TreeCorr 5.1.2
Python module for computing 2-point correlation functions
License: BSD License

.. image:: https://travis-ci.org/rmjarvis/TreeCorr.svg?branch=main
        :target: https://travis-ci.org/rmjarvis/TreeCorr
.. image:: https://codecov.io/gh/rmjarvis/TreeCorr/branch/main/graph/badge.svg
        :target: https://codecov.io/gh/rmjarvis/TreeCorr

TreeCorr is a package for efficiently computing 2-point and 3-point correlation
functions.

- The code is hosted at https://github.com/rmjarvis/TreeCorr
- It can compute correlations of regular number counts, weak lensing shears, or
  scalar quantities such as convergence or CMB temperature fluctutations.
- 2-point correlations may be auto-correlations or cross-correlations.  This
  includes shear-shear, count-shear, count-count, kappa-kappa, etc.  (Any
  combination of shear, kappa, and counts.)
- 3-point correlations currently can only be auto-correlations.  This includes
  shear-shear-shear, count-count-count, and kappa-kappa-kappa.  The cross
  varieties are planned to be added in the near future.
- Both 2- and 3-point functions can be done with the correct curved-sky
  calculation using RA, Dec coordinates, on a Euclidean tangent plane, or in
  3D using either (RA,Dec,r) or (x,y,z) positions.
- The front end is in Python, which can be used as a Python module or as a
  standalone executable using configuration files. (The executable is corr2
  for 2-point and corr3 for 3-point.)
- The actual computation of the correlation functions is done in C++ using ball
  trees (similar to kd trees), which make the calculation extremely efficient.
- When available, OpenMP is used to run in parallel on multi-core machines.
- Approximate running time for 2-point shear-shear is ~30 sec * (N/10^6) / core
  for a bin size b=0.1 in log(r).  It scales as b^(-2).  This is the slowest
  of the various kinds of 2-point correlations, so others will be a bit faster,
  but with the same scaling with N and b.
- The running time for 3-point functions are highly variable depending on the
  range of triangle geometries you are calculating.  They are significantly
  slower than the 2-point functions, but many orders of magnitude faster than
  brute force algorithms.
- **If you use TreeCorr in published research, please reference:
  Jarvis, Bernstein, & Jain, 2004, MNRAS, 352, 338**
  (I'm working on new paper about TreeCorr, including some of the improvements
  I've made since then, but this will suffice as a reference for now.)
- If you use the three-point multipole functionality of TreeCorr, please also
  reference **Porth et al, 2023, arXiv:2309.08601**
- Record on the Astrophyics Source Code Library: http://ascl.net/1508.007
- Developed by Mike Jarvis.  Fee free to contact me with questions or comments
  at mikejarvis17 at gmail.  Or post an issue (see below) if you have any
  problems with the code.

The code is licensed under a FreeBSD license.  Essentially, you can use the
code in any way you want, but if you distribute it, you need to include the
file ``TreeCorr_LICENSE`` with the distribution.  See that file for details.


Installation
------------

The easiest ways to install TreeCorr are either with pip::

    pip install treecorr

or with conda::

    conda install -c conda-forge treecorr

If you have previously installed TreeCorr, and want to upgrade to a new
released version, you should do::

    pip install treecorr --upgrade

or::

    conda update -c conda-forge treecorr

Depending on the write permissions of the python distribution for your specific
system, you might need to use one of the following variants for pip installation::

    sudo pip install treecorr
    pip install treecorr --user

The latter installs the Python module into ``~/.local/lib/python3.X/site-packages``,
which is normally already in your PYTHONPATH, but it puts the executables
``corr2`` and ``corr3`` into ``~/.local/bin`` which is probably not in your PATH.
To use these scripts, you should add this directory to your PATH.  If you would
rather install into a different prefix rather than ~/.local, you can use::

    pip install treecorr --install-option="--prefix=PREFIX"

This would install the executables into ``PREFIX/bin`` and the Python module
into ``PREFIX/lib/python3.X/site-packages``.


If you would rather download the tarball and install TreeCorr yourself,
that is also relatively straightforward:

1. Download TreeCorr
^^^^^^^^^^^^^^^^^^^^

   You can download the latest tarball from::

        https://github.com/rmjarvis/TreeCorr/releases/

   Or you can clone the repository using either of the following::

        git clone git@github.com:rmjarvis/TreeCorr.git
        git clone https://github.com/rmjarvis/TreeCorr.git

   which will start out in the current stable release branch.

   Either way, cd into the TreeCorr directory.

2. Install dependencies
^^^^^^^^^^^^^^^^^^^^^^^

   All required dependencies should be installed automatically for you by
   pip or conda, so you should not need to worry about these.  But if you
   are interested, the dependencies are:

    - numpy
    - pyyaml
    - LSSTDESC.Coord
    - pybind11

   They can all be installed at once by running::

        pip install -r requirements.txt

   or::

        conda install -c conda-forge treecorr --only-deps

   .. note::

        Several additional modules are not required for basic TreeCorr operations, but are
        potentially useful.

        - fitsio is required for reading FITS catalogs or writing to FITS output files.
        - pandas will signficantly speed up reading from ASCII catalogs.
        - pandas and pyarrow are required for reading Parquet files.
        - h5py is required for reading HDF5 catalogs.
        - mpi4py is required for running TreeCorr across multiple machines using MPI.

        These are all pip installable::

            pip install fitsio
            pip install pandas
            pip install pyarrow
            pip install h5py
            pip install mpi4py

        But they are not installed with TreeCorr automatically.

        Also, beware that many HPC machines (e.g. NERSC) have special instructions for installing
        mpi4py, so the above command may not work on such systems.  If you have trouble, look
        for specialized instructions about how to install mpi4py properly on your system.


