PyFJCore 1.0.1

Description:

PyFJCore 1.0.1

PyFJCore



PyFJCore is a Python wrapper of FastJet Core functionality with additional NumPy support. In contrast with the pyjet package, PyFJCore wraps all the methods/functions in fjcore and works with regular NumPy arrays instead of structured one. In contrast with the Python extension to the main FastJet library, this package can be built in a portable manner, including on Windows, and is available on PyPI.
Current version of fjcore: 3.4.0
Documentation
The FastJet documentation and manual contain helpful information for the classes and methods in PyFJCore. Not all FastJet classes are wrapped in PyFJCore, primarily just PseudoJet, JetDefinition, ClusterSequence, and Selector.
PseudoJet
Particles are represented in FastJet by PseudoJet objects. PseudoJets can be constructed from Cartesian momenta using the constructor, pyfjcore.PseudoJet(px, py, pz, e). They can be constructed from hadronic momenta as pyfjcore.PtYPhiM(pt, y, phi, [mass]), where the mass is optional and is taken to be zero if not present.
PseudoJets have a user index which is set to -1 by default. It can be set using the set_user_index(index) method and accessed with the user_index() method. An arbitrary Python object can also be associated with a PseudoJet using the set_python_info(pyobj) method, and accessed as python_info().
PseudoJetContainer
A PseudoJetContainer is useful for efficiently working with a list/vector of PseudoJets. In C++, it is a struct holding a std::vector<PseudoJet>, which allows the user to control SWIG's automatic coercion to/from native Python containers. Such coercion can be useful, but can also be inefficient since it requires a lot of copying. This coercion is still possible if desired by explicit tuple/list construction, e.g. tuple(pjcontainer) or list(pjcontainer). A PseudoJetContainer can be indexed, assigned to, or modified (by deleting elements) as if it were a list of PseudoJets. The wrapper code has been modified so that methods that accept const std::vector<PseudoJet> & will accept a PseudoJetContainer without any copying. The vector property can be used to access the underlying vectorPseudoJet (SWIG's wrapper of std::vector<fastjet::PseudoJet>) directly.
PseudoJetContainers con be constructed directly from an iterable of PseudoJets, or more commonly from NumPy arrays of particle kinematics (see the functions ptyphim_array_to_pseudojets, epxpypz_array_to_pseudojets, array_to_pseudojets below). Given a PseudoJetContainer, a NumPy array of the particle kinematics can be obtained using the methods ptyphim_array, epxpypz_array, and array, which correspond to the functions pseudojets_to_ptyphim_array, pseudojets_to_epxpypz_array, and pseudojets_to_array below. The user indices of the PseudoJets can be obtained as an integer NumPy array using the user_indices() method.
NumPy conversion functions
pyfjcore.ptyphim_array_to_pseudojets(ptyphims)

Converts a 2D array of particles, each as (pt, y, phi, [mass]), to PseudoJets (the mass is optional). Any additional features (columns after the initial four) of the array are set as the Python user info of the PseudoJets. This also sets the user_index of the PseudoJets to their position in the input array.
pyfjcore.epxpypz_array_to_pseudojets(epxpypzs)

Converts a 2D array of particles, each as (E, px, py, pz), to PseudoJets. Any additional features (columns after the initial four) of the array are set as the Python user info of the PseudoJets. This also sets the user_index of the PseudoJets to their position in the input array.
pyfjcore.array_to_pseudojets(particles, pjrep=pyfjcore.ptyphim)

Converts a 2D array of particles to PseudoJets. The format of the particles kinematics is determined by the pjrep argument. The PseudoJetRepresentation enum can take the values ptyphim, ptyphi, epxpypz. The first two values cause this function to invoke ptyphim_array_to_pseudojets and the third invokes epxpypz_array_to_pseudojets. Any additional features (columns) of the array are set as the Python user info of the PseudoJets. This also sets the user_index of the PseudoJets to their position in the input array.
pyfjcore.pseudojets_to_ptyphim_array(pseudojets, mass=True, phi_std=False, phi_ref=None, float32=False)

Converts a collection of PseudoJets (PseudoJetContainer or a Python iterable) to a 2D NumPy array of (pt, y, phi, [mass]) values, where the presence of the mass is determine by the keyword argument. phi_std determines if the phi values will be in the range [−π,π) or [0,2π). phi_ref, if not None, the phi values will lie within π of phi_ref. The float32 argument controls if the resulting array will be single-precision (can be useful to avoid extraneous copying, if 32-bit floats will be ultimately used).
pyfjcore.pseudojets_to_epxpypz_array(pseudojets, float32=False)

Converts a collection of PseudoJets (PseudoJetContainer or a Python iterable) to a 2D NumPy array of (E, px, py, pz) values. The float32 argument controls if the resulting array will be single-precision (can be useful to avoid extraneous copying, if 32-bit floats will be ultimately used).
pyfjcore.pseudojets_to_array(pseudojets, pjrep=pyfjcore.ptyphim, float32=False)

Converts a collection of PseudoJets (PseudoJetContainer or a Python iterable) to a 2D NumPy array of particles in the representation determined by the pjrep keyword argument (valid options are pyfjcore.ptyphim, pyfjcore.epxpypz, pyfjcore.ptyphi). The float32 argument controls if the resulting array will be single-precision (can be useful to avoid extraneous copying, if 32-bit floats will be ultimately used).
pyfjcore.user_indices(pseudojets)

Extracts the user indices from a collection of PseudoJets (PseudoJetContainer or a Python iterable) and returns them as a NumPy array of integers.
Version History
1.0.x
1.0.0

Restored PseudoJetContainer by explicitly overloading methods where const std::vector<PseudoJet> & is accepted as an argument. Methods that previously returned std::vector<PseudoJet> now return PseudoJetContainer.
EventGeometry and Piranha packages are now built using pyfjcore to provide basic FastJet classes.
fjcore.cc is compiled into a shared library that is linked into the Python extension.

