nbodykit.algorithms.fftrecon¶
Classes
|
FFT based Lagrangian reconstruction algorithm in a periodic box. |
- class nbodykit.algorithms.fftrecon.FFTRecon(data, ran, Nmesh, bias=1.0, f=0.0, los=[0, 0, 1], R=20, position='Position', revert_rsd_random=False, scheme='LGS', BoxSize=None)[source]¶
FFT based Lagrangian reconstruction algorithm in a periodic box.
References
Eisenstein et al, 2007 http://adsabs.harvard.edu/abs/2007ApJ…664..675E Section 3, paragraph starting with ‘Restoring in full the …’
We follow a cleaner description in Schmitfull et al 2015,
Table I, and text below. Schemes are LGS, LF2 and LRR.
A slight difference against the paper is that Redshift distortion and bias are corrected in the linear order. The Random shifting followed Martin White’s suggestion to exclude the RSD by default. (with default revert_rsd_random=False.)
- Parameters
data (CatalogSource,) – the data catalog, e.g. halos. data.attrs[‘BoxSize’] is used if argument BoxSize is not given.
ran (CatalogSource) – the random catalog, e.g. from a UniformCatalog object.
Nmesh (int) – The size of the FFT Mesh. Rule of thumb is that the size of a mesh cell shall be 2 ~ 4 times smaller than the smoothing length, R.
revert_rsd_random (boolean) – Revert the rsd for randoms as well as data. There are two conventions. either reverting rsd displacement in data displacement only(False) or in both data and randoms (True). Default is False.
R (float) – The radius of smoothing. 10 to 20 Mpc/h is usually cool.
bias (float) – The bias of the data catalog.
f (float) – The growth rate; if non-zero, correct for RSD
los (list) – The direction of the line of sight for RSD. Usually (default) [0, 0, 1].
position (string) – column to use for picking up the Position of the objects.
BoxSize (float or array_like) – the size of the periodic box, default is to infer from the data.
scheme (string) – The reconstruction scheme. LGS is the standard reconstruction (Lagrangian growth shift). LF2 is the F2 Lagrangian reconstruction. LRR is the random-random Lagrangian reconstruction.
- Attributes
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 onmode
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 onmode
.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
run
work_with
- __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
- __len__()¶
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)
; seeapply()
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 onmode
- Parameters
func (callable or a
MeshFilter
object) – func(x, y) where x is a list ofr
(k
) values that broadcasts into a full array, whenmode
is ‘real’ (‘complex’); the value of x depends onkind
.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
- property 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
- 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.
- 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 onmode
.This will call
to_real_field()
orto_complex_field()
based onmode
.- 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]¶
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()¶
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.