3. Install
^^^^^^^^^^

   You can then install TreeCorr from the local distribution.  Typically this would be the
   command::

        pip install .

   If you don't have write permission in your python distribution, you might need
   to use::

        pip install . --user

   In addition to installing the Python module ``treecorr``, this will install
   the executables ``corr2`` and ``corr3`` in a ``bin`` folder somewhere on your
   system.  Look for a line like::

        Installing corr2 script to /anaconda3/bin

   or similar in the output to see where the scripts are installed.  If the
   directory is not in your path, you will also get a warning message at the
   end letting you know which directory you should add to your path if you want
   to run these scripts.


4. Run Tests (optional)
^^^^^^^^^^^^^^^^^^^^^^^

   If you want to run the unit tests, you can do the following::

        pip install -r test_requirements.txt
        cd tests
        pytest


Two-point Correlations
----------------------

This software is able to compute a variety of two-point correlations:

:NN:  The normal two-point correlation function of number counts (typically
      galaxy counts).

:GG:  Two-point shear-shear correlation function.

:KK:  Nominally the two-point kappa-kappa correlation function, although any
      scalar quantity can be used as "kappa".  In lensing, kappa is the
      convergence, but this could be used for temperature, size, etc.

:NG:  Cross-correlation of counts with shear.  This is what is often called
      galaxy-galaxy lensing.

:NK:  Cross-correlation of counts with kappa.  Again, "kappa" here can be any scalar
      quantity.

:KG:  Cross-correlation of convergence with shear.  Like the NG calculation, but
      weighting the pairs by the kappa values the foreground points.

There are also additional combinations involving complex fields with different spin
than 2 (shear is a spin-2 field).  See `Two-point Correlation Functions
<https://rmjarvis.github.io/TreeCorr/_build/html/correlation2.html>`_ for more details.

Three-point Correlations
------------------------

Three point correlation functions are significantly more complicated, being functions
of three parameters defining the triangle size and shape, rather than just a single
separation.  For cross-correlations, there are also issues related to whether one wants
to allow the different catalogs to take all possible vertices in the triangles are be
fixed to a particular vertex.

This software is able to compute the following three-point auto-correlations:

:NNN: Three-point correlation function of number counts.

:GGG: Three-point shear correlation function.  We use the "natural components"
      called Gamma, described by Schneider & Lombardi (2003) (Astron.Astrophys.
      397, 809) using the triangle centroid as the reference point.

:KKK: Three-point kappa correlation function.  Again, "kappa" here can be any
      scalar quantity.

It is also possible to compute cross correlations combining two of these types, such
as NNG, NKK, KGK, etc..  The ordering of the letters indicates which type is placed
at which numbered vertex in the triangles where the first vertex is opposite d1, the
second opposite d2, and the third opposite d3.  The meaning of the three side lengths
is particular to the choice of binning.

See `Three-point Correlation Functions
<https://rmjarvis.github.io/TreeCorr/_build/html/correlation3.html>`_ for more details.

Running corr2 and corr3
-----------------------

The executables corr2 and corr3 each take one required command-line argument,
which is the name of a configuration file::

    corr2 config_file
    corr3 config_file

A sample configuration file for corr2 is provided, called sample.params.
See `Configuration Parameters <https://rmjarvis.github.io/TreeCorr/_build/html/params.html>`_
for the complete documentation about the allowed parameters.

You can also specify parameters on the command line after the name of
the configuration file. e.g.::

    corr2 config_file file_name=file1.dat gg_file_name=file1.out
    corr2 config_file file_name=file2.dat gg_file_name=file2.out
    ...

This can be useful when running the program from a script for lots of input
files.

See `Using configuration files <https://rmjarvis.github.io/TreeCorr/_build/html/scripts.html>`_
for more details.

Using the Python module
-----------------------

The typical usage in python is in three stages:

1. Define one or more Catalogs with the input data to be correlated.
2. Define the correlation function that you want to perform on those data.
3. Run the correlation by calling ``process``.
4. Maybe write the results to a file or use them in some way.

For instance, computing a shear-shear correlation from an input file stored
in a fits file would look something like the following::

    >>> import treecorr
    >>> cat = treecorr.Catalog('cat.fits', ra_col='RA', dec_col='DEC',
    ...                        ra_units='degrees', dec_units='degrees',
    ...                        g1_col='GAMMA1', g2_col='GAMMA2')
    >>> gg = treecorr.GGCorrelation(min_sep=1., max_sep=100., bin_size=0.1,
    ...                             sep_units='arcmin')
    >>> gg.process(cat)
    >>> xip = gg.xip  # The xi_plus correlation function
    >>> xim = gg.xim  # The xi_minus correlation function
    >>> gg.write('gg.out')  # Write results to a file

For more details, see our slightly longer `Getting Started Guide
<https://rmjarvis.github.io/TreeCorr/_build/html/guide.html>`_.

Or for a more involved worked example, see our `Jupyter notebook tutorial
<https://github.com/rmjarvis/TreeCorr/blob/main/tests/Tutorial.ipynb>`_.

And for the complete details about all aspects of the code, see the `Sphinx-generated
documentation <http://rmjarvis.github.io/TreeCorr>`_.


Reporting bugs
--------------

If you find a bug running the code, please report it at:

https://github.com/rmjarvis/TreeCorr/issues

Click "New Issue", which will open up a form for you to fill in with the
details of the problem you are having.


Requesting features
-------------------

If you would like to request a new feature, do the same thing.  Open a new
issue and fill in the details of the feature you would like added to TreeCorr.
Or if there is already an issue for your desired feature, please add to the
discussion, describing your use case.  The more people who say they want a
feature, the more likely I am to get around to it sooner than later.