Merge pull request #122 from carlgogo/master

VIP v0.9.0. Integration with DS9 is back! Docs updated. Small fixes.

docs/source/readme.rst

@@ -69,12 +69,12 @@ TL;DR setup guide
 
 Installation and dependencies
 -----------------------------
-The benefits of using a Python package manager (distribution), such as Anaconda or
-Canopy, are many. Mainly, it brings easy and robust package management and
-avoids 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 Macos. I personally recommend using Miniconda which you
-can find here: https://conda.io/miniconda.html.
+The benefits of using a Python package manager (distribution), such as
+(ana)conda or Canopy, are many. Mainly, it brings easy and robust package
+management and avoids 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 Macos. I personally recommend using Miniconda which
+you can find here: https://conda.io/miniconda.html.
 
 ``VIP`` depends on existing packages from the Python ecosystem, such as
 ``numpy``, ``scipy``, ``matplotlib``, ``pandas``, ``astropy``, ``scikit-learn``,
@@ -141,12 +141,9 @@ you could use ``conda``:
 
   $ conda install opencv
 
-``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.
+``VIP`` contains a class ``vip_hci.fits.ds9`` that enables, through ``pyds9``,
+the interaction with a DS9 window (displaying numpy arrays, controlling the
+display options, etc).
 
 Also, optionally you can install the Intel Math Kernel Library (MKL)
 optimizations provided that you have Anaconda(>v2.5) and ``conda`` on your
@@ -159,7 +156,7 @@ computations. Run:
 
 Starting from version 0.8.0 ``VIP`` offers the possibility of computing SVDs
 on GPU by using ``cupy``. This remains an optional requirement, to be installed
-by the user, as it requires having a real (good) GPU card and a proper CUDA
+by the user, as it requires having a decent GPU card and a proper CUDA
 environment.
 
 Loading VIP

docs/source/vip_hci.conf.rst

@@ -1,5 +1,5 @@
-vip\_hci.conf package
-=====================
+vip\_hci\.conf package
+======================
 
 .. automodule:: vip_hci.conf
     :members:
@@ -9,32 +9,32 @@ vip\_hci.conf package
 Submodules
 ----------
 
-vip\_hci.conf.mem module
-------------------------
+vip\_hci\.conf\.mem module
+--------------------------
 
 .. automodule:: vip_hci.conf.mem
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.conf.param module
---------------------------
+vip\_hci\.conf\.param module
+----------------------------
 
 .. automodule:: vip_hci.conf.param
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.conf.timing module
----------------------------
+vip\_hci\.conf\.timing module
+-----------------------------
 
 .. automodule:: vip_hci.conf.timing
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.conf.utils\_conf module
---------------------------------
+vip\_hci\.conf\.utils\_conf module
+----------------------------------
 
 .. automodule:: vip_hci.conf.utils_conf
     :members:

docs/source/vip_hci.exlib.rst

@@ -1,5 +1,5 @@
-vip\_hci.exlib package
-======================
+vip\_hci\.exlib package
+=======================
 
 .. automodule:: vip_hci.exlib
     :members:
@@ -9,8 +9,8 @@ vip\_hci.exlib package
 Submodules
 ----------
 
-vip\_hci.exlib.iuwt module
---------------------------
+vip\_hci\.exlib\.iuwt module
+----------------------------
 
 .. automodule:: vip_hci.exlib.iuwt
     :members:

docs/source/vip_hci.fits.rst

@@ -1,5 +1,5 @@
-vip\_hci.fits package
-=====================
+vip\_hci\.fits package
+======================
 
 .. automodule:: vip_hci.fits
     :members:
@@ -9,12 +9,20 @@ vip\_hci.fits package
 Submodules
 ----------
 
-vip\_hci.fits.fits module
--------------------------
+vip\_hci\.fits\.fits module
+---------------------------
 
 .. automodule:: vip_hci.fits.fits
     :members:
     :undoc-members:
     :show-inheritance:
 
+vip\_hci\.fits\.vipds9 module
+-----------------------------
+
+.. automodule:: vip_hci.fits.vipds9
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 

docs/source/vip_hci.frdiff.rst

@@ -1,5 +1,5 @@
-vip\_hci.frdiff package
-=======================
+vip\_hci\.frdiff package
+========================
 
 .. automodule:: vip_hci.frdiff
     :members:
@@ -9,8 +9,8 @@ vip\_hci.frdiff package
 Submodules
 ----------
 
-vip\_hci.frdiff.framediff module
---------------------------------
+vip\_hci\.frdiff\.framediff module
+----------------------------------
 
 .. automodule:: vip_hci.frdiff.framediff
     :members:

docs/source/vip_hci.llsg.rst

@@ -1,5 +1,5 @@
-vip\_hci.llsg package
-=====================
+vip\_hci\.llsg package
+======================
 
 .. automodule:: vip_hci.llsg
     :members:
@@ -9,16 +9,16 @@ vip\_hci.llsg package
 Submodules
 ----------
 
-vip\_hci.llsg.llsg module
--------------------------
+vip\_hci\.llsg\.llsg module
+---------------------------
 
