Library for pseudo-Cl computation
NaMaster is a C library, Python module and standalone program to compute full-sky angular cross-power spectra of masked, spin-0 and spin-2 fields with an arbitrary number of known contaminants using a pseudo-Cl (aka MASTER) approach. The code also implements E/B-mode purification and is available in both full-sky and flat-sky modes.
There are different ways to install NaMaster. In rough order of complexity, they are:
Unless you care about optimizing the code, it's worth giving this one a go. The conda recipe for NaMaster is currently hosted on conda-forge (infinite kudos to Mat Becker for this). In this case, installing NaMaster means simply running:
conda install -c conda-forge namaster
If that works for you and you don't care about optimizing the code too much, skip the rest of this section. If you don't have admin permissions, you can give virtual environments a try (or else follow the instructions below).
NaMaster is also hosted on PyPI. Installing it should be as simple as running:
python -m pip install pymaster [--user]
--user if you don't have admin permissions). Note that this will compile the code on your machine, so you'll need to have installed its dependencies.
If all the above fail, try to install NaMaster from its source. You should first clone this github repository. Then follow these steps:
1. Install dependencies.
Install the dependencies listed here. Note that some of them (libsharp and HEALPix) may not be necessary, as pymaster will attempt to install them automatically.
2. Install the python module
Installing the python module
pymaster should be as simple as running
python setup.py install [--user]
or, even better, if you can use
pip install . [--user]
where the optional
--user flag can be used if you don't have admin privileges.
You can check that the python installation works by running the unit tests:
python -m unittest discover -v
Note that the
test directory, containing all unit tests, also contains all the sample python scripts described in the documentation.
If you installed
pip, you can uninstall everything by running
pip uninstall pymaster
Note that the C library is automatically compiled when installing the python module. If you care about the C library at all, or you have trouble compiling it, see the next section.
3. Install the C code (optional)
scripts/install_libnmt.sh contains the instructions run by
setup.py to compile the C library (
libnmt.a). You may have to edit this file or make sure to include any missing compilation flags if
setup.py encounters issues compiling the library.
If you need the C library for your own code,
scripts/install_libnmt.sh installs it in
_deps/include. Note that the script process will also generate an executable
namaster, residing in
_deps/bin that can be used to compute power spectra. The use of this program is discouraged over using the python module.
You can check that the C code works by running
If all the checks pass, you're good to go.
Installing on Mac
NaMaster can be installed on Mac using any of the methods above as long as you have either the
clang compiler with OpenMP capabilities or the
gcc compiler. Both can be accessed via homebrew. If you don't have either, you can still try the conda installation above.
Note: NaMaster is not supported on Windows machines yet.
The following sources of documentation are available for users:
- Python documentation: also available in readthedocs
- Scientific documentation: description of the methods implemented in NaMaster
- C API documentation: description of the C library functionality and the NaMaster executable.
NaMaster has the following dependencies, which should be present in your system before you can install the code from source:
- GSL. Version 2 required (note in certain systems you may also need to install
openblas- see this issue.
- FFTW. Version 3 required. Install with
--enable-openmpand potentially also
- cfitsio. Any version >3 should work.
Besides these, NaMaster will attempt to install the following two dependencies. If this fails, or if you'd like to use your own preinstalled versions, follow these instructions:
- libsharp. Libsharp is automatically installed with NaMaster.
setup.pyattempts to download and install libsharp automatically. This is done by running the script
scripts/install_libsharp.sh. If you encounter any trouble during this step, inspect the contents of that file. Libsharp gets installed in
_deps/include. However, if you want to use your own preinstalled version of libsharp, you should simlink it into the directory
_deps, such that
_deps/lib/libsharp.acan be seen. See instructions in NERSC_installation.md for more details on libsharp.
- HEALPix. Like libsharp, HEALPix is automatically installed by
setup.pyby running the script
scripts/install_libchealpix.sh(have a look there if you run into trouble). HEALPix gets installed in
_deps/include. However, if you want to use your own preinstalled version , you should simlink it into the directory
_deps, such that
_deps/lib/libchealpix.acan be seen. Any version >2 should work. Only the C libraries are needed.
Licensing, credits and feedback
You are welcome to re-use the code, which is open source and freely available under terms consistent with BSD 3-Clause licensing (see LICENSE).
If you use NaMaster for any scientific publication, we kindly ask you to cite this github repository and the companion paper https://arxiv.org/abs/1809.09603. Special kudos should go to the following heroes for their contributions to the code:
- Mat Becker (@beckermr)
- Giulio Fabbian (@gfabbian)
- Martina Gerbino (@mgerbino)
- Daniel Lenz (@DanielLenz)
- Zack Li (@xzackli)
- Thibaut Louis (@thibautlouis)
For feedback, please contact the author via github issues or email (email@example.com).
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