nbodykit.source.catalog.halos.HaloCatalog(source, cosmo, redshift, mdef='vir', mass='Mass', position='Position', velocity='Velocity')[source]¶Bases: nbodykit.base.catalog.CatalogSource
A wrapper CatalogSource of halo objects to interface nicely with
halotools.sim_manager.UserSuppliedHaloCatalog.
| Parameters: |
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Attributes
attrs |
A dictionary storing relevant meta-data about the CatalogSource. |
columns |
All columns in the CatalogSource, including those hard-coded into the class’s defintion and override columns provided by the user. |
csize |
The total, collective size of the CatalogSource, i.e., summed across all ranks. |
hardcolumns |
A list of the hard-coded columns in the CatalogSource. |
size |
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use_cache |
If set to True, use the built-in caching features of dask to cache data in memory. |
Methods
Concentration() |
The halo concentration, computed using nbodykit.transform.HaloConcentration(). |
Mass() |
The halo mass column, assumed to be in units of \(M_\odot/h\). |
Position() |
The halo position column, assumed to be in units of \(\mathrm{Mpc}/h\). |
Radius() |
The halo radius, computed using nbodykit.transform.HaloRadius(). |
Selection() |
A boolean column that selects a subset slice of the CatalogSource. |
Value() |
When interpolating a CatalogSource on to a mesh, the value of this array is used as the Value that each particle contributes to a given mesh cell. |
Velocity() |
The halo velocity column, assumed to be in units of km/s. |
VelocityOffset() |
The redshift-space distance offset due to the velocity in units of distance. |
Weight() |
The column giving the weight to use for each particle on the mesh. |
compute(*args, **kwargs) |
Our version of dask.compute() that computes multiple delayed dask collections at once. |
copy() |
Return a copy of the CatalogSource object |
get_hardcolumn(col) |
Construct and return a hard-coded column. |
make_column(array) |
Utility function to convert a numpy array to a dask.array.Array. |
read(columns) |
Return the requested columns as dask arrays. |
save(output, columns[, datasets, header]) |
Save the CatalogSource to a bigfile.BigFile. |
to_halotools([BoxSize, selection]) |
Return the CatalogSource as a halotools.sim_manager.UserSuppliedHaloCatalog. |
to_mesh([Nmesh, BoxSize, dtype, interlaced, …]) |
Convert the CatalogSource to a MeshSource, using the specified parameters. |
update_csize() |
Set the collective size, csize. |
Concentration()[source]¶The halo concentration, computed using nbodykit.transform.HaloConcentration().
This uses the analytic formulas for concentration from Dutton and Maccio 2014.
Radius()[source]¶The halo radius, computed using nbodykit.transform.HaloRadius().
Assumed units of \(\mathrm{Mpc}/h\).
Selection()¶A boolean column that selects a subset slice of the CatalogSource.
By default, this column is set to True for all particles.
Value()¶When interpolating a CatalogSource on to a mesh, the value of this array is used as the Value that each particle contributes to a given mesh cell.
The mesh field is a weighted average of Value, with the weights
given by Weight.
By default, this array is set to unity for all particles.
VelocityOffset()[source]¶The redshift-space distance offset due to the velocity in units of distance. The assumed units are \(\mathrm{Mpc}/h\).
This multiplies Velocity by \(1 / (a 100 E(z)) = 1 / (a H(z)/h)\).
Weight()¶The column giving the weight to use for each particle on the mesh.
The mesh field is a weighted average of Value, with the weights
given by Weight.
By default, this array is set to unity for all particles.
__delitem__(col)¶Delete a column; cannot delete a “hard-coded” column
__getitem__(sel)¶The following types of indexing are supported:
__len__()¶The local size of the CatalogSource on a given rank.
__setitem__(col, value)¶Add columns to the CatalogSource, overriding any existing columns
with the name col.
attrs¶A dictionary storing relevant meta-data about the CatalogSource.
columns¶All columns in the CatalogSource, including those hard-coded into the class’s defintion and override columns provided by the user.
compute(*args, **kwargs)¶Our version of dask.compute() that computes
multiple delayed dask collections at once.
This should be called on the return value of read()
to converts any dask arrays to numpy arrays.
If use_cache is True, this internally caches data, using
dask’s built-in cache features.
| Parameters: | args (object) – Any number of objects. If the object is a dask collection, it’s computed and the result is returned. Otherwise it’s passed through unchanged. |
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Notes
The dask default optimizer induces too many (unnecesarry) IO calls – we turn this off feature off by default. Eventually we want our own optimizer probably.
copy()¶Return a copy of the CatalogSource object
| Returns: | the new CatalogSource object holding the copied data columns |
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| Return type: | CatalogCopy |
csize¶The total, collective size of the CatalogSource, i.e., summed across all ranks.
It is the sum of size across all available ranks.
get_hardcolumn(col)¶Construct and return a hard-coded column.
These are usually produced by calling member functions marked by the @column decorator.
Subclasses may override this method and the hardcolumns attribute to bypass the decorator logic.
hardcolumns¶A list of the hard-coded columns in the CatalogSource.
These columns are usually member functions marked by @column decorator.
Subclasses may override this method and use get_hardcolumn() to
bypass the decorator logic.
logger = <logging.Logger object>¶make_column(array)¶Utility function to convert a numpy array to a dask.array.Array.
read(columns)¶Return the requested columns as dask arrays.
| Parameters: | columns (list of str) – the names of the requested columns |
|---|---|
| Returns: | the list of column data, in the form of dask arrays |
| Return type: | list of dask.array.Array |
save(output, columns, datasets=None, header='Header')¶Save the CatalogSource to a bigfile.BigFile.
Only the selected columns are saved and attrs are saved in
header. The attrs of columns are stored in the datasets.
| Parameters: |
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size¶to_halotools(BoxSize=None, selection='Selection')[source]¶Return the CatalogSource as a halotools.sim_manager.UserSuppliedHaloCatalog.
The Halotools catalog only holds the local data, although halos are
labeled via the halo_id column using the global index.
| Parameters: | |
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| Returns: | cat – the Halotools halo catalog, storing the local halo data |
| Return type: |
to_mesh(Nmesh=None, BoxSize=None, dtype='f4', interlaced=False, compensated=False, window='cic', weight='Weight', value='Value', selection='Selection', position='Position')¶Convert the CatalogSource to a MeshSource, using the specified parameters.
| Parameters: |
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| Returns: | mesh – a mesh object that provides an interface for gridding particle data onto a specified mesh |
| Return type: |
update_csize()¶Set the collective size, csize.
This function should be called in __init__() of a subclass,
after size has been set to a valid value (not NotImplemented)
use_cache¶If set to True, use the built-in caching features of dask
to cache data in memory.