***************** The GUI interface ***************** by Rolf Schmidt Enable by selecting `gui` in your :file:`hooke.cfg`.:: [user interfaces] command line = False gui = True 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): # Folders (`F5`) # Playlists (`F6`) # Commands (or Settings and commands) (`F7`) # Properties (`F8`) # Assistant (`F9`) # Results (`F10`) # Output (`F11`) # Note (`F12`) .. img:: 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. Above the windows you see the navigation toolbar to switch from one curve to another (next/previous). 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 plot (and from the playlist in the playlists panel) * legend: show or hide the legend * use_zero: display `0` instead of e.g. `0.00` on the axes * decimals (x_decimals, y_decimals): set the decimal places for the x and y axes * prefixes(x_prefix, y_prefix): set the prefix for the x and y axes These are global settings. Individual plots can be customised with the same options (except hide_curve_extension) by setting `preferences` in the plot plugin. Folders ======= Here you can navigate your file system and double click on a saved playlist to open it. You can change the initial folder by modifying `workdir` in the `preferences` (core plugin). Playlists ========= You can manage several playlists in this window. As the GUI is rather flexible, it is possible to display the curves from different playlists side by side to compare them (relatively handy when comparing different fit parameters). You can double-click a file in the playlist to display it in the plot area. Deleting entire playlists or single files can be accomplished by right-clicking and selecting `Delete`. 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. Selecting a plugin or command will display the associated help in the `Assistant`_ window. You can edit the properties of the selected command in the `Properties`_ window and click `Execute` to run the selected command. If you do not need to modify any properties, you can also double-click a command to run it. Properties ========== The properties for the command selected in the `Commands`_ window are displayed here. Edit the properties to your satisfaction (some need to be confirmed by hitting enter, this seems to be a problem in wxPropertyGrid) and click the `Execute` button to run the selected command. Floating point values are limited to a certain number of decimals (limitation of wxPropertyGrid?) so be careful when using floating point values. Assistant ========= Selecting a plugin or command in the `Commands`_ window will display the associated help here. The help for the plugin should give a general description of the plugin. The help for a command should describe the properties available for this command and suggest reasonable default values if possible. Feel free to point out missing help content. Results ======= The results from the `autopeak` or `multidistance` commands are displayed here. Initially, all results are checked (i.e. visible). If you want to hide a result, simply uncheck it. Hidden curves will not be exported either. You can only display one type of fit result (WLC, FJC, etc.) at a time and you can switch between result types (results plugin - show_results). Output ====== The Output window serves as a log where pertinent information is displayed. If something does not work the way you expect it, have a look here to see if there is more information available. Note ==== A note can be added to every curve: enter your note and click `Update note`. With the copylog command (core plugin) you can copy all the files with a note to a different folder. General remarks =============== Ignore the text on the `Welcome` tab. This tab is more like a proof of principle and will contain a short how-to in the future (once the howto is written). Hooke's GUI will remember the size and position of the main window (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 Hooke will always start with the last used perspective and you can switch from one perspective to another by selecting a perspective from the perspectives menu. After deleting a perspective, the radio indicator in the perspectives menu disappears (known bug in wxPython). This is only a visual problem and does not affect anything else. 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.