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TreeCorr 3.3.7

Python module for computing 2-point correlation functions

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.)
  • 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 way to install TreeCorr is with pip:

sudo pip install TreeCorr

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

sudo pip install TreeCorr --upgrade

To install TreeCorr on a system where you do not have sudo privileges, you can do:

pip install TreeCorr --user

This installs the Python module into ~/.local/lib/python2.7/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/python2.7/site-packages.

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

  1. Dependencies: All dependencies should be installed automatically for you by setup.py, so you should not need to worry about these. But if you are interested, the dependencies are:

    • numpy
    • future
    • fitsio
    • pandas
    • pyyaml
    • cffi

    The last dependency is the only one that typically could cause any problems, since it in turn depends on a library called libffi. This is a common thing to have installed already on linux machines, so it is likely that you won’t have any trouble with it, but if you get errors about “ffi.h” not being found, then you may need to either install it yourself or update your paths to include the directory where ffi.h is found.

    1. Installing libffi on linux systems:

      If you have root access on your system, then one of the following should work to install libffi:

      apt-get install libffi-dev
      yum install libffi-devel
      
    2. Installing libffi on Mac systems:

      It should be installed as part of the XCode libraries after running:

      xcode-select --install
      
    3. Installing libffi manually:

      If neither of the above methods works for you, you can install it yourself with the following commands:

      wget ftp://sourceware.org:/pub/libffi/libffi-3.2.1.tar.gz
      tar xfz libffi-3.2.1.tar.gz
      cd libffi-3.2.1
      ./configure --prefix={prefix}
      make
      make install
      cp */include/ffi*.h {prefix}/include
      cd ..
      

      where {prefix} is wherever you want the code to be installed. e.g. /home/username.

    4. Updating your system paths:

      If you used option (c) above and {prefix} is not /usr/local or similar, then you might need to update some system paths to let the compiler know where to look for the header file and library. Similarly, if libffi was already installed, but it is in a non-standard location where gcc doesn’t look by default, then this also applies. (Try locate ffi.h to see if it shows up somewhere.)

      Assuming ffi.h is in {prefix}/include/ffi/ and libffi.so (or libffi.dylib on Macs) is in {prefix}/lib/, then the following commands should be put in your .bashrc or .bash_profile file:

      export C_INCLUDE_PATH=$C_INCLUDE_PATH:{prefix}/include
      export LIBRARY_PATH=$LIBRARY_PATH:{prefix}/lib
      export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:{prefix}/lib
      

      Or if you use C shell, put the following in .cshrc or equivalent file:

      setenv C_INCLUDE_PATH "$C_INCLUDE_PATH":{prefix}/include
      setenv LIBRARY_PATH "$LIBRARY_PATH":{prefix}/lib
      setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":{prefix}/lib
      
  2. Download the zip file or tarball for the latest release from:

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

  3. Unzip the archive with either of the following (depending on which kind of archive you downloaded):

    unzip TreeCorr-3.3.7.zip
    tar xvzf TreeCorr-3.3.7.tar.gz
    

    It will unzip into the directory TreeCorr-3.3.7. Change to that directory:

    cd TreeCorr-3.3.7
    
  4. Install with the normal setup.py options. Typically this would be the command:

    python setup.py install --prefix=~
    

    This will install the executable corr2 at:

    /your/home/directory/bin/corr2
    

    It will also install the Python module called treecorr which you can use from within Python.

    Note

    There is a bug with numpy that it sometimes doesn’t install correctly when included as a setup.py dependency:

    https://github.com/numpy/numpy/issues/1458

    The bug was marked closed in 2012, but I’ve gotten it with numpy versions since then. Installation failed with a traceback that ended with:

    File "/private/tmp/easy_install-xl4gri/numpy-1.8.2/numpy/core/setup.py", line 631, in configuration
    
    AttributeError: 'Configuration' object has no attribute 'add_define_macros'
    

    The workaround if this happens for you seems to be to install numpy separately with:

    easy_install numpy
    

    Then the normal TreeCorr installation should work correctly.

  5. (optional) If you want to run the unit tests, you can do the following:

    cd tests
    nosetests
    

Two-point Correlations

This software is able to compute several varieties 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.

Three-point Correlations

This software is currently only able to compute 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 [Astron.Astrophys. 397 (2003) 809-818] using the triangle centroid as the reference point.
KKK:Three-point kappa correlation function. Again, “kappa” here can be any scalar quantity.

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 the TreeCorr wiki page

https://github.com/rmjarvis/TreeCorr/wiki/Configuration-Parameters

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.

Using the Python module

Here we only give a quick overview. A Jupyter notebook tutorial here:

https://github.com/rmjarvis/TreeCorr/blob/master/tests/Tutorial.ipynb

goes into more detail. And full Sphinx-generated documentation can be found at:

http://rmjarvis.github.io/TreeCorr/html/index.html

The TreeCorr module is called treecorr in Python. Typical usage for computing the shear-shear correlation function looks 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

The different correlation functions each have their own class. You can access the Python documentation by calling help on the appropriate class to get more details about the different kwarg options, attributes, and methods for each:

>>> help(NNCorrelation)
>>> help(GGCorrelation)
>>> help(KKCorrelation)
>>> help(NGCorrelation)
>>> help(NKCorrelation)
>>> help(KGCorrelation)
>>> help(NNNCorrelation)
>>> help(GGGCorrelation)
>>> help(KKKCorrelation)

You can also leverage the configuration file apparatus from within Python using a Python dict for the configuration parameters:

>>> import treecorr
>>> config = treecorr.read_config(config_file)
>>> config['file_name'] = 'file1.dat'
>>> config['gg_file_name'] = 'file1.out'
>>> treecorr.corr2(config)
>>> config['file_name'] = 'file2.dat'
>>> config['gg_file_name'] = 'file2.out'
>>> treecorr.corr2(config)

However, the Python module gives you much more flexibility in how to specify the input and output, including going directly from and to numpy arrays within Python. For a slightly longer “Getting Started” guide see the wiki page:

https://github.com/rmjarvis/TreeCorr/wiki/Guide-to-using-TreeCorr-in-Python

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.

 
File Type Py Version Uploaded on Size
TreeCorr-3.3.7.tar.gz (md5) Source 2017-04-12 418KB