diff --git a/docs/source/index.rst b/docs/source/index.rst index 140dde4..7b6e6d9 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -12,9 +12,27 @@ each piece of analytical instrumentation. **autopew** `outputs `__ 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 `__ What is **autopew** not? @@ -42,3 +60,11 @@ The current development plan for **autopew** can be found `here `__ .. 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 index f55c900..46902c7 100644 --- 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 `__ - - 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 index 680a5f1..fecb746 100644 --- 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 `__ +is a great way to install python and included popular software for editing and interacting +with python script such as `Spyder `__ and +`Jupyter `__. + +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 `__ is a great jumping off +point. diff --git a/docs/source/usage/outputs.rst b/docs/source/usage/outputs.rst index 0107392..d12fbc8 100644 --- 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 `__. 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.