pyjet
Advanced tools
:warning:pyjet is deprecated, largely unmaintained, and superseded:warning:
pyjet has been maintained minimalistically over the past couple of years. In the meantime a new project started, to provide a modern Pythonic jet-finding package in the Scikit-HEP ecosystem.
fastjet provides official FastJet bindings to Python and Awkward Array.
Refer to the GitHub repository for details. <https://github.com/scikit-hep/fastjet>_
.. image:: https://img.shields.io/pypi/v/pyjet.svg :target: https://pypi.python.org/pypi/pyjet :alt: PyPI version
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1197493.svg :target: https://doi.org/10.5281/zenodo.1197493 :alt: Zenodo link
.. image:: https://github.com/scikit-hep/pyjet/workflows/Main/badge.svg?branch=master :target: https://github.com/scikit-hep/pyjet/actions :alt: Test status
.. image:: https://dev.azure.com/scikit-hep/pyjet/_apis/build/status/scikit-hep.pyjet?branchName=master :target: https://dev.azure.com/scikit-hep/pyjet/_build/latest?definitionId=8&branchName=master :alt: Wheel builds
.. image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/scikit-hep/pyjet/master?urlpath=lab/tree/notebooks/PyjetDemo.ipynb :alt: Binder
pyjet allows you to perform jet clustering with FastJet <http://fastjet.fr/>_
on NumPy <http://www.numpy.org/>_ arrays. By default pyjet only depends on
NumPy and internally uses FastJet's standalone fjcore release. The interface
code is written in Cython <http://cython.org/>_ that then becomes compiled
C++, so it's fast. Remember that if you use pyjet then you are using FastJet
and should cite the papers listed here <http://fastjet.fr/about.html>_.
Python <http://docs.python-guide.org/en/latest/starting/installation/>__ (3.7+)Numpy <https://scipy.org/install.html>__pyjet provides the cluster() function that takes a NumPy array as input
and returns a ClusterSequence from which you can access the jets:
.. code-block:: python
from pyjet import cluster from pyjet.testdata import get_event
vectors = get_event() sequence = cluster(vectors, R=1.0, p=-1) jets = sequence.inclusive_jets() # list of PseudoJets exclusivejets = sequence.exclusive_jets(3) # Find the cluster history when there are 3 jets
The input is given in the form of a structured array <https://docs.scipy.org/doc/numpy/user/basics.rec.html>_ in numpy. The first four fields of the input array vectors must be either:
.. code-block:: python
np.dtype([('pT', 'f8'), ('eta', 'f8'), ('phi', 'f8'), ('mass', 'f8')])
or if cluster(..., ep=True):
.. code-block:: python
np.dtype([('E', 'f8'), ('px', 'f8'), ('py', 'f8'), ('pz', 'f8')])
Note that the field names of the input array need not match 'pT', 'eta', 'phi',
'mass' etc. pyjet only assumes that the first four fields are those quantities.
This array may also have additional fields of any type. Additional fields will
then become attributes of the PseudoJet objects.
See the examples <https://github.com/scikit-hep/pyjet/tree/master/examples>_ to
get started:
.. image:: https://github.com/scikit-hep/pyjet/raw/master/examples/jet_areas.png
To simply use the built-in FastJet source, from your virtual environment, run::
python -m pip install pyjet
And you're good to go! If you have a old version of pip (<10), you will need to have Cython and Numpy already installed to build from source - however on most systems, you should get a binary wheel.
Get example.py and run it::
curl -O https://raw.githubusercontent.com/scikit-hep/pyjet/master/examples/example.py
python example.py
jet# pT eta phi mass #constit.
