nbodykit.source.mesh.species

Classes

MultipleSpeciesCatalogMesh(source, Nmesh, …) A subclass of CatalogMesh designed to paint the density field from a sum of multiple types of particles.
class nbodykit.source.mesh.species.MultipleSpeciesCatalogMesh(source, Nmesh, BoxSize, dtype, selection, position, weight, value, interlaced, compensated, resampler)[source]

A subclass of CatalogMesh designed to paint the density field from a sum of multiple types of particles.

The compute() function paints the density field summed over all particle species.

Parameters:
  • source (CatalogSource) – the input catalog that we wish to interpolate to a mesh
  • BoxSize – the size of the box
  • Nmesh (int, 3-vector) – the number of cells per mesh side
  • dtype (str) – the data type of the values stored on mesh
  • weight (str) – column in source that specifies the weight value for each particle in the source to use when gridding
  • value (str) – column in source that specifies the field value for each particle; the mesh stores a weighted average of this column
  • selection (str) – column in source that selects the subset of particles to grid
  • position (str, optional) – column in source specifying the position coordinates; default is Position
Attributes:
actions

A list of actions to apply to the density field when interpolating to the mesh.

attrs

A dictionary storing relevant meta-data about the CatalogSource.

Methods

apply(func[, kind, mode]) Return a view of the mesh, with actions updated to apply the specified function, either in Fourier space or configuration space, based on mode
compute([mode, Nmesh]) Compute / Fetch the mesh object into memory as a RealField or ComplexField object.
preview([axes, Nmesh, root]) Gather the mesh into as a numpy array, with (reduced) resolution.
save(output[, dataset, mode]) Save the mesh as a BigFileMesh on disk, either in real or complex space.
to_complex_field([out]) Convert the mesh source to the Fourier-space field, returning a pmesh.pm.ComplexField object.
to_field([mode, out]) Return the mesh as a pmesh Field object, either in Fourier space or configuration space, based on mode.
to_real_field([normalize]) Paint the density field holding the sum of all particle species, returning a RealField object.
view() Return a “view” of the MeshSource, in the spirit of numpy’s ndarray view.
paint  
__finalize__(other)

Finalize the creation of a MeshSource object by copying over attributes from a second MeshSource.

Parameters:other (MeshSource) – the second MeshSource to copy over attributes from
__getitem__(key)[source]

If indexed by a species name, return a CatalogMesh object holding only the data columns for that species with the same parameters as the current object.

If not a species name, this has the same behavior as CatalogSource.__getitem__().

__len__()

Length of a mesh source is zero

actions

A list of actions to apply to the density field when interpolating to the mesh.

This stores tuples of (mode, func, kind); see apply() for more details.

apply(func, kind='wavenumber', mode='complex')

Return a view of the mesh, with actions updated to apply the specified function, either in Fourier space or configuration space, based on mode

Parameters:
  • func (callable or a MeshFilter object) – func(x, y) where x is a list of r (k) values that broadcasts into a full array, when mode is ‘real’ (‘complex’); the value of x depends on kind. y is the value of the mesh field on the corresponding locations.
  • kind (string, optional) –

    if a MeshFilter object is given as func, this is ignored. The kind of value in x.

    • When mode is ‘complex’:
      • ’wavenumber’ means wavenumber from [- 2 pi / L * N / 2, 2 pi / L * N / 2).
      • ’circular’ means circular frequency from [- pi, pi).
      • ’index’ means [0, Nmesh )
    • When mode is ‘real’:
      • ’relative’ means distance from [-0.5 Boxsize, 0.5 BoxSize).
      • ’index’ means [0, Nmesh )
  • mode ('complex' or 'real', optional) – if a MeshFilter object is given as func, this is ignored. whether to apply the function to the mesh in configuration space or Fourier space
Returns:

a view of the mesh object with the actions attribute updated to include the new action

Return type:

MeshSource

attrs

A dictionary storing relevant meta-data about the CatalogSource.

compute(mode='real', Nmesh=None)

Compute / Fetch the mesh object into memory as a RealField or ComplexField object.

preview(axes=None, Nmesh=None, root=0)

Gather the mesh into as a numpy array, with (reduced) resolution. The result is broadcast to all ranks, so this uses \(\mathrm{Nmesh}^3\) per rank.

Parameters:
  • Nmesh (int, array_like) – The desired Nmesh of the result. Be aware this function allocates memory to hold a full Nmesh on each rank.
  • axes (int, array_like) – The axes to project the preview onto., e.g. (0, 1)
  • root (int, optional) – the rank number to treat as root when gathering to a single rank
Returns:

out – An numpy array holding the real density field.

Return type:

array_like

save(output, dataset='Field', mode='real')

Save the mesh as a BigFileMesh on disk, either in real or complex space.

Parameters:
  • output (str) – name of the bigfile file
  • dataset (str, optional) – name of the bigfile data set where the field is stored
  • mode (str, optional) – real or complex; the form of the field to store
to_complex_field(out=None)

Convert the mesh source to the Fourier-space field, returning a pmesh.pm.ComplexField object.

Not implemented in the base class, unless object is a view.

to_field(mode='real', out=None)

Return the mesh as a pmesh Field object, either in Fourier space or configuration space, based on mode.

This will call to_real_field() or to_complex_field() based on mode.

Parameters:mode ('real' or 'complex') – the return type of the field
Returns:either a RealField of ComplexField, storing the value of the field on the mesh
Return type:RealField, ComplexField
to_real_field(normalize=True)[source]

Paint the density field holding the sum of all particle species, returning a RealField object.

Meta-data computed for each particle is stored in the attrs attribute of the returned RealField, with keys that are prefixed by the species name. In particular, the total shot noise for the mesh is defined as:

\[P_\mathrm{shot} = \sum_i (W_i/W_\mathrm{tot})^2 P_{\mathrm{shot},i},\]

where the sum is over all species in the catalog, W_i is the sum of the Weight column for the \(i^\mathrm{th}\) species, and \(W_\mathrm{tot}\) is the sum of \(W_i\) across all species.

Parameters:normalize (bool, optional) – if True, normalize the density field as \(1+\delta\), dividing by the total mean number of objects per cell, as given by the num_per_cell meta-data value in attrs
Returns:the RealField holding the painted density field, with a attrs dictionary attribute holding the meta-data
Return type:RealField
view()

Return a “view” of the MeshSource, in the spirit of numpy’s ndarray view.

This returns a new MeshSource whose memory is owned by self.

Note that for CatalogMesh objects, this is overidden by the CatalogSource.view function.