nbodykit.base.mesh

Classes

MeshSource(comm, Nmesh, BoxSize, dtype) Base class for a source in the form of data on an input grid.
class nbodykit.base.mesh.MeshSource(comm, Nmesh, BoxSize, dtype)[source]

Base class for a source in the form of data on an input grid.

The MeshSource object remembers the original source together with a sequence of transformations (added via the apply method).

dtype is the type of the real numbers, either ‘f4’ or ‘f8’.

Parameters:
  • comm – the global MPI communicator
  • Nmesh (int, array_like) – the number of cells per grid size
  • BoxSize (array_like) – the size of the box
  • dtype (str) – the desired data type of the grid

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
paint([mode, Nmesh]) Paint the density on the mesh and apply any transformation functions specified in actions.
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([out, normalize]) Convert the mesh source to the configuration-space field, returning a pmesh.pm.RealField object.
view() Return a “view” of the MeshSource, in the spirit of numpy’s ndarray view.
__finalize__(other)[source]

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
__len__()[source]

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')[source]

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) – 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) –

    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) – 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.

paint(mode='real', Nmesh=None)[source]

Paint the density on the mesh and apply any transformation functions specified in actions.

The return type of the pmesh Field object is specified by mode. This calls to_field() to convert the mesh to a Field.

See the documentation on painting for more details on painting catalogs to a mesh.

Parameters:
  • mode ('real' or 'complex') – the type of the returned Field object, either a RealField or ComplexField
  • Nmesh (int or array_like, or None) – If given and different from the intrinsic Nmesh of the source, resample the mesh to the given resolution
Returns:

either a RealField of ComplexField, with the functions in actions applied to it
Return type:

RealField, ComplexField
preview(axes=None, Nmesh=None, root=0)[source]

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')[source]

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)[source]

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)[source]

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(out=None, normalize=True)[source]

Convert the mesh source to the configuration-space field, returning a pmesh.pm.RealField object.

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

view()[source]

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.