HBTplus Python toolbox

Python module with helpers for analysis of dark matter haloes from HBTplus halo finder.

Usage

Makefile is used to document computation of targets for any given values of gravity, snapshot, f or density profile parameters. run.sh and submit.sh demonstrate sample calculation and submission to a batch queue.

Readers

  • HBTReader: general utility class, from HBTplus
  • HBTHistoryReader: provides an efficient collapsed mass history (CMH) calculation
  • HBTProfileReader: provides halo and subhalo density profile reader & calculation; does not perform fitting - this is done in src.process.prof()
  • HBTEnvironmentReader: calculates environmental proxies, as described in Haas+2012 and Shi+2017 (only $D_{N,f}$)

Modules

hbtp

HBTReader module.

Python module containing HBTReader class, used for analysis of HBT+ halo finder output.

Example:

class hbtp.ConfigReader(config_file)

Bases: object

Class to read the config files (i.e. Parameters.log).

class hbtp.HBTReader(subhalo_path)

Bases: object

Class to read the HBTPlus outputs.

To use it, initialize the reader with the directory in which Parameters.log is stored - it is written by HBT during runtime.

Parameters:subhalo_path (str) – directory with config files
GetExclusiveParticles(isnap=-1)

Loads an exclusive set of particles for subhaloes at isnap

Duplicate particles are assigned to the lowest mass subhaloes.

GetFileName(isnap, ifile=0, filetype='Sub')

Returns filename of an HBT snapshot

Parameters:
  • isnap (int) – snapshot of the file
  • ifile (int) – (default=0) index for sub-snapshots
  • filetype (str) – (default=’Sub’) ‘Src’, ‘Sub’ or ‘HaloSize’
Returns:

HBT snaphost filename
Return type:

(str)
GetHostHalo(HostHaloId, isnap=-1)

Returns spatial information of a specific FoF group.

Parameters:
  • HostHaloId (int) – host halo id
  • isnap (int) – snapshot number
Returns:

(numpy.ndarray) single FoF group in a structured array
GetHostMergerTree(HostHaloId, isnap=-1, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)

Builds a FoF merger tree starting at a host halo ID.

Prints a graph which can be consumed by [Dot](graphviz.org] software.

Parameters:
  • HostHaloId (int) – a halo at which to root a tree
  • isnap (int) – (default = -1) snapshot number
  • file (File) – (default=sys.stdout) default output for a Dot diagram
Returns:

multiply embedded list with a tree, i.e. [1, [2, 3]]
Return type:

(list)
GetNumberOfSubhalos(isnap=-1)

Retunrs number of subhaloes in a snapshot.

Parameters:isnap (int) – (default = -1) snapshot number
GetParticleProperties(subindex, isnap=-1)

Returns subhalo particle properties for subhalo with index subindex.

Values are returned in the order they appear in the file, subindex==trackId for single file output (but not for mpi multiple-file outputs)

GetProgenitorHaloes(HostHaloId, isnap=-1)

Returns progenitors of a given host halo.

Given a HostHaloId and a snapshot number, it finds all subhaloes within the host, follows their track ids to the previous snapshot, checks if they are the main / central subhalo (by Rank values), finds those subhaloes’ hosts and keeps the unique IDs. Filtering by Rank is necessary to remove fly-by and re-merger events.

Parameters:
  • HostHaloId (int) – host halo id
  • isnap (int) – (default=-1) snapshot number
Returns:

array of host halo ids of progenitors
Return type:

(numpy.ndarray)
GetScaleFactor(isnap)

Reads scale factor at a given snapshot.

GetScaleFactorDict()

Returns a dictionary that maps snapshot_index to ScaleFactor.

GetSub(trackId, isnap=-1)

Loads a subhalo with the given trackId at snapshot isnap.

GetSubsOfHost(HostHaloId, isnap=-1)

Loads all subhaloes belonging to a host halo.

Uses information from Membership/GroupedTrackIds.

Parameters:
  • HostHaloId (int) – row number
  • isnap (int) – (default = -1)
Returns:

array of TrackIds, or empty array if FoF does

not host subhalos
Return type:

(numpy.ndarray)
GetTrack(trackId, fields=None, MaxSnap=None)

Loads an entire track of the given trackId.

