Merge pull request #52 from carlgogo/master

VIP version 0.5.2 changes:

VERSION

@@ -1 +1 @@
-0.5.1
+0.5.2

docs/source/faq.rst

@@ -1,68 +1,87 @@
 
 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:
+First things first. Please make sure you have the latest version of ``VIP``.
+Please go and check the repository now!
+
+
+On linux, why do I get a matplotlib related error when importing ``VIP``?
+*ImportError: Matplotlib qt-based backends require an external PyQt4, PyQt5,
+or PySide package to be installed, but it was not found.*
+You may need to change the matplotlib backend. Find your matplotlibrc
+configuration file and change the backend from WXAgg to TkAgg. More info here:
+http://matplotlib.org/faq/usage_faq.html#what-is-a-backend. On linux the
+matplotlibrc file is located in:
+
+.. code-block:: bash
+
+  $HOME/.config/matplotlib/matplotlibrc
+
+
+Why do I get, in OSX, the following RuntimeError?
+*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 related issue. Read the link in the previous
+answer. It can be solved setting the backend to WXAgg or TkAgg.
+
+
+The ``VIP`` setup.py script doesn't finish the job, it seems to be stuck.
+What do I do?
+This is very unlikely to happen with the latest versions of pip, setuptools
+and ``VIP``'s setup script. Anyway, if this happens kill the process
+(Ctrl + C) and start it again by re-running the setup command. A workaround
+is to install the problematic dependency before executing ``VIP`` setup:
 
 .. code-block:: bash
 
-  $ conda install --channel https://conda.anaconda.org/astropy photutils
+  $ pip install <problematic_dependency>
+
 
-- 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:
+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:
 
 .. code-block:: bash
 
   $ 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:
+
+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, it is the default library used although it is optional.
+You can install it with conda:
+
+.. code-block:: bash
+
+  $ conda install opencv
+
+
+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
+them using your system's package management tool.
+
+
+Why Python crashes when using some of the parallel functions, e.g.
+``pca_adi_annular`` 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.
+
+
+I get an error: ValueError: "unknown locale: UTF-8" when importing ``VIP``.
+It's not ``VIP``'s fault. The problem must be solved if you add these lines in
+your ~/.bash_profile:
 
 .. code-block:: bash
 

docs/source/index.rst

@@ -38,8 +38,8 @@ the github repository.
 
 The goal of ``VIP`` is to incorporate robust, efficient, easy-to-use, well-documented
 and open source implementations of high-contrast image processing algorithms to
-the interested scientific community. The main repository of ``VIP`` resides on Github,
-the standard for scientific open source code distribution, using Git as a
+the interested scientific community. The main repository of ``VIP`` resides on
+Github, the standard for scientific open source code distribution, using Git as a
 version control system. Github is a repository hosting service with an amazing
 web front-end for source-code management and collaboration. It provides features
 such as access control, bug tracking, feature requests, task management, and
@@ -48,11 +48,12 @@ wikis for every project.
 ``VIP`` is being developed in Python 2.7, a modern open source high-level programming
 language, able to express a large amount of functionality per line of code.
 Python has a vast ecosystem of scientific open source libraries/packages (e.g.
-numpy, scipy, astropy, scikit-learn, scikit-image) and many well-known libraries
-have python bindings as well (e.g. opencv). On top of that exist a great tool,
-the Jupyter (né IPython) notebook. A notebook file is simple a JSON document,
-containing text, source code, rich media output, and metadata. It allows to
-combine data analysis and visualization into an easily sharable format.
+``numpy``, ``scipy``, ``astropy``, ``scikit-learn``, ``scikit-image``) and many
+well-known libraries have python bindings as well (e.g. ``opencv``). On top of
+that exist a great tool, the ``Jupyter`` (né ``IPython``) notebook. A notebook
+file is simple a JSON document, containing text, source code, rich media output,
+and metadata. It allows to combine data analysis and visualization into an
+easily sharable format.
 
 
 Jupyter notebook tutorial
@@ -65,38 +66,18 @@ Jupyter notebook tutorial
 Quick Setup Guide
 ------------------
 
-Get the code from github by downloading it as a zip file or by cloning the
-repository (make sure your system has git installed):
+Run:
 
 .. code-block:: bash
 
-  $ git clone https://github.com/vortex-exoplanet/VIP.git
-
-Install opencv. If you use Anaconda run:
-
-.. code-block:: bash
-
-  $ conda install opencv
-
-From the root of the ``VIP`` package:
-
-.. code-block:: bash
-
-  $ python setup.py develop
-
-Start Python (IPython or Jupyter notebook) and check if the setup worked fine by
-importing ``VIP``:
-
-.. code-block:: python
-
-  import vip
-
+   $ pip install git+https://github.com/vortex-exoplanet/VIP.git
 
 
 Installation and dependencies
 ------------------------------
 
-You can find a more detailed description of ``VIP``'s dependencies here.
+Here you can find a more detailed description of ``VIP``'s dependencies, how to
+clone the repository and install ``Opencv`` (optional).
 
