-force curves, use the plot toolbar under the plot. A more detailed
-description is available on the
-[http://matplotlib.sourceforge.net/users/navigation_toolbar.html
-matplotlib website].
-
-== Some plugins and commands ==
- * replot (plot): replots the current force curve from scratch eliminating any secondary plots
- * fjc/fjcPEG/wlc (fit): do not use any of these commands directly, they are not implemented properly yet. However, the properties you set for these commands are used for the autopeak command
- * plotmanipulators (core): select the plotmanipulators you want to use and arrange them in the proper order
- * test (test): use this for testing purposes. You find do_test in hooke.py
- * clear_results (results): deletes all fitting results from the curve
- * show_results (results): select which fitting results should be displayed on the plot
- * overlay (export): exports all retraction curves in a playlist on the same scale. This is achieved by determining the maximum x window and adding x(max) and x(min) to all curves that are shorter than the maximum x window. Make sure to filter your playlist before running this command!
-
-== Basic analysis and autopeak ==
-Please follow the steps for basic analysis described [BasicAnalysis here]. Instead of typing in the command at the command-line, select it in the Commands window, set your properties in the Properties window and click on 'Execute'.
-
-The [Brief_Autopeak_HowTo autopeak] tutorial is also applicable. In Hooke(GUI) you need to setup the type of fit you want to use: in the Properties of the autopeak command (autopeak plugin) select wlc, fjc or fjcPEG from the dropdown list for the fit_function.
-
-If you run different fits (e.g. WLC and FJC) you can switch the display of the results with the show_results command (results plugin).
-
-== Brief plugin/Properties tutorial ==
-Have a look at the files in the _plugins_ folder. The python files contain the plotmanipulators (i.e. plotmanip_NAME), commands (i.e. do_COMMAND) and auxilliary methods. The ini files contain the information for the Properties window. You can already use a fair number of datatypes (e.g. integer, float, boolean, list, color, etc.) and more can be added. Be careful when using floats as there is a limit to the number of decimals (see above). The plotmanipulators and commands should read the properties directly from the ini file instead of having them passed to them as arguments. For the time being, accessor methods are located in hooke.py (e.g. GetBoolFromConfig()).
-A more detailed description will be made available.
+force curves, use the plot toolbar under the plot. A more detailed
+description is available on the `Matplotlib website`_
+
+.. _Matplotlib website:
+ http://matplotlib.sourceforge.net/users/navigation_toolbar.html
+
+Some plugins and commands
+=========================
+
+* overlay (export): exports all retraction curves in a playlist on the
+ same scale. This is achieved by determining the maximum x window and
+ adding x(max) and x(min) to all curves that are shorter than the
+ maximum x window. Make sure to filter your playlist before running
+ this command!
+
+.. todo:: Implement overlay.
+
+Basic analysis and autopeak
+===========================
+
+.. todo:: Implement autopeak. Bring in autopeak tutorial from the wiki?
+
+Please follow the steps in the :doc:`tutorial`. Instead of typing in
+the command at the command-line, select it in the `Commands`_ window,
+set your properties in the `Properties`_ window and click on
+`Execute` back in the `Commands`_ window.
+
+The :doc:`autopeak` tutorial is also applicable. You need to setup the
+type of fit you want to use: in the Properties of the autopeak command
+(autopeak plugin) select `WLC`, `FJC` or `FJC_PEG` from the dropdown
+list for the `polymer model` argument of `polymer fit`.
+
+Fast curve reviewing and saving
+===============================
+.. todo:: Update curve review tutorial section.
+
+When automatic routines are not good enough to filter your data, use
+``review`` command to cycle through your playlist presenting ten
+curves in the same graph. You can then enter the numbers of the
+interesting curves and automatically save a copy of them into another
+directory.