av, make_MW_extinction_rv
 from .objects.base_object import LSST_BANDS
 from .objects.base_object import ROMAN_BANDS
+from .sso_catalog_creator import SsoCatalogCreator
 
 """
 Code to create a sky catalog for particular object types
@@ -197,7 +198,8 @@ def __init__(self, parts, area_partition=None, skycatalog_root=None,
                  no_flux=False, flux_parallel=16, galaxy_nside=32,
                  galaxy_stride=1000000, provenance=None,
                  dc2=False, sn_object_type='sncosmo', galaxy_type='cosmodc2',
-                 include_roman_flux=False, star_input_fmt='sqlite'):
+                 include_roman_flux=False, star_input_fmt='sqlite',
+                 sso_truth=None, sso_sed=None, sso_partition='healpixel'):
         """
         Store context for catalog creation
 
@@ -244,6 +246,9 @@ def __init__(self, parts, area_partition=None, skycatalog_root=None,
         galaxy_type     Currently allowed values are cosmodc2 and diffsky
         include_roman_flux Calculate and write Roman flux values
         star_input_fmt  May be either 'sqlite' or 'parquet'
+        sso_truth       Directory containing Sorcha output
+        sso_sed         Path to sed file to be used for all SSOs
+        sso_partition   Whether to partition by time or by healpixels
 
         Might want to add a way to specify template for output file name
         and template for input sedLookup file name.
@@ -291,6 +296,7 @@ def __init__(self, parts, area_partition=None, skycatalog_root=None,
                 self._star_truth = _star_db
             elif self._star_input_fmt == 'parquet':
                 self._star_truth = _star_parquet
+
         self._cat = None
 
         self._parts = parts
@@ -326,6 +332,11 @@ def __init__(self, parts, area_partition=None, skycatalog_root=None,
         self._dc2 = dc2
         self._include_roman_flux = include_roman_flux
         self._obs_sed_factory = None
+        self._sso_sed_factory = None               # do we need this?
+        self._sso_creator = SsoCatalogCreator(self, sso_truth, sso_sed)
+        self._sso_truth = self._sso_creator.sso_truth
+        self._sso_sed = self._sso_creator.sso_sed
+        self._sso_partition = sso_partition
 
     def _make_tophat_columns(self, dat, names, cmp):
         '''
@@ -357,8 +368,8 @@ def create(self, catalog_type):
 
         Parameters
         ----------
-        catalog_type   string    Currently 'galaxy' and 'pointsource' are
-                                 the only values allowed
+        catalog_type   string    Currently 'galaxy', 'pointsource'
+                                 and 'sso' are the only values allowed
         Return
         ------
         None
@@ -373,6 +384,12 @@ def create(self, catalog_type):
                 self.create_pointsource_catalog()
             if not self._no_flux:
                 self.create_pointsource_flux_catalog()
+        elif catalog_type == ('sso'):
+            if not self._flux_only:
+                self._sso_creator.create_sso_catalog()
+            if not self._main_only:
+                self._sso_creator.create_sso_flux_catalog()
+
         else:
             raise NotImplementedError(f'CatalogCreator.create: unsupported catalog type {catalog_type}')
 
@@ -1081,6 +1098,9 @@ def write_config(self, overwrite=False, path_only=False):
             inputs['sn_truth'] = self._sn_truth
         if self._star_truth:
             inputs['star_truth'] = self._star_truth
+        if self._sso_truth:
+            inputs['sso_truth'] = self._sso_truth
+            inputs['sso_sed'] = self._sso_sed
         config.add_key('provenance', assemble_provenance(self._pkg_root,
                                                          inputs=inputs))
 

skycatalogs/objects/base_object.py

@@ -240,7 +240,7 @@ def _get_sed_from_file(self, fpath, redshift=0):
             sed = sed.atRedshift(redshift)
         return sed
 
-    def get_gsobject_components(self, gsparams=None, rng=None):
+    def get_gsobject_components(self, gsparams=None, rng=None, exposure=None):
         """
         Return a dictionary of the GSObject components for the
         sky catalogs object, keyed by component name.
@@ -570,7 +570,10 @@ def __contains__(self, obj):
         return id in self._id
 
     def __len__(self):
-        return len(self._id)
+        if self._id is not None:
+            return len(self._id)
+        else:
+            return 0
 
     # def __iter__(self):   Standard impl based on __getitem__ should be ok
     # def __reversed__(self):   Default implementation ok
@@ -654,8 +657,14 @@ def __init__(self):
 
     def append_collection(self, coll):
         old = self._total_len
-        self._total_len += len(coll)
-        self._located.append(LocatedCollection(coll, old, self._total_len))
+        if isinstance(coll, ObjectCollection):
+            self._total_len += len(coll)
+            self._located.append(LocatedCollection(coll, old, self._total_len))
+        else:  #  list of collections
+            for c in coll:
+                self._total_len += len(c)
+                self._located.append(LocatedCollection(c, old, self._total_len))
+                old = self._total_len
 
     def append_object_list(self, object_list):
         for e in object_list._located:

skycatalogs/objects/gaia_object.py

@@ -203,9 +203,11 @@ def load_collection(region, skycatalog, mjd=None):
         rv1 = np.zeros(len(df))
         epNa = 2400000.5  # "part A" of starting and ending epochs for MJDs.
         ep2b = mjd
-        pm_outputs = erfa.pmsafe(df['coord_ra'], df['coord_dec'],
-                                 df['pm_ra'], df['pm_dec'], df['parallax'],
-                                 rv1, epNa, df['epoch'], epNa, ep2b)
+        pm_outputs = erfa.pmsafe(np.array(df['coord_ra']),
+                                 np.array(df['coord_dec']),
+                                 np.array(df['pm_ra']), np.array(df['pm_dec']),
+                                 np.array(df['parallax']),
+                                 rv1, epNa, np.array(df['epoch']), epNa, ep2b)
         # Update ra, dec values.
         df['coord_ra'] = pm_outputs[0]
         df['coord_dec'] = pm_outputs[1]

skycatalogs/objects/snana_object.py

@@ -92,7 +92,7 @@ def get_observer_sed_component(self, component, mjd=None):
         if mjd is None:
             mjd = self._belongs_to._mjd
         if mjd is None:
-            txt = 'SnananObject._get_sed: no mjd specified for this call\n'
+            txt = 'SnananObject.get_observer_sed_component: no mjd specified for this call\n'
             txt += 'nor when generating object list'
             raise ValueError(txt)
         sed, _ = self._get_sed(mjd=mjd)