1 983.280 -0.868 2.905 36.457 34
2 901.745 0.221 -0.252 51.850 34
3 67.994 -1.194 -0.200 11.984 32
4 12.465 0.433 0.673 5.461 13
5 6.568 -2.629 1.133 2.099 9
6 6.498 -1.828 -2.248 3.309 6
The 6th jet has the following constituents:
PseudoJet(pt=0.096, eta=-2.166, phi=-2.271, mass=0.000)
PseudoJet(pt=2.200, eta=-1.747, phi=-1.972, mass=0.140)
PseudoJet(pt=1.713, eta=-2.037, phi=-2.469, mass=0.940)
PseudoJet(pt=0.263, eta=-1.682, phi=-2.564, mass=0.140)
PseudoJet(pt=1.478, eta=-1.738, phi=-2.343, mass=0.940)
PseudoJet(pt=0.894, eta=-1.527, phi=-2.250, mass=0.140)
Get the constituents as an array (pT, eta, phi, mass):
[( 0.09551261, -2.16560157, -2.27109083, 4.89091390e-06)
( 2.19975694, -1.74672746, -1.97178728, 1.39570000e-01)
( 1.71301882, -2.03656511, -2.46861524, 9.39570000e-01)
( 0.26339374, -1.68243005, -2.56397904, 1.39570000e-01)
( 1.47781519, -1.7378898 , -2.34304346, 9.39570000e-01)
( 0.89353864, -1.52729244, -2.24973202, 1.39570000e-01)]
or (E, px, py, pz):
[( 0.42190436, -0.06155242, -0.07303395, -0.41095089)
( 6.50193926, -0.85863306, -2.02526044, -6.11692764)
( 6.74203628, -1.33952806, -1.06775374, -6.45273802)
( 0.74600384, -0.22066287, -0.1438199 , -0.68386087)
( 4.43164941, -1.0311407 , -1.05862485, -4.07096881)
( 2.15920027, -0.56111108, -0.69538886, -1.96067711)]
Reclustering the constituents of the hardest jet with the kt algorithm
[PseudoJet(pt=983.280, eta=-0.868, phi=2.905, mass=36.457)]
Go back in the clustering sequence to when there were two jets
PseudoJet(pt=946.493, eta=-0.870, phi=2.908, mass=20.117)
PseudoJet(pt=36.921, eta=-0.800, phi=2.821, mass=4.119)
Ask how many jets there are with a given dcut
There are 9 jets with a dcut of 0.5
Get the jets with the given dcut
1 PseudoJet(pt=308.478, eta=-0.865, phi=2.908, mass=2.119)
2 PseudoJet(pt=256.731, eta=-0.868, phi=2.906, mass=0.140)
3 PseudoJet(pt=142.326, eta=-0.886, phi=2.912, mass=0.829)
4 PseudoJet(pt=135.971, eta=-0.870, phi=2.910, mass=0.140)
5 PseudoJet(pt=91.084, eta=-0.864, phi=2.899, mass=1.530)
6 PseudoJet(pt=30.970, eta=-0.831, phi=2.822, mass=2.124)
7 PseudoJet(pt=7.123, eta=-0.954, phi=2.939, mass=1.017)
8 PseudoJet(pt=5.951, eta=-0.626, phi=2.818, mass=0.748)
9 PseudoJet(pt=4.829, eta=-0.812, phi=3.037, mass=0.384)
To take advantage of the full FastJet library, including the jet area
calculations and the optimized O(NlnN) kt and anti-kt algorithms,
you can first build and install FastJet and then install
pyjet with the --external-fastjet flag. Before building FastJet you will
need to install CGAL <http://www.cgal.org/>_ and GMP <https://gmplib.org/>_.
On a Debian-based system (Ubuntu)::
sudo apt-get install libcgal-dev libcgal11v5 libgmp-dev libgmp10
On an RPM-based system (Fedora)::
sudo dnf install gmp.x86_64 gmp-devel.x86_64 CGAL.x86_64 CGAL-devel.x86_64
On Mac OS::
brew install cgal gmp wget
Then run pyjet's install-fastjet.sh script::
curl -O https://raw.githubusercontent.com/scikit-hep/pyjet/master/install-fastjet.sh chmod +x install-fastjet.sh sudo ./install-fastjet.sh
Now install pyjet like::
python -m pip install numpy Cython python setup.py install --external-fastjet
pyjet will now use the external FastJet installation on your system.
The package is indifferent to particular units, which are merely "propagated"
through the code. We do recommend that the HEP units be used, as defined
in the units module of the hepunits package <https://github.com/scikit-hep/hepunits>_.
It is worth noting that the azimuthal angle phi is expressed in radians and varies from pi to pi.
If you want to setup for development::
python3 -m venv .env source .env/bin/activate pip install -e .[dev] pytest
FAQs
The interface between FastJet and NumPy
We found that pyjet demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 3 open source maintainers collaborating on the project.
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