 .. automodule:: vip_hci.llsg.llsg
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.llsg.thresholding module
----------------------------------
+vip\_hci\.llsg\.thresholding module
+-----------------------------------
 
 .. automodule:: vip_hci.llsg.thresholding
     :members:

docs/source/vip_hci.madi.rst

@@ -1,5 +1,5 @@
-vip\_hci.madi package
-=====================
+vip\_hci\.madi package
+======================
 
 .. automodule:: vip_hci.madi
     :members:
@@ -9,8 +9,8 @@ vip\_hci.madi package
 Submodules
 ----------
 
-vip\_hci.madi.adi\_source module
---------------------------------
+vip\_hci\.madi\.adi\_source module
+----------------------------------
 
 .. automodule:: vip_hci.madi.adi_source
     :members:

docs/source/vip_hci.negfc.rst

@@ -1,5 +1,5 @@
-vip\_hci.negfc package
-======================
+vip\_hci\.negfc package
+=======================
 
 .. automodule:: vip_hci.negfc
     :members:
@@ -9,40 +9,40 @@ vip\_hci.negfc package
 Submodules
 ----------
 
-vip\_hci.negfc.mcmc\_sampling module
-------------------------------------
+vip\_hci\.negfc\.mcmc\_sampling module
+--------------------------------------
 
 .. automodule:: vip_hci.negfc.mcmc_sampling
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.negfc.nested\_sampling module
---------------------------------------
+vip\_hci\.negfc\.nested\_sampling module
+----------------------------------------
 
 .. automodule:: vip_hci.negfc.nested_sampling
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.negfc.simplex\_fmerit module
--------------------------------------
+vip\_hci\.negfc\.simplex\_fmerit module
+---------------------------------------
 
 .. automodule:: vip_hci.negfc.simplex_fmerit
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.negfc.simplex\_optim module
-------------------------------------
+vip\_hci\.negfc\.simplex\_optim module
+--------------------------------------
 
 .. automodule:: vip_hci.negfc.simplex_optim
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.negfc.utils\_negfc module
-----------------------------------
+vip\_hci\.negfc\.utils\_negfc module
+------------------------------------
 
 .. automodule:: vip_hci.negfc.utils_negfc
     :members:

docs/source/vip_hci.nmf.rst

@@ -1,5 +1,5 @@
-vip\_hci.nmf package
-====================
+vip\_hci\.nmf package
+=====================
 
 .. automodule:: vip_hci.nmf
     :members:
@@ -9,8 +9,8 @@ vip\_hci.nmf package
 Submodules
 ----------
 
-vip\_hci.nmf.nmf\_fullfr module
--------------------------------
+vip\_hci\.nmf\.nmf\_fullfr module
+---------------------------------
 
 .. automodule:: vip_hci.nmf.nmf_fullfr
     :members:

docs/source/vip_hci.pca.rst

@@ -1,5 +1,5 @@
-vip\_hci.pca package
-====================
+vip\_hci\.pca package
+=====================
 
 .. automodule:: vip_hci.pca
     :members:
@@ -9,32 +9,32 @@ vip\_hci.pca package
 Submodules
 ----------
 
-vip\_hci.pca.pca\_fullfr module
--------------------------------
+vip\_hci\.pca\.pca\_fullfr module
+---------------------------------
 
 .. automodule:: vip_hci.pca.pca_fullfr
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.pca.pca\_local module
-------------------------------
+vip\_hci\.pca\.pca\_local module
+--------------------------------
 
 .. automodule:: vip_hci.pca.pca_local
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.pca.svd module
------------------------
+vip\_hci\.pca\.svd module
+-------------------------
 
 .. automodule:: vip_hci.pca.svd
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.pca.utils\_pca module
-------------------------------
+vip\_hci\.pca\.utils\_pca module
+--------------------------------
 
 .. automodule:: vip_hci.pca.utils_pca
     :members:

docs/source/vip_hci.phot.rst

@@ -1,5 +1,5 @@
-vip\_hci.phot package
-=====================
+vip\_hci\.phot package
+======================
 
 .. automodule:: vip_hci.phot
     :members:
@@ -9,40 +9,40 @@ vip\_hci.phot package
 Submodules
 ----------
 
-vip\_hci.phot.contrcurve module
--------------------------------
+vip\_hci\.phot\.contrcurve module
+---------------------------------
 
 .. automodule:: vip_hci.phot.contrcurve
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.phot.detection module
-------------------------------
+vip\_hci\.phot\.detection module
+--------------------------------
 
 .. automodule:: vip_hci.phot.detection
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.phot.fakecomp module
------------------------------
+vip\_hci\.phot\.fakecomp module
+-------------------------------
 
 .. automodule:: vip_hci.phot.fakecomp
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.phot.frame\_analysis module
-------------------------------------
+vip\_hci\.phot\.frame\_analysis module
+--------------------------------------
 
 .. automodule:: vip_hci.phot.frame_analysis
     :members:
     :undoc-members:
     :show-inheritance:
 
-vip\_hci.phot.snr module
-------------------------
+vip\_hci\.phot\.snr module
+--------------------------
 
 .. automodule:: vip_hci.phot.snr
     :members: