pixell 0.9.5

pixell

pixell

pixell is a library for loading, manipulating and analyzing maps stored in rectangular pixelization. It is mainly targeted for use with maps of the sky (e.g. CMB intensity and polarization maps, stacks of 21 cm intensity maps, binned galaxy positions or shear) in cylindrical projection, but its core functionality is more general. It extends numpy’s ndarray to an ndmap class that associates a World Coordinate System (WCS) with a numpy array. It includes tools for Fourier transforms (through numpy or pyfft) and spherical harmonic transforms (through libsharp) of such maps and tools for visualization (through the Python Image Library).

• Free software: BSD license

• Documentation: https://pixell.readthedocs.io.

• Tutorials

Dependencies

• Python>=3.6

• gcc/gfortran or Intel compilers (clang might not work out of the box)

• libsharp (downloaded and installed)

• automake (for libsharp compilation)

• healpy, Cython, astropy, numpy, scipy, matplotlib, pyyaml, h5py, Pillow (Python Image Library)

Installing

For installation instructions specific to NERSC/cori, see NERSC.

For installation instructions specific to MacOS X, see MACOSX (h/t Thibaut Louis).

For all other, below are general instructions.

To install, clone this repository and run:

$ python setup.py install --user

To test the installation, you can run:

$ python setup.py test

You may need to install pytest for the above to work (with pip install pytest –user).

Existing libsharp installation (optional)

Libsharp is installed automatically by setup.py. The installation script will attempt to automatically git clone the latest version and compile it. If instead you want to use an existing libsharp installation, you can do so by symlinking the libsharp directory into a directory called _deps in the root directory, such that pixell/_deps/libsharp/libsharp/sharp.h exists. If you’re convinced that the libsharp library is successfully compiled, add an empty file named pixell/_deps/libsharp/libsharp/success.txt to ensure pixell’s setup.py knows of your existing installation.

Intel compilers

Intel compilers might require a two step installation as follows

$ python setup.py build_ext -i --fcompiler=intelem --compiler=intelem
$ python setup.py install --user

On some systems, further specification might be required (make sure to get a fresh copy of the repository before trying out a new install method), e.g.:

$ LDSHARED="icc -shared" LD=icc LINKCC=icc CC=icc python setup.py build_ext -i --fcompiler=intelem --compiler=intelem
$ python setup.py install --user

Development workflow (recommended)

If you are a developer, run:

$ python setup.py build_ext -i
$ py.test

and add the cloned directory to your Python path so that changes you make in any python file are immediately reflected. e.g., in your .bashrc file,

export PYTHONPATH=$PYTHONPATH:/path/to/cloned/pixell/directory

If you also need non-Python code to be recompiled, run:

$ python setup.py clean

before the above steps.

To test the installation under development mode, you can run:

$ py.test

This requires the pytest Python package to be installed.

Contributions

If you have write access to this repository, please:

1. create a new branch

2. push your changes to that branch

3. merge or rebase to get in sync with master

4. submit a pull request on github

If you do not have write access, create a fork of this repository and proceed as described above. For more details, see Contributing.

History

0.1.0 (2018-06-15)

• First release on PyPI.

0.5.2 (2019-01-22)

• API for most modules is close to converged

• Significant number of bug fixes and new features

• Versioning system implemented through versioneer and bumpversion

• Automated pixel level tests for discovering effects of low-level changes

0.6.0 (2019-09-18)

Changes relative to 0.5.2 include:

• Improvements in accuracy for map extent, area and Fourier wavenumbers

• Spherical harmonic treatment consistent with healpy

• Additional helper functions, e.g enmap.insert

• Helper arguments, e.g. physical normalization for enmap.fft

• Bug fixes e.g. in rand_alm

• Improved installation procedure and documentation

0.9.5 (2020-06-20)

Changes relative to 0.6.0 include:

• Ability to read compressed FITS images

• Fixed a bug to make aberration and modulation accurate to all orders

• Expanded alm2cl to handle full cross-spectra and broadcasting