LoadHostHalos(isnap=-1, selection=None)

Returns spatial properties of FoF groups for a snapshot.

Parameters:
  • isnap (int) – snapshot number
  • selection (tuple) – (default = None) selection query being passed on
  • HBT file (to) –
Returns:

(numpy.ndarray) host haloes matching the selection
LoadNestedSubhalos(isnap=-1, selection=None)

Load the list of nested subhalo indices for each subhalo

Parameters:isnap (int) – (default = -1) snapshot number
Returns:array of nested indices
Return type:(numpy.ndarray)
LoadParticles(isnap=-1, subindex=None, filetype='Sub')

Loads subhalo particle list at snapshot

If subindex is given, only load subhalo of the given index (the order it appears in the file, subindex==trackId for single file output, but not for mpi multiple-file outputs). Otherwise loads all the subhaloes.

Default filetype (Sub) will load subhalo particles. Filetype Src loads source subhalo particles instead (for debugging purpose only).

Parameters:
  • isnap (int) – (default=-1) snapshot number
  • subindex (int) – (default=None) index of a subhalo
  • filetype (str) – (default=’Sub’) HBT file type
LoadSubhalos(isnap=-1, selection=None, show_progress=False)

Load all subhaloes from a snapshot.

Note

selection=('Rank', 'Nbound') will load only the Rank and Nbound fields of subhaloes; selection=3 will only load subhalo with subindex 3; default will load all fields of all subhaloes. You can also use numpy slice for selection, e.g. selection=np.s_[:10, 'Rank','HostHaloId'] will select the Rank and HostHaloId of the first 10 subhaloes. You can also specify multiple subhaloes by passing a list of (ordered) subindex, e.g., selection=((1,2,3),). However, currently only a single subhalo can be specified for multiple-file HBT data (not restricted for single-file data).

Note

Subindex specifies the order of the subhalo in the file at the current snapshot, i.e., subhalo=AllSubhalo[subindex]. subindex == trackId for single file output, but subindex != trackId for mpi multiple-file outputs.

Parameters:
  • isnap (int) – (default = -1) snapshot
  • selection (numpy.s_) – (default = None) can be a single field, a list of the field names or a single subhalo index
  • show_progress (bool) – (default = False)
OpenFile(isnap, ifile=0, filetype='Sub', mode='r')

Opens HDF5 file.

Parameters:
  • isnap (int) – snapshot of the file
  • ifile (int) – (default=0) index for sub-snapshots
  • filetype (str) – (default=’Sub’) ‘Src’, ‘Sub’ or ‘HaloSize’
  • mode (chr) – (default=’r’) file handle mode
Returns:

HDF5 HBT file handle
Return type:

(File)
Snapshots()
hbtp.PeriodicDistance(x, y, BoxSize, axis=-1)
hbtp.distance(x, y, axis=-1)
hbtp.get_hbt_snapnum(snapname)

Extracts snapshot number from a filename.

Parameters:snapname (str) – name of snapshot file
Returns:snapshot number
Return type:(int)

src.cmh

src.mt

src.mt.main(grav, snap, host)

Construct & output merger tree

Parameters:
  • grav (str) – Gravity (GR_b64n512 or fr6_b64n512)
  • snap (int) – Snapshot number (between 122 and 10)
  • host (int) – Host halo ID

src.process

src.query

src.query.main(grav, snap, min_part_num=1000)

Query & filter halo IDs.

Parameters:
  • grav (str) – Gravity (GR_b64n512 or fr6_b64n512)
  • snap (int) – Snapshot number (between 122 and 9)
  • min_part_num (int) – Minimum number of particles

src.read

src.read.cmh(grav, snap, f=0.02)
src.read.ids(grav, snap, prefix='ids')
src.read.snaps()

src.split_by_Dnf

src.split_by_Dnf.bin(data, by, nbins)
src.split_by_Dnf.main(grav, snap)

Split halo ids into 2 groups, below and above percentile range in log10(D_Nf).

Parameters:
  • grav (str) – Gravity (GR_b64n512 or fr6_b64n512)
  • snap (int) – Snapshot number (between 122 and 9)