Merge branch 'CHANGE_finish_Maven_migration'

README.md

@@ -13,7 +13,7 @@ http://sass.readthedocs.io/en/latest/
 
 ## Usage
 
-## API Notice ##
+## API notice ##
 
 The API for SASS is still under development and may change until major
 version 1.0.0. Any methods or classes that are marked as deprecated
@@ -23,28 +23,31 @@ will be removed by this release.
 
 1. Download the latest .jar from [releases].
 2. Download the latest .jar from
-   [ALICA_ACPack](https://github.com/LEB-EPFL/ALICA_ACPack).
+   [ALICA_ACPack](https://github.com/LEB-EPFL/ALICA_ACPack/releases).
 3. If using SASS as a ImageJ/Fiji plugin, place the SASS jar in
    `<IMAGEJ_ROOT>/plugins` and the ALICA_ACPack jar in
    `<IMAGEJ_ROOT>/jars`. Otherwise, place both jars in the same
-   folder.
-
-**If you are using v0.7.0 and below, you do not need to download and
-install the ALICA_ACPack.jar**.
+   folder of your choosing.
+
+**Note:** The SASS .jar file that is found in the releases is an
+uber-jar, i.e. it contains all the dependencies that are necessary to
+run.
 
-### As standalone application
+### As a standalone application
  - Executing the .jar file by double-clicking on it launches a
    BeanShell console. Example scripts can be found in `/scripts/`
    folder.
  - Running SASS from command line: `java -jar <SASS-jar-name> --help`
    brings up available options, such as executing a script, or an
    interactive session within the terminal.
 
-### As FIJI plugin
+### As Fiji plugin
+ - If launching Fiji from the command line, launch it from within the
+   Fiji directory so that the ALICA_ACPack.jar is properly found.
  - `Plugins -> SASS -> Simulation` launches an interactive simulator
    (not all options are available through the GUI).
  - `Plugins -> SASS -> Command Prompt` launches BeanShell
-   console. Generated images can be analyzed immediately with FIJI.
+   console. Generated images can be analyzed immediately with Fiji.
 
 ## Where to find help
 

docs/source/quickstart.rst

@@ -2,14 +2,25 @@ Quickstart
 ==========
 
 .. contents::
-   :depth: 2
+   :depth: 3
 
 Installation
 ++++++++++++
 
-SASS is a `Fiji <http://fiji.sc/>`_ plugin and therefore may be
-installed like other plugins.
+SASS is both a standalone application and a `Fiji <http://fiji.sc/>`_
+plugin.
 
+Standalone
+----------
+1. Download the latest .jar file from the `SASS releases page
+   <https://github.com/MStefko/SASS/releases>`_.
+2. You will also need to download the latest `ALICA_ACPack
+   <https://github.com/LEB-EPFL/ALICA_ACPack>`_ .jar, which contains
+   the run-time components for control systems simulations.
+3. Place both .jars in the folder of your choosing.
+
+Fiji
+----
 1. Download the latest .jar file from the `SASS releases page
    <https://github.com/MStefko/SASS/releases>`_.
 2. You will also need to download the latest `ALICA_ACPack
@@ -23,3 +34,43 @@ installed like other plugins.
 You should now see *SASS* appear as a menu item in the the *Plugins*
 menu.
 
+Run a simulation
+++++++++++++++++
+
+Standalone
+----------
+
+Before starting, make sure that you have a copy of the file
+`example_random_2d_fluorophores.bsh
+<https://github.com/LEB-EPFL/SASS/blob/master/scripts/example_random_2d_fluorophores.bsh>`_
+from the SASS respository's *scripts* folder. When using SASS in
+standalone mode, it is most commonly used as a command line
+application.
+
+1. From the command line, navigate to the folder where you placed the
+   SASS .jar file that you downloaded in the installation step.
+2. Enter the command `java -jar SASS_-<VERSION>.jar -s
+   example_random_2d_fluorophores.bsh`.
+3. If you want to save the simulation's output, ensure that any call
+   to the `saveStack(...)` method is uncommented inside the script and
+   rerun the simulation.
+
+Fiji
+----
+
+1. Launch Fiji. (If you're launch Fiji from the command line, ensure
+   that you are first in the Fiji root directory.)
+2. Navigate to *Plugins > SASS > Simulator*.
+3. Ensure that **Manual** is selected in the *Controller* drop-down
+   box.
+4. Click the *Initialize* button.
+5. Rearrange the windows so that you can find the dialog with the
+   controller set point and the *Start* and *Stop* buttons.
+6. Click *Start* to start the simulation. You should see images begin
+   streaming into the simulation's image stack.
+7. Click the *Stop* button to pause the simulation.
+8. Change the *Controller setpoint* value and click *Start* again to
+   resume the simulation with a new laser power.
+
+
+