Functions
CompensateCIC (w, v) 
Return the Fourierspace kernel that accounts for the convolution of the gridded field with the CIC window function in configuration space 
CompensateCICShotnoise (w, v) 
Return the Fourierspace kernel that accounts for the convolution of the gridded field with the CIC window function in configuration space, as well as the approximate aliasing correction to the first order 
CompensatePCS (w, v) 
Return the Fourierspace kernel that accounts for the convolution of the gridded field with the PCS window function in configuration space. 
CompensatePCSShotnoise (w, v) 
Return the Fourierspace kernel that accounts for the convolution of the gridded field with the PCS window function in configuration space, as well as the approximate aliasing correction to first order 
CompensateTSC (w, v) 
Return the Fourierspace kernel that accounts for the convolution of the gridded field with the TSC window function in configuration space. 
CompensateTSCShotnoise (w, v) 
Return the Fourierspace kernel that accounts for the convolution of the gridded field with the TSC window function in configuration space, as well as the approximate aliasing correction to the first order 
get_compensation (interlaced, resampler) 
Return the compensation function, which corrects for the windowing kernel. 
Classes
CatalogMesh (source, Nmesh, BoxSize, Position) 
A mesh generated by resampling a Catalog with the given parameters. 
nbodykit.source.mesh.catalog.
CatalogMesh
(source, Nmesh, BoxSize, Position, dtype='f4', resampler='cic', compensated=False, interlaced=False, Value=None, Selection=None, Weight=None, **kwargs)[source]¶A mesh generated by resampling a Catalog with the given parameters.
The original CatalogSource object is stored as the base
attribute.
Parameters: 


‘Weight’, ‘Value’, ‘Selection’, ‘Position’ are items of the collection that can be reassigned after the creation of the object.
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 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 Fourierspace 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]) 
Paint the density field, by interpolating the position column on to the mesh. 
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 

__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: 


Returns:  a view of the mesh object with the 
Return type: 
attrs
¶A dictionary storing relevant metadata 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:  

Returns:  out – An numpy array holding the real density field. 
Return type:  array_like 
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: 

to_complex_field
(out=None)¶Convert the mesh source to the Fourierspace 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
(out=None, normalize=True)[source]¶Paint the density field, by interpolating the position column on to the mesh.
This computes the following metadata attributes in the process of
painting, returned in the attrs
attributes of the returned
RealField object:
N
Note
The density field on the mesh is normalized as \(1+\delta\), such that the collective mean of the field is unity.
See the documentation on painting for more details on painting catalogs to a mesh.
Returns:  real – the painted real field; this has a attrs dict storing metadata 

Return type:  pmesh.pm.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.
nbodykit.source.mesh.catalog.
CompensateCIC
(w, v)[source]¶Return the Fourierspace kernel that accounts for the convolution of the gridded field with the CIC window function in configuration space
Note
see equation 18 (with p=2) of Jing et al 2005
Parameters: 


nbodykit.source.mesh.catalog.
CompensateCICShotnoise
(w, v)[source]¶Return the Fourierspace kernel that accounts for the convolution of the gridded field with the CIC window function in configuration space, as well as the approximate aliasing correction to the first order
Note
see equation 20 of Jing et al 2005
Parameters: 


nbodykit.source.mesh.catalog.
CompensatePCS
(w, v)[source]¶Return the Fourierspace kernel that accounts for the convolution of the gridded field with the PCS window function in configuration space.
Note
see equation 18 (with p=4) of Jing et al 2005
Parameters: 


nbodykit.source.mesh.catalog.
CompensatePCSShotnoise
(w, v)[source]¶Return the Fourierspace kernel that accounts for the convolution of the gridded field with the PCS window function in configuration space, as well as the approximate aliasing correction to first order
Note
YF: I derived this by fitting the result to s ** 3 according to the form given in equation 20 of Jing et al. It must be possible to derive this manually.
Parameters: 


nbodykit.source.mesh.catalog.
CompensateTSC
(w, v)[source]¶Return the Fourierspace kernel that accounts for the convolution of the gridded field with the TSC window function in configuration space.
Note
see equation 18 (with p=3) of Jing et al 2005
Parameters: 


nbodykit.source.mesh.catalog.
CompensateTSCShotnoise
(w, v)[source]¶Return the Fourierspace kernel that accounts for the convolution of the gridded field with the TSC window function in configuration space, as well as the approximate aliasing correction to the first order
Note
see equation 20 of Jing et al 2005
Parameters: 


nbodykit.source.mesh.catalog.
get_compensation
(interlaced, resampler)[source]¶Return the compensation function, which corrects for the windowing kernel.
The compensation function is computed as:
interlaced = True
:
 CompensateCIC()
if using CIC window
 CompensateTSC()
if using TSC window
 CompensatePCS()
if using PCS windowinterlaced = False
:
 CompensateCICShotnoise()
if using CIC window
 CompensateTSCShotnoise()
if using TSC window
 CompensatePCSShotnoise()
if using PCS window