nbodykit.algorithms.convpower.catalogmesh

Classes

FKPCatalogMesh(source, BoxSize, BoxCenter, …) A subclass of MultipleSpeciesCatalogMesh designed to paint a FKPCatalog to a mesh.
class nbodykit.algorithms.convpower.catalogmesh.FKPCatalogMesh(source, BoxSize, BoxCenter, Nmesh, dtype, selection, comp_weight, fkp_weight, nbar, value='Value', position='Position', interlaced=False, compensated=False, resampler='cic')[source]

A subclass of MultipleSpeciesCatalogMesh designed to paint a FKPCatalog to a mesh.

The multiple species here are data and randoms CatalogSource objects, where randoms is a catalog of randomly distributed objects with no instrinsic clustering that defines the survey volume.

The position of the catalogs are re-centered to the [-L/2, L/2] where L is the size of the Cartesian box.

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
  • selection (str) – column in source that selects the subset of particles to grid to the mesh
  • comp_weight (str) – the completeness weight column name
  • fkp_weight (str) – the FKP weight column name
  • nbar (str) – the n(z) column name
  • position (str, optional) – column in source specifying the position coordinates; default is Position
Attributes:
actions

The actions to apply to the interpolated density field, optionally included the compensation correction.

attrs

A dictionary storing relevant meta-data about the CatalogSource.

compensated

Boolean flag to indicate whether to correct for the windowing kernel introduced when interpolating the discrete particles to a continuous field.

interlaced

Whether to use interlacing when interpolating the density field.

resampler

String specifying the name of the interpolation kernel when gridding the density field.

window

Methods

RecenteredPosition(name) The Position of the objects, re-centered on the mesh to the range [-BoxSize/2, BoxSize/2].
TotalWeight(name) The total weight for the mesh is the completenes weight times the FKP weight.
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.
recenter_box(BoxSize, BoxCenter) Re-center the box by applying the new box center to the column specified by position.
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() Paint the FKP density field, returning a RealField.
view() Return a “view” of the MeshSource, in the spirit of numpy’s ndarray view.
weighted_total(name) Compute the weighted total number of objects, using either the data or randoms source:
paint  
RecenteredPosition(name)[source]

The Position of the objects, re-centered on the mesh to the range [-BoxSize/2, BoxSize/2].

This subtracts BoxCenter from attrs from the original position array.

TotalWeight(name)[source]

The total weight for the mesh is the completenes weight times the FKP weight.

__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

The actions to apply to the interpolated density field, optionally included the compensation correction.

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.

compensated

Boolean flag to indicate whether to correct for the windowing kernel introduced when interpolating the discrete particles to a continuous field.

See the documentation for further details.

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

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

interlaced

Whether to use interlacing when interpolating the density field. See the documentation for further details.

See also: Section 3.1 of Sefusatti et al. 2015

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

recenter_box(BoxSize, BoxCenter)[source]

Re-center the box by applying the new box center to the column specified by position.

This ensures that the position column is always re-centered to [-L/2,L/2] where L is the BoxSize.

resampler

String specifying the name of the interpolation kernel when gridding the density field.

See the documentation for further details.

Note

Valid values must be in pmesh.resampler.methods

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()[source]

Paint the FKP density field, returning a RealField.

Given the data and randoms catalogs, this paints:

\[F(x) = w_\mathrm{fkp}(x) * [w_\mathrm{comp}(x)*n_\mathrm{data}(x) - \alpha * w_\mathrm{comp}(x)*n_\mathrm{randoms}(x)]\]

This computes the following meta-data attributes in the process of painting, returned in the attrs attributes of the returned RealField object:

  • randoms.W, data.W :
    the weighted sum of randoms and data objects; see weighted_total()
  • alpha : float
    the ratio of data.W to randoms.W
  • randoms.norm, data.norm : float
    the power spectrum normalization; see normalization()
  • randoms.shotnoise, data.shotnoise: float
    the shot noise for each sample; see shotnoise()
  • shotnoise : float
    the total shot noise, equal to the sum of randoms.shotnoise and data.shotnoise
  • randoms.num_per_cell, data.num_per_cell : float
    the mean number of weighted objects per cell for each sample
  • num_per_cell : float
    the mean number of weighted objects per cell

For further details on the meta-data, see the documentation.

Returns:the field object holding the FKP density field in real space
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.

weighted_total(name)[source]

Compute the weighted total number of objects, using either the data or randoms source:

This is the sum of the completeness weights:

\[W = \sum w_\mathrm{comp}\]