0.4.x
0.4.0

Incompatibility with FastJet Python extension fixed by adding virtual methods to PseudoJet, PseudoJetStructureBase, CompositeJetStructure, and ClusterSequenceStructure that were removed in fjcore due to lack of area support.

0.3.x
0.3.0

Memory leak (and subsequent crash) detected in EnergyFlow testing of PyFJCore. Removing PseudoJetContainer for now.

0.2.x
0.2.1

Fixed typechecking so that PseudoJetContainer is accepted in overloaded functions such as Selector::operator().

0.2.0

Built against older NumPy properly; added pyproject.toml file.

0.1.x
0.1.2

Renamed some PseudoJetRepresentation constants.
Updated documentation.

0.1.1

Fixed several bugs, including an inability to pass a PseudoJetContainer to the ClusterSequence constructor due to SWIG's typechecking.

0.1.0

First version released on PyPI.

References
PyFJCore relies critically on the fjcore header and source files, which in turn are created from the main FastJet library. So if you use this package in your research, please cite the FastJet package and publications.
Summary of changes to fjcore

fjcore.hh

Changed namespace from fjcore to fastjet to facilitate interoperability with the FastJet Python extension.
Added back virtual methods to PseudoJet, PseudoJetStructureBase, CompositeJetStructure, and ClusterSequenceStructure that were removed in fjcore due to lack of area support. This is critical for ensuring compatibility with the FastJet Python extension.
Wrapped some code in IsBaseAndDerived that SWIG cannot parse with #ifndef SWIG_PREPROCESSOR and #endif. Since SWIG doesn't need this code for anything, it parses the file correctly without affecting the actual compilation.
Changed templated ClusterSequence constructor to an untemplated version using PseudoJet as the former template type.
Added methods that accept PseudoJetContainer anywhere that const std::vector<PseudoJet> & is an argument.



fjcore README
// fjcore -- extracted from FastJet v3.4.0 (http://fastjet.fr)
//
// fjcore constitutes a digest of the main FastJet functionality.
// The files fjcore.hh and fjcore.cc are meant to provide easy access to these
// core functions, in the form of single files and without the need of a full
// FastJet installation:
//
// g++ main.cc fjcore.cc
//
// with main.cc including fjcore.hh.
//
// A fortran interface, fjcorefortran.cc, is also provided. See the example
// and the Makefile for instructions.
//
// The results are expected to be identical to those obtained by linking to
// the full FastJet distribution.
//
// NOTE THAT, IN ORDER TO MAKE IT POSSIBLE FOR FJCORE AND THE FULL FASTJET
// TO COEXIST, THE FORMER USES THE "fjcore" NAMESPACE INSTEAD OF "fastjet".
//
// In particular, fjcore provides:
//
// - access to all native pp and ee algorithms, kt, anti-kt, C/A.
// For C/A, the NlnN method is available, while anti-kt and kt
// are limited to the N^2 one (still the fastest for N < 100k particles)
// - access to selectors, for implementing cuts and selections
// - access to all functionalities related to pseudojets (e.g. a jet's
// structure or user-defined information)
//
// Instead, it does NOT provide:
//
// - jet areas functionality
// - background estimation
// - access to other algorithms via plugins
// - interface to CGAL
// - fastjet tools, e.g. filters, taggers
//
// If these functionalities are needed, the full FastJet installation must be
// used. The code will be fully compatible, with the sole replacement of the
// header files and of the fjcore namespace with the fastjet one.
//
// fjcore.hh and fjcore.cc are not meant to be human-readable.
// For documentation, see the full FastJet manual and doxygen at http://fastjet.fr
//
// Like FastJet, fjcore is released under the terms of the GNU General Public
// License version 2 (GPLv2). If you use this code as part of work towards a
// scientific publication, whether directly or contained within another program
// (e.g. Delphes, MadGraph, SpartyJet, Rivet, LHC collaboration software frameworks,
// etc.), you should include a citation to
//
// EPJC72(2012)1896 [arXiv:1111.6097] (FastJet User Manual)
// and, optionally, Phys.Lett.B641 (2006) 57 [arXiv:hep-ph/0512210]
//
//FJSTARTHEADER
// $Id$
//
// Copyright (c) 2005-2021, Matteo Cacciari, Gavin P. Salam and Gregory Soyez
//
//----------------------------------------------------------------------
// This file is part of FastJet (fjcore).
//
// FastJet is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// The algorithms that underlie FastJet have required considerable
// development. They are described in the original FastJet paper,
// hep-ph/0512210 and in the manual, arXiv:1111.6097. If you use
// FastJet as part of work towards a scientific publication, please
// quote the version you use and include a citation to the manual and
// optionally also to hep-ph/0512210.
//
// FastJet is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with FastJet. If not, see <http://www.gnu.org/licenses/>.
//----------------------------------------------------------------------
//FJENDHEADER