rmjc/vip

VIP is a package/pipeline for angular, reference star and spectral differential imaging for exoplanet detection through high-contrast imaging.

Vortex Image Processing pipeline (VIP)

Please cite Gomez Gonzalez et al. 2016 (in prep.) whenever you publish data reduced with VIP.

VIP is registered on the Astrophysics Source Code Library [ascl:1603.003].

VIP is a package/pipeline for angular, reference star and spectral differential imaging for exoplanet detection through high-contrast imaging. VIP is being developed in Python 2.7.

VIP is being developed within the VORTEX team @ University of Liege (Belgium). It's in alpha version meaning that the code will change drastically before the first release version. If you want to report a bug, suggest a feature or add a feature please contact the main developer at cgomez [at] ulg.ac.be or through github.

Documentation

VIP tutorial (Jupyter notebook) was removed from the main VIP repository. It will be updated and released in a separate repository. Documentation in HTML and PDF will be produced when VIP paper is published.

Quick Setup Guide

Install opencv. If you use Anaconda run:

$ conda install opencv

From the root of the VIP package:

$ python setup.py develop

Installation and dependencies

Having a python distribution installed, such as Canopy or Anaconda, will allow easy and robust package management and avoid messing up with your system's default python. An alternative is to use package managers like apt-get for Ubuntu or Homebrew/MacPorts/Fink for OSX. I personally recommend using Anaconda which you can grab it from here: https://www.continuum.io/downloads.

A setup.py file (Setuptools Python package) is included in the root folder of VIP. It takes care of installing most of the requirements for you. VIP depends on existing packages from the Python ecosystem, such as numpy, scipy, matplotlib, pandas, astropy, scikit-learn, scikit-image, photutils, emcee, etc.

VIP ships a stripped-down version of RO.DS9 (Russell Owen) for convenient xpaset/xpaget based interaction with DS9. VIP contains a class vipDS9 that works on top of RO.DS9 containing several useful methods for DS9 control such as displaying arrays, manipulating regions, controlling the display options, etc. VipDS9 functionality will only be available if you have DS9 and XPA installed on your system PATH.

OpenCV (Open source Computer Vision) is used for fast image processing operations. Opencv and its python bindings are usually difficult to install (can't be processed from the setup.py requirements) but fortunately with just one command we'll get it ready.

Make sure to install OpenCV before running setup.py and make sure you have a C compiler installed in your system, like g++. With conda (anaconda) just type:

$ conda install opencv

For installing VIP in your system run setup.py:

$ python setup.py install

The code is in continuous development and will be changing often. It's preferred to 'install' with the develop flag:

$ python setup.py develop

In any case wait a couple of minutes until all the requirements are satisfied.

FAQ

• The VIP setup doesn't finish the job, it seems to be stuck. What do I do? We have experienced a few times that the setup script hangs while installing photutils. The reason why it crashes when compiling its own modules is unknown. We recommend to kill the process (Ctrl + C) and restart it again by re-running the setup command. A workaround is to install photutils before executing VIP setup:

$ conda install --channel https://conda.anaconda.org/astropy photutils

• Why the setup fails complaining about the lack of a Fortran compiler? Fortran compilers are apparently needed for compiling Scipy from source. Make sure there is a Fortran compiler in your system. A workaround is to install Scipy through conda before running the setup script:

$ conda install scipy

• Why do I get and error related to importing cv2 package when importing VIP? cv2 is the name of opencv bindings for python. This library is needed for fast image transformations. You have to install by following the aforementioned instructions.
• Why do I get a warning related to DS9/XPA when importing VIP? Please make sure you have DS9 and XPA in your system path. Try installing it with your system package management tool.
• Why Python crashes when using some of the parallel functions, e.g. pca_adi_annular_quad and run_mcmc_astrometry? These functions require running SVD on several processes and this can be problematic depending on the linear algebra libraries on your machine. We've encountered this problem on OSX systems that use the ACCELERATE library for linear algebra calculations (default in every OSX system). For this library the multiprocessing is broken. A workaround is to compile Python against other linear algebra library (e.g. OPENBLAS). An quick-n-easy fix is to install the latest ANACONDA (2.5 or later) distribution which ships MKL library and effectively replaces ACCELERATE on OSX systems. On linux with the default LAPACK/BLAS libraries VIP successfully distributes the SVDs among all the existing cores.
• Why do I get, in linux, a matplotlib related error when importing VIP? (Matplotlib backend_wx and backend_wxagg require wxPython >=2.8) If you use Canopy python distro then this is caused by the combination linux/Canopy. Nothing to do with the VIP pipeline. You may need to change the matplotlib backend. Find your matplotlibrc configuration file and change the backend from WXAgg to Qt4Agg. More info here: http://matplotlib.org/faq/usage_faq.html#what-is-a-backend
• Why do I get, in OSX, the RuntimeError shown below? (Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends.) Again, this is a matplotlib-backend issue (not VIP related). Read the link in the previous question. It can be solved setting the backend to WXAgg or TkAgg.
• I get an error: ValueError: "unknown locale: UTF-8" when importing VIP. It's not a VIP related problem. The problem must be solved if you add these lines in your ~/.bash_profile:

export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8