nbodykit.source.mesh.
BigFileMesh
(path, dataset, comm=None, **kwargs)[source]¶A MeshSource object that reads a mesh from disk using bigfile
.
This can read meshes that have been stored with the
save()
function of MeshSource objects.
Parameters:  

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 () 
Return the ComplexField stored on disk. 
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 () 
Return the RealField stored on disk. 
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
¶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')¶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.
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.
Parameters: 

to_complex_field
()[source]¶Return the ComplexField stored on disk.
Note
The mesh stored on disk must be stored with mode=complex
Returns:  real – an arraylike object holding the mesh loaded from disk in Fourier space 

Return type:  pmesh.pm.ComplexField 
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]¶Return the RealField stored on disk.
Note
The mesh stored on disk must be stored with mode=real
Returns:  real – an arraylike object holding the mesh loaded from disk in configuration space 

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.
LinearMesh
(Plin, BoxSize, Nmesh, seed=None, unitary_amplitude=False, inverted_phase=False, remove_variance=None, comm=None)[source]¶A MeshSource object that generates a RealField
density
mesh from a linear power spectrum function \(P(k)\).
Parameters: 


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 () 
Return a ComplexField, generating from the linear power spectrum. 
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 configurationspace 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)¶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
¶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')¶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.
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.
Parameters: 

to_complex_field
()[source]¶Return a ComplexField, generating from the linear power spectrum.
Note
The density field is normalized to \(1+\delta\) such that the mean of the return field in real space is unity.
Returns:  an arraylike object holding the generated linear density field in Fourier space 

Return type:  pmesh.pm.ComplexField 
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)¶Convert the mesh source to the configurationspace 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.
nbodykit.source.mesh.
FieldMesh
(field)[source]¶A MeshSource initialized from an inmemory Field object, either a
pmesh.pm.RealField
or pmesh.pm.ComplexField
.
Note
The original field object is never modified by this source.
Parameters:  

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 () 
Return a copy of the (possibly resampled) input ComplexField 
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 () 
Return a copy of the (possibly resampled) input RealField 
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
¶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')¶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.
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.
Parameters: 

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 
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.
ArrayMesh
(array, BoxSize, comm=None, root=0, **kwargs)[source]¶A MeshSource initalized from an inmemory numpy array.
Note
The inmemory array must be fully hosted by the root rank.
Parameters: 


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 () 
Convert the mesh source to the configurationspace 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)¶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
¶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')¶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.
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.
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
()[source]¶Convert the mesh source to the configurationspace 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.
nbodykit.source.mesh.
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.
MultipleSpeciesCatalogMesh
(source, Nmesh, BoxSize, dtype, selection, position, weight, value, interlaced, compensated, resampler)[source]¶A subclass of CatalogMesh
designed to paint the density field from a sum of multiple types
of particles.
The compute()
function paints the density field summed over
all particle species.
Parameters: 


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 ([normalize]) 
Paint the density field holding the sum of all particle species, returning a RealField object. 
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 

__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
¶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')¶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.
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.
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
(normalize=True)[source]¶Paint the density field holding the sum of all particle species,
returning a RealField
object.
Metadata computed for each particle is stored in the attrs
attribute of the returned RealField, with keys that are prefixed by
the species name. In particular, the total shot noise for the
mesh is defined as:
where the sum is over all species in the catalog, W_i
is the
sum of the Weight
column for the \(i^\mathrm{th}\) species,
and \(W_\mathrm{tot}\) is the sum of \(W_i\) across all species.
Parameters:  normalize (bool, optional) – if True , normalize the density field as \(1+\delta\),
dividing by the total mean number of objects per cell, as given
by the num_per_cell metadata value in attrs 

Returns:  the RealField holding the painted density field, with a
attrs dictionary attribute holding the metadata 
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.