nbodykit.base.mesh

Classes

MeshFilter()

A filter function that can be applied to a Mesh Refer to nbodykit.filters for a list of filters.

MeshSource(comm, Nmesh, BoxSize, dtype)

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

class nbodykit.base.mesh.MeshFilter[source]

A filter function that can be applied to a Mesh Refer to nbodykit.filters for a list of filters.

Attributes
kind
mode

Methods

filter(x, v)

Apply a filter based on coordinate variables x and field value v.

filter(x, v)[source]

Apply a filter based on coordinate variables x and field value v.

It shall return the new field value with the same shape of v. :param x: a list of arrays for the coordiantes of v :type x: list

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 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([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.

paint

__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

property 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 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

property attrs

A dictionary storing relevant meta-data about the CatalogSource.

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

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

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.