Support Libraries

In general, we will try to avoid re-implementing complex mathematical algorithms, and use instead a small set of well-tested, community supported packages. All packages chosen have large developer bases, and a wide community of users, ensuring long-term support.

The following are support libraries that are allowed when developing CTA Pipeline algorithms. Any new dependencies must be discussed with the software manager.

Math/Stats

A large variety of advanced math and statistcs functions can be found in the numpy (data structures and numerics) and scipy packages (advanced mathematics).

• NumPy user guide : https://docs.scipy.org/doc/numpy/user/ (more high-level)

• NumPy reference : https://docs.scipy.org/doc/numpy/reference/

• SciPy user guide : https://docs.scipy.org/doc/scipy/tutorial/index.html

• SciPy reference : https://docs.scipy.org/doc/scipy/reference/index.html

Specific functionality:

• scipy.stats: statistical models (pdfs, random sampling, etc) for discrete or continuous distributions

• scipy.linalg: fast linear algebra operations

• scipy.optimize: fitting and minimization

• scipy.integrate: integration, including multivariate integration

• scipy.signal: signal processing

• scipy.interpolate: interpolation of multi-variate datasets

• scipy.spatial: spatial algorithms (clustering, nearest neighbors)

• scipy.special: special functions

these functions are all based on numpy.ndarray data structures, which provide c-like speeds.

Multivariate Analysis and Machine Learning

SciKit-Learn, an extension of SciPy, provides very friendly and well-documented interface to a wide variety of MVA techniques, both for classification and regression.

• Decision Trees

• Support vector machines

• Random Forrests

• Perceptrons

• Clustering

• Dimensionality Reduction

• training/cross-checks

• etc.

Astronomical Calculations

AstroPy is the accepted package for all astronomical calculations. Specifically:

• astropy.coordinates: coordinate transforms and frames

• astropy.time: time transformations and frames

• astropy.wcs: projections

• astropy.io: low-level FITS access

• astropy.units: unit quantities with automatic propegation and cross-checks

• astropy.table: quick and easy reading of tables in nearly any format (FITS, ascii, HDF, VO, etc)

• astropy.convolution: convolution and filtering (built upon scipy.signal, but with more robust defaults)

subpackages of Astropy that are not marked as “reasonable stable” or “mature” should be avoided until their interfaces are solidified. The list can be found on the astropy documentation page, under the list current status of subpackages

Tabular Data Processing

We support the following systems to process and manipulate tabular data (e.g.

an event list):

• astropy.table: for small table manipulations

• pytables: for direct manipulation of tables in HDF5 files (faster than other systems for large on-disk files)

low-level FITS Table Access

FITS Tables can be read via astropy.table, or astropy.io.fits, however these implementations are not intended for efficient access to very large files (As they access all tables column-wise). In the case we want to load GBs or more of data in a FITS table, the fitsio module should be used instead. It is a simple wrapper for libCFITSIO, and supports efficient row-wise table access.

low-level HDF5 Table Access

For HDF5 input/output we use pytables directly and h5py through astropy.tables.

Model Fitting

We support only scipy.optimize, iminuit, and scikit-learn fitting systems.

Graphics and Plotting

We support the following:

• matplotlib (recommended for most cases)

• bokeh (for web-guis)

Parallelization and Speed-ups

Since execution speed is important in some algorithms (particularly those called per-event), the speed of python can be a hindrance to performance. The following methods to improve speed are allowed in ctapipe:

Use NumPy operations

One of the easiest way to speed up code is to attempt to avoid for-loops (which are slow) by using numpy vector and matrix operations instead, as well as libraries that use them internally (like scipy and astropy). This requires no special support, but can sometimes be conceptually difficult to achieve. If it is not possible, use one of the following supported methods.

Use Numba

numba allows you to automatically compile a python function via the LLVM compiler backend the first time a funciton is called (“just in time compilation”). The advantage over cython is that there is no special syntax, and no compilation step, however as a somewhat “black-box” it does not always improve your code without some help. See the numba documentation for more info.

Use C/C++ code and wrap it

Currently, ctapipe does not have any AoT compiled components. External C/C++ libraries should provide python bindings, e.g. via pybind11.