***************** The GUI interface ***************** Orignially by Rolf Schmidt . Run the GUI with:: $ ./bin/hk.py --ui gui Alternatively, select `gui` in your config file (see :doc:`config`):: [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): * Commands (`F5`) * Folders (`F6`) * Note (`F7`) * Output (`F8`) * Playlists (`F9`) * Properties (`F10`) * Results (`F11`) .. 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. Underneath the menus at thte top of the window there is a navigation toolbar to switch from one curve to another (next/previous). Plot area ========= The plot area displays the current curve. You can select the data column to use as the x axis using the dropdown menu in the plot navigation bar (under the plot, not to be confused with the navigation bar under the menus). You can select the columns to plot by clicking the `y column(s)` button and checking interesting columns. We suggest you stick to columns with a single unit, and not try and dispay, for example, both meters and newtons on the same y axis. You can move about the plot using its navigation toolbar. See the `Matplotlib manual`_ for details. .. _Matplotlib manual: http://matplotlib.sourceforge.net/users/navigation_toolbar.html You can measure distances and forces directly in the plot. If you want to know the coordinates of a single point, left click on it. The index and coordinates of the nearest data point will be displayed in the status bar along with the x and y coordinates of your click. To find the distance between two points, just issue the command ``delta``. You will be asked to click two points. When you click a point, a blue dot should appear. When you click the second point, the distances will appear in the output panel. Hooke automatically adjusts the position of the clicked point to the nearest point in the graph, so you will be always measuring distances and forces between points in the graph. .. todo:: Implement blue dots and click handler. 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). .. todo:: Implement folders panel. 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`. .. todo:: Do we need side-by-side comparison? How did this work in the old GUI? 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 properties in the `Properties`_ window. You can edit the properties 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. Mousing over a plugin or command in the `Commands`_ window will display the associated help in a tooltip. 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. 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. .. todo:: Document new, non-PropGrid :mod:`~hooke.ui.gui.panel.propertyeditor`. 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). .. todo:: Results panel not yet re-implemented. Output ====== The Output window serves as a log where pertinent information is displayed. The output is generally the same as what you would see if you were running the commands from the command line. Note ==== A note can be added to every curve: enter your note and click `Update note`. With the `note filter playlist` command (`playlist` plugin) you can copy all the curves with a note into a new playlist. General remarks =============== Read :doc:`hacking` for an overview of how Hooke works internally and :doc:`config` for more information about configuring Hooke. 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 the config file, see :doc:`config`). You can arrange the panels any which way you like and save this arrangement as a perspective. .. 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 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 `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.