Interface
=========
-
Starting Hooke's GUI for the first time, you will see the central plot
area with the current plot surrounded by the following windows (the `F*`
key toggles the visibility of the panel):
# Output (`F11`)
# Note (`F12`)
-.. img:: img/gui_screenshot.jpg
+.. image:: img/gui_screenshot.jpg
Initially, the window will be rather small in order to work with small
screen resolutions. Adjust the size and position to your liking.
Plot area
=========
-
The plot area can be customised by setting `preferences` in the core plugin.
* hide_curve_extension: hides the curve extension in the title of the
Commands (or Settings and commands)
===================================
-
All available commands are listed under their corresponding plugin. In
order to see a plugin and its commands, you have to edit
:file:`hooke.conf` and enable th plugin in the plugins section.
(stored in ~/.hooke-gui.cfg). You can arrange the panels any which
way you like and save this arrangement as a perspective.
-.. img:: img/gui_perspective.jpg
+.. image:: img/gui_perspective.jpg
Hooke will always start with the last used perspective and you can
switch from one perspective to another by selecting a perspective from
In order to pan the plot, zoom in and out and export the plot of your
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.
+description is available on the `matplotlib website`_
+
+.. _matplotlib website:
+ http://matplotlib.sourceforge.net/users/navigation_toolbar.html
+
+
+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 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`.
+
+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 `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 plot manipulators (i.e. `plotmanip_NAME`), commands
+(i.e. `do_COMMAND`) and auxilliary methods. The :file:`*.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 :file:`*.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.
projects / hooke.git / commitdiff