Merge pull request #8 from drombas/new_doc

DOC: add tutorials and installation instructions

README.md

@@ -8,7 +8,7 @@ A MATLAB Toolbox for retinal OCT image analysis.
 ![fig_readme](https://user-images.githubusercontent.com/50577357/198825276-a70c2cc9-6fd4-408c-8adb-d9f7fcd8d6de.png)
 
 ## What can I do with RETIMAT?
-- Read propietary OCT files (.vol, .e2e, .img, .fda, .xml)
+- Read OCT files: .vol, .e2e, .img, .fda, .xml (OCT Explorer)
 - Visualization
     - Raw images (OCT, fundus) + en-face maps (thickness, reflectance)
     - Summary reports
@@ -26,4 +26,4 @@ A MATLAB Toolbox for retinal OCT image analysis.
 3. Take a look into the tutorials
 
 ## Contact
-For help, feedback or collaboration inquiries please contact dromero@mondragon.edu
+For help, feedback or collaboration inquiries please contact dromero[email protected]

doc/conf.py

@@ -8,9 +8,9 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'RETIMAT'
-copyright = '2023, David Romero-Bascones'
 author = 'David Romero-Bascones'
-release = '1.0.0'
+version = '1.0.0'
+release = version
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -20,13 +20,20 @@
 templates_path = ['_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
+add_module_names = False # show only function name
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'bizstyle'
+html_theme = 'classic'
 html_static_path = ['_static']
-
+html_sidebars = {'**': ['globaltoc.html', 'sourcelink.html', 'searchbox.html']}
+html_show_sphinx = False
+html_title = f'{project} {version}'
+html_domain_indices = False
+html_use_index = False
+html_show_sourcelink = False
+html_show_copyright = False
 
 # -- MATLAB configuration ----------------------------------------------------
 primary_domain = 'mat'

doc/functions.rst

@@ -2,30 +2,36 @@
 Functions
 =========
 
-These are the functions implemented in RETIMAT
+These are all the functions implemented in RETIMAT
 
 
 File reading
 ============
 .. automodule:: io
-.. autofunction:: io.read_xml_iowa
+
+.. autofunction:: io.read_vol
 
 ----
 
-.. autofunction:: io.read_bin
+.. autofunction:: io.read_e2e
 
 ----
 
-.. autofunction:: io.read_e2e
+.. autofunction:: io.read_img
 
 ----
 
-.. autofunction:: io.read_vol
+.. autofunction:: io.read_bin
 
 ----
 
 .. autofunction:: io.read_fda
 
+----
+
+.. autofunction:: io.read_xml_iowa
+
+----
 
 Spatial analysis
 ================

doc/index.rst

@@ -3,18 +3,42 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to RETIMAT's documentation!
-===================================
+Home
+====
 
+RETIMAT is MATLAB toolbox for retinal OCT image analysis.
+
+.. image:: https://user-images.githubusercontent.com/50577357/198825276-a70c2cc9-6fd4-408c-8adb-d9f7fcd8d6de.png
+  :width: 1000
+  :alt: Alternative text
+
+What can I do with RETIMAT
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+* Read OCT files: ``vol``, ``e2e``, ``fda``, ``img``, ``OCTExplorer``
+* Visualize images
+* Feature extraction: thickness, foveal pit morphology, texture
+
+How to install it
+^^^^^^^^^^^^^^^^^
+
+1. Download the code from `here <https://zenodo.org/record/7313091#.ZDVXQLxBz1s>`_
+2. Unzip the downloaded file
+3. Execute the ``startup.m`` script from the main folder
+4. Follow the tutorials or reach out for help
+
+How to use it
+^^^^^^^^^^^^^
+.. toctree::
+   :hidden:
+
+   self
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
+   tutorials
    functions
 
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+Contact
+^^^^^^^
+For help, feedback or collaboration inquiries please contact [email protected]