Documentation for console and settings

doc/source/index.rst

@@ -24,7 +24,6 @@ Contents:
    usage
    plugins
    extending
-   apidoc/spykeviewer
 
 Indices and tables
 ==================

doc/source/installation.rst

@@ -73,7 +73,7 @@ https://github.com/rproepp/spykeviewer.
 The master branch (selected by default) always contains the current stable
 version. If you want the latest development version (not recommended unless
 you need some features that do not exist in the stable version yet), select
-the development branch. You can download the repository from the GitHub page
+the develop branch. You can download the repository from the GitHub page
 or clone it using git and then install from the resulting folder::
 
 $ python setup.py install

doc/source/usage.rst

@@ -35,6 +35,8 @@ formats that have a
 to use a file format that is not supported by Neo, you can write a plugin:
 :ref:`ioplugins`.
 
+.. _selections:
+
 Selections
 ----------
 Now that a file was loaded, some entries have appeared in the ``Navigation``
@@ -139,7 +141,9 @@ a number of plugins that enable you to create various plots from your data.
 Select the ``Plugins`` dock (located next to the ``Filter`` dock in the
 initial layout) to see the list of available plugins. To start a plugin,
 simply double-click it or select it and then click on "Run Plugin" in the
-plugin toolbar or menu.
+plugin toolbar or menu. You can also start a plugin in a different process
+(so that you can continue using Spyke Viewer while the plugin is busy) by
+selecting "Start with Remote Script" in the "Plugins" menu.
 
 For example, if you start the "Signal Plot" plugin, it will create a plot of
 selected analog signals. Try selecting Segment 3, Tetrode 2 and Channels 3
@@ -159,7 +163,75 @@ learn more about the included plugins and how to use them, go to
 Using the Console
 -----------------
 
+With the integrated console, you can use the full power of Python in Spyke
+Viewer, with access to your selected data. Open the ``Console`` dock by
+clicking on the "View" menu and selecting "Console". You can explore your
+workspace using the ``Variable Explorer`` dock and view your previous
+commands with the ``Command History`` dock. Some packages like scipy_ and
+:mod:`neo` are imported on startup, the message in the console shows which.
+The console features autocompletion (press the Tab key to complete with the
+selected entry) and docstring popups.
+
+The most important objects in the console environment are ``current`` and
+``selections``. ``current`` gives you access to your currently selected data,
+``selections`` contains all stored selections (which you can manage using
+the "Selections" menu, see selections_). For example,
+
+>>> current.spike_trains()
+
+gives a list of your currently selected spike trains. Both ``current`` and
+the entries of ``selections`` are
+:class:`spykeutils.plugin.data_provider.DataProvider` objects, refer to the
+documentation for details of the methods provided by this class.
+
+As an example, to view the total amount of spikes in your selected spike
+trains for each trial, enter the following lines:
+
+>>> trains = current.spike_trains_by_segment()
+>>> for s, st in trains.iteritems():
+...     print s.name, '-', sum((len(train) for train in st)), 'spikes'
+
+Note that the variables used in these lines have now appeared in the
+``Variable Explorer`` dock.
+
+
 .. _settings:
 
 Settings
 --------
+
+The Spyke Viewer settings can be accessed by opening the "View" menu and
+selecting "Settings". You can adjust various paths in the settings:
+
+**Selection path**
+    The path where your selections are stored when you exit Spyke Viewer. This
+    is also the default directory when using "Save Selection Set..." or
+    "Load Selection Set.." in the "File" menu.
+
+**Filter path**
+    The directory where your filter hierarchy and activation states are stored
+    when you exit Spyke Viewer. Your filters are stored as regular Python
+    files with some special annotation comments, so you can edit them in your
+    favourite editor.
+
+**Data path**
+    This directory is important when you are using the data storage features
+    of :class:`spykeutils.plugin.analysis_plugin.AnalysisPlugin`.
+
+**Remote script**
+    A script file that is executed when you use "Start with remote script"
+    action for a plugin. The default script simply starts the plugin locally,
+    but you can write a different script for other purposes, e.g. starting it
+    on a server.
+
+**Plugin paths**
+    These are the search paths for plugins. They will be recursively searched
+    for Python files containing AnalysisPlugin classes. Subdirectories will be
+    displayed as nodes in the ``Plugins`` dock.
+
+    In addition, your IO plugins also have to stored be in one of the plugin
+    paths. The search for IO plugins is not recursive, so you have to put
+    them directly into one of the paths in this list.
+
+
+.. _`scipy`: http://scipy.org/

spykeviewer/ui/main_window.py

@@ -199,9 +199,8 @@ def get_dir(self, objtxt):
         ns = {'current': self.provider, 'selections': self.selections,
               'np': numpy, 'sp': scipy, 'plt': plt, 'guiplt': guiplt,
               'pq': quantities, 'neo': neo, 'spykeutils': spykeutils}
-        msg = ('current and selections can be used as in the start() ' +
-        ' method of a plugin.\n\n' +
-        'Modules imported at startup: numpy as np, scipy as sp, ' +
+        msg = ('current and selections can be used to access selected data'
+        '\n\nModules imported at startup: numpy as np, scipy as sp, ' +
         pltmsg + 'quantities as pq, neo, spykeutils')
 
         self.console = FixedInternalShell(self.consoleDock, namespace=ns,