Merge pull request #423 from brechmos-stsci/make-markdown

Moved all documentation to markdown from RsT (shiver)

Author: Craig Jones

README.rst renamed to README.md

@@ -1,29 +1,21 @@
-CubeViz
---------------------------------
-
-.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
-    :target: http://www.astropy.org
-    :alt: Powered by Astropy Badge
+# CubeViz
 
+![](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)
 
 For documentation see http://cubeviz.readthedocs.io/en/latest/
 
-Release 0.2.0
--------------
+## Release 0.2.0
 
 We are pleased to announce the release of CubeViz, a visualization and analysis tool for data cubes from integral field units (IFUs). This is an early release (v0.2.0) and we would appreciate your feedback.  It is built on top of the “glue” visualization tool.
 
-.. role:: bash(code)
-   :language: bash
-   
 To install:
-  * Install minconda3 if it is not on your system
-  * To install, type: :bash:`$ conda create -n cubeviz020 -c glueviz cubeviz`
+  * Install [Minconda3](https://conda.io/miniconda.html) if it is not on your system
+  * To install, type: `$ conda create -n cubeviz020 -c glueviz cubeviz`
 
 To run:
-  * Activate the environment: :bash:`$ source activate cubeviz020`
-  * Run cubeviz: :bash:`$ cubeviz`
-  * Once done, deactivate the environment: :bash:`source deactivate`
+  * Activate the environment: `$ source activate cubeviz020`
+  * Run cubeviz: `$ cubeviz`
+  * Once done, deactivate the environment: `source deactivate`
 
 More installation instructions will be on the RTD page (currently incorrectly displaying the wrong docs and appears to be an RTD bug).
 
@@ -35,10 +27,9 @@ If you run into any issues or have suggestions for new features, we encourage yo
 
 This release requires Python 3.5 or 3.6.
 
-.. image:: /docs/images/CubeViz_splitviewer.png
+![](/docs/images/CubeViz_splitviewer.png)
 
 
-License
--------
+# License
 
 This project is Copyright (c) JDADF Developers and licensed under the terms of the BSD 3-Clause license. See the licenses folder for more information.

docs/functionality.rst renamed to docs/functionality.md

@@ -1,4 +1,4 @@
-#Overview of Basic CubeViz Functionality
+# Overview of Basic CubeViz Functionality
 
 CubeViz has two main "modes:" Split Image Viewer and Single Image Viewer.
 CubeViz starts in the Split Image Viewer which shows the flux, error,
@@ -14,11 +14,9 @@ In addition to the image viewers which display the data cube in
 its spatial axes (RA, DEC), a spectrum viewer shows the spectral axis
 (wavelength).
 
-.. image::  images/CubeViz_splitviewer.png 
-   :align:   center
+![](images/CubeViz_splitviewer.png?raw=true)
 
-.. image::  images/CubeViz_singleviewer.png	     
-   :align:   center
+![](images/CubeViz_singleviewer.png?raw=true)
 
 Caption: Screen shots of the split image viewer (top) and single
 image viewer (bottom) are shown.
@@ -28,7 +26,7 @@ is displayed in the image viewer, and a spectrum of the entire cube
 (collapsed wavelength space using an average) is shown in black in the
 spectrum viewer.
 
-##Using the Image Viewers
+## Using the Image Viewers
 
 To manipulate an image displayed in an image viewer, the user should
 click on that image and then the "Show viewer options" button in the
@@ -41,9 +39,7 @@ The user can hide the control panel again by clicking on the
 The user can also interact with the image panels using the menu bar
 across the top:
 
-.. figure::  images/upper_panel.png	     
-   :align:   center
-
+![](images/upper_panel.png?raw=true)
 
 This is below the very top glue menu bar.  The left-most part of the menu
 bar shows three pull-down menus which list the extension of the loaded
@@ -71,7 +67,7 @@ to hide the coordinate axes and tool bars on the image viewers.
 (Finally, there is another button to sync the viewers?)
 
 
-##Selecting a Region in the Image Viewers      
+## Selecting a Region in the Image Viewers      
 
 Regions can be selected in the image viewers. If they are spatial
 regions (RA, DEC), the cube will be collapsed in wavelength space