 .. toctree::
    :maxdepth: 2
@@ -106,8 +87,8 @@ You can find a more detailed description of ``VIP``'s dependencies here.
 Frequently asked questions
 ---------------------------
 
-Check out this questions if you find problems when installing or running ``VIP`` for
-the first time.
+Check out this questions if you find problems when installing or running ``VIP``
+for the first time.
 
 .. toctree::
    :maxdepth: 2
@@ -126,14 +107,14 @@ image rotation, pixel temporal and spatial subsampling. On top of that several
 pre-processing functions are available such as re-centering and bad frame
 detection.
 
-For Angular differential imaging (ADI) data several point spread gunction
+For Angular differential imaging (ADI) data several point spread function
 subtraction techniques are available, from a simple median subtraction to
 different low-rank approximations. Principal Component Analysis (PCA) methods
 are implemented in different flavours. Also PCA can process RDI and multiple
 channel SDI (IFS) data. ``VIP`` contains a first version of the Local Low-rank plus
 Sparse plus Gaussian-noise decomposition (LLSG, Gomez Gonzalez et al. 2016).
 
-Functions for Signal-to-noise ratio (S/R) estimation, S/R map generation are
+Functions for Signal-to-noise ratio (S/N) estimation and S/N map generation are
 included.
 
 Flux and position of point-like sources are estimated using the Negative Fake

docs/source/install.rst

@@ -8,39 +8,49 @@ Homebrew/MacPorts/Fink for OSX. I personally recommend using Anaconda which you
 can find 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) provides fast c++ image processing
-operations and is used by VIP (whenever it's possible) instead of python based
-libraries such as ndimage or scikit-image. This dependency is tricky to get
-install/compile, but having Anaconda python distribution the process takes just
-a command provided that you have a C compiler installed in your system, like g++.
-We'll use conda (core component of Anaconda) in this shell/terminal command:
+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`` (by 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.
+
+First, get the code from github by downloading it as a zip file or by cloning the
+repository (make sure your system has git installed):
+
+.. code-block:: bash
+
+  $ git clone https://github.com/vortex-exoplanet/VIP.git
+
+``Opencv`` (Open source Computer Vision) provides fast c++ image processing
+operations and is used by ``VIP`` for basic image transformations. Starting from
+version 0.5.2 of ``VIP`` the dependency on ``opencv`` is optional. If you don't
+have/want the ``opencv`` python bindings, ``VIP`` will use the much slower
+``ndimage/scikit-image`` libraries transparently. Installing ``opencv`` library
+is tricky, but having Anaconda python distribution (``conda`` package manager)
+the process takes just a command (this is an optional step):
 
 .. code-block:: bash
 
   $ conda install opencv
 
-For installing VIP in your system run setup.py:
+For installing ``VIP`` in your system run setup.py:
 
 .. code-block:: bash
 
   $ python setup.py install
 
-The code is in continuous development and will be changing often. It's preferred
-to 'install' with the develop flag:
+Wait a minute until all the requirements are satisfied. Finally start Python
+(or IPython/Jupyter notebook if you prefer) and check that you are able to
+import ``VIP``:
 
-.. code-block:: bash
+.. code-block:: python
 
-  $ python setup.py develop
+  import vip
 
-In any case wait a couple of minutes until all the requirements are satisfied.
+Hopefully you will see the welcome message of ``VIP``.

readme.rst

@@ -35,15 +35,11 @@ Documentation can be found in http://vip.readthedocs.io/.
 
 Quick Setup Guide
 ------------------
-Install opencv. If you use Anaconda run:
+Run:
 
 .. code-block:: bash
-  
-  $ conda install opencv
 
-From the root of the VIP package:
-
-.. code-block:: bash
-
-  $ python setup.py develop   
+   $ pip install git+https://github.com/vortex-exoplanet/VIP.git
 
+Read the documentation for a detailed installation procedure (and optionally,
+how to install ``Opencv``).

requirements

@@ -0,0 +1,17 @@
+cython
+numpy >= 1.8
+scipy >= 0.17
+astropy >= 1.0.2
+photutils >= 0.2.2
+scikit-learn >= 0.17
+scikit-image >= 0.11
+emcee >= 2.1
+corner >= 1.0.2
+pandas >= 0.18
+matplotlib >= 1.4.3
+psutil
+pytest
+image_registration
+FITS_tools
+pywavelets
+pyprind