nbodykit.source.mesh¶
- class nbodykit.source.mesh.ArrayMesh(array, BoxSize, comm=None, root=0, **kwargs)[source]¶
A MeshSource initalized from an in-memory numpy array.
Note
The in-memory array must be fully hosted by the root rank.
- Parameters
array (numpy.ndarray) – the numpy array holding the field data; this must be fully hosted by the rank specified by
root
BoxSize (float, 3-vector) – the size of the box
root (int, optional) – the root rank holding the array data
**kwargs – additional meta-data to store
- 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
- __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.
- class 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 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.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 onmode
.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
- 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()[source]¶
Return the ComplexField stored on disk.
Note
The mesh stored on disk must be stored with
mode=complex
- Returns
real – an array-like 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 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]¶
Return the RealField stored on disk.
Note
The mesh stored on disk must be stored with
mode=real
- Returns
real – an array-like object holding the mesh loaded from disk in configuration space
- Return type
- 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.
- class 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
source (CatalogSource) – the input catalog that we are viewing as a mesh
BoxSize – the size of the box
Nmesh (int, 3-vector) – the number of cells per mesh side
dtype (str) – the data type of the values stored on mesh
Weight (array_like, Column, None) – column that specifies the weight value for each particle in the
source
to use when griddingValue (array_like, Column, None) – column that specifies the field value for each particle; the mesh stores a weighted average of this column
Selection (array_like, Column, None) – column that selects the subset of particles to grid to the mesh
Position (array_like, Column, None) – column in
source
specifying the position coordinates; default isPosition
interlaced (bool, optional) – use the interlacing technique of Sefusatti et al. 2015 to reduce the effects of aliasing on Fourier space quantities computed from the mesh
compensated (bool, optional) – whether to correct for the window introduced by the grid interpolation scheme
window (str, optional) – the string specifying which window interpolation scheme to use; see
pmesh.window.methods
‘Weight’, ‘Value’, ‘Selection’, ‘Position’ are items of the collection that can be reassigned after the creation of the object.
- Attributes
actions
The actions to apply to the interpolated density field, optionally included the compensation correction.
attrs
A dictionary storing relevant meta-data 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.
interlaced
Whether to use interlacing when interpolating the density field.
resampler
String specifying the name of the interpolation kernel when gridding the density field.
- window
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
.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
- property 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 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.
- property 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.
- property 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
- property 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.
- 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(out=None, normalize=True)[source]¶
Paint the density field, by interpolating the position column on to the mesh.
This computes the following meta-data attributes in the process of painting, returned in the
attrs
attributes of the returned RealField object:- Nint
the (unweighted) total number of objects painted to the mesh
- Wfloat
the weighted number of total objects, equal to the collective sum of the ‘weight’ column
- shotnoisefloat
the Poisson shot noise, equal to the volume divided by
N
- num_per_cellfloat
the mean number of weighted objects per cell
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 meta-data- Return type
- 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.
- class nbodykit.source.mesh.FieldMesh(field)[source]¶
A MeshSource initialized from an in-memory Field object, either a
pmesh.pm.RealField
orpmesh.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 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.Return a copy of the (possibly re-sampled) input ComplexField
to_field
([mode, out])Return the mesh as a
pmesh
Field object, either in Fourier space or configuration space, based onmode
.Return a copy of the (possibly re-sampled) 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
- 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_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
- 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.
- class 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
Plin (callable) – the callable linear power spectrum function, which takes the wavenumber as its single argument
BoxSize (float, 3-vector of floats) – the size of the box to generate the grid on
Nmesh (int, 3-vector of int) – the number of the mesh cells per side
seed (int, optional) – the global random seed, used to set the seeds across all ranks
remove_variance (bool, optional) –
Deprecated since version 0.2.9: use
unitary_amplitude
insteadunitary_amplitude (bool, optional) –
True
to remove variance from the complex field by fixing the amplitude to \(P(k)\) and only the phase is random.inverted_phase (bool, optional) –
True
to invert phase of the complex field by fixing the amplitude to \(P(k)\) and only the phase is random.comm (MPI communicator) – the MPI communicator
- 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.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 onmode
.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)¶
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()[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 array-like 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 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(out=None, normalize=True)¶
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.
- class 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
source (CatalogSource) – the input catalog that we wish to interpolate to a mesh
BoxSize – the size of the box
Nmesh (int, 3-vector) – the number of cells per mesh side
dtype (str) – the data type of the values stored on mesh
weight (str) – column in
source
that specifies the weight value for each particle in thesource
to use when griddingvalue (str) – column in
source
that specifies the field value for each particle; the mesh stores a weighted average of this columnselection (str) – column in
source
that selects the subset of particles to gridposition (str, optional) – column in
source
specifying the position coordinates; default isPosition
- Attributes
actions
The actions to apply to the interpolated density field, optionally included the compensation correction.
attrs
A dictionary storing relevant meta-data 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.
interlaced
Whether to use interlacing when interpolating the density field.
resampler
String specifying the name of the interpolation kernel when gridding the density field.
- window
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
.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
- property 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 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.
- property 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.
- property 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
- property 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.
- 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(normalize=True)[source]¶
Paint the density field holding the sum of all particle species, returning a
RealField
object.Meta-data 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:\[P_\mathrm{shot} = \sum_i (W_i/W_\mathrm{tot})^2 P_{\mathrm{shot},i},\]where the sum is over all species in the catalog,
W_i
is the sum of theWeight
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 thenum_per_cell
meta-data value inattrs
- Returns
the RealField holding the painted density field, with a
attrs
dictionary attribute holding the meta-data- 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.