Docs update

Started getting started page and updated the landing page.
morganjwilliams · Apr 28, 2020 · 724a257 · 724a257
1 parent 44c2deb
commit 724a257
Show file tree

Hide file tree

Showing 4 changed files with 77 additions and 10 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -12,9 +12,27 @@ each piece of analytical instrumentation. **autopew** `outputs <usage/outputs.ht
 currently included a .scancsv file which can be directly imported into `Chromium <http://www.teledynecetac.com/support/software>`__
 laser ablation navigation software.
 
-.. image:: _static/transform_concept.png
-   :align: center
-   :width: 70%
+
+Why use **autopew**
+----------------------
+**autopew** is designed for easy referencing between analytical equipment and/or images.
+This allows the time spend on analytical equipment to be more effectively used for
+data collection rather than spending valuable time locating the areas of interest.
+
+This software also allows for tracking of the context of in-situ microanalysis by
+allowing reference to large images and areas which will allow for new insights into
+what effects chemistry of given particles with reference to their location and
+micro-environment. We can then track the analysis between different analytical
+equipment and make inferences on  macroscale processes from well characterised
+in-situ microanalysis [1].
+
+Although primarily designed for use of laser ablation analysis on geological material
+this software can be used for any microanalytical technique, from electron
+microprobe analysis, x-ray fluorescence mapping, and any scanning electron microscopy work.
+
+.. seealso::
+
+  For outlined examples of how autopew is used, see `Examples <usage/examples.html>`__
 
 
 What is **autopew** not?
@@ -42,3 +60,11 @@ The current development plan for **autopew** can be found `here <future.html>`__
 
 .. note:: This documentation is a work in progress and is updated regularly. Contact
           the maintainers with any specific questions/requests.
+
+
+References
+-------------
+[1] Pearce, M. A., Godel, B. M., Fisher, L. A., Schoneveld, L. E.,
+Cleverly, J. S., Oliver, N. H. S., and  Nugus, M., 2017, Microscale data to
+macroscale processes: a review of microcharacterization applied to mineral
+systems: Geological Society, London, Special Publications,, v. 453
diff --git a/docs/source/usage/examples.rst b/docs/source/usage/examples.rst
@@ -9,25 +9,27 @@ using these examples, please visit the installation and getting started pages.
   `Installation <../installation.html>`__ ,
   `Getting Started <gettingstarted.html>`__
 
-
-
 Use Cases
 --------------
 
-autopew is designed for easy referencing between analytical equipment and/or images.
-Here we outline some use cases as well as what is required for use.
+Here we outline some common use cases as well as what is required for use. This
+includes translating from pixel coordinates on images to analytical stages and
+translating between analytical stages directly.
 
 .. toctree::
    :maxdepth: 1
 
    usecases
 
+.. image:: ../_static/transform_concept.png
+  :align: center
+  :width: 50%
 
 
 Workflows
 -----------------
 
-Here we outline the workflows for use of **autopew**
+This set of pages walks you through how to use **autopew** for each use case.
 
 .. toctree::
    :glob:

diff --git a/docs/source/usage/gettingstarted.rst b/docs/source/usage/gettingstarted.rst
@@ -1,2 +1,41 @@
 Getting Started
 =================
+
+.. note::
+
+  This page is under construction. Feel free to send through suggestions or questions.
+
+Set up
+-------
+To use this software you need in install Python. `Anaconda <https://www.anaconda.com/>`__
+is a great way to install python and included popular software for editing and interacting
+with python script such as `Spyder <https://www.spyder-ide.org/>`__ and
+`Jupyter <https://jupyter.org/>`__.
+
+Installation
+--------------
+.. seealso::
+
+  `Installation <../installation.html>`__
+
+For in depth installation processes see the page above. For most purposes you
+should be able to install **autopew** by typing the following in a terminal ("Anaconda Prompt"
+application on your computer if you're using Anaconda)
+
+.. code-block:: bash
+
+   pip install autopew
+
+If you're already installed autopew and would like the most up-to-date version,
+type this into a terminal:
+
+.. code-block:: bash
+
+   pip install --upgrade autopew
+
+Writing and editing code
+---------------------------
+**autopew** is designed to be very beginner friendly, but if you're completely
+new to python consider visiting some free online courses about the basic Python
+concepts. `Codecademy <https://www.codecademy.com/>`__ is a great jumping off
+point.
diff --git a/docs/source/usage/outputs.rst b/docs/source/usage/outputs.rst
@@ -5,9 +5,9 @@ Output Types
 .scancsv
 -------------------------
 The .scancsv current output is compatible with a Photonmachines (Teledyne) laser
-running on Chromium (TM) .
+running on `Chromium <http://www.teledynecetac.com/support/software>`__.
 This allows for rapid input of X,Y coordinates into the laser system with spot
 labels either read from the source file, or numbered sequentially.
 
 Currently all other settings; including focus (z), spot size and laser conditions
-need to be changed manually after import into the laser. 
+need to be changed manually after import into the laser.