docs/index.md

@@ -0,0 +1,32 @@
+# CubeViz: Visualization & Analysis Tool for Data Cubes from Integral Field Units (IFUs)
+
+CubeViz is an visualization and analysis toolbox for data cubes from [integral field units (IFUs)](https://jwst-docs.stsci.edu/display/JPP/Introduction+to+IFU+Spectroscopy).  It is built as part of the [glue visualiztion tool](http://glueviz.org).  CubeViz is designed to work with data cubes from the [NIRSpec](https://jwst-docs.stsci.edu/display/JTI/NIRSpec+IFU+Spectroscopy) and [MIRI](https://jwst-docs.stsci.edu/display/JTI/MIRI+Medium-Resolution+Spectroscopy) instruments on [JWST](https://jwst-docs.stsci.edu/display/HOM/JWST+User+Documentation+Home), and will work with data cubes from any IFU.  It uses the [specutils](https://specutils.readthedocs.io/en/latest/) package from [Astropy](http://www.astropy.org).
+
+The core functionality of CubeViz currently includes the ability to:
+  * view the wavelength slices (RA, DEC) in a data cube,
+  * view flux, error, and data quality slices simultaneously,
+  * view spectra from selected spatial (RA, DEC) regions,
+  * smooth cubes spactially (RA, DEC) and spectrally (wavelength), and
+  * create and display contour maps.
+
+Future functionality will include the ability to:
+  * collapse cubes over selected wavelength regions,
+  * fit spectral lines,
+  * create moment maps,
+  * create kinematic maps (rotation velocity and velocity dispersion),
+  * create RGB images from regions collapsed in wavelength space (i.e., linemaps),
+  * perform continuum subtraction,  
+  * overlay spectral line lists,
+  * save edited cubes,
+  * create publication quality figures,
+  * output astropy commands,
+  * match spatial resolution among selected data cubes,
+  * bin data into constant signal-to-noise regions,
+  * mock slit observations
+  * accurate spectro-photometry
+
+# Reference/API
+
+  * [Installation](installation.md)
+  * [Functionality](functionality.md)
+  * [Reading in Data](readingindata.md)

docs/index.rst

@@ -4,7 +4,7 @@ CubeViz is packaged in the Conda environment system and therefore requires Minic
 
 ## Installing Miniconda 
 
-Follow the Miniconda `installation instructions <https://conda.io/miniconda.html>`_ found on the Miniconda website. When asked whether miniconda should be appended to your system PATH, make sure to select yes.
+Follow the Miniconda [installation instructions](https://conda.io/miniconda.html) found on the Miniconda website. When asked whether miniconda should be appended to your system PATH, make sure to select yes.
 
 Note that we have encountered issues with older versions of Miniconda, so if you already have it installed, it might be a good idea to update it.
 

docs/installation.rst renamed to docs/installation.md

@@ -1,18 +1,14 @@
-***************
-Reading-in Data
-***************
+# Reading-in Data
 
 CubeViz will be able to read in NIRSpec and MIRI IFU data straight from the pipeline or archive.  It includes data loaders for many but not all ground-based IFUs.
 
-CubeViz uses simple [yaml] (https://learn.getgrav.org/advanced/yaml) files as data loaders.  Examples are given below.  In short, the yaml file tells CubeViz which axes in the cube are RA, DEC, and wavelength, and the units used, among other things.
+CubeViz uses simple [yaml](https://learn.getgrav.org/advanced/yaml) files as data loaders.  Examples are given below.  In short, the yaml file tells CubeViz which axes in the cube are RA, DEC, and wavelength, and the units used, among other things.
 
-If you have trouble loading your data cube into CubeViz, please email [Susan Kassin] (https://www.susankassin.com/contact/).  It would be helpfu a link to your data cube is provided.
+If you have trouble loading your data cube into CubeViz, please email [Susan Kassin](https://www.susankassin.com/contact/).  It would be helpfu a link to your data cube is provided.
 
-+++++++++++++++++++++++++++++++++++++++++++++++++++++
-Reading in an Example Data Cube
-+++++++++++++++++++++++++++++++++++++++++++++++++++++
+# Reading in an Example Data Cube
 
-An example data cube from the [MaNGA Survey] (http://www.sdss.org/surveys/manga/) can be found on the bottom of [this website] (http://skyserver.sdss.org/dr13/en/tools/explore/summary.aspx?ra=205.4384&dec=27.004754).  To download the data cube, click on "LIN Data Cube" or "LOG Data Cube" to dowload a data cube with a linear or log wavelength axis, respectively.
+An example data cube from the [MaNGA Survey](http://www.sdss.org/surveys/manga/) can be found on the bottom of [this website](http://skyserver.sdss.org/dr13/en/tools/explore/summary.aspx?ra=205.4384&dec=27.004754).  To download the data cube, click on "LIN Data Cube" or "LOG Data Cube" to dowload a data cube with a linear or log wavelength axis, respectively.
 
 Start up CubeViz by typing "cubeviz" on the command line, following the
 installation instructions (:ref:'installation.rst').  CubeViz should start
@@ -22,9 +18,7 @@ should appear.  In the dialog box, select the data cube you wish to load and
 select the relevant data loader using the drop down menu on the bottom.
 For the MaNGA cube, select "manga (*)."  The data cube should load.
 
-+++++++++++++++++++++++++++++++++++++++++++++++++++++
-Reading in an Unsupported Data Cube
-+++++++++++++++++++++++++++++++++++++++++++++++++++++
+# Reading in an Unsupported Data Cube
 
 If your data cube does not automatically load with one of the
 pre-existing data loaders in the "Open Data" dialog box, you can