API Reference¶
Working with Merger Trees¶
The load
can load all supported
merger tree formats. Once loaded, the
save_arbor
and
save_tree
functions can be
used to save the entire arbor or individual trees.
load (filename[, method]) |
Load an Arbor, determine the type automatically. |
Arbor (filename) |
Base class for all Arbor classes. |
add_alias_field (alias, field[, units, force_add]) |
Add a field as an alias to another field. |
add_analysis_field (name, units[, dtype, default]) |
Add an empty field to be filled by analysis operations. |
add_derived_field (name, function[, units, …]) |
Add a field that is a function of other fields. |
add_vector_field (name) |
Add vector fields for a set of x,y,z component fields. |
save_arbor (**kwargs) |
Save the arbor to a file. |
select_halos (criteria[, trees, select_from, …]) |
Select halos from the arbor based on a set of criteria given as a string. |
set_selector (selector, *args, **kwargs) |
Sets the tree node selector to be used. |
TreeNode (uid[, arbor, root]) |
Class for objects stored in Arbors. |
get_leaf_nodes ([selector]) |
Get all leaf nodes from the tree of which this is the head. |
get_root_nodes () |
Get all root nodes from the forest to which this node belongs. |
get_node (selector, index) |
Get a single TreeNode from a tree. |
save_tree ([filename, fields]) |
Save the tree to a file. |
TreeNodeSelector (function[, args, kwargs]) |
The TreeNodeSelector is responsible for choosing which one of a halo’s ancestors to return when querying the line of main progenitors for a halo. |
TreeNodeSelector (function[, args, kwargs]) |
The TreeNodeSelector is responsible for choosing which one of a halo’s ancestors to return when querying the line of main progenitors for a halo. |
add_tree_node_selector (name, function) |
Add a TreeNodeSelector to the registry of known selectors, so they can be chosen with set_selector . |
max_field_value (ancestors, field) |
Return the TreeNode with the maximum value of the given field. |
min_field_value (ancestors, field) |
Return the TreeNode with the minimum value of the given field. |
get_yt_selection ([above, below, equal, …]) |
Get a selection of halos meeting given criteria. |
get_nodes_from_selection (container) |
Generate TreeNodes from a yt data container. |
ytds |
Load as a yt dataset. |
Visualizing Merger Trees¶
Functionality for plotting merger trees.
TreePlot (tree[, dot_kwargs, node_function, …]) |
Make a simple merger tree plot using pydot and graphviz. |
save ([filename]) |
Save the merger tree plot. |
Analysis Pipeline¶
Machinery for creating a pipeline of analysis to be run on halos in a merger tree.
AnalysisPipeline ([output_dir]) |
Initialize an AnalysisPipeline. |
add_operation (function, *args, **kwargs) |
Add an operation to the AnalysisPipeline. |
add_recipe (function, *args, **kwargs) |
Add a recipe to the AnalysisPipeline. |
process_target (target) |
Process a node through the AnalysisPipeline. |
AnalysisOperation (function, *args, **kwargs) |
An analysis task performed by an AnalysisPipeline. |
Parallelism¶
Functions for iterating over trees and/or nodes in parallel.
parallel_trees (trees[, save_every, …]) |
Iterate over a list of trees in parallel. |
parallel_tree_nodes (tree[, group, njobs, …]) |
Iterate over nodes in a single tree in parallel. |
parallel_nodes (trees[, group, save_every, …]) |
Iterate over all nodes in a list of trees in parallel. |
Internal Classes¶
Base Classes¶
All frontends inherit from these base classes for arbor, fields, and i/o.
Arbor (filename) |
Base class for all Arbor classes. |
SegmentedArbor (filename) |
Arbor subclass for multi-file datasets where an entire merger tree is contained within a file (i.e., no overlap). |
CatalogArbor (filename) |
Base class for Arbors created from a series of halo catalog files where the descendent ID for each halo has been pre-determined. |
Detector |
Base class for detecting field dependencies and testing operations. |
FieldDetector (arbor[, name]) |
A fake field data container used to calculate dependencies. |
SelectionDetector (arbor) |
A TreeNode-like object to test select_halos criteria. |
FieldInfoContainer (arbor) |
A container for information about fields. |
FieldContainer (arbor) |
A container for field data. |
FieldIO (arbor[, default_dtype]) |
Base class for FieldIO classes. |
TreeFieldIO (arbor[, default_dtype]) |
IO class for getting fields for a tree. |
DefaultRootFieldIO (arbor[, default_dtype]) |
Class for getting root fields from arbors that have no specialized storage for root fields. |
DataFile (filename) |
Base class for data files. |
CatalogDataFile (filename, arbor) |
Base class for halo catalog files. |
Arbor Subclasses¶
Arbor subclasses for each frontend.
AHFArbor (filename[, log_filename, …]) |
Arbor for Amiga Halo Finder data. |
ConsistentTreesArbor (filename) |
Arbors loaded from consistent-trees tree_*.dat files. |
ConsistentTreesGroupArbor (filename) |
Arbors loaded from consistent-trees locations.dat files. |
ConsistentTreesHlistArbor (filename) |
Class for Arbors created from consistent-trees hlist_*.list files. |
ConsistentTreesHDF5Arbor (filename[, access]) |
Arbors loaded from consistent-trees data converted into HDF5. |
LHaloTreeArbor (*args, **kwargs) |
Arbors for LHaloTree data. |
LHaloTreeHDF5Arbor (filename[, …]) |
Arbors loaded from consistent-trees data converted into HDF5. |
MoriaArbor (filename) |
Arbors from Moria merger trees. |
RockstarArbor (filename) |
Class for Arbors created from Rockstar out_*.list files. |
TreeFarmArbor (filename) |
Class for Arbors created with TreeFarm . |
YTreeArbor (filename) |
Class for Arbors created from the save_arbor or save_tree functions. |
FieldInfo Subclasses¶
Subclasses for frontend-specific field definitions.
AHFFieldInfo (arbor) |
|
ConsistentTreesFieldInfo (arbor) |
|
ConsistentTreesHDF5FieldInfo (arbor) |
|
LHaloTreeFieldInfo (arbor) |
|
LHaloTreeHDF5FieldInfo (arbor) |
|
MoriaFieldInfo (arbor) |
|
RockstarFieldInfo (arbor) |
|
TreeFarmFieldInfo (arbor) |
FieldIO Subclasses¶
Subclasses for data i/o from a whole dataset.
ConsistentTreesTreeFieldIO (arbor[, …]) |
|
ConsistentTreesHDF5TreeFieldIO (arbor[, …]) |
|
ConsistentTreesHDF5RootFieldIO (arbor[, …]) |
Read in fields for first node in all trees/forest. |
LHaloTreeTreeFieldIO (arbor[, default_dtype]) |
|
LHaloTreeRootFieldIO (arbor[, default_dtype]) |
|
LHaloTreeHDF5TreeFieldIO (arbor[, default_dtype]) |
|
MoriaTreeFieldIO (arbor[, default_dtype]) |
|
YTreeTreeFieldIO (arbor[, default_dtype]) |
|
YTreeRootFieldIO (arbor[, default_dtype]) |
DataFile Subclasses¶
Subclasses for data i/o from individual files.
AHFDataFile (filename, arbor) |
|
ConsistentTreesDataFile (filename) |
|
ConsistentTreesHlistDataFile (filename, arbor) |
|
ConsistentTreesHDF5DataFile (filename, linkname) |
|
LHaloTreeHDF5DataFile (filename, linkname) |
|
MoriaDataFile (filename) |
|
RockstarDataFile (filename, arbor) |
|
TreeFarmDataFile (filename, arbor) |
|
YTreeDataFile (filename) |